Contacts of the helix formed by residues 59 - 88 (chain A) in PDB entry 3VWJ


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with SER 59 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  THR      3.6     3.4    +      -       -      -
     58A  PHE*     1.3    76.7    -      -       -      +
     60A  ASP*     1.3    59.4    +      -       -      +
     61A  GLN*     3.9     9.4    +      -       -      +
     62A  GLN*     3.1    24.8    +      -       -      +
     63A  TRP*     2.9    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PHE      3.9     0.2    +      -       -      -
     59A  SER*     1.3    72.5    -      -       -      +
     61A  GLN*     1.3    58.4    +      -       -      +
     62A  GLN      3.1     3.8    +      -       -      -
     63A  TRP*     4.0    13.3    +      -       -      +
     64A  GLU*     4.0    13.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  SER*     3.1     8.3    +      -       -      +
     60A  ASP*     1.3    77.6    -      -       -      +
     62A  GLN*     1.3    57.9    +      -       -      +
     64A  GLU*     4.7     6.6    -      -       -      +
     65A  THR*     3.8     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PHE*     5.0     8.5    -      -       +      -
     59A  SER*     3.1    25.2    +      -       -      +
     61A  GLN*     1.3    80.5    -      -       -      +
     63A  TRP*     1.3    59.2    +      -       -      +
     64A  GLU      3.1     2.0    -      -       -      -
     65A  THR*     3.0    30.4    +      -       -      +
     66A  LEU*     3.3    16.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  HIS*     3.6    32.3    -      +       -      -
     47A  VAL*     5.0    12.8    +      -       +      -
     48A  ARG      5.9     0.2    -      -       -      -
     49A  SER*     4.6    14.5    +      -       -      -
     54A  SER      3.8    10.1    -      -       -      -
     55A  GLN*     4.7    27.0    -      -       +      +
     58A  PHE*     5.0     8.3    -      -       +      +
     59A  SER      2.9    15.5    +      -       -      +
     60A  ASP*     4.0    10.0    +      -       -      +
     62A  GLN*     1.3    77.7    -      -       -      +
     64A  GLU*     1.3    57.8    +      -       -      +
     65A  THR      3.2     0.2    -      -       -      -
     66A  LEU*     3.6    35.2    +      -       +      +
     67A  GLN*     3.2    46.8    +      -       -      +
     70A  PHE*     6.2     1.1    -      +       -      -
    169A  PHE*     4.3    12.1    -      +       -      -
    303A  DB3      4.7     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ASP      4.0    13.4    +      -       -      +
     61A  GLN*     5.1     5.2    -      -       -      +
     62A  GLN      3.1     0.4    -      -       -      -
     63A  TRP*     1.3    77.4    -      -       -      +
     65A  THR*     1.3    60.4    +      -       -      +
     67A  GLN*     3.5    11.2    -      -       +      +
     68A  HIS*     3.0    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  GLN      3.8     6.4    +      -       -      -
     62A  GLN*     3.0    22.9    +      -       -      +
     64A  GLU*     1.3    76.8    -      -       -      +
     66A  LEU*     1.3    62.7    +      -       +      +
     68A  HIS*     3.4     6.6    +      -       +      +
     69A  ILE*     3.1    42.3    +      -       +      +
    160A  TRP*     5.0    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PHE*     4.2    30.1    -      -       +      -
     62A  GLN*     3.3    19.2    +      -       +      +
     63A  TRP*     3.6    37.0    -      -       +      +
     65A  THR*     1.3    79.1    -      -       +      +
     67A  GLN*     1.3    65.6    +      -       -      +
     69A  ILE*     3.5     9.7    +      -       +      +
     70A  PHE*     3.3    51.3    +      -       +      -
    161A  LEU*     6.3     2.0    -      -       +      -
    165A  THR*     5.2    10.3    -      -       +      -
    169A  PHE*     5.0     9.2    -      -       +      -
    303A  DB3      5.6     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ASP      5.4     2.0    -      -       -      +
     46A  THR*     3.2    18.6    -      -       +      -
     47A  VAL*     2.4    48.4    +      -       -      +
     63A  TRP*     3.2    50.0    +      -       -      +
     64A  GLU*     3.5    14.6    -      -       +      +
     65A  THR      3.2     0.2    -      -       -      -
     66A  LEU*     1.3    79.2    -      -       -      +
     68A  HIS*     1.3    61.9    +      -       -      +
     70A  PHE*     4.3     4.5    -      -       -      +
     71A  ARG*     3.4    21.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  GLU      3.0    16.5    +      -       -      +
     65A  THR*     3.8     7.4    -      -       +      +
     66A  LEU      3.3     0.2    -      -       -      -
     67A  GLN*     1.3    74.8    -      -       -      +
     69A  ILE*     1.3    69.9    +      -       +      +
     71A  ARG*     3.2    10.4    +      -       +      +
     72A  VAL*     3.2    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  THR*     3.1    32.0    +      -       +      +
     66A  LEU*     3.9     9.6    -      -       +      +
     67A  GLN      3.4     0.2    -      -       -      -
     68A  HIS*     1.3    81.7    -      -       +      +
     70A  PHE*     1.3    76.0    +      -       +      +
     72A  VAL*     3.2     9.1    +      -       -      +
     73A  TYR*     2.9    25.1    +      -       -      +
    153A  TRP*     6.2     4.3    -      -       +      -
    157A  THR*     5.3     7.0    -      -       +      -
    160A  TRP*     3.9    28.5    -      -       +      -
    161A  LEU*     4.6    22.2    -      -       +      -
    303A  DB3      4.7    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  TRP*     3.2    34.2    -      +       +      -
     47A  VAL*     4.7    15.9    -      -       +      -
     63A  TRP*     6.2     2.0    -      +       -      -
     66A  LEU*     3.3    39.9    +      -       +      +
     67A  GLN      4.3     2.5    -      -       -      +
     69A  ILE*     1.3    87.8    -      -       +      +
     71A  ARG*     1.3    60.9    +      -       -      +
     73A  TYR*     3.6     5.5    -      +       -      +
     74A  ARG*     2.9    25.1    +      -       -      +
    161A  LEU*     5.0     8.1    -      -       +      -
    303A  DB3      3.7    69.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  TRP*     4.3     8.0    -      -       -      -
     45A  ASP      5.3     9.4    -      -       -      +
     67A  GLN      3.4    12.8    +      -       -      +
     68A  HIS*     3.2    16.2    +      -       -      +
     70A  PHE*     1.3    79.7    -      -       -      +
     72A  VAL*     1.3    62.1    +      -       +      +
     74A  ARG*     3.5     8.0    +      -       -      +
     75A  SER*     3.4    20.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  HIS*     3.2    43.5    +      -       +      +
     69A  ILE*     3.6     7.2    -      -       -      +
     71A  ARG*     1.3    74.1    -      -       +      +
     73A  TYR*     1.3    62.9    +      -       -      +
     75A  SER*     3.3     6.7    +      -       -      +
     76A  SER*     2.7    39.5    +      -       -      +
    303A  DB3      4.1    17.3    -      -       -      +
     28C  PRO*     3.9    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLN*     2.7    33.7    +      -       -      -
     40A  TRP*     4.9     9.4    -      +       -      -
     69A  ILE      2.9    17.2    +      -       -      +
     70A  PHE*     3.6    11.4    -      +       -      +
     71A  ARG      3.3     0.2    -      -       -      -
     72A  VAL*     1.3    76.9    -      -       -      +
     74A  ARG*     1.3    58.6    +      -       +      +
     76A  SER*     4.4     1.3    -      -       -      -
     77A  PHE*     2.8    64.2    +      +       +      +
     98A  VAL*     4.3     6.1    -      -       -      +
    114A  PHE*     5.0     1.4    -      +       -      -
    303A  DB3      3.4   111.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  THR*     4.2    32.0    -      -       +      +
     40A  TRP*     3.1    46.8    -      -       +      +
     41A  SER      3.3    12.9    +      -       -      -
     42A  ASN*     3.1    36.8    +      -       -      +
     44A  SER      2.8    24.6    +      -       -      -
     45A  ASP*     4.4     7.7    +      -       -      +
     70A  PHE      2.9    17.0    +      -       -      +
     71A  ARG*     3.8    10.5    +      -       -      +
     72A  VAL      3.3     0.4    -      -       -      -
     73A  TYR*     1.3    83.5    -      -       +      +
     75A  SER*     1.3    56.3    +      -       -      +
     77A  PHE*     4.0     3.8    -      -       -      +
     78A  THR*     2.7    35.3    +      -       -      +
    302A  NAG      5.3     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ARG      3.4    10.8    +      -       -      -
     72A  VAL*     3.3    11.8    +      -       -      +
     74A  ARG*     1.3    77.6    -      -       -      +
     76A  SER*     1.3    67.8    +      -       -      +
     78A  THR*     3.8     5.1    +      -       -      -
     79A  ARG*     3.4    21.3    +      -       -      +
     28C  PRO*     5.5     4.3    -      -       -      +
     95C  ARG*     4.7     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL*     2.7    27.0    +      -       -      +
     73A  TYR      3.7     1.3    -      -       -      -
     75A  SER*     1.3    78.7    +      -       -      +
     77A  PHE*     1.3    59.6    +      -       -      +
     79A  ARG*     3.2     2.3    +      -       -      +
     80A  ASP*     2.8    35.7    +      -       -      +
    303A  DB3      3.2    42.3    +      -       -      -
     28C  PRO*     4.0     8.0    -      -       -      +
     95C  ARG*     3.6    15.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLN*     3.8    15.9    -      -       -      +
     16A  SER*     3.7    25.8    -      -       -      -
     18A  PHE*     4.7     1.8    -      +       -      -
     26A  THR*     5.1     2.0    -      -       +      -
     73A  TYR*     2.8    54.3    +      +       +      +
     74A  ARG*     4.0     5.2    -      -       -      +
     76A  SER*     1.3    72.3    -      -       -      +
     78A  THR*     1.3    66.6    +      -       -      +
     80A  ASP*     3.3     1.8    +      -       +      +
     81A  VAL*     3.0    51.9    +      -       +      +
     96A  LEU*     4.3    14.1    -      -       +      -
     98A  VAL*     4.3    13.5    -      -       +      -
    303A  DB3      3.7    52.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  PHE*     3.7    20.4    -      -       +      -
     24A  THR*     3.6    34.7    +      -       +      +
     26A  THR*     4.1    14.7    +      -       -      -
     74A  ARG*     2.7    23.2    +      -       -      +
     75A  SER*     4.1     6.5    -      -       -      -
     76A  SER      3.2     0.8    -      -       -      -
     77A  PHE*     1.3    79.8    -      -       -      +
     79A  ARG*     1.3    61.2    +      -       -      +
     81A  VAL      3.6     0.2    +      -       -      -
     82A  LYS*     3.2    37.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  SER      3.4    15.0    +      -       -      +
     76A  SER      3.2     4.3    +      -       -      +
     78A  THR*     1.3    79.1    -      -       -      +
     80A  ASP*     1.3    59.0    +      -       -      +
     82A  LYS*     3.4    14.9    +      -       +      +
     83A  GLU*     3.0    30.7    +      -       +      +
     94C  ASP*     2.7    32.9    +      -       -      -
     95C  ARG*     3.9    17.8    -      -       -      +
     99C  LEU      4.4     3.8    +      -       -      -
    100C  GLY*     3.8     7.5    -      -       -      -
    103C  ARG*     3.2    48.2    -      -       -      +
    105C  TYR*     3.4    15.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  SER      2.8    24.7    +      -       -      +
     77A  PHE*     3.7     7.9    -      -       +      +
     79A  ARG*     1.3    75.9    +      -       -      +
     81A  VAL*     1.3    59.8    +      -       +      +
     83A  GLU*     3.2     4.2    +      -       -      +
     84A  PHE*     2.9    40.5    +      -       +      -
    148A  LEU*     5.6     1.2    -      -       -      +
    303A  DB3      2.3    37.3    +      -       +      +
     95C  ARG*     3.0    26.9    +      -       -      -
     99C  LEU*     3.8    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  PHE*     3.8    23.6    -      -       +      -
     77A  PHE*     3.0    46.0    +      -       +      +
     78A  THR      4.2     0.2    -      -       -      +
     80A  ASP*     1.3    73.5    -      -       +      +
     82A  LYS*     1.3    66.4    +      -       -      +
     84A  PHE*     3.3     7.2    +      -       -      +
     85A  ALA*     3.0    22.7    +      -       -      +
     94A  LEU*     4.3    15.9    -      -       +      -
     96A  LEU*     3.9    22.9    -      -       +      -
    303A  DB3      4.3    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  PHE*     4.5    11.9    -      -       +      -
     20A  ASN      5.6     0.4    -      -       -      -
     21A  SER      3.6    23.2    +      -       -      +
     22A  SER*     4.9     5.1    -      -       -      +
     23A  TRP      5.9     0.2    -      -       -      -
     24A  THR*     3.9    31.4    -      -       -      +
     78A  THR*     3.2    25.2    +      -       -      +
     79A  ARG*     3.5    17.3    -      -       +      +
     81A  VAL*     1.3    78.4    -      -       -      +
     83A  GLU*     1.3    61.2    +      -       -      +
     85A  ALA*     3.5    13.7    -      -       -      +
     86A  LYS*     3.7    13.5    +      -       -      +
     92A  TYR*     3.8    19.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  ARG*     3.0    18.1    +      -       +      +
     80A  ASP*     3.7     7.0    -      -       -      +
     81A  VAL      3.1     0.2    -      -       -      -
     82A  LYS*     1.3    75.6    -      -       -      +
     84A  PHE*     1.3    64.6    +      -       -      +
     85A  ALA      3.1     1.6    -      -       -      -
     86A  LYS*     3.2    25.0    +      -       -      +
     87A  MET*     3.1    21.3    +      -       -      +
     99C  LEU*     4.2    24.0    -      -       +      +
    103C  ARG*     6.6     0.2    -      -       -      -
     48D  TYR*     3.4    18.0    +      -       -      -
     50D  TYR*     2.3    39.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  ASP*     2.9    27.6    +      -       +      +
     81A  VAL      3.3     2.7    +      -       -      +
     83A  GLU*     1.3    75.5    -      -       -      +
     85A  ALA*     1.3    58.5    +      -       -      +
     87A  MET*     4.2    19.1    -      -       +      -
     88A  LEU*     2.9    44.4    +      -       +      +
     90A  LEU*     4.4     0.2    -      -       -      +
    144A  ALA*     4.2    29.8    -      -       -      -
    147A  VAL*     4.4    11.0    -      -       +      -
    148A  LEU*     4.3    18.8    -      -       +      -
    303A  DB3      3.6    51.1    -      -       +      -
     99C  LEU*     3.6    38.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  VAL      3.0    16.2    +      -       -      +
     82A  LYS      3.5     8.7    -      -       -      +
     83A  GLU      3.1     0.2    -      -       -      -
     84A  PHE*     1.3    78.2    -      -       -      +
     86A  LYS*     1.3    62.6    +      -       -      +
     89A  ARG*     3.2     4.0    +      -       -      -
     90A  LEU*     3.1    39.0    +      -       -      +
     92A  TYR*     3.6    26.0    -      -       +      +
     94A  LEU*     3.9    20.6    -      -       +      -
    303A  DB3      5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  LYS      3.7    14.4    -      -       -      +
     83A  GLU*     3.2    30.7    +      -       -      +
     85A  ALA*     1.3    75.8    -      -       +      +
     87A  MET*     1.3    66.8    +      -       -      +
     89A  ARG*     3.5    13.0    +      -       -      +
     92A  TYR*     5.7     1.1    -      -       +      +
     48D  TYR*     2.9    25.3    +      -       -      -
     50D  TYR*     5.5     0.9    -      -       +      -
     54D  SER*     6.0     0.2    -      -       -      -
     56D  GLU*     3.6    36.6    +      -       -      +
     57D  LYS      4.9     5.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  GLU      3.1     9.8    +      -       -      +
     84A  PHE*     3.8    21.1    -      -       +      +
     86A  LYS*     1.3    82.6    -      -       -      +
     88A  LEU*     1.3    71.8    +      -       +      +
     89A  ARG*     3.2     9.1    +      -       -      +
    143A  LEU*     4.4    20.9    -      -       +      +
    147A  VAL*     4.8    11.2    -      -       +      -
     99C  LEU*     3.5    32.1    -      -       +      -
     50D  TYR*     3.5    53.1    -      -       +      -
     54D  SER*     4.8    12.5    +      -       -      +
     56D  GLU*     4.5     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  PHE*     2.9    32.3    +      -       +      +
     87A  MET*     1.3    89.9    -      -       +      +
     89A  ARG*     1.3    66.5    +      -       -      +
     90A  LEU*     2.9    34.9    +      -       +      +
    140A  TRP*     3.7    43.9    -      -       +      +
    143A  LEU*     3.7    39.9    -      -       +      -
    144A  ALA*     4.9     6.7    -      -       +      +
    303A  DB3      4.7     3.1    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il