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Tidy folder structure

Thomas Forest 5 years ago
parent
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249a0e21d4
6 changed files with 2715 additions and 0 deletions
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  1. 268 0
      data/1est.dssp
  2. 2414 0
      data/1est.pdb
  3. 0 0
      doc/Notice.pdf
  4. 0 0
      doc/Sujets_Projets_Courts_2019_2020.pdf
  5. 0 0
      doc/kabsch1983.pdf
  6. 33 0
      doc/notes.org

+ 268 - 0
data/1est.dssp View File

1 
+==== Secondary Structure Definition by the program DSSP, CMBI version by M.L. Hekkelman/2010-10-21 ==== DATE=2012-03-20        .
2 
+REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637                                                              .
3 
+HEADER    HYDROLASE                               17-MAY-76   1EST                                                             .
4 
+COMPND   2 MOLECULE: PORCINE PANCREATIC ELASTASE;                                                                              .
5 
+SOURCE   2 ORGANISM_SCIENTIFIC: SUS SCROFA;                                                                                    .
6 
+AUTHOR    L.SAWYER,D.M.SHOTTON,H.C.WATSON                                                                                      .
7 
+  240  1  4  4  0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN)                .
8 
+ 10891.8   ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)                                                                         .
9 
+  162 67.5   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J)  , SAME NUMBER PER 100 RESIDUES                              .
10 
+    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS IN     PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
11 
+   82 34.2   TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
12 
+    1  0.4   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES                              .
13 
+    2  0.8   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES                              .
14 
+    6  2.5   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES                              .
15 
+    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES                              .
16 
+    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES                              .
17 
+    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES                              .
18 
+    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES                              .
19 
+   26 10.8   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES                              .
20 
+   30 12.5   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES                              .
21 
+   10  4.2   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES                              .
22 
+    1  0.4   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES                              .
23 
+  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30     *** HISTOGRAMS OF ***           .
24 
+  0  0  0  1  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0    RESIDUES PER ALPHA HELIX         .
25 
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0    PARALLEL BRIDGES PER LADDER      .
26 
+  6  2  2  5  2  1  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0    ANTIPARALLEL BRIDGES PER LADDER  .
27 
+  0  0  0  0  0  1  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0    LADDERS PER SHEET                .
28 
+  #  RESIDUE AA STRUCTURE BP1 BP2  ACC     N-H-->O    O-->H-N    N-H-->O    O-->H-N    TCO  KAPPA ALPHA  PHI   PSI    X-CA   Y-CA   Z-CA
29 
+    1   16 A V    >         0   0    1      0, 0.0     3,-0.6     0, 0.0     2,-0.4   0.000 360.0 360.0 360.0 108.5  -11.1   33.8   35.9
30 
+    2   17 A V  B 3   +A  182   0A   7    180,-2.5   180,-1.9     1,-0.2   134,-0.1  -0.776 360.0   8.1 -84.5 125.5  -14.7   34.4   34.8
31 
+    3   18 A G  T 3  S+     0   0   43    132,-0.7    -1,-0.2    -2,-0.4     2,-0.1   0.798 100.7 136.9  80.5  24.5  -16.0   37.9   35.4
32 
+    4   19 A G    <   -     0   0   25     -3,-0.6     2,-0.3   144,-0.1   144,-0.2  -0.371  45.8-132.5-100.0 170.1  -12.7   39.3   36.5
33 
+    5   20 A T  E     -B  147   0B  84    142,-2.6   142,-2.6    -2,-0.1     2,-0.1  -0.899  35.7 -86.0-114.8 165.7  -10.6   42.4   35.9
34 
+    6   21 A E  E     -B  146   0B 116     -2,-0.3   140,-0.2   140,-0.2     2,-0.1  -0.432  44.9-137.8 -79.6 125.3   -6.9   42.9   35.0
35 
+    7   22 A A        -     0   0    5    138,-2.6     2,-0.4    -2,-0.1    -1,-0.1  -0.325  18.7-104.2 -76.0 161.6   -4.6   43.0   38.0
36 
+    8   23 A Q    >>  -     0   0  133     -2,-0.1     3,-1.8     1,-0.1     4,-0.7  -0.782  31.7-116.3 -93.7 129.2   -1.7   45.3   38.6
37 
+    9   24 A R  T 34 S+     0   0  109     -2,-0.4     3,-0.2     1,-0.3    -1,-0.1   0.849 114.3  36.3 -25.9 -47.2    1.8   43.9   38.0
38 
+   10   25 A N  T 34 S+     0   0   94      1,-0.2    -1,-0.3     2,-0.1    99,-0.0   0.291  95.3  90.4 -95.2  -8.1    2.8   44.3   41.6
39 
+   11   26 A S  T <4 S+     0   0   37     -3,-1.8    -1,-0.2     1,-0.2    -2,-0.2   0.961  98.4  20.4 -54.7 -58.2   -0.5   43.5   43.2
40 
+   12   27 A W    ><  +     0   0   25     -4,-0.7     3,-1.5    -3,-0.2    -1,-0.2  -0.621  69.2 166.5-120.7  81.0   -0.2   39.7   43.6
41 
+   13   28 A P  T 3   +     0   0   33      0, 0.0    97,-2.2     0, 0.0    45,-0.2   0.352  68.6  62.2 -95.3  15.7    3.5   38.8   43.6
42 
+   14   29 A S  T 3  S+     0   0    8     95,-0.2    20,-2.3    97,-0.1     2,-0.3   0.326  76.6 113.3-108.5 -13.4    3.3   35.3   44.9
43 
+   15   30 A Q  E <   -I   33   0C   7     -3,-1.5    43,-0.5    18,-0.2    44,-0.4  -0.580  48.5-171.3 -63.8 119.9    1.2   34.1   42.0
44 
+   16   31 A I  E     -IJ  32  57C   0     16,-1.8    16,-0.9    -2,-0.3     2,-0.6  -0.912  22.1-128.7-115.2 158.2    3.1   31.7   39.7
45 
+   17   32 A S  E     -IJ  31  56C   0     39,-2.0    39,-1.6    -2,-0.3     2,-0.7  -0.944  15.4-154.0-107.5 111.1    2.4   30.1   36.3
46 
+   18   33 A L  E     -IJ  30  55C   0     12,-3.3    11,-2.8    -2,-0.6    12,-1.8  -0.891  24.0-178.6 -87.1 102.6    2.7   26.3   36.2
47 
+   19   34 A Q  E     -IJ  28  54C   9     35,-2.7    35,-2.4    -2,-0.7     2,-0.3  -0.916  17.2-152.0-107.9 142.4    3.6   25.5   32.6
48 
+   20   35 A Y  E     -IJ  27  53C  71      7,-2.4     7,-2.9    -2,-0.4     2,-1.0  -0.873  31.0-106.6-113.2 142.2    4.2   22.1   30.9
49 
+   21   36 A R  E     -I   26   0C 135     31,-1.9     2,-1.3    -2,-0.3    31,-0.3  -0.731  31.4-167.7 -73.6  92.0    6.5   21.6   27.9
50 
+   22   36AA S  E >   -I   25   0C  61      3,-1.9     3,-1.8    -2,-1.0     2,-0.8  -0.855  54.9 -82.7 -81.6  69.3    4.0   21.1   25.1
51 
+   23   36BA G  T 3  S+     0   0   62     -2,-1.3    -1,-0.0     1,-0.3    -2,-0.0  -0.301 119.0  14.6  77.3 -82.9    6.5   19.8   22.6
52 
+   24   36CA S  T 3  S+     0   0  125     -2,-0.8    -1,-0.3    -3,-0.1     2,-0.2   0.665 132.2  17.5 -91.7 -40.1    8.1   22.9   21.1
53 
+   25   37 A S  E <  S-I   22   0C  71     -3,-1.8    -3,-1.9    -5,-0.1     2,-0.4  -0.696  82.8 -90.0-126.0-175.0    7.0   25.4   23.6
54 
+   26   38 A W  E     -I   21   0C  62     -5,-0.3     2,-0.4    -2,-0.2    -5,-0.2  -0.868  32.7-158.1-108.7 135.8    5.6   25.9   27.1
55 
+   27   39 A A  E     -I   20   0C  27     -7,-2.9    -7,-2.4    -2,-0.4     2,-0.1  -0.981  20.2-119.7-120.1 134.7    1.9   25.9   28.0
56 
+   28   40 A H  E     +I   19   0C  20     -2,-0.4    -9,-0.2    -9,-0.2     3,-0.1  -0.359  40.9 157.2 -70.1 115.2    0.1   27.3   31.0
57 
+   29   41 A T  E     -     0   0C  43    -11,-2.8     2,-0.3     1,-0.4   159,-0.3   0.628  58.1  -2.9-106.4 -36.8   -1.8   24.6   32.8
58 
+   30   42 A a  E     -I   18   0C   5    -12,-1.8   -12,-3.3   157,-0.1    -1,-0.4  -0.967  58.7-112.8-148.2 173.7   -2.2   25.9   36.4
59 
+   31   43 A G  E     +I   17   0C   1    157,-2.2    12,-0.4    -2,-0.3     2,-0.3  -0.344  32.4 176.1 -99.5-179.3   -1.6   28.6   39.0
60 
+   32   44 A G  E     -I   16   0C   0    -16,-0.9   -16,-1.8    10,-0.1     2,-0.4  -0.974  26.9-114.8-175.2 173.1    0.5   28.4   42.2
61 
+   33   45 A T  E     -IK  15  41C   0      8,-2.4     8,-3.1    -2,-0.3     2,-0.5  -0.984  19.4-137.8-134.2 111.0    1.9   30.1   45.2
62 
+   34   46 A L  E     + K   0  40C   1    -20,-2.3    78,-2.4    -2,-0.4     6,-0.2  -0.643  32.3 164.7 -63.9 105.3    5.5   30.8   45.9
63 
+   35   47 A I  E     +     0   0C   2      4,-2.4     2,-0.3    -2,-0.5     5,-0.2   0.535  67.1  17.3 -97.6 -30.9    5.9   30.0   49.6
64 
+   36   48 A R  E >  S- K   0  39C  96      3,-2.0     3,-1.0    74,-0.1    -1,-0.4  -0.928  88.1-102.9-129.9 166.3    9.7   29.7   49.8
65 
+   37   49 A Q  T 3  S+     0   0   89     -2,-0.3    66,-2.6     1,-0.3    64,-0.1   0.812 128.2  23.2 -64.0 -14.6   12.4   31.0   47.3
66 
+   38   50 A N  T 3  S+     0   0   36     64,-0.2    61,-2.8    62,-0.1     2,-0.4   0.168 113.8  82.0-131.0  -1.6   12.6   27.4   46.2
67 
+   39   51 A W  E <   -KL  36  98C   4     -3,-1.0    -4,-2.4    59,-0.2    -3,-2.0  -0.991  52.1-170.3-117.0 136.2    9.2   26.0   47.3
68 
+   40   52 A V  E     -KL  34  97C   0     57,-1.8    57,-2.8    -2,-0.4     2,-0.6  -0.937  12.2-148.4-126.4 128.5    5.9   26.3   45.4
69 
+   41   53 A M  E     +KL  33  96C   0     -8,-3.1    -8,-2.4    -2,-0.4    55,-0.2  -0.928  35.5 144.7-100.3 111.3    2.4   25.4   46.7
70 
+   42   54 A T  E     - L   0  95C   0     53,-2.8    53,-2.6    -2,-0.6     2,-0.4  -0.619  51.2 -75.2-130.3-177.2   -0.1   24.1   44.0
71 
+   43   55 A A        -     0   0    0    -12,-0.4     4,-0.5    51,-0.3     3,-0.4  -0.802  28.0-137.3 -89.2 133.1   -2.9   21.6   43.5
72 
+   44   56 A A  S >  S+     0   0    0     -2,-0.4     3,-1.4     1,-0.2    -1,-0.1   0.858 102.7  68.7 -56.6 -24.6   -2.1   17.9   43.2
73 
+   45   57 A H  G >  S+     0   0   77      1,-0.3     3,-1.2     2,-0.2     4,-0.2   0.870  95.0  56.2 -69.4 -23.5   -4.6   17.7   40.4
74 
+   46   58 A a  G 3  S+     0   0   14     -3,-0.4    -1,-0.3     1,-0.3     3,-0.2   0.659 107.8  45.1 -77.9 -35.1   -2.3   19.8   38.3
75 
+   47   59 A V  G <  S+     0   0   18     -3,-1.4    -1,-0.3    -4,-0.5    -2,-0.2  -0.036  78.8 108.1-104.1  23.0    0.7   17.5   38.6
76 
+   48   60 A D    <   +     0   0   48     -3,-1.2     2,-0.3     2,-0.1    -1,-0.1   0.870  68.2  65.3 -60.8 -49.5   -1.2   14.2   38.0
77 
+   49   61 A R  S    S-     0   0  200     -4,-0.2     2,-2.1    -3,-0.2     0, 0.0  -0.675  93.3-116.2 -88.3 123.5    0.3   13.6   34.5
78 
+   50   62 A E        +     0   0  197     -2,-0.3     2,-0.1     2,-0.0    -1,-0.1  -0.540  62.6 141.6 -59.5  79.9    4.0   13.0   34.2
79 
+   51   63 A L        -     0   0   77     -2,-2.1     2,-0.6   -29,-0.0   -29,-0.1  -0.323  60.5 -94.9-111.8 172.9    4.9   16.1   32.2
80 
+   52   64 A T        -     0   0   89    -31,-0.3   -31,-1.9    -2,-0.1     2,-0.3  -0.952  48.2-161.6 -97.4 107.4    7.9   18.5   32.3
81 
+   53   65 A F  E     -J   20   0C  13     -2,-0.6    21,-1.2   -33,-0.2     2,-0.3  -0.791  16.0-176.9 -96.7 141.4    7.0   21.4   34.5
82 
+   54   65AA R  E     -JM  19  73C  54    -35,-2.4   -35,-2.7    -2,-0.3     2,-0.4  -0.942  16.8-142.2-131.1 142.9    8.4   24.9   34.8
83 
+   55   66 A V  E     -JM  18  72C   0     17,-3.1    17,-2.5    -2,-0.3     2,-0.5  -0.929  10.4-160.0-106.3 123.6    7.4   27.7   37.2
84 
+   56   67 A V  E     -JM  17  71C   0    -39,-1.6   -39,-2.0    -2,-0.4     3,-0.4  -0.992   7.1-169.9-110.0 109.2    7.4   31.3   36.1
85 
+   57   68 A V  E     +JM  16  70C   3     13,-2.1    13,-1.8    -2,-0.5    52,-0.1  -0.712  69.7  32.4 -93.7 144.0    7.5   33.9   38.8
86 
+   58   69 A G  S    S+     0   0    5    -43,-0.5    10,-0.3    50,-0.5     2,-0.3   0.859  83.5 155.8  85.5  19.4    6.9   37.6   37.9
87 
+   59   70 A E        +     0   0   16    -44,-0.4    -1,-0.2    -3,-0.4     3,-0.1  -0.691  16.8 149.1 -76.5 149.4    4.5   36.8   35.1
88 
+   60   71 A H  S    S+     0   0   11      1,-0.3    85,-1.2    -2,-0.3     2,-0.6   0.363  73.8  32.7-139.1 -53.2    1.8   39.2   33.9
89 
+   61   72 A N  B >   -O  144   0D  13      3,-0.4     3,-1.1    83,-0.2    -1,-0.3  -0.928  64.4-161.0-118.8  99.2    1.3   38.6   30.2
90 
+   62   73 A L  T 3  S+     0   0   33     81,-2.3    -1,-0.2    -2,-0.6    82,-0.1   0.935  93.9  41.7 -39.8 -44.0    1.8   34.9   29.3
91 
+   63   74 A N  T 3  S+     0   0  124     80,-0.2     2,-0.4    -3,-0.1    -1,-0.2   0.296 112.7  61.8 -93.8   3.1    2.2   35.7   25.7
92 
+   64   75 A Q  S <  S-     0   0  104     -3,-1.1     2,-0.5    79,-0.2    -3,-0.4  -0.988  85.7-108.4-142.6 133.9    4.4   38.8   26.1
93 
+   65   76 A N        -     0   0  121     -2,-0.4    -3,-0.1     1,-0.2    -2,-0.1  -0.602  29.9-179.8 -59.3 105.7    7.8   39.7   27.7
94 
+   66   77 A N        -     0   0   17     -2,-0.5    -1,-0.2    -5,-0.1    -4,-0.0   0.393  36.5-131.3 -83.3 -13.3    7.0   41.6   30.8
95 
+   67   78 A G  S    S+     0   0   59      1,-0.1    -8,-0.1     0, 0.0    -2,-0.1   0.444  93.9  79.7  76.7  -1.9   10.7   41.9   31.6
96 
+   68   79 A T        +     0   0   29    -10,-0.3    -1,-0.1    40,-0.0    40,-0.1   0.274  64.1 122.5-116.0   4.0   10.1   40.7   35.1
97 
+   69   80 A E        -     0   0   26    -13,-0.1     2,-0.4    40,-0.0   -11,-0.2  -0.315  40.5-164.6 -79.5 141.0    9.9   37.0   34.5
98 
+   70   81 A Q  E     -M   57   0C  49    -13,-1.8   -13,-2.1     2,-0.1     2,-0.6  -0.953   9.8-154.8-121.2 119.7   12.0   34.3   36.2
99 
+   71   82 A Y  E     +M   56   0C 122     -2,-0.4     2,-0.3   -15,-0.2   -15,-0.2  -0.869  21.8 167.5-100.7 111.3   11.9   30.8   34.6
100 
+   72   83 A V  E     -M   55   0C  16    -17,-2.5   -17,-3.1    -2,-0.6     2,-0.1  -0.975  26.9-129.4-129.4 140.2   12.7   27.9   36.9
101 
+   73   84 A G  E     -M   54   0C  33     -2,-0.3    27,-2.6   -19,-0.2     2,-0.6  -0.430  23.2-115.3 -83.5 158.2   12.4   24.1   36.6
102 
+   74   85 A V  E     +N   99   0C  30    -21,-1.2    25,-0.3    25,-0.3   -21,-0.2  -0.937  29.4 176.8 -97.2 110.4   10.8   21.8   39.1
103 
+   75   86 A Q  E     +     0   0C 114     23,-2.3     2,-0.4    -2,-0.6    24,-0.2   0.792  68.1  24.6 -84.6 -23.2   13.2   19.3   40.6
104 
+   76   87 A K  E     -N   98   0C  89     22,-2.1    22,-2.0     2,-0.0     2,-0.5  -0.995  58.5-159.7-154.3 127.3   10.8   17.6   43.0
105 
+   77   88 A I  E     -N   97   0C  71     -2,-0.4     2,-0.6    20,-0.2    20,-0.2  -0.986   7.1-173.8-113.1 114.4    7.1   17.0   43.3
106 
+   78   89 A V  E     -N   96   0C  27     18,-3.0    18,-2.6    -2,-0.5     2,-0.3  -0.948   6.6-172.4-110.9  97.6    5.5   16.1   46.6
107 
+   79   90 A V  E     -N   95   0C  63     -2,-0.6    16,-0.2    16,-0.2    14,-0.1  -0.692  40.7 -92.6 -90.1 133.3    1.8   15.2   46.3
108 
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113 
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118 
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132 
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134 
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147 
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150 
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152 
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154 
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155 
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158 
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160 
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161 
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168 
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169 
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170 
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171 
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173 
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174 
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180 
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181 
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183 
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184 
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185 
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186 
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187 
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188 
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189 
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190 
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191 
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194 
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+  178  186 A D  S    S-     0   0   64      3,-0.5    39,-0.3    39,-0.2     4,-0.1   0.407  76.7-122.3 -65.2 -17.0  -23.0   34.7   42.3
207 
+  179  187 A G  S    S+     0   0   15     37,-0.5    38,-0.2     2,-0.4    36,-0.1   0.474 101.1  68.5  89.9  -8.0  -23.1   33.2   38.8
208 
+  180  188 A V  S    S+     0   0   93      1,-0.3     2,-0.4    36,-0.1    -1,-0.1   0.727  98.0  41.2-104.1 -43.1  -21.1   36.1   37.4
209 
+  181  188AA R  S    S+     0   0   86    -32,-0.1    -4,-0.7  -178,-0.1    -3,-0.5  -0.805  70.9 114.4-115.8 138.2  -17.7   35.7   39.0
210 
+  182  189 A S  B     -A    2   0A   4   -180,-1.9  -180,-2.5    -2,-0.4    33,-0.1  -0.977  56.0 -76.6-169.6-171.2  -15.7   32.5   39.5
211 
+  183  190 A G        -     0   0    1     -2,-0.3     2,-0.3    31,-0.2   -52,-0.0  -0.345  44.3-176.9-104.0 152.9  -12.6   30.3   38.8
212 
+  184  191 A d    >   -     0   0    5     -2,-0.1     3,-2.4    25,-0.1     4,-0.3  -0.827  41.5 -42.9-145.6 170.9  -12.2   28.3   35.6
213 
+  185  192 A Q  T 3  S+     0   0   98     -2,-0.3   -51,-2.0     1,-0.2  -155,-0.1  -0.422 125.9  28.4 -42.1 107.7  -10.0   25.9   33.8
214 
+  186  193 A G  T 3  S+     0   0    9    -53,-0.2   -54,-0.5  -157,-0.2    -1,-0.2   0.186  96.8  86.0 126.5 -26.7   -6.5   27.1   34.3
215 
+  187  194 A D    X   +     0   0    0     -3,-2.4     3,-1.6  -157,-0.2    19,-0.3   0.477  62.7 128.8 -72.2 -23.1   -6.9   28.8   37.6
216 
+  188  195 A S  T 3  S+     0   0   27     -4,-0.3  -157,-2.2  -159,-0.3    19,-0.2  -0.175  70.3  15.4 -38.1 139.2   -6.3   25.5   39.5
217 
+  189  196 A G  T 3  S+     0   0    0     17,-2.8    -1,-0.2     1,-0.3  -156,-0.2   0.452 101.8 123.2  81.1 -18.3   -3.7   25.4   42.2
218 
+  190  197 A G    <   -     0   0    0     -3,-1.6    16,-2.7  -158,-0.1    -1,-0.3  -0.244  62.4 -81.3 -84.4 170.1   -3.7   29.1   42.3
219 
+  191  198 A P  E     - G   0 205B   0      0, 0.0   -61,-1.2     0, 0.0     2,-0.6  -0.465  14.6-154.4-101.4 140.4   -4.5   31.3   45.3
220 
+  192  199 A L  E     -CG 129 204B   0     12,-1.4    11,-2.3   -63,-0.2    12,-1.2  -0.987  25.4-154.9-103.9  93.1   -7.4   32.7   47.2
221 
+  193  200 A H  E     -CG 128 202B   6    -65,-2.5   -65,-2.4    -2,-0.6     2,-0.4  -0.804  12.2-170.0 -73.9 115.1   -6.2   35.9   48.8
222 
+  194  201 A b  E     -CG 127 201B   1      7,-2.7     7,-2.0    -2,-0.8     2,-0.8  -0.802  22.4-126.6-115.7 135.5   -8.2   36.8   51.9
223 
+  195  202 A L  E     + G   0 200B  62    -69,-2.5     2,-0.4    -2,-0.4     5,-0.2  -0.694  40.8 160.8 -85.0  96.5   -8.0   40.0   53.8
224 
+  196  203 A V  E >   - G   0 199B  45      3,-3.1     3,-1.3    -2,-0.8    -2,-0.0  -0.979  67.9 -10.3-119.8 134.1   -7.3   39.3   57.4
225 
+  197  204 A N  T 3  S-     0   0  163     -2,-0.4    -1,-0.1     1,-0.2     3,-0.1   0.924 128.1 -57.4  46.9  36.6   -5.9   41.8   60.0
226 
+  198  205 A G  T 3  S+     0   0   70      1,-0.2     2,-0.4    -3,-0.1    -1,-0.2   0.623 120.7 106.4  78.7   7.7   -5.2   44.2   57.1
227 
+  199  206 A Q  E <   -G  196   0B 107     -3,-1.3    -3,-3.1    -5,-0.1     2,-0.5  -0.979  69.2-128.1-124.4 133.8   -3.0   41.5   55.5
228 
+  200  207 A Y  E     +G  195   0B  98     -2,-0.4     2,-0.3    -5,-0.2   -87,-0.3  -0.765  32.5 179.3 -80.1 116.3   -3.6   39.3   52.4
229 
+  201  208 A A  E     -G  194   0B   6     -7,-2.0    -7,-2.7    -2,-0.5     2,-1.1  -0.926  35.5-113.7-119.3 146.3   -3.0   35.6   53.1
230 
+  202  209 A V  E     +G  193   0B   3    -89,-2.8    -9,-0.2    -2,-0.3     3,-0.1  -0.804  44.9 159.8 -82.0  87.7   -3.4   32.6   50.8
231 
+  203  210 A H  E     +     0   0B   9    -11,-2.3    23,-1.4    -2,-1.1    24,-0.4   0.677  56.9  48.1 -81.0 -19.7   -6.3   30.8   52.4
232 
+  204  211 A G  E     -GH 192 225B   0    -12,-1.2   -12,-1.4    21,-0.2     2,-0.5  -0.863  53.3-158.1-137.2 147.4   -7.3   28.8   49.3
233 
+  205  212 A V  E     -GH 191 224B   0     19,-0.7    19,-2.4    -2,-0.3   -32,-0.1  -0.977  41.9-114.4-119.8  98.9   -5.8   26.5   46.6
234 
+  206  213 A T  E     + H   0 223B   4    -16,-2.7   -17,-2.8    -2,-0.5    17,-0.2  -0.204  49.1 159.7 -38.5 107.5   -8.2   26.5   43.5
235 
+  207  214 A S  E     -     0   0B   4     15,-2.6     2,-0.3     1,-0.3    16,-0.2   0.758  47.0 -19.2 -98.6 -70.9   -9.5   22.9   43.3
236 
+  208  215 A F  E     - H   0 222B  29     14,-1.3    14,-2.3  -120,-0.1    -1,-0.3  -0.881  38.8-159.4-145.4 164.5  -12.7   22.5   41.3
237 
+  209  216 A V        -     0   0   25     -2,-0.3     5,-0.1    12,-0.2    12,-0.1  -0.821  49.1 -63.4-126.1-179.6  -15.8   24.0   39.7
238 
+  210  217 A S  B >   -R  213   0G  12      3,-0.6     3,-1.4     9,-0.4     9,-0.0  -0.396  33.0-134.7 -75.9 130.8  -19.2   22.6   38.6
239 
+  211  217AA R  T 3  S+     0   0  246      1,-0.2    -1,-0.1    -2,-0.1     3,-0.1   0.797 108.0  65.4 -48.8 -26.8  -19.1   20.2   35.6
240 
+  212  218 A L  T 3  S-     0   0  146      1,-0.3     2,-0.2     2,-0.1    -1,-0.2   0.674 124.8 -69.1 -72.1 -15.8  -22.0   22.3   34.4
241 
+  213  219 A G  B <   -R  210   0G   8     -3,-1.4    -3,-0.6     1,-0.1    -1,-0.3  -0.773  46.2 -82.4 144.1 176.4  -19.6   25.2   34.0
242 
+  214  220 A d  S    S+     0   0    1     -2,-0.2     2,-1.2     1,-0.2    -4,-0.3   0.957 111.3  44.5 -80.2 -56.5  -17.5   27.7   35.8
243 
+  215  221 A N  S    S+     0   0   49    -36,-0.1     2,-0.5   -33,-0.1    -1,-0.2  -0.763  75.1 154.9 -98.9  76.4  -19.8   30.5   36.8
244 
+  216  221AA V  B >   -S  219   0H  36     -2,-1.2     3,-2.1     3,-0.5   -37,-0.5  -0.979  48.8-112.0-111.6 119.4  -22.8   28.7   38.1
245 
+  217  222 A T  T 3  S+     0   0   79     -2,-0.5   -39,-0.2     1,-0.3   -40,-0.1  -0.458 104.7   7.8 -48.4 117.0  -25.2   30.3   40.6
246 
+  218  223 A R  T 3  S+     0   0  119    -41,-2.5    -1,-0.3    -2,-0.1   -40,-0.1   0.709 106.5  99.9  76.5  12.5  -24.9   28.4   43.9
247 
+  219  224 A K  B <   -S  216   0H  45     -3,-2.1    -3,-0.5    -5,-0.1    -9,-0.4  -0.544  60.6-171.7-118.3  72.8  -22.0   26.5   42.7
248 
+  220  225 A P        -     0   0    1      0, 0.0   -44,-0.2     0, 0.0     2,-0.1  -0.013  34.3 -89.4 -69.8 151.9  -19.0   28.4   44.2
249 
+  221  226 A T  E     -F  175   0B   1    -46,-2.1   -46,-1.6   -12,-0.1     2,-0.5  -0.510  43.7-137.5 -62.5 121.8  -15.4   27.8   43.4
250 
+  222  227 A V  E     -FH 174 208B   0    -14,-2.3   -15,-2.6   -48,-0.2   -14,-1.3  -0.917  22.2-171.1 -94.7 120.3  -14.0   25.2   45.8
251 
+  223  228 A F  E     -FH 173 206B   0    -50,-2.8   -50,-2.1    -2,-0.5     2,-0.5  -0.858  30.1-109.9-106.1 153.7  -10.6   25.8   47.3
252 
+  224  229 A T  E     -FH 172 205B   4    -19,-2.4     2,-1.4    -2,-0.3   -19,-0.7  -0.768  38.7-121.6 -87.1 108.9   -8.3   23.6   49.4
253 
+  225  230 A R  E >   - H   0 204B  30    -54,-1.9     3,-2.5    -2,-0.5     4,-0.3  -0.641  24.6-164.7 -59.4  86.1   -8.3   25.1   52.9
254 
+  226  231 A V  G >  S+     0   0    0    -23,-1.4     3,-2.3    -2,-1.4     4,-0.4   0.815  82.1  67.9 -40.7 -32.9   -4.5   25.8   53.3
255 
+  227  232 A S  G 3  S+     0   0    3    -24,-0.4  -109,-2.7     1,-0.3    -1,-0.3   0.594  94.1  58.1 -71.9 -13.5   -5.0   26.2   57.1
256 
+  228  233 A A  G <  S+     0   0   44     -3,-2.5    -1,-0.3  -111,-0.2    -2,-0.2   0.511 109.8  42.4 -85.2 -21.4   -5.8   22.5   57.4
257 
+  229  234 A Y  S <> S+     0   0   14     -3,-2.3     4,-2.8    -4,-0.3    -2,-0.2   0.266  75.4 110.8-108.8  -2.3   -2.5   21.4   55.9
258 
+  230  235 A I  H  > S+     0   0   21     -4,-0.4     4,-2.5     2,-0.2     5,-0.2   0.920  80.8  52.1 -41.8 -42.0   -0.1   23.9   57.6
259 
+  231  236 A S  H  > S+     0   0   81      2,-0.2     4,-2.6     1,-0.2    -1,-0.2   0.898 111.8  44.9 -62.3 -45.3    1.4   21.0   59.6
260 
+  232  237 A W  H  > S+     0   0   37      2,-0.2     4,-2.8     1,-0.2     5,-0.2   0.942 109.5  55.7 -67.9 -40.1    2.0   18.9   56.5
261 
+  233  238 A I  H  X S+     0   0    1     -4,-2.8     4,-2.3     1,-0.2    -2,-0.2   0.883 111.3  44.7 -64.3 -33.7    3.5   21.8   54.6
262 
+  234  239 A N  H  X S+     0   0   71     -4,-2.5     4,-2.7     1,-0.2     5,-0.2   0.920 111.2  52.1 -78.7 -38.2    6.0   22.4   57.3
263 
+  235  240 A N  H  X S+     0   0  102     -4,-2.6     4,-2.0     2,-0.2    -1,-0.2   0.897 111.5  47.2 -66.5 -37.2    6.9   18.8   57.7
264 
+  236  241 A V  H >< S+     0   0   14     -4,-2.8     3,-0.5     2,-0.2    -2,-0.2   0.938 112.9  47.3 -72.7 -39.7    7.6   18.3   54.0
265 
+  237  242 A I  H >< S+     0   0   22     -4,-2.3     3,-1.2     1,-0.3    -1,-0.2   0.873 113.6  48.4 -75.6 -24.9    9.7   21.5   53.7
266 
+  238  243 A A  H 3< S+     0   0   82     -4,-2.7    -1,-0.3     1,-0.3    -2,-0.2   0.780 109.6  50.3 -89.9 -22.3   11.7   20.6   56.7
267 
+  239  244 A S  T <<        0   0   87     -4,-2.0    -1,-0.3    -3,-0.5    -2,-0.2   0.044 360.0 360.0 -95.3   3.2   12.4   17.0   55.7
268 
+  240  245 A N    <         0   0   89     -3,-1.2    -1,-0.3    -5,-0.1    -2,-0.2  -0.112 360.0 360.0-125.9 360.0   13.5   18.4   52.3

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+ 2414 - 0
data/1est.pdb


Notice.pdf → doc/Notice.pdf View File


Sujets_Projets_Courts_2019_2020.pdf → doc/Sujets_Projets_Courts_2019_2020.pdf View File


kabsch1983.pdf → doc/kabsch1983.pdf View File


+ 33 - 0
doc/notes.org View File

1 
+Dépôt output DSSP:
2 
+http://ftp.cbi.pku.edu.cn/pub/database/DSSP/latest_release/
3 
+
4 
+
5 
+structure basée sur liaisons H
6 
+
7 
+- n-turns : liaison H entre CO et NH du res i+n, ou n = [3,4,5]
8 
+- bridges : LH avec res non proches
9 
+
10 
+* hélices : 4-turns répétés
11 
+* brins beta : repetition bridges
12 
+
13 
+common imperfections : helical kinks + beta-bulges
14 
+
15 
+propriétés déduites geométriquement : bends, chirality, SS bonds, solvent exposure
16 
+
17 
+
18 
+Hbond(i,j) = [E<-0.5kcal/mole]
19 
+
20 
+electrostatic interaction energy between twho H-bonding groups by placing partial charges on the C,O(+q1,-q1) and N,H(-q2,+q2) atoms
21 
+
22 
+E = q1q2(1/r(ON) + 1/r(CH) - 1/r(OH) - 1/r(CN))*f
23 
+avec
24 
+q1 = 0.42e
25 
+q2 = 0.20e
26 
+e la charge élémentaire d'un electro (e = 1,602 176 634 ×10−19 C)
27 
+r en angström
28 
+f (facteur de dimmensionnalité) = 332
29 
+E en kcal/mol
30 
+
31 
+Bonne LH si E <= -3 kcal/mol
32 
+
33 
+Cutoff choisi permet une distance N-O jusqu'à 2.2 Angström