Contacts of the helix formed by residues 57 - 78 (chain A) in PDB entry 4PIM


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 TYR 57 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  PRO      5.6     0.9    -      -       -      +
     55A  GLU      3.1    15.3    +      -       -      +
     56A  TYR*     1.3    71.2    -      -       -      +
     58A  PRO*     1.4    77.0    -      -       +      +
     59A  THR      3.2     0.6    +      -       -      -
     60A  ARG*     3.5    16.4    +      -       +      +
     61A  THR*     2.6    40.6    +      -       -      +
    194A  ASP*     2.6    40.6    +      -       -      -
    197A  LYS*     2.9    35.1    +      -       +      -
    201A  ARG*     3.9    35.9    -      -       +      +
    202A  LEU*     3.3    15.5    -      -       +      +
    205A  ALA*     3.9    18.1    -      -       +      +
    206A  TYR*     5.5     0.7    -      +       -      -
    286A  LYS*     4.6     0.2    +      -       -      -
    313A  ASP*     4.3     6.5    -      -       +      +
    314A  PHE*     5.3     0.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with PRO 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  TYR*     3.2    41.1    -      -       +      +
     57A  TYR*     1.4   119.0    -      -       +      +
     59A  THR*     1.3    62.5    +      -       -      +
     61A  THR*     3.7     1.6    -      -       -      +
     62A  GLU*     2.9    28.0    +      -       -      +
    161A  GLY*     5.1     6.3    -      -       -      +
    194A  ASP*     3.8    12.8    -      -       +      +
    205A  ALA*     5.0     0.9    -      -       +      -
    206A  TYR*     4.9     3.4    -      -       +      +
    286A  LYS*     5.3     0.2    -      -       -      +
    314A  PHE*     4.3    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  THR*     3.4    39.8    -      -       +      +
     56A  TYR*     3.4    21.3    +      -       -      -
     57A  TYR      3.3     0.8    -      -       -      -
     58A  PRO*     1.3    78.4    -      -       -      +
     60A  ARG*     1.3    59.1    +      -       -      +
     62A  GLU*     3.9     4.2    -      -       -      +
     63A  ALA*     2.9    31.4    +      -       +      +
     91A  GLU*     5.7     5.2    -      -       +      +
     92A  LYS*     4.7    23.3    +      -       +      +
    161A  GLY*     6.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  THR      4.2     3.4    +      -       -      -
     52A  ARG*     3.6    17.8    +      -       -      +
     53A  LEU      2.8    26.6    +      -       -      -
     54A  PRO*     3.0    30.5    +      -       -      +
     56A  TYR      3.3    19.5    +      -       -      -
     57A  TYR*     3.6    15.5    -      -       +      +
     59A  THR*     1.3    79.4    -      -       -      +
     61A  THR*     1.3    62.1    +      -       -      +
     63A  ALA*     3.7     7.3    -      -       -      +
     64A  GLN*     3.0    29.1    +      -       -      +
     67A  ARG*     5.0     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  TYR*     2.6    37.5    +      -       -      +
     58A  PRO*     3.7     3.4    -      -       -      -
     60A  ARG*     1.3    78.4    -      -       -      +
     62A  GLU*     1.3    65.1    +      -       -      +
     64A  GLN*     3.3     6.8    +      -       -      +
     65A  ILE*     3.1    23.0    +      -       +      +
    309A  ASP*     3.4    40.1    -      -       +      +
    313A  ASP*     4.1     8.6    +      -       +      +
    314A  PHE*     3.6    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PRO      2.9    16.8    +      -       -      +
     59A  THR*     3.9     2.8    -      -       -      +
     61A  THR*     1.3    76.2    -      -       -      +
     63A  ALA*     1.3    63.7    +      -       -      +
     65A  ILE*     3.1     7.0    +      -       -      +
     66A  LEU*     3.0    25.7    +      -       +      +
     92A  LYS*     2.6    37.8    +      -       +      -
    160A  LEU*     3.3    21.1    -      -       -      +
    161A  GLY*     2.9    28.6    +      -       -      -
    192A  GLY*     3.7     0.9    -      -       -      -
    314A  PHE*     3.3    36.8    -      -       +      -
    316A  LEU*     3.7    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  THR*     2.9    21.0    +      -       +      +
     60A  ARG*     3.7     8.7    -      -       -      +
     62A  GLU*     1.3    77.6    -      -       -      +
     64A  GLN*     1.3    57.1    +      -       -      +
     66A  LEU*     3.3     3.1    +      -       -      -
     67A  ARG*     2.7    47.5    +      -       -      +
     91A  GLU*     4.7    10.5    -      -       -      +
     92A  LYS*     4.4    20.1    -      -       +      +
     95A  MSE      3.6     9.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ARG      3.0    18.3    +      -       -      +
     61A  THR*     3.7     6.1    -      -       -      +
     63A  ALA*     1.3    72.5    -      -       -      +
     65A  ILE*     1.3    66.7    +      -       +      +
     67A  ARG*     2.7    40.7    +      -       -      +
     68A  THR*     3.1    48.5    +      -       +      +
    309A  ASP*     6.2     4.0    -      -       +      -
    310A  PRO*     6.4     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  THR      3.1    16.5    +      -       -      +
     62A  GLU*     3.1     6.5    +      -       -      +
     64A  GLN*     1.3    78.8    -      -       +      +
     66A  LEU*     1.3    61.7    +      -       -      +
     68A  THR*     3.3     6.4    +      -       -      -
     69A  ARG*     3.0    26.6    +      -       +      +
     73A  ILE*     5.5     1.1    -      -       +      -
    307A  TRP*     3.8    28.5    -      -       +      +
    308A  THR*     4.1     4.3    -      -       -      +
    309A  ASP*     3.7    28.0    -      -       +      +
    314A  PHE*     3.7    42.0    -      -       +      +
    315A  GLY*     4.7     0.9    -      -       -      +
    316A  LEU*     3.6    20.9    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     62A  GLU*     3.0    18.5    +      -       +      +
     63A  ALA      3.7     6.1    -      -       -      +
     65A  ILE*     1.3    76.7    -      -       -      +
     67A  ARG*     1.3    63.1    +      -       -      +
     70A  SER*     2.9    32.3    +      -       -      +
     73A  ILE*     3.7    26.0    -      -       +      -
     92A  LYS*     3.6    49.4    -      -       +      +
     95A  MSE      3.7    14.3    -      -       +      +
     96A  LEU*     4.1    18.4    -      -       +      -
    160A  LEU*     4.3    11.4    -      -       +      -
    190A  LEU*     4.4     7.2    -      -       +      -
    316A  LEU*     3.7    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ARG      5.0     1.2    +      -       -      -
     63A  ALA*     2.7    28.3    +      -       -      +
     64A  GLN*     2.7    58.5    +      -       -      +
     65A  ILE      3.3     0.6    -      -       -      -
     66A  LEU*     1.3    74.5    -      -       -      +
     68A  THR*     1.3    63.2    +      -       +      +
     70A  SER*     4.6     5.0    +      -       -      -
     91A  GLU*     4.3    12.1    +      -       -      -
     95A  MSE      3.4    34.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  GLN*     3.1    41.3    +      -       -      +
     65A  ILE*     3.3     8.7    +      -       -      -
     66A  LEU      3.1     0.2    -      -       -      -
     67A  ARG*     1.3    85.2    -      -       +      +
     69A  ARG*     1.3    74.0    +      -       -      +
     70A  SER      3.8     0.4    -      -       -      -
     71A  ALA      5.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ILE*     3.0    16.9    +      -       +      +
     66A  LEU      3.9     0.2    -      -       -      -
     68A  THR*     1.3    97.2    +      -       -      +
     70A  SER*     1.3    63.8    +      -       -      +
     71A  ALA*     3.2     3.6    -      -       -      +
     72A  GLU*     3.0    36.6    +      -       -      +
     73A  ILE*     2.9    28.7    +      -       +      +
    307A  TRP*     3.7    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     2.9    21.6    +      -       -      -
     67A  ARG      4.6     4.7    +      -       -      -
     68A  THR      3.8     1.0    -      -       -      -
     69A  ARG*     1.3    76.0    -      -       -      +
     71A  ALA*     1.3    65.8    +      -       -      +
     73A  ILE*     3.3    12.3    +      -       -      +
     74A  ILE*     3.0    28.6    +      -       -      +
     95A  MSE      4.0    26.6    +      -       -      +
     96A  LEU*     4.7     7.2    -      -       -      -
     99A  ALA*     3.8    12.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  THR      5.6     0.2    -      -       -      -
     69A  ARG      3.2     1.2    -      -       -      -
     70A  SER*     1.3    83.5    +      -       -      +
     72A  GLU*     1.3    56.3    +      -       -      +
     74A  ILE*     3.5     3.0    +      -       -      +
     75A  SER*     2.9    29.5    +      -       -      -
     99A  ALA*     4.4     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ARG*     3.0    41.6    +      -       -      +
     71A  ALA*     1.3    75.1    -      -       -      +
     73A  ILE*     1.3    60.9    +      -       -      +
     75A  SER*     3.4     6.8    +      -       -      -
     76A  ALA*     2.9    31.1    +      -       +      +
    305A  HIS*     4.1    17.9    +      -       +      +
    307A  TRP*     2.7    35.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ILE      5.2     0.2    -      -       -      +
     66A  LEU*     3.7    30.7    -      -       +      -
     69A  ARG*     2.9    28.5    +      -       +      +
     70A  SER*     3.3     8.9    +      -       -      +
     72A  GLU*     1.3    77.1    -      -       -      +
     74A  ILE*     1.3    59.8    +      -       +      +
     76A  ALA*     3.2     3.8    +      -       -      +
     77A  ALA*     2.9    27.7    +      -       -      +
     96A  LEU*     4.2    10.1    -      -       +      -
    156A  LEU*     4.7     6.5    -      -       +      -
    190A  LEU*     4.0    30.7    -      -       +      -
    307A  TRP*     3.6    40.2    -      -       +      -
    316A  LEU*     4.7     5.4    -      -       +      -
    318A  LEU*     4.6     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  SER      3.0    19.3    +      -       -      +
     71A  ALA*     3.9     3.8    -      -       -      +
     73A  ILE*     1.3    73.4    -      -       -      +
     75A  SER*     1.3    61.8    +      -       -      +
     77A  ALA*     3.9     2.7    -      -       +      +
     78A  GLY*     2.9    28.2    +      -       -      -
     79A  ALA      4.4     1.9    +      -       -      +
     96A  LEU*     3.9    17.9    -      -       +      +
     99A  ALA*     3.4    37.9    -      -       +      +
    100A  MSE      3.4    33.9    -      -       +      -
    103A  ALA*     4.3     5.4    -      -       +      -
    105A  LEU*     4.2    17.0    -      -       +      +
    156A  LEU*     3.9    25.6    -      -       +      -
----------------------------------------------------------
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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  ALA      2.9    18.1    +      -       -      -
     72A  GLU*     3.7     7.6    -      -       -      -
     74A  ILE*     1.3    78.7    -      -       -      +
     76A  ALA*     1.3    63.6    +      -       -      +
     77A  ALA      3.4     0.2    +      -       -      -
     78A  GLY*     3.6     8.3    +      -       -      -
    103A  ALA*     6.5     0.4    -      -       -      -
    105A  LEU*     5.9     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  GLU*     2.9    19.1    +      -       +      +
     73A  ILE*     3.5     6.7    -      -       -      +
     75A  SER*     1.3    79.2    -      -       -      +
     77A  ALA*     1.3    60.7    +      -       -      +
    154A  ARG*     5.1     3.6    +      -       -      -
    188A  SER*     5.0     0.9    +      -       -      -
    305A  HIS*     3.6    34.1    -      -       +      +
    307A  TRP*     4.8     0.9    -      -       +      -
    318A  LEU*     3.8    16.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ILE      2.9    16.8    +      -       -      +
     74A  ILE*     4.0     4.0    -      -       +      +
     75A  SER      3.3     0.2    -      -       -      -
     76A  ALA*     1.3    78.7    -      -       -      +
     78A  GLY*     1.3    64.4    +      -       -      +
     79A  ALA*     3.1    14.6    +      -       +      +
    154A  ARG*     3.2    21.2    +      -       -      -
    156A  LEU*     4.1    30.7    -      -       +      -
    186A  GLY      4.2     1.6    -      -       -      +
    188A  SER*     3.9    20.4    +      -       -      +
    318A  LEU*     4.2     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ILE      2.9    14.9    +      -       -      -
     75A  SER      3.6     6.5    +      -       -      -
     76A  ALA      3.5     2.0    -      -       -      -
     77A  ALA*     1.3    76.4    -      -       -      +
     79A  ALA*     1.3    60.7    +      -       -      +
     80A  ASP      4.1     0.3    +      -       -      -
    105A  LEU*     4.5    18.1    -      -       -      +
    154A  ARG*     3.2    21.9    +      -       -      +
----------------------------------------------------------
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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