Contacts of the helix formed by residues 491 - 504 (chain B) in PDB entry 3GJN


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 491 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489B  PHE*     3.5     0.6    -      -       -      +
    490B  LYS*     1.3    81.1    +      -       -      +
    492B  PHE*     1.3    61.2    +      -       -      +
    493B  ASP*     3.1    11.7    +      -       -      +
    494B  ASP*     2.7    31.4    +      -       -      +
    495B  PHE      3.3    14.2    +      -       -      -
    556B  TYR*     3.1    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 492 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491B  SER*     1.3    73.1    -      -       -      +
    493B  ASP*     1.3    58.1    +      -       -      +
    495B  PHE*     3.5    28.2    -      +       -      +
    496B  ARG*     3.1    24.1    +      -       +      +
    543B  LEU*     4.4    32.8    -      -       +      -
    545B  ALA*     4.8    18.2    -      -       +      -
    556B  TYR*     3.3    31.4    +      +       +      -
    561B  ILE*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 493 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491B  SER*     3.1    10.0    +      -       -      +
    492B  PHE*     1.3    76.9    -      -       -      +
    494B  ASP*     1.3    64.9    +      -       -      +
    495B  PHE      3.0     1.3    -      -       -      -
    496B  ARG*     2.8    40.6    +      -       -      +
    497B  LYS*     3.0    35.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 494 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488B  GLU      4.5     0.5    -      -       -      +
    489B  PHE*     3.6     8.1    -      -       -      -
    490B  LYS*     2.9    55.4    +      -       +      +
    491B  SER*     2.7    18.4    +      -       -      +
    493B  ASP*     1.3    76.3    -      -       -      +
    495B  PHE*     1.3    62.3    +      -       -      +
    497B  LYS*     3.5    15.4    +      -       -      +
    498B  LYS*     3.2    50.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 495 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453B  ALA*     4.0    18.6    -      -       +      -
    476B  VAL*     5.5     1.1    -      -       +      -
    484B  LEU*     3.6    29.4    -      -       +      -
    489B  PHE*     3.9    31.2    -      +       +      +
    491B  SER      3.3    12.1    +      -       -      +
    492B  PHE*     3.5    31.0    -      +       -      +
    493B  ASP      3.0     0.6    -      -       -      -
    494B  ASP*     1.3    80.7    -      -       -      +
    496B  ARG*     1.3    66.7    +      -       -      +
    498B  LYS*     3.3     1.9    +      -       -      +
    499B  PHE*     3.0    30.3    +      +       +      +
    543B  LEU*     4.4    11.9    -      -       +      -
    556B  TYR*     4.1    16.6    -      +       +      -
    558B  MET*     4.0    17.9    -      -       +      -
    561B  ILE*     4.0    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 496 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    492B  PHE*     3.1    14.2    +      -       +      +
    493B  ASP*     2.8    37.5    +      -       -      +
    495B  PHE*     1.3    77.4    -      -       -      +
    497B  LYS*     1.3    88.2    +      -       -      +
    499B  PHE*     3.4     2.6    +      -       -      +
    500B  TRP*     3.1    45.7    +      -       -      +
    524B  GLY      2.3    35.8    +      -       -      -
    525B  LYS*     3.8     8.5    -      -       -      +
    526B  ALA*     4.3     9.0    -      -       -      +
    543B  LEU*     3.4    35.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 497 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493B  ASP*     3.0    23.3    +      -       -      +
    494B  ASP*     3.5    20.9    -      -       -      +
    496B  ARG*     1.3   102.7    -      -       -      +
    498B  LYS*     1.4    58.1    +      -       +      +
    500B  TRP*     3.1     2.9    +      -       -      -
    501B  GLU*     3.0    34.6    +      -       -      +
    523B  VAL      4.7    10.4    +      -       -      +
    524B  GLY*     3.6    26.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 498 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484B  LEU*     4.0     7.0    -      -       +      -
    487B  LYS*     4.4    16.8    -      -       +      +
    488B  GLU      4.9     6.8    +      -       -      +
    489B  PHE*     3.9    25.8    -      -       +      -
    490B  LYS*     5.5     2.0    -      -       -      +
    494B  ASP*     3.2    41.9    +      -       -      +
    495B  PHE      3.3     0.6    +      -       -      +
    497B  LYS*     1.4    72.8    -      -       -      +
    499B  PHE*     1.3    65.8    +      -       -      +
    500B  TRP      3.2     0.4    -      -       -      -
    501B  GLU*     3.5    24.4    -      -       +      +
    502B  GLU*     3.1    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 499 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464B  TRP*     4.1     8.3    -      +       -      -
    476B  VAL*     4.1    26.0    -      -       +      -
    477B  PRO*     4.3     3.1    -      -       +      -
    480B  ILE*     3.7    25.5    -      -       +      +
    484B  LEU*     3.9    19.9    -      -       +      +
    495B  PHE*     3.0    29.1    +      +       +      +
    496B  ARG*     3.5     6.5    -      -       -      +
    498B  LYS*     1.3    78.9    -      -       -      +
    500B  TRP*     1.3    98.0    +      +       -      +
    502B  GLU*     3.4     2.6    +      -       -      +
    503B  VAL*     3.1    39.9    +      -       +      +
    543B  LEU*     3.7    26.7    -      -       +      -
    561B  ILE*     6.1     0.2    -      -       +      -
    563B  VAL*     4.0    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 500 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464B  TRP*     3.8    21.5    -      +       -      -
    465B  LEU*     4.7     2.0    -      -       +      -
    496B  ARG*     3.1    45.8    +      -       -      +
    497B  LYS      3.1     3.8    +      -       -      +
    499B  PHE*     1.3   103.6    -      +       -      +
    501B  GLU*     1.3    60.3    +      -       -      +
    503B  VAL*     3.0    24.9    +      -       +      +
    504B  SER      3.0     8.8    +      -       -      -
    513B  PHE*     4.7     0.9    -      +       -      -
    521B  MET*     3.4    28.4    -      -       +      +
    524B  GLY      4.1     4.7    -      -       -      +
    525B  LYS      3.9    13.5    -      -       -      +
    526B  ALA*     3.5    24.2    -      -       +      +
    527B  PRO*     3.5    37.7    -      -       +      -
    541B  PHE*     4.1    13.6    +      -       +      -
    543B  LEU*     4.3     9.0    -      -       +      +
    563B  VAL*     3.7    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 501 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497B  LYS*     3.0    19.5    +      -       -      +
    498B  LYS*     3.5    39.5    +      -       -      +
    500B  TRP*     1.3    72.5    -      -       -      +
    502B  GLU*     1.3    60.5    +      -       +      +
    504B  SER*     2.8    18.9    +      -       -      -
    505B  LYS*     3.0    28.7    -      -       -      +
    521B  MET      3.4    12.1    +      -       -      +
    522B  LYS*     3.4    26.0    -      -       -      +
    523B  VAL*     4.0    11.3    -      -       -      +
    524B  GLY*     4.3     1.6    -      -       -      -
    522C  LYS*     6.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 502 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480B  ILE*     3.8    19.0    -      -       +      +
    483B  LYS*     3.2    26.5    -      -       +      +
    484B  LEU*     4.0    15.0    -      -       +      -
    487B  LYS*     3.2    20.9    +      -       -      -
    498B  LYS      3.1    20.2    +      -       -      +
    499B  PHE      3.9     3.6    -      -       -      +
    500B  TRP      3.2     0.2    -      -       -      -
    501B  GLU*     1.3    73.3    -      -       +      +
    503B  VAL*     1.3    69.4    +      -       -      +
    504B  SER      2.8     2.8    +      -       -      -
    505B  LYS*     3.1    12.0    +      -       -      +
    506B  ASP*     3.1    24.1    +      -       -      +
    515C  ARG*     2.8    40.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 503 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464B  TRP*     3.7    30.1    -      -       +      -
    480B  ILE*     3.8    25.8    -      -       +      -
    499B  PHE*     3.1    43.3    +      -       +      +
    500B  TRP*     3.0    12.8    +      -       +      +
    502B  GLU*     1.3    77.8    -      -       -      +
    504B  SER*     1.3    61.6    +      -       -      +
    506B  ASP      3.4     4.0    +      -       -      -
    509B  LEU*     3.6    11.8    -      -       +      +
    510B  SER      3.4    18.0    +      -       -      -
    513B  PHE*     4.0     9.0    -      -       +      -
    521B  MET*     4.0    17.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 504 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    500B  TRP      3.0     2.6    +      -       -      -
    501B  GLU      2.8    17.5    +      -       -      -
    502B  GLU      2.8     1.2    -      -       -      -
    503B  VAL*     1.3    81.5    -      -       -      +
    505B  LYS*     1.3    55.2    +      -       -      +
    506B  ASP      3.5     0.4    -      -       -      -
    510B  SER*     3.1    22.3    +      -       -      -
    518B  ASN*     4.0    16.4    +      -       -      +
    521B  MET*     3.5    26.0    -      -       -      -
    522B  LYS*     3.5    12.2    +      -       -      -
    504C  SER      4.1     5.9    -      -       -      +
    510C  SER*     5.0     0.2    -      -       -      -
    518C  ASN*     4.8     1.2    -      -       -      +
    522C  LYS*     3.5    28.1    +      -       -      -
----------------------------------------------------------
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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