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Thomas Forest
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# Implementation of the DSSP approach for secondary structure assignation
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Attempt to implement the historic 1983 version of DSSP (Define Secondary Structure of Proteins): Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 222577-2637. PMID: 6667333; UI: 84128824.
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## Getting Started
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These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
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### Prerequisites
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You need to have **Python 3** and **Conda** on your machine, as it will be used to deploy the running environnement of DSSP.
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This program has been tested for Python 3.7.4.
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### Installing
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Use conda to create the environnement
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```
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conda env create --file environment.yml
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```
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Load your environnement
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```
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conda activate dssp
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```
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You should be ready to run the program, by calling, for example
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```
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python3 src/dssp.py data/1est.pdb
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```
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## Author
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* **FOREST Thomas** - *M2BI* - [Univ-Paris-Diderot.fr](https://www.univ-paris-diderot.fr/) - thomas.forest@etu.univ-paris-diderot.fr
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## License
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This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details
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## Acknowledgments
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* Hat tip to anyone whose code was used
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* Inspiration
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* etc
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HEADER RIBONUCLEASE INHIBITOR 09-MAY-94 1BTA
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TITLE THREE-DIMENSIONAL SOLUTION STRUCTURE AND 13C ASSIGNMENTS OF
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TITLE 2 BARSTAR USING NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
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COMPND MOL_ID: 1;
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COMPND 2 MOLECULE: BARSTAR;
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COMPND 3 CHAIN: A;
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COMPND 4 ENGINEERED: YES
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SOURCE MOL_ID: 1;
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SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS AMYLOLIQUEFACIENS;
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SOURCE 3 ORGANISM_TAXID: 1390
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KEYWDS RIBONUCLEASE INHIBITOR
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EXPDTA SOLUTION NMR
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AUTHOR M.J.LUBIENSKI,M.BYCROFT,S.M.V.FREUND,A.R.FERSHT
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REVDAT 2 24-FEB-09 1BTA 1 VERSN
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REVDAT 1 31-JUL-94 1BTA 0
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JRNL AUTH M.J.LUBIENSKI,M.BYCROFT,S.M.FREUND,A.R.FERSHT
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JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE AND 13C
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JRNL TITL 2 ASSIGNMENTS OF BARSTAR USING NUCLEAR MAGNETIC
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JRNL TITL 3 RESONANCE SPECTROSCOPY.
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JRNL REF BIOCHEMISTRY V. 33 8866 1994
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JRNL REFN ISSN 0006-2960
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JRNL PMID 8043574
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JRNL DOI 10.1021/BI00196A003
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REMARK 1
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REMARK 1 REFERENCE 1
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REMARK 1 AUTH R.W.HARTLEY
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REMARK 1 TITL BARNASE AND BARSTAR: TWO SMALL PROTEINS TO FOLD
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REMARK 1 TITL 2 AND FIT TOGETHER
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REMARK 1 REF TRENDS BIOCHEM.SCI. V. 14 450 1989
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REMARK 1 REFN ISSN 0968-0004
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REMARK 2
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REMARK 2 RESOLUTION. NOT APPLICABLE.
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REMARK 3
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REMARK 3 REFINEMENT.
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REMARK 3 PROGRAM : X-PLOR
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REMARK 3 AUTHORS : BRUNGER
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REMARK 3
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REMARK 3 OTHER REFINEMENT REMARKS: NULL
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REMARK 4
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REMARK 4 1BTA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
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REMARK 100
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REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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REMARK 210
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REMARK 210 EXPERIMENTAL DETAILS
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REMARK 210 EXPERIMENT TYPE : NMR
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REMARK 210 TEMPERATURE (KELVIN) : NULL
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REMARK 210 PH : NULL
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REMARK 210 IONIC STRENGTH : NULL
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REMARK 210 PRESSURE : NULL
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REMARK 210 SAMPLE CONTENTS : NULL
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REMARK 210
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REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
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REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
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REMARK 210 SPECTROMETER MODEL : NULL
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REMARK 210 SPECTROMETER MANUFACTURER : NULL
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REMARK 210
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REMARK 210 STRUCTURE DETERMINATION.
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REMARK 210 SOFTWARE USED : NULL
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REMARK 210 METHOD USED : NULL
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REMARK 210
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REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
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REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
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REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
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REMARK 210
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REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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REMARK 210
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REMARK 210 REMARK: NULL
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REMARK 215
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REMARK 215 NMR STUDY
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REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
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REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
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REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
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REMARK 215 THESE RECORDS ARE MEANINGLESS.
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REMARK 500
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REMARK 500 GEOMETRY AND STEREOCHEMISTRY
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REMARK 500 SUBTOPIC: TORSION ANGLES
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REMARK 500
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REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
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REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
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REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
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REMARK 500
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REMARK 500 STANDARD TABLE:
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REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
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REMARK 500
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REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
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REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
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REMARK 500
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REMARK 500 M RES CSSEQI PSI PHI
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REMARK 500 PRO A 27 -179.66 -57.36
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REMARK 500 TYR A 30 105.85 -38.41
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REMARK 500 GLU A 32 3.60 50.07
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REMARK 500 TRP A 44 -66.63 177.13
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REMARK 500 LEU A 62 -32.03 -33.51
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REMARK 500 GLU A 64 106.99 -12.37
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REMARK 500 ASN A 65 32.13 73.69
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REMARK 500 ASP A 83 65.33 -109.29
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REMARK 500 THR A 85 98.90 -52.92
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REMARK 500
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REMARK 500 REMARK: NULL
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REMARK 500
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REMARK 500 GEOMETRY AND STEREOCHEMISTRY
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REMARK 500 SUBTOPIC: PLANAR GROUPS
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REMARK 500
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REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
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REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
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REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
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REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
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REMARK 500 AN RMSD GREATER THAN THIS VALUE
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REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
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REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
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REMARK 500
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REMARK 500 M RES CSSEQI RMS TYPE
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REMARK 500 ARG A 11 0.17 SIDE_CHAIN
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REMARK 500 ARG A 54 0.31 SIDE_CHAIN
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REMARK 500 ARG A 75 0.11 SIDE_CHAIN
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REMARK 500
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REMARK 500 REMARK: NULL
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REMARK 900
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REMARK 900 RELATED ENTRIES
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REMARK 900 RELATED ID: 1BTB RELATED DB: PDB
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DBREF 1BTA A 1 89 UNP P11540 BARS_BACAM 1 89
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SEQRES 1 A 89 LYS LYS ALA VAL ILE ASN GLY GLU GLN ILE ARG SER ILE
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SEQRES 2 A 89 SER ASP LEU HIS GLN THR LEU LYS LYS GLU LEU ALA LEU
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SEQRES 3 A 89 PRO GLU TYR TYR GLY GLU ASN LEU ASP ALA LEU TRP ASP
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SEQRES 4 A 89 CYS LEU THR GLY TRP VAL GLU TYR PRO LEU VAL LEU GLU
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SEQRES 5 A 89 TRP ARG GLN PHE GLU GLN SER LYS GLN LEU THR GLU ASN
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SEQRES 6 A 89 GLY ALA GLU SER VAL LEU GLN VAL PHE ARG GLU ALA LYS
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SEQRES 7 A 89 ALA GLU GLY CYS ASP ILE THR ILE ILE LEU SER
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HELIX 1 H1 SER A 14 ALA A 25 1 12
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HELIX 2 H2 ASN A 33 GLY A 43 1 11
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HELIX 3 H3 PHE A 56 THR A 63 1 8
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HELIX 4 H4 GLU A 68 GLY A 81 1 14
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SHEET 1 SH1 3 LYS A 1 ASN A 6 0
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SHEET 2 SH1 3 LEU A 49 ARG A 54 1
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SHEET 3 SH1 3 ASP A 83 SER A 89 1
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CISPEP 1 TYR A 47 PRO A 48 0 0.92
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CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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ORIGX1 1.000000 0.000000 0.000000 0.00000
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ORIGX2 0.000000 1.000000 0.000000 0.00000
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ORIGX3 0.000000 0.000000 1.000000 0.00000
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SCALE1 1.000000 0.000000 0.000000 0.00000
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SCALE2 0.000000 1.000000 0.000000 0.00000
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SCALE3 0.000000 0.000000 1.000000 0.00000
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ATOM 1 N LYS A 1 -8.655 5.770 8.371 1.00 1.40 N
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ATOM 2 CA LYS A 1 -7.542 5.187 9.163 1.00 0.52 C
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ATOM 3 C LYS A 1 -6.210 5.619 8.561 1.00 0.39 C
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ATOM 4 O LYS A 1 -6.156 6.468 7.693 1.00 0.33 O
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ATOM 5 CB LYS A 1 -7.641 3.666 9.159 1.00 1.53 C
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ATOM 6 CG LYS A 1 -7.750 3.179 10.602 1.00 2.38 C
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ATOM 7 CD LYS A 1 -9.158 3.466 11.126 1.00 3.11 C
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ATOM 8 CE LYS A 1 -9.145 4.744 11.965 1.00 3.58 C
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ATOM 9 NZ LYS A 1 -9.497 4.416 13.375 1.00 4.21 N
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ATOM 25 N LYS A 2 -5.128 5.066 9.028 1.00 0.51 N
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ATOM 26 CA LYS A 2 -3.813 5.485 8.490 1.00 0.44 C
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ATOM 27 C LYS A 2 -2.931 4.277 8.172 1.00 0.41 C
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ATOM 28 O LYS A 2 -3.040 3.218 8.757 1.00 0.58 O
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ATOM 29 CB LYS A 2 -3.138 6.383 9.534 1.00 0.63 C
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ATOM 30 CG LYS A 2 -1.624 6.134 9.604 1.00 1.04 C
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ATOM 31 CD LYS A 2 -0.967 7.224 10.453 1.00 0.93 C
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ATOM 32 CE LYS A 2 0.116 7.929 9.634 1.00 0.63 C
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ATOM 33 NZ LYS A 2 1.057 8.630 10.551 1.00 1.43 N
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ATOM 47 N ALA A 3 -2.040 4.474 7.250 1.00 0.27 N
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ATOM 48 CA ALA A 3 -1.086 3.403 6.848 1.00 0.30 C
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ATOM 49 C ALA A 3 0.316 4.013 6.751 1.00 0.30 C
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ATOM 50 O ALA A 3 0.469 5.207 6.586 1.00 0.54 O
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ATOM 51 CB ALA A 3 -1.491 2.834 5.486 1.00 0.34 C
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ATOM 57 N VAL A 4 1.342 3.214 6.860 1.00 0.30 N
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ATOM 58 CA VAL A 4 2.725 3.769 6.780 1.00 0.27 C
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ATOM 59 C VAL A 4 3.643 2.773 6.074 1.00 0.26 C
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ATOM 60 O VAL A 4 3.842 1.667 6.535 1.00 0.33 O
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ATOM 61 CB VAL A 4 3.250 4.021 8.194 1.00 0.30 C
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ATOM 62 CG1 VAL A 4 4.617 4.709 8.122 1.00 0.35 C
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ATOM 63 CG2 VAL A 4 2.262 4.915 8.946 1.00 0.35 C
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ATOM 73 N ILE A 5 4.210 3.153 4.961 1.00 0.23 N
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ATOM 74 CA ILE A 5 5.117 2.213 4.245 1.00 0.23 C
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ATOM 75 C ILE A 5 6.570 2.567 4.552 1.00 0.25 C
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ATOM 76 O ILE A 5 7.176 3.388 3.893 1.00 0.27 O
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ATOM 77 CB ILE A 5 4.879 2.300 2.742 1.00 0.23 C
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ATOM 78 CG1 ILE A 5 3.360 2.231 2.478 1.00 0.23 C
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ATOM 79 CG2 ILE A 5 5.620 1.142 2.061 1.00 0.24 C
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ATOM 80 CD1 ILE A 5 3.034 1.246 1.346 1.00 0.22 C
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ATOM 92 N ASN A 6 7.134 1.947 5.547 1.00 0.27 N
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ATOM 93 CA ASN A 6 8.545 2.232 5.905 1.00 0.31 C
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ATOM 94 C ASN A 6 9.466 1.399 5.009 1.00 0.31 C
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ATOM 95 O ASN A 6 9.611 0.207 5.189 1.00 0.35 O
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ATOM 96 CB ASN A 6 8.759 1.859 7.370 1.00 0.37 C
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ATOM 97 CG ASN A 6 8.067 2.890 8.264 1.00 0.65 C
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ATOM 98 OD1 ASN A 6 7.534 3.869 7.782 1.00 1.48 O
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ATOM 99 ND2 ASN A 6 8.054 2.711 9.557 1.00 1.13 N
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ATOM 106 N GLY A 7 10.078 2.017 4.035 1.00 0.33 N
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ATOM 107 CA GLY A 7 10.976 1.261 3.114 1.00 0.36 C
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ATOM 108 C GLY A 7 12.182 0.718 3.879 1.00 0.35 C
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ATOM 109 O GLY A 7 12.583 -0.414 3.694 1.00 0.46 O
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ATOM 113 N GLU A 8 12.767 1.509 4.735 1.00 0.38 N
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ATOM 114 CA GLU A 8 13.946 1.022 5.505 1.00 0.43 C
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ATOM 115 C GLU A 8 13.659 -0.390 6.019 1.00 0.39 C
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ATOM 116 O GLU A 8 14.559 -1.170 6.260 1.00 0.45 O
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ATOM 117 CB GLU A 8 14.207 1.950 6.696 1.00 0.53 C
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ATOM 118 CG GLU A 8 14.064 3.409 6.256 1.00 1.39 C
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ATOM 119 CD GLU A 8 14.660 4.324 7.328 1.00 1.74 C
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ATOM 120 OE1 GLU A 8 14.225 4.232 8.464 1.00 2.30 O
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ATOM 121 OE2 GLU A 8 15.540 5.100 6.994 1.00 2.19 O
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ATOM 128 N GLN A 9 12.408 -0.720 6.195 1.00 0.35 N
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ATOM 129 CA GLN A 9 12.051 -2.069 6.699 1.00 0.38 C
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ATOM 130 C GLN A 9 11.745 -3.001 5.523 1.00 0.35 C
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ATOM 131 O GLN A 9 12.213 -4.121 5.468 1.00 0.40 O
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ATOM 132 CB GLN A 9 10.811 -1.937 7.578 1.00 0.43 C
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ATOM 133 CG GLN A 9 11.027 -0.819 8.600 1.00 0.50 C
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ATOM 134 CD GLN A 9 11.790 -1.365 9.805 1.00 1.06 C
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ATOM 135 OE1 GLN A 9 12.979 -1.155 9.931 1.00 1.97 O
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ATOM 136 NE2 GLN A 9 11.151 -2.059 10.705 1.00 1.49 N
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ATOM 145 N ILE A 10 10.952 -2.550 4.591 1.00 0.32 N
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ATOM 146 CA ILE A 10 10.597 -3.408 3.424 1.00 0.34 C
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ATOM 147 C ILE A 10 11.825 -4.171 2.934 1.00 0.31 C
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ATOM 148 O ILE A 10 12.893 -3.617 2.765 1.00 0.35 O
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ATOM 149 CB ILE A 10 10.059 -2.546 2.281 1.00 0.37 C
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ATOM 150 CG1 ILE A 10 8.683 -2.005 2.655 1.00 0.51 C
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ATOM 151 CG2 ILE A 10 9.933 -3.402 1.018 1.00 0.35 C
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ATOM 152 CD1 ILE A 10 7.689 -3.158 2.715 1.00 0.78 C
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ATOM 164 N ARG A 11 11.668 -5.440 2.692 1.00 0.33 N
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ATOM 165 CA ARG A 11 12.794 -6.261 2.200 1.00 0.37 C
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ATOM 166 C ARG A 11 12.423 -6.834 0.830 1.00 0.39 C
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ATOM 167 O ARG A 11 13.251 -7.368 0.120 1.00 0.48 O
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ATOM 168 CB ARG A 11 13.035 -7.400 3.184 1.00 0.50 C
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ATOM 169 CG ARG A 11 13.677 -6.844 4.458 1.00 0.57 C
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ATOM 170 CD ARG A 11 15.105 -7.376 4.589 1.00 1.27 C
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ATOM 171 NE ARG A 11 15.489 -7.404 6.030 1.00 1.87 N
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ATOM 172 CZ ARG A 11 16.544 -8.065 6.417 1.00 2.53 C
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ATOM 173 NH1 ARG A 11 16.881 -9.170 5.815 1.00 3.26 N
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ATOM 174 NH2 ARG A 11 17.261 -7.620 7.412 1.00 2.99 N
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|
||||||
ATOM 188 N SER A 12 11.174 -6.725 0.458 1.00 0.37 N
|
|
||||||
ATOM 189 CA SER A 12 10.732 -7.258 -0.860 1.00 0.45 C
|
|
||||||
ATOM 190 C SER A 12 9.270 -6.869 -1.096 1.00 0.42 C
|
|
||||||
ATOM 191 O SER A 12 8.619 -6.289 -0.242 1.00 0.37 O
|
|
||||||
ATOM 192 CB SER A 12 10.862 -8.781 -0.865 1.00 0.56 C
|
|
||||||
ATOM 193 OG SER A 12 11.282 -9.221 0.419 1.00 1.44 O
|
|
||||||
ATOM 199 N ILE A 13 8.741 -7.185 -2.245 1.00 0.47 N
|
|
||||||
ATOM 200 CA ILE A 13 7.324 -6.831 -2.520 1.00 0.46 C
|
|
||||||
ATOM 201 C ILE A 13 6.445 -7.446 -1.435 1.00 0.41 C
|
|
||||||
ATOM 202 O ILE A 13 5.579 -6.799 -0.887 1.00 0.36 O
|
|
||||||
ATOM 203 CB ILE A 13 6.908 -7.370 -3.892 1.00 0.56 C
|
|
||||||
ATOM 204 CG1 ILE A 13 5.570 -6.749 -4.313 1.00 0.63 C
|
|
||||||
ATOM 205 CG2 ILE A 13 6.753 -8.888 -3.812 1.00 0.64 C
|
|
||||||
ATOM 206 CD1 ILE A 13 5.564 -5.246 -4.010 1.00 0.57 C
|
|
||||||
ATOM 218 N SER A 14 6.669 -8.690 -1.109 1.00 0.46 N
|
|
||||||
ATOM 219 CA SER A 14 5.851 -9.332 -0.047 1.00 0.44 C
|
|
||||||
ATOM 220 C SER A 14 5.859 -8.424 1.179 1.00 0.37 C
|
|
||||||
ATOM 221 O SER A 14 4.837 -8.162 1.781 1.00 0.35 O
|
|
||||||
ATOM 222 CB SER A 14 6.453 -10.689 0.312 1.00 0.50 C
|
|
||||||
ATOM 223 OG SER A 14 5.481 -11.469 0.996 1.00 1.07 O
|
|
||||||
ATOM 229 N ASP A 15 7.009 -7.928 1.541 1.00 0.34 N
|
|
||||||
ATOM 230 CA ASP A 15 7.097 -7.021 2.709 1.00 0.30 C
|
|
||||||
ATOM 231 C ASP A 15 6.187 -5.819 2.475 1.00 0.24 C
|
|
||||||
ATOM 232 O ASP A 15 5.470 -5.386 3.353 1.00 0.23 O
|
|
||||||
ATOM 233 CB ASP A 15 8.536 -6.538 2.871 1.00 0.30 C
|
|
||||||
ATOM 234 CG ASP A 15 9.056 -6.939 4.254 1.00 0.33 C
|
|
||||||
ATOM 235 OD1 ASP A 15 8.483 -7.843 4.840 1.00 1.17 O
|
|
||||||
ATOM 236 OD2 ASP A 15 10.015 -6.335 4.705 1.00 1.08 O
|
|
||||||
ATOM 241 N LEU A 16 6.211 -5.283 1.288 1.00 0.25 N
|
|
||||||
ATOM 242 CA LEU A 16 5.347 -4.111 0.980 1.00 0.23 C
|
|
||||||
ATOM 243 C LEU A 16 3.898 -4.464 1.298 1.00 0.22 C
|
|
||||||
ATOM 244 O LEU A 16 3.233 -3.804 2.073 1.00 0.21 O
|
|
||||||
ATOM 245 CB LEU A 16 5.470 -3.779 -0.505 1.00 0.28 C
|
|
||||||
ATOM 246 CG LEU A 16 4.802 -2.436 -0.784 1.00 0.31 C
|
|
||||||
ATOM 247 CD1 LEU A 16 5.341 -1.386 0.188 1.00 0.31 C
|
|
||||||
ATOM 248 CD2 LEU A 16 5.110 -2.013 -2.219 1.00 0.39 C
|
|
||||||
ATOM 260 N HIS A 17 3.413 -5.509 0.701 1.00 0.22 N
|
|
||||||
ATOM 261 CA HIS A 17 2.018 -5.941 0.944 1.00 0.22 C
|
|
||||||
ATOM 262 C HIS A 17 1.874 -6.363 2.405 1.00 0.19 C
|
|
||||||
ATOM 263 O HIS A 17 0.786 -6.432 2.941 1.00 0.19 O
|
|
||||||
ATOM 264 CB HIS A 17 1.715 -7.120 0.024 1.00 0.26 C
|
|
||||||
ATOM 265 CG HIS A 17 1.994 -6.716 -1.397 1.00 0.32 C
|
|
||||||
ATOM 266 ND1 HIS A 17 1.294 -5.699 -2.026 1.00 0.38 N
|
|
||||||
ATOM 267 CD2 HIS A 17 2.895 -7.181 -2.324 1.00 0.40 C
|
|
||||||
ATOM 268 CE1 HIS A 17 1.779 -5.586 -3.276 1.00 0.44 C
|
|
||||||
ATOM 269 NE2 HIS A 17 2.756 -6.465 -3.510 1.00 0.45 N
|
|
||||||
ATOM 277 N GLN A 18 2.969 -6.639 3.055 1.00 0.19 N
|
|
||||||
ATOM 278 CA GLN A 18 2.905 -7.047 4.475 1.00 0.19 C
|
|
||||||
ATOM 279 C GLN A 18 2.501 -5.844 5.322 1.00 0.17 C
|
|
||||||
ATOM 280 O GLN A 18 1.541 -5.888 6.067 1.00 0.18 O
|
|
||||||
ATOM 281 CB GLN A 18 4.275 -7.553 4.927 1.00 0.21 C
|
|
||||||
ATOM 282 CG GLN A 18 4.092 -8.654 5.975 1.00 0.55 C
|
|
||||||
ATOM 283 CD GLN A 18 5.461 -9.139 6.452 1.00 1.31 C
|
|
||||||
ATOM 284 OE1 GLN A 18 6.390 -8.363 6.557 1.00 2.11 O
|
|
||||||
ATOM 285 NE2 GLN A 18 5.626 -10.399 6.749 1.00 2.02 N
|
|
||||||
ATOM 294 N THR A 19 3.229 -4.764 5.217 1.00 0.17 N
|
|
||||||
ATOM 295 CA THR A 19 2.882 -3.573 6.019 1.00 0.17 C
|
|
||||||
ATOM 296 C THR A 19 1.519 -3.063 5.542 1.00 0.17 C
|
|
||||||
ATOM 297 O THR A 19 0.682 -2.691 6.328 1.00 0.18 O
|
|
||||||
ATOM 298 CB THR A 19 3.976 -2.492 5.860 1.00 0.20 C
|
|
||||||
ATOM 299 OG1 THR A 19 4.593 -2.276 7.121 1.00 0.22 O
|
|
||||||
ATOM 300 CG2 THR A 19 3.371 -1.165 5.396 1.00 0.21 C
|
|
||||||
ATOM 308 N LEU A 20 1.286 -3.056 4.258 1.00 0.16 N
|
|
||||||
ATOM 309 CA LEU A 20 -0.022 -2.590 3.751 1.00 0.18 C
|
|
||||||
ATOM 310 C LEU A 20 -1.104 -3.472 4.365 1.00 0.17 C
|
|
||||||
ATOM 311 O LEU A 20 -2.183 -3.040 4.683 1.00 0.24 O
|
|
||||||
ATOM 312 CB LEU A 20 -0.050 -2.738 2.232 1.00 0.19 C
|
|
||||||
ATOM 313 CG LEU A 20 0.878 -1.705 1.588 1.00 0.20 C
|
|
||||||
ATOM 314 CD1 LEU A 20 0.822 -1.851 0.068 1.00 0.23 C
|
|
||||||
ATOM 315 CD2 LEU A 20 0.434 -0.292 1.981 1.00 0.21 C
|
|
||||||
ATOM 327 N LYS A 21 -0.794 -4.716 4.530 1.00 0.16 N
|
|
||||||
ATOM 328 CA LYS A 21 -1.760 -5.680 5.122 1.00 0.16 C
|
|
||||||
ATOM 329 C LYS A 21 -2.011 -5.324 6.586 1.00 0.17 C
|
|
||||||
ATOM 330 O LYS A 21 -3.123 -5.365 7.059 1.00 0.19 O
|
|
||||||
ATOM 331 CB LYS A 21 -1.173 -7.088 5.035 1.00 0.17 C
|
|
||||||
ATOM 332 CG LYS A 21 -2.174 -8.100 5.593 1.00 0.29 C
|
|
||||||
ATOM 333 CD LYS A 21 -1.414 -9.229 6.292 1.00 0.68 C
|
|
||||||
ATOM 334 CE LYS A 21 -2.407 -10.255 6.837 1.00 1.26 C
|
|
||||||
ATOM 335 NZ LYS A 21 -1.733 -11.101 7.860 1.00 1.94 N
|
|
||||||
ATOM 349 N LYS A 22 -0.991 -4.980 7.317 1.00 0.18 N
|
|
||||||
ATOM 350 CA LYS A 22 -1.204 -4.631 8.741 1.00 0.20 C
|
|
||||||
ATOM 351 C LYS A 22 -2.006 -3.335 8.817 1.00 0.23 C
|
|
||||||
ATOM 352 O LYS A 22 -3.074 -3.277 9.390 1.00 0.29 O
|
|
||||||
ATOM 353 CB LYS A 22 0.142 -4.442 9.432 1.00 0.22 C
|
|
||||||
ATOM 354 CG LYS A 22 0.148 -5.278 10.717 1.00 0.83 C
|
|
||||||
ATOM 355 CD LYS A 22 1.553 -5.339 11.302 1.00 1.43 C
|
|
||||||
ATOM 356 CE LYS A 22 1.494 -6.033 12.671 1.00 2.18 C
|
|
||||||
ATOM 357 NZ LYS A 22 2.827 -6.602 13.001 1.00 2.84 N
|
|
||||||
ATOM 371 N GLU A 23 -1.495 -2.303 8.219 1.00 0.22 N
|
|
||||||
ATOM 372 CA GLU A 23 -2.195 -1.004 8.212 1.00 0.26 C
|
|
||||||
ATOM 373 C GLU A 23 -3.621 -1.224 7.716 1.00 0.24 C
|
|
||||||
ATOM 374 O GLU A 23 -4.587 -1.066 8.436 1.00 0.27 O
|
|
||||||
ATOM 375 CB GLU A 23 -1.450 -0.080 7.250 1.00 0.29 C
|
|
||||||
ATOM 376 CG GLU A 23 -0.006 0.098 7.725 1.00 0.35 C
|
|
||||||
ATOM 377 CD GLU A 23 0.032 1.057 8.914 1.00 1.53 C
|
|
||||||
ATOM 378 OE1 GLU A 23 -1.026 1.364 9.438 1.00 2.29 O
|
|
||||||
ATOM 379 OE2 GLU A 23 1.120 1.471 9.280 1.00 2.27 O
|
|
||||||
ATOM 386 N LEU A 24 -3.737 -1.599 6.480 1.00 0.23 N
|
|
||||||
ATOM 387 CA LEU A 24 -5.066 -1.859 5.871 1.00 0.23 C
|
|
||||||
ATOM 388 C LEU A 24 -5.767 -2.996 6.618 1.00 0.22 C
|
|
||||||
ATOM 389 O LEU A 24 -6.953 -3.209 6.467 1.00 0.24 O
|
|
||||||
ATOM 390 CB LEU A 24 -4.848 -2.277 4.418 1.00 0.21 C
|
|
||||||
ATOM 391 CG LEU A 24 -4.150 -1.150 3.658 1.00 0.25 C
|
|
||||||
ATOM 392 CD1 LEU A 24 -3.120 -1.750 2.701 1.00 0.20 C
|
|
||||||
ATOM 393 CD2 LEU A 24 -5.184 -0.352 2.862 1.00 0.40 C
|
|
||||||
ATOM 405 N ALA A 25 -5.043 -3.736 7.416 1.00 0.21 N
|
|
||||||
ATOM 406 CA ALA A 25 -5.667 -4.860 8.158 1.00 0.22 C
|
|
||||||
ATOM 407 C ALA A 25 -6.369 -5.796 7.170 1.00 0.21 C
|
|
||||||
ATOM 408 O ALA A 25 -7.501 -6.191 7.366 1.00 0.23 O
|
|
||||||
ATOM 409 CB ALA A 25 -6.670 -4.292 9.152 1.00 0.26 C
|
|
||||||
ATOM 415 N LEU A 26 -5.693 -6.152 6.112 1.00 0.21 N
|
|
||||||
ATOM 416 CA LEU A 26 -6.293 -7.062 5.095 1.00 0.24 C
|
|
||||||
ATOM 417 C LEU A 26 -6.438 -8.468 5.690 1.00 0.28 C
|
|
||||||
ATOM 418 O LEU A 26 -5.795 -8.792 6.669 1.00 0.30 O
|
|
||||||
ATOM 419 CB LEU A 26 -5.371 -7.117 3.872 1.00 0.23 C
|
|
||||||
ATOM 420 CG LEU A 26 -4.954 -5.697 3.483 1.00 0.21 C
|
|
||||||
ATOM 421 CD1 LEU A 26 -3.954 -5.751 2.337 1.00 0.26 C
|
|
||||||
ATOM 422 CD2 LEU A 26 -6.187 -4.909 3.043 1.00 0.23 C
|
|
||||||
ATOM 434 N PRO A 27 -7.280 -9.262 5.077 1.00 0.34 N
|
|
||||||
ATOM 435 CA PRO A 27 -7.526 -10.643 5.529 1.00 0.41 C
|
|
||||||
ATOM 436 C PRO A 27 -6.221 -11.438 5.555 1.00 0.39 C
|
|
||||||
ATOM 437 O PRO A 27 -5.165 -10.932 5.233 1.00 0.31 O
|
|
||||||
ATOM 438 CB PRO A 27 -8.489 -11.230 4.490 1.00 0.48 C
|
|
||||||
ATOM 439 CG PRO A 27 -8.880 -10.091 3.514 1.00 0.48 C
|
|
||||||
ATOM 440 CD PRO A 27 -8.054 -8.852 3.890 1.00 0.38 C
|
|
||||||
ATOM 448 N GLU A 28 -6.289 -12.685 5.931 1.00 0.50 N
|
|
||||||
ATOM 449 CA GLU A 28 -5.058 -13.519 5.972 1.00 0.53 C
|
|
||||||
ATOM 450 C GLU A 28 -4.729 -13.997 4.558 1.00 0.49 C
|
|
||||||
ATOM 451 O GLU A 28 -3.622 -14.407 4.273 1.00 0.51 O
|
|
||||||
ATOM 452 CB GLU A 28 -5.295 -14.732 6.871 1.00 0.67 C
|
|
||||||
ATOM 453 CG GLU A 28 -5.557 -14.268 8.305 1.00 1.14 C
|
|
||||||
ATOM 454 CD GLU A 28 -5.237 -15.405 9.276 1.00 1.65 C
|
|
||||||
ATOM 455 OE1 GLU A 28 -4.380 -16.210 8.953 1.00 2.31 O
|
|
||||||
ATOM 456 OE2 GLU A 28 -5.856 -15.452 10.327 1.00 2.20 O
|
|
||||||
ATOM 463 N TYR A 29 -5.686 -13.952 3.671 1.00 0.47 N
|
|
||||||
ATOM 464 CA TYR A 29 -5.426 -14.409 2.279 1.00 0.44 C
|
|
||||||
ATOM 465 C TYR A 29 -5.020 -13.218 1.409 1.00 0.37 C
|
|
||||||
ATOM 466 O TYR A 29 -4.999 -13.312 0.198 1.00 0.38 O
|
|
||||||
ATOM 467 CB TYR A 29 -6.686 -15.061 1.704 1.00 0.51 C
|
|
||||||
ATOM 468 CG TYR A 29 -7.900 -14.250 2.087 1.00 0.66 C
|
|
||||||
ATOM 469 CD1 TYR A 29 -8.300 -13.171 1.290 1.00 1.29 C
|
|
||||||
ATOM 470 CD2 TYR A 29 -8.627 -14.579 3.237 1.00 1.53 C
|
|
||||||
ATOM 471 CE1 TYR A 29 -9.428 -12.421 1.643 1.00 1.43 C
|
|
||||||
ATOM 472 CE2 TYR A 29 -9.756 -13.829 3.590 1.00 1.75 C
|
|
||||||
ATOM 473 CZ TYR A 29 -10.156 -12.750 2.793 1.00 1.24 C
|
|
||||||
ATOM 474 OH TYR A 29 -11.268 -12.011 3.140 1.00 1.57 O
|
|
||||||
ATOM 484 N TYR A 30 -4.694 -12.103 2.017 1.00 0.32 N
|
|
||||||
ATOM 485 CA TYR A 30 -4.275 -10.903 1.222 1.00 0.28 C
|
|
||||||
ATOM 486 C TYR A 30 -3.419 -11.366 0.035 1.00 0.32 C
|
|
||||||
ATOM 487 O TYR A 30 -2.281 -11.759 0.193 1.00 0.38 O
|
|
||||||
ATOM 488 CB TYR A 30 -3.462 -9.958 2.121 1.00 0.29 C
|
|
||||||
ATOM 489 CG TYR A 30 -3.006 -8.741 1.339 1.00 0.20 C
|
|
||||||
ATOM 490 CD1 TYR A 30 -3.750 -8.286 0.243 1.00 0.47 C
|
|
||||||
ATOM 491 CD2 TYR A 30 -1.832 -8.068 1.715 1.00 0.48 C
|
|
||||||
ATOM 492 CE1 TYR A 30 -3.319 -7.163 -0.477 1.00 0.49 C
|
|
||||||
ATOM 493 CE2 TYR A 30 -1.400 -6.943 0.995 1.00 0.49 C
|
|
||||||
ATOM 494 CZ TYR A 30 -2.145 -6.493 -0.102 1.00 0.25 C
|
|
||||||
ATOM 495 OH TYR A 30 -1.724 -5.388 -0.814 1.00 0.36 O
|
|
||||||
ATOM 505 N GLY A 31 -3.974 -11.339 -1.151 1.00 0.39 N
|
|
||||||
ATOM 506 CA GLY A 31 -3.215 -11.796 -2.357 1.00 0.51 C
|
|
||||||
ATOM 507 C GLY A 31 -2.004 -10.892 -2.611 1.00 0.58 C
|
|
||||||
ATOM 508 O GLY A 31 -1.214 -11.146 -3.495 1.00 1.36 O
|
|
||||||
ATOM 512 N GLU A 32 -1.870 -9.835 -1.853 1.00 0.56 N
|
|
||||||
ATOM 513 CA GLU A 32 -0.726 -8.877 -2.011 1.00 0.54 C
|
|
||||||
ATOM 514 C GLU A 32 -0.533 -8.420 -3.470 1.00 0.54 C
|
|
||||||
ATOM 515 O GLU A 32 0.377 -7.671 -3.760 1.00 0.59 O
|
|
||||||
ATOM 516 CB GLU A 32 0.582 -9.491 -1.474 1.00 0.66 C
|
|
||||||
ATOM 517 CG GLU A 32 0.741 -10.947 -1.915 1.00 1.51 C
|
|
||||||
ATOM 518 CD GLU A 32 2.052 -11.506 -1.358 1.00 1.87 C
|
|
||||||
ATOM 519 OE1 GLU A 32 3.044 -10.799 -1.410 1.00 2.36 O
|
|
||||||
ATOM 520 OE2 GLU A 32 2.040 -12.632 -0.890 1.00 2.37 O
|
|
||||||
ATOM 527 N ASN A 33 -1.373 -8.817 -4.389 1.00 0.51 N
|
|
||||||
ATOM 528 CA ASN A 33 -1.203 -8.335 -5.792 1.00 0.53 C
|
|
||||||
ATOM 529 C ASN A 33 -1.891 -6.977 -5.927 1.00 0.50 C
|
|
||||||
ATOM 530 O ASN A 33 -2.423 -6.444 -4.974 1.00 0.56 O
|
|
||||||
ATOM 531 CB ASN A 33 -1.811 -9.321 -6.806 1.00 0.54 C
|
|
||||||
ATOM 532 CG ASN A 33 -2.420 -10.533 -6.096 1.00 0.62 C
|
|
||||||
ATOM 533 OD1 ASN A 33 -1.721 -11.465 -5.752 1.00 1.57 O
|
|
||||||
ATOM 534 ND2 ASN A 33 -3.703 -10.559 -5.864 1.00 0.82 N
|
|
||||||
ATOM 541 N LEU A 34 -1.918 -6.429 -7.107 1.00 0.48 N
|
|
||||||
ATOM 542 CA LEU A 34 -2.609 -5.125 -7.305 1.00 0.47 C
|
|
||||||
ATOM 543 C LEU A 34 -4.108 -5.392 -7.331 1.00 0.40 C
|
|
||||||
ATOM 544 O LEU A 34 -4.911 -4.621 -6.852 1.00 0.37 O
|
|
||||||
ATOM 545 CB LEU A 34 -2.204 -4.539 -8.650 1.00 0.55 C
|
|
||||||
ATOM 546 CG LEU A 34 -0.749 -4.072 -8.606 1.00 0.64 C
|
|
||||||
ATOM 547 CD1 LEU A 34 -0.358 -3.503 -9.971 1.00 0.82 C
|
|
||||||
ATOM 548 CD2 LEU A 34 -0.590 -2.986 -7.539 1.00 0.61 C
|
|
||||||
ATOM 560 N ASP A 35 -4.469 -6.494 -7.911 1.00 0.39 N
|
|
||||||
ATOM 561 CA ASP A 35 -5.897 -6.886 -8.018 1.00 0.36 C
|
|
||||||
ATOM 562 C ASP A 35 -6.467 -7.173 -6.632 1.00 0.30 C
|
|
||||||
ATOM 563 O ASP A 35 -7.614 -6.894 -6.351 1.00 0.28 O
|
|
||||||
ATOM 564 CB ASP A 35 -5.975 -8.167 -8.833 1.00 0.38 C
|
|
||||||
ATOM 565 CG ASP A 35 -5.683 -7.865 -10.303 1.00 0.43 C
|
|
||||||
ATOM 566 OD1 ASP A 35 -6.344 -7.000 -10.853 1.00 1.24 O
|
|
||||||
ATOM 567 OD2 ASP A 35 -4.803 -8.506 -10.856 1.00 1.06 O
|
|
||||||
ATOM 572 N ALA A 36 -5.676 -7.742 -5.769 1.00 0.29 N
|
|
||||||
ATOM 573 CA ALA A 36 -6.180 -8.058 -4.401 1.00 0.25 C
|
|
||||||
ATOM 574 C ALA A 36 -6.124 -6.799 -3.563 1.00 0.22 C
|
|
||||||
ATOM 575 O ALA A 36 -7.111 -6.353 -3.016 1.00 0.22 O
|
|
||||||
ATOM 576 CB ALA A 36 -5.310 -9.125 -3.749 1.00 0.29 C
|
|
||||||
ATOM 582 N LEU A 37 -4.967 -6.217 -3.477 1.00 0.21 N
|
|
||||||
ATOM 583 CA LEU A 37 -4.820 -4.966 -2.697 1.00 0.19 C
|
|
||||||
ATOM 584 C LEU A 37 -5.987 -4.058 -3.064 1.00 0.16 C
|
|
||||||
ATOM 585 O LEU A 37 -6.706 -3.539 -2.224 1.00 0.16 O
|
|
||||||
ATOM 586 CB LEU A 37 -3.502 -4.299 -3.095 1.00 0.21 C
|
|
||||||
ATOM 587 CG LEU A 37 -3.539 -2.815 -2.724 1.00 0.20 C
|
|
||||||
ATOM 588 CD1 LEU A 37 -3.557 -2.667 -1.201 1.00 0.22 C
|
|
||||||
ATOM 589 CD2 LEU A 37 -2.302 -2.115 -3.290 1.00 0.24 C
|
|
||||||
ATOM 601 N TRP A 38 -6.173 -3.884 -4.333 1.00 0.17 N
|
|
||||||
ATOM 602 CA TRP A 38 -7.277 -3.046 -4.821 1.00 0.16 C
|
|
||||||
ATOM 603 C TRP A 38 -8.577 -3.613 -4.303 1.00 0.16 C
|
|
||||||
ATOM 604 O TRP A 38 -9.345 -2.951 -3.643 1.00 0.16 O
|
|
||||||
ATOM 605 CB TRP A 38 -7.315 -3.093 -6.341 1.00 0.18 C
|
|
||||||
ATOM 606 CG TRP A 38 -8.456 -2.267 -6.801 1.00 0.18 C
|
|
||||||
ATOM 607 CD1 TRP A 38 -9.708 -2.718 -6.963 1.00 0.21 C
|
|
||||||
ATOM 608 CD2 TRP A 38 -8.476 -0.860 -7.128 1.00 0.18 C
|
|
||||||
ATOM 609 NE1 TRP A 38 -10.508 -1.672 -7.389 1.00 0.23 N
|
|
||||||
ATOM 610 CE2 TRP A 38 -9.785 -0.502 -7.508 1.00 0.20 C
|
|
||||||
ATOM 611 CE3 TRP A 38 -7.487 0.125 -7.138 1.00 0.17 C
|
|
||||||
ATOM 612 CZ2 TRP A 38 -10.099 0.802 -7.885 1.00 0.22 C
|
|
||||||
ATOM 613 CZ3 TRP A 38 -7.785 1.430 -7.507 1.00 0.19 C
|
|
||||||
ATOM 614 CH2 TRP A 38 -9.093 1.778 -7.885 1.00 0.20 C
|
|
||||||
ATOM 625 N ASP A 39 -8.815 -4.850 -4.599 1.00 0.17 N
|
|
||||||
ATOM 626 CA ASP A 39 -10.061 -5.500 -4.130 1.00 0.18 C
|
|
||||||
ATOM 627 C ASP A 39 -10.283 -5.117 -2.672 1.00 0.18 C
|
|
||||||
ATOM 628 O ASP A 39 -11.394 -5.091 -2.182 1.00 0.21 O
|
|
||||||
ATOM 629 CB ASP A 39 -9.927 -7.017 -4.254 1.00 0.21 C
|
|
||||||
ATOM 630 CG ASP A 39 -10.613 -7.488 -5.537 1.00 0.29 C
|
|
||||||
ATOM 631 OD1 ASP A 39 -10.045 -7.286 -6.598 1.00 1.13 O
|
|
||||||
ATOM 632 OD2 ASP A 39 -11.695 -8.044 -5.438 1.00 1.06 O
|
|
||||||
ATOM 637 N CYS A 40 -9.222 -4.807 -1.977 1.00 0.17 N
|
|
||||||
ATOM 638 CA CYS A 40 -9.354 -4.412 -0.556 1.00 0.19 C
|
|
||||||
ATOM 639 C CYS A 40 -9.797 -2.948 -0.466 1.00 0.19 C
|
|
||||||
ATOM 640 O CYS A 40 -10.745 -2.623 0.218 1.00 0.23 O
|
|
||||||
ATOM 641 CB CYS A 40 -8.001 -4.580 0.132 1.00 0.21 C
|
|
||||||
ATOM 642 SG CYS A 40 -7.334 -6.221 -0.239 1.00 0.58 S
|
|
||||||
ATOM 648 N LEU A 41 -9.117 -2.057 -1.142 1.00 0.17 N
|
|
||||||
ATOM 649 CA LEU A 41 -9.497 -0.625 -1.076 1.00 0.18 C
|
|
||||||
ATOM 650 C LEU A 41 -10.943 -0.424 -1.548 1.00 0.21 C
|
|
||||||
ATOM 651 O LEU A 41 -11.729 0.247 -0.908 1.00 0.45 O
|
|
||||||
ATOM 652 CB LEU A 41 -8.562 0.173 -1.981 1.00 0.17 C
|
|
||||||
ATOM 653 CG LEU A 41 -7.117 -0.285 -1.776 1.00 0.19 C
|
|
||||||
ATOM 654 CD1 LEU A 41 -6.189 0.625 -2.567 1.00 0.18 C
|
|
||||||
ATOM 655 CD2 LEU A 41 -6.760 -0.219 -0.289 1.00 0.31 C
|
|
||||||
ATOM 667 N THR A 42 -11.284 -0.971 -2.679 1.00 0.26 N
|
|
||||||
ATOM 668 CA THR A 42 -12.650 -0.794 -3.226 1.00 0.28 C
|
|
||||||
ATOM 669 C THR A 42 -13.665 -1.664 -2.479 1.00 0.32 C
|
|
||||||
ATOM 670 O THR A 42 -14.826 -1.704 -2.836 1.00 0.55 O
|
|
||||||
ATOM 671 CB THR A 42 -12.649 -1.174 -4.708 1.00 0.26 C
|
|
||||||
ATOM 672 OG1 THR A 42 -11.870 -2.347 -4.894 1.00 0.29 O
|
|
||||||
ATOM 673 CG2 THR A 42 -12.054 -0.026 -5.525 1.00 0.40 C
|
|
||||||
ATOM 681 N GLY A 43 -13.262 -2.363 -1.452 1.00 0.27 N
|
|
||||||
ATOM 682 CA GLY A 43 -14.258 -3.210 -0.729 1.00 0.31 C
|
|
||||||
ATOM 683 C GLY A 43 -13.627 -3.900 0.484 1.00 0.27 C
|
|
||||||
ATOM 684 O GLY A 43 -13.610 -5.112 0.574 1.00 0.32 O
|
|
||||||
ATOM 688 N TRP A 44 -13.125 -3.148 1.425 1.00 0.25 N
|
|
||||||
ATOM 689 CA TRP A 44 -12.519 -3.775 2.630 1.00 0.23 C
|
|
||||||
ATOM 690 C TRP A 44 -11.944 -2.689 3.540 1.00 0.23 C
|
|
||||||
ATOM 691 O TRP A 44 -12.415 -2.466 4.637 1.00 0.27 O
|
|
||||||
ATOM 692 CB TRP A 44 -11.402 -4.721 2.201 1.00 0.24 C
|
|
||||||
ATOM 693 CG TRP A 44 -10.808 -5.362 3.411 1.00 0.26 C
|
|
||||||
ATOM 694 CD1 TRP A 44 -9.735 -4.894 4.085 1.00 0.27 C
|
|
||||||
ATOM 695 CD2 TRP A 44 -11.233 -6.571 4.106 1.00 0.30 C
|
|
||||||
ATOM 696 NE1 TRP A 44 -9.470 -5.739 5.146 1.00 0.31 N
|
|
||||||
ATOM 697 CE2 TRP A 44 -10.366 -6.788 5.202 1.00 0.34 C
|
|
||||||
ATOM 698 CE3 TRP A 44 -12.274 -7.493 3.891 1.00 0.35 C
|
|
||||||
ATOM 699 CZ2 TRP A 44 -10.527 -7.879 6.058 1.00 0.41 C
|
|
||||||
ATOM 700 CZ3 TRP A 44 -12.439 -8.592 4.750 1.00 0.43 C
|
|
||||||
ATOM 701 CH2 TRP A 44 -11.567 -8.785 5.831 1.00 0.45 C
|
|
||||||
ATOM 712 N VAL A 45 -10.925 -2.016 3.089 1.00 0.25 N
|
|
||||||
ATOM 713 CA VAL A 45 -10.304 -0.949 3.912 1.00 0.26 C
|
|
||||||
ATOM 714 C VAL A 45 -11.350 0.112 4.253 1.00 0.25 C
|
|
||||||
ATOM 715 O VAL A 45 -12.264 0.362 3.493 1.00 0.37 O
|
|
||||||
ATOM 716 CB VAL A 45 -9.165 -0.300 3.125 1.00 0.30 C
|
|
||||||
ATOM 717 CG1 VAL A 45 -8.436 0.706 4.017 1.00 0.42 C
|
|
||||||
ATOM 718 CG2 VAL A 45 -8.181 -1.377 2.661 1.00 0.28 C
|
|
||||||
ATOM 728 N GLU A 46 -11.215 0.751 5.382 1.00 0.21 N
|
|
||||||
ATOM 729 CA GLU A 46 -12.197 1.808 5.755 1.00 0.23 C
|
|
||||||
ATOM 730 C GLU A 46 -11.566 3.177 5.505 1.00 0.22 C
|
|
||||||
ATOM 731 O GLU A 46 -10.440 3.435 5.880 1.00 0.22 O
|
|
||||||
ATOM 732 CB GLU A 46 -12.600 1.688 7.231 1.00 0.30 C
|
|
||||||
ATOM 733 CG GLU A 46 -11.576 0.848 7.993 1.00 1.31 C
|
|
||||||
ATOM 734 CD GLU A 46 -12.107 0.545 9.395 1.00 1.80 C
|
|
||||||
ATOM 735 OE1 GLU A 46 -13.089 -0.173 9.493 1.00 2.43 O
|
|
||||||
ATOM 736 OE2 GLU A 46 -11.524 1.036 10.347 1.00 2.28 O
|
|
||||||
ATOM 743 N TYR A 47 -12.285 4.047 4.861 1.00 0.22 N
|
|
||||||
ATOM 744 CA TYR A 47 -11.744 5.402 4.559 1.00 0.22 C
|
|
||||||
ATOM 745 C TYR A 47 -12.564 6.446 5.329 1.00 0.26 C
|
|
||||||
ATOM 746 O TYR A 47 -13.586 6.110 5.892 1.00 0.29 O
|
|
||||||
ATOM 747 CB TYR A 47 -11.851 5.623 3.045 1.00 0.24 C
|
|
||||||
ATOM 748 CG TYR A 47 -10.868 4.720 2.323 1.00 0.24 C
|
|
||||||
ATOM 749 CD1 TYR A 47 -9.830 4.081 3.021 1.00 1.25 C
|
|
||||||
ATOM 750 CD2 TYR A 47 -10.994 4.520 0.945 1.00 1.21 C
|
|
||||||
ATOM 751 CE1 TYR A 47 -8.935 3.251 2.342 1.00 1.27 C
|
|
||||||
ATOM 752 CE2 TYR A 47 -10.094 3.692 0.272 1.00 1.20 C
|
|
||||||
ATOM 753 CZ TYR A 47 -9.067 3.058 0.970 1.00 0.29 C
|
|
||||||
ATOM 754 OH TYR A 47 -8.181 2.239 0.301 1.00 0.34 O
|
|
||||||
ATOM 764 N PRO A 48 -12.102 7.682 5.359 1.00 0.27 N
|
|
||||||
ATOM 765 CA PRO A 48 -10.858 8.134 4.685 1.00 0.25 C
|
|
||||||
ATOM 766 C PRO A 48 -9.620 7.409 5.219 1.00 0.22 C
|
|
||||||
ATOM 767 O PRO A 48 -9.455 7.234 6.406 1.00 0.30 O
|
|
||||||
ATOM 768 CB PRO A 48 -10.761 9.631 5.010 1.00 0.28 C
|
|
||||||
ATOM 769 CG PRO A 48 -11.970 10.004 5.902 1.00 0.33 C
|
|
||||||
ATOM 770 CD PRO A 48 -12.815 8.738 6.097 1.00 0.32 C
|
|
||||||
ATOM 778 N LEU A 49 -8.744 7.000 4.338 1.00 0.20 N
|
|
||||||
ATOM 779 CA LEU A 49 -7.502 6.298 4.775 1.00 0.19 C
|
|
||||||
ATOM 780 C LEU A 49 -6.301 7.182 4.462 1.00 0.19 C
|
|
||||||
ATOM 781 O LEU A 49 -6.335 7.998 3.567 1.00 0.20 O
|
|
||||||
ATOM 782 CB LEU A 49 -7.362 4.977 3.994 1.00 0.18 C
|
|
||||||
ATOM 783 CG LEU A 49 -5.885 4.560 3.861 1.00 0.17 C
|
|
||||||
ATOM 784 CD1 LEU A 49 -5.350 4.066 5.209 1.00 0.20 C
|
|
||||||
ATOM 785 CD2 LEU A 49 -5.759 3.447 2.816 1.00 0.16 C
|
|
||||||
ATOM 797 N VAL A 50 -5.222 6.985 5.157 1.00 0.21 N
|
|
||||||
ATOM 798 CA VAL A 50 -4.003 7.770 4.857 1.00 0.22 C
|
|
||||||
ATOM 799 C VAL A 50 -2.919 6.786 4.408 1.00 0.20 C
|
|
||||||
ATOM 800 O VAL A 50 -2.748 5.736 4.987 1.00 0.21 O
|
|
||||||
ATOM 801 CB VAL A 50 -3.555 8.555 6.114 1.00 0.26 C
|
|
||||||
ATOM 802 CG1 VAL A 50 -2.135 8.158 6.542 1.00 0.26 C
|
|
||||||
ATOM 803 CG2 VAL A 50 -3.567 10.051 5.802 1.00 0.29 C
|
|
||||||
ATOM 813 N LEU A 51 -2.167 7.122 3.409 1.00 0.19 N
|
|
||||||
ATOM 814 CA LEU A 51 -1.081 6.210 2.976 1.00 0.18 C
|
|
||||||
ATOM 815 C LEU A 51 0.228 6.969 3.109 1.00 0.18 C
|
|
||||||
ATOM 816 O LEU A 51 0.745 7.517 2.155 1.00 0.20 O
|
|
||||||
ATOM 817 CB LEU A 51 -1.267 5.748 1.523 1.00 0.17 C
|
|
||||||
ATOM 818 CG LEU A 51 -0.106 4.823 1.149 1.00 0.19 C
|
|
||||||
ATOM 819 CD1 LEU A 51 -0.195 3.543 1.973 1.00 0.21 C
|
|
||||||
ATOM 820 CD2 LEU A 51 -0.185 4.451 -0.328 1.00 0.18 C
|
|
||||||
ATOM 832 N GLU A 52 0.760 7.014 4.296 1.00 0.19 N
|
|
||||||
ATOM 833 CA GLU A 52 2.031 7.743 4.505 1.00 0.21 C
|
|
||||||
ATOM 834 C GLU A 52 3.158 6.861 3.988 1.00 0.19 C
|
|
||||||
ATOM 835 O GLU A 52 3.789 6.122 4.721 1.00 0.19 O
|
|
||||||
ATOM 836 CB GLU A 52 2.213 8.030 5.996 1.00 0.24 C
|
|
||||||
ATOM 837 CG GLU A 52 3.642 8.508 6.256 1.00 0.30 C
|
|
||||||
ATOM 838 CD GLU A 52 3.650 9.471 7.444 1.00 0.64 C
|
|
||||||
ATOM 839 OE1 GLU A 52 2.717 9.420 8.229 1.00 1.28 O
|
|
||||||
ATOM 840 OE2 GLU A 52 4.588 10.244 7.550 1.00 1.44 O
|
|
||||||
ATOM 847 N TRP A 53 3.385 6.915 2.708 1.00 0.20 N
|
|
||||||
ATOM 848 CA TRP A 53 4.436 6.072 2.099 1.00 0.20 C
|
|
||||||
ATOM 849 C TRP A 53 5.813 6.694 2.321 1.00 0.24 C
|
|
||||||
ATOM 850 O TRP A 53 6.142 7.720 1.760 1.00 0.38 O
|
|
||||||
ATOM 851 CB TRP A 53 4.175 5.945 0.603 1.00 0.24 C
|
|
||||||
ATOM 852 CG TRP A 53 4.807 4.689 0.123 1.00 0.23 C
|
|
||||||
ATOM 853 CD1 TRP A 53 6.084 4.326 0.376 1.00 0.25 C
|
|
||||||
ATOM 854 CD2 TRP A 53 4.223 3.620 -0.671 1.00 0.21 C
|
|
||||||
ATOM 855 NE1 TRP A 53 6.325 3.103 -0.214 1.00 0.26 N
|
|
||||||
ATOM 856 CE2 TRP A 53 5.210 2.627 -0.872 1.00 0.24 C
|
|
||||||
ATOM 857 CE3 TRP A 53 2.948 3.416 -1.234 1.00 0.21 C
|
|
||||||
ATOM 858 CZ2 TRP A 53 4.946 1.474 -1.601 1.00 0.25 C
|
|
||||||
ATOM 859 CZ3 TRP A 53 2.684 2.251 -1.974 1.00 0.23 C
|
|
||||||
ATOM 860 CH2 TRP A 53 3.682 1.284 -2.156 1.00 0.25 C
|
|
||||||
ATOM 871 N ARG A 54 6.627 6.069 3.124 1.00 0.26 N
|
|
||||||
ATOM 872 CA ARG A 54 7.992 6.607 3.371 1.00 0.35 C
|
|
||||||
ATOM 873 C ARG A 54 8.988 5.823 2.515 1.00 0.49 C
|
|
||||||
ATOM 874 O ARG A 54 8.781 4.663 2.219 1.00 1.33 O
|
|
||||||
ATOM 875 CB ARG A 54 8.346 6.446 4.849 1.00 0.44 C
|
|
||||||
ATOM 876 CG ARG A 54 8.545 7.825 5.481 1.00 0.88 C
|
|
||||||
ATOM 877 CD ARG A 54 8.772 7.667 6.985 1.00 1.09 C
|
|
||||||
ATOM 878 NE ARG A 54 10.009 8.396 7.382 1.00 1.40 N
|
|
||||||
ATOM 879 CZ ARG A 54 10.254 8.632 8.637 1.00 1.87 C
|
|
||||||
ATOM 880 NH1 ARG A 54 10.719 7.683 9.399 1.00 2.47 N
|
|
||||||
ATOM 881 NH2 ARG A 54 10.035 9.816 9.133 1.00 2.46 N
|
|
||||||
ATOM 895 N GLN A 55 10.062 6.439 2.107 1.00 0.53 N
|
|
||||||
ATOM 896 CA GLN A 55 11.050 5.709 1.264 1.00 0.46 C
|
|
||||||
ATOM 897 C GLN A 55 10.308 5.032 0.111 1.00 0.53 C
|
|
||||||
ATOM 898 O GLN A 55 10.193 3.826 0.056 1.00 1.30 O
|
|
||||||
ATOM 899 CB GLN A 55 11.759 4.650 2.111 1.00 0.55 C
|
|
||||||
ATOM 900 CG GLN A 55 13.251 4.974 2.186 1.00 1.05 C
|
|
||||||
ATOM 901 CD GLN A 55 13.542 5.750 3.472 1.00 1.22 C
|
|
||||||
ATOM 902 OE1 GLN A 55 12.710 5.822 4.354 1.00 1.82 O
|
|
||||||
ATOM 903 NE2 GLN A 55 14.698 6.338 3.616 1.00 1.89 N
|
|
||||||
ATOM 912 N PHE A 56 9.791 5.807 -0.801 1.00 0.64 N
|
|
||||||
ATOM 913 CA PHE A 56 9.035 5.228 -1.949 1.00 0.57 C
|
|
||||||
ATOM 914 C PHE A 56 10.002 4.576 -2.944 1.00 0.71 C
|
|
||||||
ATOM 915 O PHE A 56 10.000 3.374 -3.124 1.00 1.62 O
|
|
||||||
ATOM 916 CB PHE A 56 8.267 6.356 -2.637 1.00 0.62 C
|
|
||||||
ATOM 917 CG PHE A 56 7.213 5.805 -3.572 1.00 0.57 C
|
|
||||||
ATOM 918 CD1 PHE A 56 6.938 4.430 -3.629 1.00 1.37 C
|
|
||||||
ATOM 919 CD2 PHE A 56 6.504 6.690 -4.386 1.00 1.31 C
|
|
||||||
ATOM 920 CE1 PHE A 56 5.953 3.951 -4.507 1.00 1.40 C
|
|
||||||
ATOM 921 CE2 PHE A 56 5.522 6.212 -5.260 1.00 1.40 C
|
|
||||||
ATOM 922 CZ PHE A 56 5.249 4.842 -5.323 1.00 0.79 C
|
|
||||||
ATOM 932 N GLU A 57 10.824 5.355 -3.595 1.00 0.67 N
|
|
||||||
ATOM 933 CA GLU A 57 11.784 4.768 -4.576 1.00 0.65 C
|
|
||||||
ATOM 934 C GLU A 57 12.637 3.708 -3.882 1.00 0.58 C
|
|
||||||
ATOM 935 O GLU A 57 13.002 2.709 -4.467 1.00 0.58 O
|
|
||||||
ATOM 936 CB GLU A 57 12.703 5.861 -5.118 1.00 0.80 C
|
|
||||||
ATOM 937 CG GLU A 57 11.991 6.634 -6.229 1.00 1.16 C
|
|
||||||
ATOM 938 CD GLU A 57 12.794 7.891 -6.571 1.00 1.75 C
|
|
||||||
ATOM 939 OE1 GLU A 57 13.812 8.110 -5.935 1.00 2.34 O
|
|
||||||
ATOM 940 OE2 GLU A 57 12.378 8.612 -7.462 1.00 2.41 O
|
|
||||||
ATOM 947 N GLN A 58 12.961 3.924 -2.638 1.00 0.58 N
|
|
||||||
ATOM 948 CA GLN A 58 13.786 2.942 -1.899 1.00 0.60 C
|
|
||||||
ATOM 949 C GLN A 58 12.982 1.655 -1.731 1.00 0.53 C
|
|
||||||
ATOM 950 O GLN A 58 13.524 0.569 -1.730 1.00 0.56 O
|
|
||||||
ATOM 951 CB GLN A 58 14.158 3.516 -0.530 1.00 0.69 C
|
|
||||||
ATOM 952 CG GLN A 58 15.064 4.735 -0.723 1.00 0.94 C
|
|
||||||
ATOM 953 CD GLN A 58 16.526 4.322 -0.542 1.00 1.56 C
|
|
||||||
ATOM 954 OE1 GLN A 58 16.810 3.268 -0.008 1.00 2.34 O
|
|
||||||
ATOM 955 NE2 GLN A 58 17.472 5.114 -0.966 1.00 1.94 N
|
|
||||||
ATOM 964 N SER A 59 11.685 1.773 -1.611 1.00 0.52 N
|
|
||||||
ATOM 965 CA SER A 59 10.829 0.560 -1.473 1.00 0.52 C
|
|
||||||
ATOM 966 C SER A 59 10.318 0.172 -2.859 1.00 0.44 C
|
|
||||||
ATOM 967 O SER A 59 9.371 -0.576 -3.002 1.00 0.48 O
|
|
||||||
ATOM 968 CB SER A 59 9.639 0.859 -0.562 1.00 0.65 C
|
|
||||||
ATOM 969 OG SER A 59 9.861 0.266 0.709 1.00 1.39 O
|
|
||||||
ATOM 975 N LYS A 60 10.954 0.675 -3.881 1.00 0.41 N
|
|
||||||
ATOM 976 CA LYS A 60 10.532 0.342 -5.266 1.00 0.42 C
|
|
||||||
ATOM 977 C LYS A 60 11.614 -0.520 -5.922 1.00 0.44 C
|
|
||||||
ATOM 978 O LYS A 60 11.326 -1.436 -6.666 1.00 0.55 O
|
|
||||||
ATOM 979 CB LYS A 60 10.356 1.636 -6.062 1.00 0.51 C
|
|
||||||
ATOM 980 CG LYS A 60 9.518 1.361 -7.311 1.00 1.03 C
|
|
||||||
ATOM 981 CD LYS A 60 9.317 2.665 -8.084 1.00 1.61 C
|
|
||||||
ATOM 982 CE LYS A 60 9.529 2.412 -9.575 1.00 2.36 C
|
|
||||||
ATOM 983 NZ LYS A 60 10.507 3.397 -10.112 1.00 3.11 N
|
|
||||||
ATOM 997 N GLN A 61 12.860 -0.228 -5.655 1.00 0.51 N
|
|
||||||
ATOM 998 CA GLN A 61 13.963 -1.020 -6.264 1.00 0.62 C
|
|
||||||
ATOM 999 C GLN A 61 14.010 -2.425 -5.651 1.00 0.60 C
|
|
||||||
ATOM 1000 O GLN A 61 13.841 -3.416 -6.332 1.00 0.66 O
|
|
||||||
ATOM 1001 CB GLN A 61 15.297 -0.315 -6.006 1.00 0.73 C
|
|
||||||
ATOM 1002 CG GLN A 61 15.326 1.021 -6.751 1.00 1.14 C
|
|
||||||
ATOM 1003 CD GLN A 61 16.704 1.221 -7.385 1.00 1.66 C
|
|
||||||
ATOM 1004 OE1 GLN A 61 17.499 0.303 -7.440 1.00 2.16 O
|
|
||||||
ATOM 1005 NE2 GLN A 61 17.024 2.390 -7.868 1.00 2.39 N
|
|
||||||
ATOM 1014 N LEU A 62 14.264 -2.497 -4.372 1.00 0.64 N
|
|
||||||
ATOM 1015 CA LEU A 62 14.358 -3.820 -3.661 1.00 0.71 C
|
|
||||||
ATOM 1016 C LEU A 62 13.391 -4.833 -4.276 1.00 0.67 C
|
|
||||||
ATOM 1017 O LEU A 62 13.653 -6.019 -4.302 1.00 0.94 O
|
|
||||||
ATOM 1018 CB LEU A 62 13.995 -3.678 -2.170 1.00 0.78 C
|
|
||||||
ATOM 1019 CG LEU A 62 13.609 -2.241 -1.817 1.00 0.78 C
|
|
||||||
ATOM 1020 CD1 LEU A 62 12.330 -1.844 -2.561 1.00 0.66 C
|
|
||||||
ATOM 1021 CD2 LEU A 62 13.367 -2.146 -0.310 1.00 0.94 C
|
|
||||||
ATOM 1033 N THR A 63 12.276 -4.379 -4.770 1.00 0.58 N
|
|
||||||
ATOM 1034 CA THR A 63 11.298 -5.309 -5.376 1.00 0.70 C
|
|
||||||
ATOM 1035 C THR A 63 10.933 -4.785 -6.761 1.00 0.81 C
|
|
||||||
ATOM 1036 O THR A 63 9.802 -4.445 -7.030 1.00 0.89 O
|
|
||||||
ATOM 1037 CB THR A 63 10.042 -5.450 -4.482 1.00 0.65 C
|
|
||||||
ATOM 1038 OG1 THR A 63 8.893 -5.599 -5.300 1.00 0.72 O
|
|
||||||
ATOM 1039 CG2 THR A 63 9.848 -4.231 -3.559 1.00 0.52 C
|
|
||||||
ATOM 1047 N GLU A 64 11.921 -4.721 -7.629 1.00 0.95 N
|
|
||||||
ATOM 1048 CA GLU A 64 11.731 -4.227 -9.035 1.00 1.21 C
|
|
||||||
ATOM 1049 C GLU A 64 10.247 -4.117 -9.389 1.00 1.18 C
|
|
||||||
ATOM 1050 O GLU A 64 9.570 -5.108 -9.578 1.00 1.53 O
|
|
||||||
ATOM 1051 CB GLU A 64 12.403 -5.214 -9.993 1.00 1.55 C
|
|
||||||
ATOM 1052 CG GLU A 64 12.903 -4.472 -11.231 1.00 1.91 C
|
|
||||||
ATOM 1053 CD GLU A 64 14.052 -5.257 -11.865 1.00 2.44 C
|
|
||||||
ATOM 1054 OE1 GLU A 64 14.291 -6.373 -11.432 1.00 3.09 O
|
|
||||||
ATOM 1055 OE2 GLU A 64 14.675 -4.730 -12.771 1.00 2.79 O
|
|
||||||
ATOM 1062 N ASN A 65 9.732 -2.920 -9.470 1.00 1.70 N
|
|
||||||
ATOM 1063 CA ASN A 65 8.289 -2.761 -9.802 1.00 1.68 C
|
|
||||||
ATOM 1064 C ASN A 65 7.456 -3.157 -8.582 1.00 0.85 C
|
|
||||||
ATOM 1065 O ASN A 65 6.375 -3.697 -8.706 1.00 1.09 O
|
|
||||||
ATOM 1066 CB ASN A 65 7.944 -3.685 -10.974 1.00 2.27 C
|
|
||||||
ATOM 1067 CG ASN A 65 6.828 -3.063 -11.814 1.00 2.89 C
|
|
||||||
ATOM 1068 OD1 ASN A 65 6.854 -1.884 -12.103 1.00 3.24 O
|
|
||||||
ATOM 1069 ND2 ASN A 65 5.844 -3.815 -12.224 1.00 3.66 N
|
|
||||||
ATOM 1076 N GLY A 66 7.968 -2.928 -7.401 1.00 0.56 N
|
|
||||||
ATOM 1077 CA GLY A 66 7.225 -3.330 -6.177 1.00 1.20 C
|
|
||||||
ATOM 1078 C GLY A 66 6.279 -2.227 -5.680 1.00 0.91 C
|
|
||||||
ATOM 1079 O GLY A 66 5.073 -2.381 -5.677 1.00 1.26 O
|
|
||||||
ATOM 1083 N ALA A 67 6.826 -1.155 -5.185 1.00 0.39 N
|
|
||||||
ATOM 1084 CA ALA A 67 5.996 -0.071 -4.590 1.00 0.46 C
|
|
||||||
ATOM 1085 C ALA A 67 5.313 0.846 -5.615 1.00 0.34 C
|
|
||||||
ATOM 1086 O ALA A 67 4.352 1.513 -5.286 1.00 0.53 O
|
|
||||||
ATOM 1087 CB ALA A 67 6.909 0.777 -3.713 1.00 0.64 C
|
|
||||||
ATOM 1093 N GLU A 68 5.778 0.935 -6.823 1.00 0.27 N
|
|
||||||
ATOM 1094 CA GLU A 68 5.129 1.851 -7.769 1.00 0.38 C
|
|
||||||
ATOM 1095 C GLU A 68 3.751 1.292 -8.176 1.00 0.39 C
|
|
||||||
ATOM 1096 O GLU A 68 2.884 2.021 -8.617 1.00 0.49 O
|
|
||||||
ATOM 1097 CB GLU A 68 6.069 2.020 -8.971 1.00 0.51 C
|
|
||||||
ATOM 1098 CG GLU A 68 5.274 2.020 -10.258 1.00 1.38 C
|
|
||||||
ATOM 1099 CD GLU A 68 6.148 2.521 -11.410 1.00 1.57 C
|
|
||||||
ATOM 1100 OE1 GLU A 68 6.989 3.370 -11.165 1.00 1.83 O
|
|
||||||
ATOM 1101 OE2 GLU A 68 5.961 2.047 -12.518 1.00 2.27 O
|
|
||||||
ATOM 1108 N SER A 69 3.544 0.011 -8.034 1.00 0.39 N
|
|
||||||
ATOM 1109 CA SER A 69 2.227 -0.585 -8.417 1.00 0.47 C
|
|
||||||
ATOM 1110 C SER A 69 1.196 -0.382 -7.297 1.00 0.37 C
|
|
||||||
ATOM 1111 O SER A 69 0.120 0.157 -7.510 1.00 0.35 O
|
|
||||||
ATOM 1112 CB SER A 69 2.405 -2.082 -8.669 1.00 0.58 C
|
|
||||||
ATOM 1113 OG SER A 69 2.127 -2.366 -10.033 1.00 0.90 O
|
|
||||||
ATOM 1119 N VAL A 70 1.509 -0.818 -6.106 1.00 0.34 N
|
|
||||||
ATOM 1120 CA VAL A 70 0.544 -0.662 -4.984 1.00 0.27 C
|
|
||||||
ATOM 1121 C VAL A 70 0.107 0.793 -4.912 1.00 0.20 C
|
|
||||||
ATOM 1122 O VAL A 70 -1.057 1.098 -4.748 1.00 0.20 O
|
|
||||||
ATOM 1123 CB VAL A 70 1.215 -1.063 -3.671 1.00 0.31 C
|
|
||||||
ATOM 1124 CG1 VAL A 70 0.288 -0.737 -2.499 1.00 0.29 C
|
|
||||||
ATOM 1125 CG2 VAL A 70 1.504 -2.565 -3.687 1.00 0.41 C
|
|
||||||
ATOM 1135 N LEU A 71 1.033 1.696 -5.048 1.00 0.24 N
|
|
||||||
ATOM 1136 CA LEU A 71 0.663 3.134 -5.002 1.00 0.23 C
|
|
||||||
ATOM 1137 C LEU A 71 -0.340 3.411 -6.113 1.00 0.23 C
|
|
||||||
ATOM 1138 O LEU A 71 -1.335 4.061 -5.909 1.00 0.23 O
|
|
||||||
ATOM 1139 CB LEU A 71 1.897 3.996 -5.229 1.00 0.30 C
|
|
||||||
ATOM 1140 CG LEU A 71 1.476 5.464 -5.305 1.00 0.35 C
|
|
||||||
ATOM 1141 CD1 LEU A 71 1.177 5.986 -3.899 1.00 0.36 C
|
|
||||||
ATOM 1142 CD2 LEU A 71 2.605 6.290 -5.924 1.00 0.43 C
|
|
||||||
ATOM 1154 N GLN A 72 -0.083 2.914 -7.289 1.00 0.28 N
|
|
||||||
ATOM 1155 CA GLN A 72 -1.027 3.138 -8.419 1.00 0.30 C
|
|
||||||
ATOM 1156 C GLN A 72 -2.417 2.716 -7.977 1.00 0.25 C
|
|
||||||
ATOM 1157 O GLN A 72 -3.408 3.314 -8.334 1.00 0.25 O
|
|
||||||
ATOM 1158 CB GLN A 72 -0.583 2.279 -9.617 1.00 0.35 C
|
|
||||||
ATOM 1159 CG GLN A 72 -1.789 1.868 -10.473 1.00 1.18 C
|
|
||||||
ATOM 1160 CD GLN A 72 -1.304 1.317 -11.813 1.00 1.42 C
|
|
||||||
ATOM 1161 OE1 GLN A 72 -1.069 2.064 -12.742 1.00 1.78 O
|
|
||||||
ATOM 1162 NE2 GLN A 72 -1.144 0.029 -11.955 1.00 1.97 N
|
|
||||||
ATOM 1171 N VAL A 73 -2.487 1.666 -7.230 1.00 0.23 N
|
|
||||||
ATOM 1172 CA VAL A 73 -3.797 1.162 -6.774 1.00 0.20 C
|
|
||||||
ATOM 1173 C VAL A 73 -4.352 2.055 -5.661 1.00 0.16 C
|
|
||||||
ATOM 1174 O VAL A 73 -5.547 2.201 -5.514 1.00 0.16 O
|
|
||||||
ATOM 1175 CB VAL A 73 -3.590 -0.254 -6.268 1.00 0.21 C
|
|
||||||
ATOM 1176 CG1 VAL A 73 -4.840 -0.752 -5.547 1.00 0.20 C
|
|
||||||
ATOM 1177 CG2 VAL A 73 -3.258 -1.151 -7.468 1.00 0.26 C
|
|
||||||
ATOM 1187 N PHE A 74 -3.501 2.649 -4.873 1.00 0.15 N
|
|
||||||
ATOM 1188 CA PHE A 74 -4.001 3.529 -3.773 1.00 0.14 C
|
|
||||||
ATOM 1189 C PHE A 74 -4.501 4.858 -4.358 1.00 0.16 C
|
|
||||||
ATOM 1190 O PHE A 74 -5.460 5.440 -3.887 1.00 0.18 O
|
|
||||||
ATOM 1191 CB PHE A 74 -2.868 3.807 -2.778 1.00 0.14 C
|
|
||||||
ATOM 1192 CG PHE A 74 -2.926 2.806 -1.651 1.00 0.12 C
|
|
||||||
ATOM 1193 CD1 PHE A 74 -3.895 2.932 -0.650 1.00 0.16 C
|
|
||||||
ATOM 1194 CD2 PHE A 74 -2.007 1.751 -1.608 1.00 0.16 C
|
|
||||||
ATOM 1195 CE1 PHE A 74 -3.946 2.003 0.395 1.00 0.18 C
|
|
||||||
ATOM 1196 CE2 PHE A 74 -2.058 0.822 -0.563 1.00 0.19 C
|
|
||||||
ATOM 1197 CZ PHE A 74 -3.027 0.949 0.439 1.00 0.19 C
|
|
||||||
ATOM 1207 N ARG A 75 -3.859 5.334 -5.388 1.00 0.19 N
|
|
||||||
ATOM 1208 CA ARG A 75 -4.271 6.610 -6.018 1.00 0.23 C
|
|
||||||
ATOM 1209 C ARG A 75 -5.453 6.341 -6.929 1.00 0.24 C
|
|
||||||
ATOM 1210 O ARG A 75 -6.368 7.124 -7.030 1.00 0.33 O
|
|
||||||
ATOM 1211 CB ARG A 75 -3.119 7.150 -6.851 1.00 0.26 C
|
|
||||||
ATOM 1212 CG ARG A 75 -1.995 7.625 -5.930 1.00 0.54 C
|
|
||||||
ATOM 1213 CD ARG A 75 -1.790 9.130 -6.107 1.00 1.28 C
|
|
||||||
ATOM 1214 NE ARG A 75 -1.186 9.394 -7.445 1.00 1.38 N
|
|
||||||
ATOM 1215 CZ ARG A 75 -1.177 10.604 -7.930 1.00 1.76 C
|
|
||||||
ATOM 1216 NH1 ARG A 75 -1.310 11.627 -7.134 1.00 2.43 N
|
|
||||||
ATOM 1217 NH2 ARG A 75 -1.032 10.790 -9.212 1.00 2.43 N
|
|
||||||
ATOM 1231 N GLU A 76 -5.429 5.219 -7.581 1.00 0.22 N
|
|
||||||
ATOM 1232 CA GLU A 76 -6.544 4.838 -8.482 1.00 0.23 C
|
|
||||||
ATOM 1233 C GLU A 76 -7.787 4.692 -7.616 1.00 0.21 C
|
|
||||||
ATOM 1234 O GLU A 76 -8.839 5.219 -7.917 1.00 0.23 O
|
|
||||||
ATOM 1235 CB GLU A 76 -6.206 3.501 -9.129 1.00 0.24 C
|
|
||||||
ATOM 1236 CG GLU A 76 -5.555 3.723 -10.494 1.00 0.30 C
|
|
||||||
ATOM 1237 CD GLU A 76 -6.631 4.058 -11.527 1.00 0.89 C
|
|
||||||
ATOM 1238 OE1 GLU A 76 -7.781 3.734 -11.282 1.00 1.65 O
|
|
||||||
ATOM 1239 OE2 GLU A 76 -6.286 4.632 -12.547 1.00 1.48 O
|
|
||||||
ATOM 1246 N ALA A 77 -7.653 4.005 -6.512 1.00 0.18 N
|
|
||||||
ATOM 1247 CA ALA A 77 -8.796 3.857 -5.591 1.00 0.17 C
|
|
||||||
ATOM 1248 C ALA A 77 -9.143 5.259 -5.113 1.00 0.19 C
|
|
||||||
ATOM 1249 O ALA A 77 -10.294 5.632 -5.003 1.00 0.20 O
|
|
||||||
ATOM 1250 CB ALA A 77 -8.403 2.975 -4.403 1.00 0.17 C
|
|
||||||
ATOM 1256 N LYS A 78 -8.133 6.059 -4.876 1.00 0.21 N
|
|
||||||
ATOM 1257 CA LYS A 78 -8.377 7.464 -4.462 1.00 0.24 C
|
|
||||||
ATOM 1258 C LYS A 78 -9.200 8.121 -5.560 1.00 0.28 C
|
|
||||||
ATOM 1259 O LYS A 78 -9.990 9.016 -5.336 1.00 0.32 O
|
|
||||||
ATOM 1260 CB LYS A 78 -7.038 8.187 -4.372 1.00 0.26 C
|
|
||||||
ATOM 1261 CG LYS A 78 -7.077 9.218 -3.247 1.00 0.32 C
|
|
||||||
ATOM 1262 CD LYS A 78 -7.173 10.619 -3.855 1.00 0.70 C
|
|
||||||
ATOM 1263 CE LYS A 78 -7.216 11.663 -2.738 1.00 0.99 C
|
|
||||||
ATOM 1264 NZ LYS A 78 -6.353 12.821 -3.109 1.00 1.50 N
|
|
||||||
ATOM 1278 N ALA A 79 -8.984 7.664 -6.756 1.00 0.28 N
|
|
||||||
ATOM 1279 CA ALA A 79 -9.690 8.204 -7.933 1.00 0.33 C
|
|
||||||
ATOM 1280 C ALA A 79 -11.110 7.645 -7.972 1.00 0.32 C
|
|
||||||
ATOM 1281 O ALA A 79 -12.027 8.262 -8.477 1.00 0.38 O
|
|
||||||
ATOM 1282 CB ALA A 79 -8.920 7.757 -9.173 1.00 0.35 C
|
|
||||||
ATOM 1288 N GLU A 80 -11.285 6.472 -7.440 1.00 0.28 N
|
|
||||||
ATOM 1289 CA GLU A 80 -12.620 5.829 -7.425 1.00 0.29 C
|
|
||||||
ATOM 1290 C GLU A 80 -13.585 6.626 -6.544 1.00 0.37 C
|
|
||||||
ATOM 1291 O GLU A 80 -14.762 6.332 -6.476 1.00 0.68 O
|
|
||||||
ATOM 1292 CB GLU A 80 -12.466 4.417 -6.865 1.00 0.32 C
|
|
||||||
ATOM 1293 CG GLU A 80 -12.076 3.469 -7.995 1.00 0.45 C
|
|
||||||
ATOM 1294 CD GLU A 80 -13.336 2.876 -8.627 1.00 0.67 C
|
|
||||||
ATOM 1295 OE1 GLU A 80 -13.927 3.543 -9.460 1.00 1.40 O
|
|
||||||
ATOM 1296 OE2 GLU A 80 -13.688 1.764 -8.269 1.00 1.30 O
|
|
||||||
ATOM 1303 N GLY A 81 -13.098 7.621 -5.858 1.00 0.39 N
|
|
||||||
ATOM 1304 CA GLY A 81 -13.987 8.421 -4.973 1.00 0.45 C
|
|
||||||
ATOM 1305 C GLY A 81 -13.572 8.186 -3.522 1.00 0.39 C
|
|
||||||
ATOM 1306 O GLY A 81 -13.963 8.908 -2.626 1.00 0.45 O
|
|
||||||
ATOM 1310 N CYS A 82 -12.776 7.179 -3.288 1.00 0.41 N
|
|
||||||
ATOM 1311 CA CYS A 82 -12.322 6.888 -1.905 1.00 0.38 C
|
|
||||||
ATOM 1312 C CYS A 82 -11.476 8.057 -1.395 1.00 0.38 C
|
|
||||||
ATOM 1313 O CYS A 82 -10.977 8.854 -2.164 1.00 0.49 O
|
|
||||||
ATOM 1314 CB CYS A 82 -11.480 5.614 -1.920 1.00 0.39 C
|
|
||||||
ATOM 1315 SG CYS A 82 -12.566 4.168 -1.820 1.00 0.63 S
|
|
||||||
ATOM 1321 N ASP A 83 -11.316 8.173 -0.105 1.00 0.32 N
|
|
||||||
ATOM 1322 CA ASP A 83 -10.510 9.298 0.444 1.00 0.37 C
|
|
||||||
ATOM 1323 C ASP A 83 -9.188 8.769 1.009 1.00 0.36 C
|
|
||||||
ATOM 1324 O ASP A 83 -8.935 8.844 2.195 1.00 0.57 O
|
|
||||||
ATOM 1325 CB ASP A 83 -11.305 9.984 1.553 1.00 0.42 C
|
|
||||||
ATOM 1326 CG ASP A 83 -10.709 11.364 1.834 1.00 0.53 C
|
|
||||||
ATOM 1327 OD1 ASP A 83 -9.782 11.437 2.624 1.00 1.11 O
|
|
||||||
ATOM 1328 OD2 ASP A 83 -11.191 12.324 1.255 1.00 1.30 O
|
|
||||||
ATOM 1333 N ILE A 84 -8.339 8.244 0.168 1.00 0.33 N
|
|
||||||
ATOM 1334 CA ILE A 84 -7.028 7.720 0.652 1.00 0.31 C
|
|
||||||
ATOM 1335 C ILE A 84 -5.965 8.818 0.503 1.00 0.34 C
|
|
||||||
ATOM 1336 O ILE A 84 -5.289 8.905 -0.503 1.00 0.67 O
|
|
||||||
ATOM 1337 CB ILE A 84 -6.622 6.513 -0.191 1.00 0.30 C
|
|
||||||
ATOM 1338 CG1 ILE A 84 -7.546 5.345 0.117 1.00 0.50 C
|
|
||||||
ATOM 1339 CG2 ILE A 84 -5.182 6.114 0.131 1.00 0.28 C
|
|
||||||
ATOM 1340 CD1 ILE A 84 -8.049 4.762 -1.198 1.00 0.34 C
|
|
||||||
ATOM 1352 N THR A 85 -5.813 9.657 1.490 1.00 0.49 N
|
|
||||||
ATOM 1353 CA THR A 85 -4.796 10.748 1.400 1.00 0.50 C
|
|
||||||
ATOM 1354 C THR A 85 -3.430 10.156 1.047 1.00 0.47 C
|
|
||||||
ATOM 1355 O THR A 85 -2.721 9.661 1.897 1.00 0.60 O
|
|
||||||
ATOM 1356 CB THR A 85 -4.702 11.468 2.749 1.00 0.61 C
|
|
||||||
ATOM 1357 OG1 THR A 85 -5.862 12.265 2.940 1.00 0.76 O
|
|
||||||
ATOM 1358 CG2 THR A 85 -3.458 12.361 2.773 1.00 0.55 C
|
|
||||||
ATOM 1366 N ILE A 86 -3.051 10.211 -0.200 1.00 0.41 N
|
|
||||||
ATOM 1367 CA ILE A 86 -1.727 9.654 -0.602 1.00 0.40 C
|
|
||||||
ATOM 1368 C ILE A 86 -0.610 10.583 -0.118 1.00 0.44 C
|
|
||||||
ATOM 1369 O ILE A 86 -0.489 11.706 -0.564 1.00 0.59 O
|
|
||||||
ATOM 1370 CB ILE A 86 -1.665 9.540 -2.126 1.00 0.38 C
|
|
||||||
ATOM 1371 CG1 ILE A 86 -2.821 8.668 -2.620 1.00 0.74 C
|
|
||||||
ATOM 1372 CG2 ILE A 86 -0.331 8.915 -2.540 1.00 0.93 C
|
|
||||||
ATOM 1373 CD1 ILE A 86 -2.613 7.223 -2.166 1.00 0.32 C
|
|
||||||
ATOM 1385 N ILE A 87 0.212 10.123 0.786 1.00 0.39 N
|
|
||||||
ATOM 1386 CA ILE A 87 1.322 10.982 1.287 1.00 0.44 C
|
|
||||||
ATOM 1387 C ILE A 87 2.659 10.368 0.860 1.00 0.44 C
|
|
||||||
ATOM 1388 O ILE A 87 3.132 9.413 1.442 1.00 0.55 O
|
|
||||||
ATOM 1389 CB ILE A 87 1.247 11.073 2.813 1.00 0.46 C
|
|
||||||
ATOM 1390 CG1 ILE A 87 0.091 11.995 3.208 1.00 0.57 C
|
|
||||||
ATOM 1391 CG2 ILE A 87 2.556 11.640 3.362 1.00 0.55 C
|
|
||||||
ATOM 1392 CD1 ILE A 87 -0.237 11.800 4.689 1.00 0.61 C
|
|
||||||
ATOM 1404 N LEU A 88 3.259 10.902 -0.170 1.00 0.50 N
|
|
||||||
ATOM 1405 CA LEU A 88 4.552 10.348 -0.662 1.00 0.52 C
|
|
||||||
ATOM 1406 C LEU A 88 5.728 11.146 -0.093 1.00 0.56 C
|
|
||||||
ATOM 1407 O LEU A 88 5.984 12.263 -0.495 1.00 0.80 O
|
|
||||||
ATOM 1408 CB LEU A 88 4.558 10.413 -2.173 1.00 0.59 C
|
|
||||||
ATOM 1409 CG LEU A 88 3.653 9.297 -2.669 1.00 0.82 C
|
|
||||||
ATOM 1410 CD1 LEU A 88 2.691 9.851 -3.697 1.00 0.94 C
|
|
||||||
ATOM 1411 CD2 LEU A 88 4.496 8.193 -3.286 1.00 1.57 C
|
|
||||||
ATOM 1423 N SER A 89 6.445 10.581 0.841 1.00 0.55 N
|
|
||||||
ATOM 1424 CA SER A 89 7.604 11.308 1.435 1.00 0.62 C
|
|
||||||
ATOM 1425 C SER A 89 8.908 10.659 0.968 1.00 0.85 C
|
|
||||||
ATOM 1426 O SER A 89 8.935 9.445 0.852 1.00 1.41 O
|
|
||||||
ATOM 1427 CB SER A 89 7.520 11.241 2.961 1.00 0.87 C
|
|
||||||
ATOM 1428 OG SER A 89 7.246 12.538 3.473 1.00 1.64 O
|
|
||||||
ATOM 1429 OXT SER A 89 9.859 11.388 0.735 1.00 1.52 O
|
|
||||||
TER 1435 SER A 89
|
|
||||||
MASTER 97 1 0 4 3 0 0 6 1434 1 0 7
|
|
||||||
END
|
|
||||||
4228
data/1est_H.pdb
4228
data/1est_H.pdb
File diff suppressed because it is too large
Load Diff
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
498
src/chem.py~
498
src/chem.py~
|
|
@ -1,498 +0,0 @@
|
||||||
import math
|
|
||||||
#from structure import *
|
|
||||||
from geom import *
|
|
||||||
|
|
||||||
class Atom:
|
|
||||||
|
|
||||||
def dist_atoms(self, atom2):
|
|
||||||
return(math.sqrt((self.coord_x-atom2.coord_x)**2 +
|
|
||||||
(self.coord_y-atom2.coord_y)**2 +
|
|
||||||
(self.coord_z-atom2.coord_z)**2))
|
|
||||||
|
|
||||||
|
|
||||||
def __init__(self, atom_id, atom_name, res_name, chain_id,
|
|
||||||
res_seq_nb, insertion_code, coordinates):
|
|
||||||
self.atom_id = atom_id
|
|
||||||
self.atom_name = atom_name
|
|
||||||
self.res_name = res_name
|
|
||||||
self.chain_id = chain_id
|
|
||||||
self.res_seq_nb = res_seq_nb
|
|
||||||
self.insertion_code = insertion_code
|
|
||||||
self.coord_x = coordinates[0]
|
|
||||||
self.coord_y = coordinates[1]
|
|
||||||
self.coord_z = coordinates[2]
|
|
||||||
self.coords = coordinates
|
|
||||||
|
|
||||||
class Structure:
|
|
||||||
def __init__(self, res):
|
|
||||||
self.res = res
|
|
||||||
|
|
||||||
class Turn(Structure):
|
|
||||||
|
|
||||||
def __init__(self, turn_type, res):
|
|
||||||
self.turn_type = turn_type
|
|
||||||
Structure.res = res
|
|
||||||
|
|
||||||
class Bridge(Structure):
|
|
||||||
|
|
||||||
def __init__(self, bridge_type, res_num, res_partner, indices):
|
|
||||||
self.bridge_type = bridge_type
|
|
||||||
self.res_num = res_num
|
|
||||||
self.res_partner = res_partner
|
|
||||||
Structure.res = res_num
|
|
||||||
self.i = indices[0]
|
|
||||||
self.j = indices[1]
|
|
||||||
|
|
||||||
class Helix(Structure):
|
|
||||||
|
|
||||||
def __init__(self, residues, res_num, helix_type):
|
|
||||||
self.residues = residues
|
|
||||||
self.res_num = res_num
|
|
||||||
Structure.res = res_num
|
|
||||||
self.helix_type = helix_type
|
|
||||||
|
|
||||||
|
|
||||||
class Residue:
|
|
||||||
def __init__(self, atoms_list, indice):
|
|
||||||
self.atoms = {}
|
|
||||||
for atom in atoms_list:
|
|
||||||
self.atoms[atom.atom_name] = atom
|
|
||||||
self.resid = atom.res_seq_nb
|
|
||||||
self.res_name = atom.res_name
|
|
||||||
self.res_letter = self.get_amino_letter(atom.res_name)
|
|
||||||
self.chain_id = atom.chain_id
|
|
||||||
self.insertion_code = atom.insertion_code
|
|
||||||
self.indice = indice
|
|
||||||
|
|
||||||
def get_amino_letter(self, res_name):
|
|
||||||
code3 = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY',
|
|
||||||
'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER',
|
|
||||||
'THR', 'TRP', 'TYR', 'VAL']
|
|
||||||
|
|
||||||
|
|
||||||
code1 = ['A','R','N','D','C','E','Q','G','H','I','L','K','M','F','P',
|
|
||||||
'S','T','W','Y','V']
|
|
||||||
|
|
||||||
return code1[code3.index(res_name)]
|
|
||||||
|
|
||||||
def h_bond(self, res2):
|
|
||||||
if("H" not in res2.atoms.keys()):
|
|
||||||
return(False)
|
|
||||||
# dimensionnal factor, in kcal/mole
|
|
||||||
f = 332
|
|
||||||
# partial charges
|
|
||||||
q1 = 0.42
|
|
||||||
q2 = 0.20
|
|
||||||
# distance between O-N atoms, in angströms
|
|
||||||
r_ON = self.atoms["O"].dist_atoms(res2.atoms["N"])
|
|
||||||
# distance between C-H atoms, in angströms
|
|
||||||
r_CH = self.atoms["C"].dist_atoms(res2.atoms["H"])
|
|
||||||
# distance between O-H atoms, in angströms
|
|
||||||
r_OH = self.atoms["O"].dist_atoms(res2.atoms["H"])
|
|
||||||
# distance between C-N atoms, in angströms
|
|
||||||
r_CN = self.atoms["C"].dist_atoms(res2.atoms["N"])
|
|
||||||
# electrostatic interaction energy, in kcal/mole
|
|
||||||
E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
|
|
||||||
return(E)
|
|
||||||
|
|
||||||
def get_turns(self, residues):
|
|
||||||
"""
|
|
||||||
Get all the turns from a specific residue.
|
|
||||||
"""
|
|
||||||
turns = {}
|
|
||||||
i = residues.index(self)
|
|
||||||
k = 0
|
|
||||||
for j in range(3,6):
|
|
||||||
if(i+j<len(residues)):
|
|
||||||
if(self.h_bond(residues[i+j])<-0.5):
|
|
||||||
k = j
|
|
||||||
if k != 0:
|
|
||||||
#print(k,"TURN", residues[i].resid, residues[i+k].resid)
|
|
||||||
return Turn(k,residues[i].resid)
|
|
||||||
|
|
||||||
return False
|
|
||||||
|
|
||||||
def get_bends(self, residues):
|
|
||||||
i = residues.index(self)
|
|
||||||
if i >=2 and i <len(residues)-2:
|
|
||||||
angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
|
|
||||||
position_vector(residues[i-2].atoms["CA"].coords)),
|
|
||||||
vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
|
|
||||||
position_vector(residues[i].atoms["CA"].coords))))
|
|
||||||
if(angle>70):
|
|
||||||
return [angle, 'S']
|
|
||||||
return [angle, '']
|
|
||||||
else:
|
|
||||||
return [360.0, '']
|
|
||||||
|
|
||||||
def get_bridges(self, residues):
|
|
||||||
bridges = {}
|
|
||||||
bridge = {}
|
|
||||||
strongest_bridge = {}
|
|
||||||
i = residues.index(self)
|
|
||||||
if(i >= 1 and i < len(residues)-4):
|
|
||||||
E_min = 0
|
|
||||||
for j in range(i+2,len(residues)-1):
|
|
||||||
# select triplet with the minimal energy
|
|
||||||
|
|
||||||
if(residues[i-1].h_bond(residues[j])<-0.5
|
|
||||||
and residues[j].h_bond(residues[i+1])<-0.5):
|
|
||||||
bridge = {'res1':residues[i-1].h_bond(residues[j]),
|
|
||||||
'res2':residues[j].h_bond(residues[i+1]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'btype':"para"}
|
|
||||||
|
|
||||||
if(residues[j-1].h_bond(residues[i])<-0.5
|
|
||||||
and residues[i].h_bond(residues[j+1])<-0.5):
|
|
||||||
bridge = {'res1':residues[j-1].h_bond(residues[i]),
|
|
||||||
'res2':residues[i].h_bond(residues[j+1]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'btype':"para"}
|
|
||||||
|
|
||||||
if(residues[i].h_bond(residues[j])<-0.5
|
|
||||||
and residues[j].h_bond(residues[i])<-0.5):
|
|
||||||
bridge = {'res1':residues[i].h_bond(residues[j]),
|
|
||||||
'res2':residues[j].h_bond(residues[i]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'btype':"anti"}
|
|
||||||
|
|
||||||
if(residues[i-1].h_bond(residues[j+1])<-0.5
|
|
||||||
and residues[j-1].h_bond(residues[i+1])<-0.5):
|
|
||||||
bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
|
|
||||||
'res2':residues[j-1].h_bond(residues[i+1]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'btype':"anti"}
|
|
||||||
|
|
||||||
if(bridge):
|
|
||||||
if(bridge['res1']+bridge['res2']<E_min):
|
|
||||||
E_min = bridge['res1']+bridge['res2']
|
|
||||||
strongest_bridge = bridge
|
|
||||||
bridge = {}
|
|
||||||
coord_bridge = [i,j]
|
|
||||||
# finally add the strongest bridge at i and j pos
|
|
||||||
if(strongest_bridge):
|
|
||||||
bridges[coord_bridge[0]] = (Bridge(strongest_bridge['btype'],
|
|
||||||
strongest_bridge['ipos'],
|
|
||||||
strongest_bridge['jpos']))
|
|
||||||
|
|
||||||
bridges[coord_bridge[1]] = (Bridge(strongest_bridge['btype'],
|
|
||||||
strongest_bridge['jpos'],
|
|
||||||
strongest_bridge['ipos']))
|
|
||||||
if(len(bridges)>0):
|
|
||||||
return(bridges[coord_bridge[0]])
|
|
||||||
else:
|
|
||||||
return(False)
|
|
||||||
|
|
||||||
def get_helix(self, residues):
|
|
||||||
"""
|
|
||||||
Return if there is an helix at a given residue,
|
|
||||||
as well as its type.
|
|
||||||
"""
|
|
||||||
i = residues.index(self)
|
|
||||||
# if there are no turns or it is the first residue, skip
|
|
||||||
if i == 0:
|
|
||||||
return False
|
|
||||||
|
|
||||||
if(self.get_turns(residues) and residues[i-1].get_turns(residues)):
|
|
||||||
#print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].indice)
|
|
||||||
return(self.get_turns(residues).turn_type, residues[i].indice)
|
|
||||||
return(False)
|
|
||||||
|
|
||||||
def get_ladder(self, residues):
|
|
||||||
#ladders = {}
|
|
||||||
i = residues.index(self)
|
|
||||||
if i != 0:
|
|
||||||
if self.get_bridges(residues):
|
|
||||||
if (residues[i-1].get_bridges(residues)):
|
|
||||||
local_bridge = self.get_bridges(residues)
|
|
||||||
consec_bridge = residues[i-1].get_bridges(residues)
|
|
||||||
if local_bridge.bridge_type == consec_bridge.bridge_type:
|
|
||||||
#print("ladder", consec_bridge.res_num, local_bridge.res_num)
|
|
||||||
ladder = {'start':consec_bridge.res_num,
|
|
||||||
'end':local_bridge.res_num,
|
|
||||||
'bridges':[consec_bridge, local_bridge]}
|
|
||||||
return ladder
|
|
||||||
return False
|
|
||||||
|
|
||||||
def get_tco(self, residues):
|
|
||||||
i = residues.index(self)
|
|
||||||
if(i!=0):
|
|
||||||
res2 = residues[i-1]
|
|
||||||
CO_res1 = vector_from_pos(self.atoms["C"].coords,
|
|
||||||
self.atoms["O"].coords)
|
|
||||||
CO_res2 = vector_from_pos(res2.atoms["C"].coords,
|
|
||||||
res2.atoms["O"].coords)
|
|
||||||
angle = vector_angles(CO_res1, CO_res2)
|
|
||||||
else:
|
|
||||||
angle = math.pi/2
|
|
||||||
return(math.cos(angle))
|
|
||||||
|
|
||||||
def get_chirality(self, residues):
|
|
||||||
i = residues.index(self)
|
|
||||||
if (i >=1 and i < len(residues)-2):
|
|
||||||
chirality = {}
|
|
||||||
angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
|
|
||||||
residues[i].atoms["CA"].coords,
|
|
||||||
residues[i+1].atoms["CA"].coords,
|
|
||||||
residues[i+2].atoms["CA"].coords)
|
|
||||||
|
|
||||||
if(angle>0 and angle<=180):
|
|
||||||
sign="+"
|
|
||||||
|
|
||||||
if(angle<=0 and angle > -180):
|
|
||||||
sign="-"
|
|
||||||
|
|
||||||
else:
|
|
||||||
angle = 360.0
|
|
||||||
sign = ''
|
|
||||||
|
|
||||||
return [angle, sign]
|
|
||||||
|
|
||||||
def get_phi_psi(self, residues):
|
|
||||||
i = residues.index(self)
|
|
||||||
if(i==0):
|
|
||||||
phi = 360.0
|
|
||||||
else:
|
|
||||||
phi = calc_dihedral(residues[i-1].atoms["C"].coords,
|
|
||||||
residues[i].atoms["N"].coords,
|
|
||||||
residues[i].atoms["CA"].coords,
|
|
||||||
residues[i].atoms["C"].coords)
|
|
||||||
if(i==len(residues)-1):
|
|
||||||
psi = 360.0
|
|
||||||
else:
|
|
||||||
psi = calc_dihedral(residues[i].atoms["N"].coords,
|
|
||||||
residues[i].atoms["CA"].coords,
|
|
||||||
residues[i].atoms["C"].coords,
|
|
||||||
residues[i+1].atoms["N"].coords)
|
|
||||||
|
|
||||||
return((phi, psi))
|
|
||||||
def get_bridges(residues):
|
|
||||||
bridges = {}
|
|
||||||
bridge = {}
|
|
||||||
strongest_bridge = {}
|
|
||||||
for i in range(1,len(residues)-4):
|
|
||||||
E_min = 0
|
|
||||||
for j in range(i+2,len(residues)-1):
|
|
||||||
# select triplet with the minimal energy
|
|
||||||
|
|
||||||
if(residues[i-1].h_bond(residues[j])<-0.5
|
|
||||||
and residues[j].h_bond(residues[i+1])<-0.5):
|
|
||||||
bridge = {'res1':residues[i-1].h_bond(residues[j]),
|
|
||||||
'res2':residues[j].h_bond(residues[i+1]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'i':residues[i].indice,
|
|
||||||
'j':residues[j].indice,
|
|
||||||
'btype':"para"}
|
|
||||||
|
|
||||||
if(residues[j-1].h_bond(residues[i])<-0.5
|
|
||||||
and residues[i].h_bond(residues[j+1])<-0.5):
|
|
||||||
bridge = {'res1':residues[j-1].h_bond(residues[i]),
|
|
||||||
'res2':residues[i].h_bond(residues[j+1]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'i':residues[i].indice,
|
|
||||||
'j':residues[j].indice,
|
|
||||||
'btype':"para"}
|
|
||||||
|
|
||||||
if(residues[i].h_bond(residues[j])<-0.5
|
|
||||||
and residues[j].h_bond(residues[i])<-0.5):
|
|
||||||
bridge = {'res1':residues[i].h_bond(residues[j]),
|
|
||||||
'res2':residues[j].h_bond(residues[i]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'i':residues[i].indice,
|
|
||||||
'j':residues[j].indice,
|
|
||||||
'btype':"anti"}
|
|
||||||
|
|
||||||
if(residues[i-1].h_bond(residues[j+1])<-0.5
|
|
||||||
and residues[j-1].h_bond(residues[i+1])<-0.5):
|
|
||||||
bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
|
|
||||||
'res2':residues[j-1].h_bond(residues[i+1]),
|
|
||||||
'ipos':residues[i].resid,
|
|
||||||
'jpos':residues[j].resid,
|
|
||||||
'i':residues[i].indice,
|
|
||||||
'j':residues[j].indice,
|
|
||||||
'btype':"anti"}
|
|
||||||
|
|
||||||
if(bridge):
|
|
||||||
if(bridge['res1']+bridge['res2']<E_min):
|
|
||||||
E_min = bridge['res1']+bridge['res2']
|
|
||||||
strongest_bridge = bridge
|
|
||||||
coord_bridge = [i,j]
|
|
||||||
bridge = {}
|
|
||||||
|
|
||||||
# finally add the strongest bridge at i and j pos
|
|
||||||
if(strongest_bridge):
|
|
||||||
|
|
||||||
bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
|
|
||||||
strongest_bridge['ipos'],
|
|
||||||
strongest_bridge['jpos'],
|
|
||||||
[strongest_bridge['i'],
|
|
||||||
strongest_bridge['j']]))
|
|
||||||
|
|
||||||
bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
|
|
||||||
strongest_bridge['ipos'],
|
|
||||||
strongest_bridge['jpos'],
|
|
||||||
[strongest_bridge['i'],
|
|
||||||
strongest_bridge['j']]))
|
|
||||||
if(len(bridges)>0):
|
|
||||||
return(bridges)
|
|
||||||
else:
|
|
||||||
return(False)
|
|
||||||
|
|
||||||
def get_ladders(bridges, residues):
|
|
||||||
ladders = {}
|
|
||||||
i = 1
|
|
||||||
while i < len(residues):
|
|
||||||
k = 1
|
|
||||||
if i in bridges.keys():
|
|
||||||
temp_bridges = [bridges[i]]
|
|
||||||
while ((i+k in bridges.keys()) and
|
|
||||||
(bridges[i].bridge_type == bridges[i+k].bridge_type)):
|
|
||||||
temp_bridges.append(bridges[i+k])
|
|
||||||
k+=1
|
|
||||||
if k>1:
|
|
||||||
#print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
|
|
||||||
ladders[i] = {'start':bridges[i].res_num,
|
|
||||||
'end':bridges[i+k-1].res_num,
|
|
||||||
'bridges':temp_bridges,
|
|
||||||
'i':i,
|
|
||||||
'j':i+k-1}
|
|
||||||
i+=k-1
|
|
||||||
else:
|
|
||||||
i+=1
|
|
||||||
return ladders
|
|
||||||
|
|
||||||
def connected_ladders(ladd_1, ladd_2):
|
|
||||||
links = []
|
|
||||||
for bridge in ladd_1['bridges']:
|
|
||||||
if bridge.res_partner in res_list(ladd_2):
|
|
||||||
return ladd_2
|
|
||||||
|
|
||||||
return False
|
|
||||||
|
|
||||||
def connected_ladders2(ladd_1, ladd_2):
|
|
||||||
links = []
|
|
||||||
for bridge in ladd_1['bridges']:
|
|
||||||
if bridge.res_partner in res_list(ladd_2):
|
|
||||||
return([ladd_1['i'], ladd_1['j'], bridge.i, bridge.j,
|
|
||||||
ladd_2['i'], ladd_2['j']])
|
|
||||||
#return ladd_2
|
|
||||||
|
|
||||||
return False
|
|
||||||
|
|
||||||
|
|
||||||
def get_sheets(ladders):
|
|
||||||
"""
|
|
||||||
Bridges between ladders.
|
|
||||||
Check if 1 bridge between one ladder and one or more other ladders.
|
|
||||||
Iterate over all residues of one ladder and check if bridge with other residues
|
|
||||||
of the other ladders.
|
|
||||||
"""
|
|
||||||
ladds = [ elem for elem in ladders.values() ]
|
|
||||||
sheets = {}
|
|
||||||
|
|
||||||
corresp = {}
|
|
||||||
for ladd1 in ladds:
|
|
||||||
for ladd2 in ladds:
|
|
||||||
if connected_ladders(ladd1, ladd2)!=False:
|
|
||||||
corresp_list = [ elem for elem in corresp.keys() ]
|
|
||||||
if ladd1['i'] not in corresp_list and ladd2['i'] not in corresp_list:
|
|
||||||
ind = len(sheets.keys())
|
|
||||||
sheets[ind] = []
|
|
||||||
sheets[ind].append(ladd1)
|
|
||||||
sheets[ind].append(ladd2)
|
|
||||||
corresp[ladd1['i']] = ind
|
|
||||||
corresp[ladd2['i']] = ind
|
|
||||||
elif ladd2 not in corresp_list and ladd1 in corresp_list:
|
|
||||||
sheets[corresp[ladd1['i']]].append(ladd2)
|
|
||||||
corresp[ladd2['i']] = corresp[ladd1['i']]
|
|
||||||
elif ladd1 not in corresp_list and ladd2 in corresp_list:
|
|
||||||
sheets[corresp[ladd2['i']]].append(ladd1)
|
|
||||||
corresp[ladd1['i']] = corresp[ladd2['i']]
|
|
||||||
|
|
||||||
return sheets
|
|
||||||
|
|
||||||
def get_sheets2(ladders):
|
|
||||||
"""
|
|
||||||
Bridges between ladders.
|
|
||||||
Check if 1 bridge between one ladder and one or more other ladders.
|
|
||||||
Iterate over all residues of one ladder and check if bridge with other residues
|
|
||||||
of the other ladders.
|
|
||||||
"""
|
|
||||||
sheets = {}
|
|
||||||
for ladder in ladders:
|
|
||||||
for ladd2 in ladders:
|
|
||||||
if connected_ladders(ladders[ladder], ladders[ladd2]):
|
|
||||||
bridge_i = connected_ladders2(ladders[ladder], ladders[ladd2])[2]
|
|
||||||
bridge_j = connected_ladders2(ladders[ladder], ladders[ladd2])[3]
|
|
||||||
print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge_i, bridge_j,
|
|
||||||
"ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j'])
|
|
||||||
|
|
||||||
|
|
||||||
def res_list(ladder):
|
|
||||||
# TODO : method in ladder class
|
|
||||||
l=[]
|
|
||||||
for i in range(ladder['i'], ladder['j']):
|
|
||||||
l.append(i)
|
|
||||||
return(l)
|
|
||||||
|
|
||||||
def build_turns_patterns(residues):
|
|
||||||
turns_3 = {}
|
|
||||||
turns_4 = {}
|
|
||||||
turns_5 = {}
|
|
||||||
for i,res in enumerate(residues):
|
|
||||||
turn = residues[i].get_turns(residues)
|
|
||||||
if(turn):
|
|
||||||
for k in range(turn.turn_type):
|
|
||||||
if turn.turn_type == 3:
|
|
||||||
turns_3[i+1+k] = turn.turn_type
|
|
||||||
if turn.turn_type == 4:
|
|
||||||
turns_4[i+1+k] = turn.turn_type
|
|
||||||
if turn.turn_type == 5:
|
|
||||||
turns_5[i+1+k] = turn.turn_type
|
|
||||||
return[turns_3, turns_4, turns_5]
|
|
||||||
|
|
||||||
def build_helix_patterns(residues):
|
|
||||||
helix_3 = {}
|
|
||||||
helix_4 = {}
|
|
||||||
helix_5 = {}
|
|
||||||
for i,res in enumerate(residues):
|
|
||||||
helix = residues[i].get_helix(residues)
|
|
||||||
if(helix):
|
|
||||||
helix_type = residues[i].get_helix(residues)[0]
|
|
||||||
helix_pos = residues[i].get_helix(residues)[1]
|
|
||||||
#print("TYPE", helix_type)
|
|
||||||
for k in range(helix_type):
|
|
||||||
if helix_type == 3:
|
|
||||||
helix_3[i+1+k] = "G"
|
|
||||||
if helix_type == 4:
|
|
||||||
helix_4[i+1+k] = "H"
|
|
||||||
if helix_type == 5:
|
|
||||||
helix_5[i+1+k] = "I"
|
|
||||||
#print(helix_3)
|
|
||||||
return[helix_3, helix_4, helix_5]
|
|
||||||
|
|
||||||
def print_helix_pattern(residues, res, helix):
|
|
||||||
i = residues.index(res)+1
|
|
||||||
if i in helix.keys():
|
|
||||||
return (helix[i])
|
|
||||||
else:
|
|
||||||
return(' ')
|
|
||||||
|
|
||||||
def print_turn_pattern(residues, res, turns):
|
|
||||||
i = residues.index(res)+1
|
|
||||||
if i in turns.keys() and not i-1 in turns.keys():
|
|
||||||
return(">")
|
|
||||||
elif i in turns.keys() and i-1 in turns.keys():
|
|
||||||
return(turns[i])
|
|
||||||
elif i not in turns.keys() and i-1 in turns.keys():
|
|
||||||
return("<")
|
|
||||||
else:
|
|
||||||
return(' ')
|
|
||||||
|
|
||||||
42
src/pdb.py
42
src/pdb.py
|
|
@ -6,10 +6,39 @@ import pymol
|
||||||
|
|
||||||
class PDBFile:
|
class PDBFile:
|
||||||
def get_content(self, filename):
|
def get_content(self, filename):
|
||||||
|
"""Get content of a PDB file
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
filename : str
|
||||||
|
The name of the file to be parsed.
|
||||||
|
|
||||||
|
This function is used to get the raw content
|
||||||
|
of the PDB file.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
list
|
||||||
|
List of lines of the PDB file.
|
||||||
|
"""
|
||||||
with open(filename) as f:
|
with open(filename) as f:
|
||||||
return(f.readlines())
|
return(f.readlines())
|
||||||
|
|
||||||
def get_header(self):
|
def get_header(self):
|
||||||
|
"""Returns header of a PDB file
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
self : PDBFile
|
||||||
|
The instance of PDB File to get the header from.
|
||||||
|
|
||||||
|
This function is used to get the header of the PDB file.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
dict
|
||||||
|
A field-formatted metadata header.
|
||||||
|
"""
|
||||||
metadata = {}
|
metadata = {}
|
||||||
for line in self.rawLines:
|
for line in self.rawLines:
|
||||||
# no need to continue if meta are complete
|
# no need to continue if meta are complete
|
||||||
|
|
@ -28,6 +57,19 @@ class PDBFile:
|
||||||
return(metadata)
|
return(metadata)
|
||||||
|
|
||||||
def get_atoms(self, filename):
|
def get_atoms(self, filename):
|
||||||
|
"""Get all atoms inside a PDB file.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
self : PDBFile
|
||||||
|
The instance of PDB File to get the header from.
|
||||||
|
filename :
|
||||||
|
The name of the file. Used to be sent to
|
||||||
|
add_hydrogens(), as it will be used by PyMOL lib.
|
||||||
|
|
||||||
|
This function is used to parse all ATOM lines and
|
||||||
|
create residues accordingly.
|
||||||
|
"""
|
||||||
self.atoms = []
|
self.atoms = []
|
||||||
self.residues = []
|
self.residues = []
|
||||||
temp_atoms = []
|
temp_atoms = []
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue