Contacts of the strand formed by residues 81 - 90 (chain B) in PDB entry 1GNG


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 LEU 81 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  GLN*     3.3    25.1    -      -       +      +
     73B  ALA      3.4    12.8    -      -       -      +
     74B  LYS*     3.8    17.7    -      -       +      +
     79B  GLY      3.6    15.3    -      -       -      +
     80B  GLU*     1.3    75.4    -      -       -      +
     82B  VAL*     1.3    65.0    +      -       -      +
    113B  ARG*     5.2     0.5    +      -       -      -
    133B  ASP*     4.4     1.6    -      -       -      +
    134B  TYR*     3.3    40.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  TYR*     5.3     0.9    -      -       +      -
     72B  GLN*     3.4     8.1    -      -       -      +
     73B  ALA*     3.0    39.9    +      -       +      +
     75B  LEU*     3.5    35.4    -      -       +      -
     80B  GLU      4.0     0.4    -      -       -      +
     81B  LEU*     1.3    80.5    -      -       -      +
     83B  ALA*     1.3    61.8    +      -       -      +
     84B  ILE*     4.2    19.3    -      -       +      -
    113B  ARG*     4.0    26.0    -      -       -      +
    131B  VAL*     4.0    10.5    -      -       +      -
    132B  LEU      3.0    15.5    -      -       -      +
    133B  ASP*     4.7     0.7    -      -       -      -
    134B  TYR*     3.8     8.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  ILE*     5.1     1.8    -      -       +      -
     70B  VAL*     4.7    11.2    -      -       +      -
     71B  TYR      3.3    10.1    -      -       -      +
     72B  GLN*     4.6     0.4    -      -       -      +
     82B  VAL*     1.3    74.5    -      -       -      +
     84B  ILE*     1.3    61.1    +      -       -      +
     85B  LYS      4.0     0.4    -      -       -      -
    130B  LEU      3.2     2.0    -      -       -      +
    131B  VAL*     3.4     2.1    -      -       -      -
    132B  LEU*     2.7    52.5    +      -       +      +
    133B  ASP      4.5     4.5    -      -       -      +
    134B  TYR*     4.3    17.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  TYR*     3.6    44.9    -      -       +      +
     59B  THR*     5.6     0.7    -      -       +      -
     70B  VAL*     3.6     2.4    -      -       -      -
     71B  TYR*     2.7    53.2    +      -       +      +
     73B  ALA*     3.9    15.9    -      -       +      +
     82B  VAL*     4.2    13.7    -      -       +      -
     83B  ALA*     1.3    77.9    -      -       -      +
     85B  LYS*     1.3    58.4    +      -       -      +
     86B  LYS*     5.1     0.9    -      -       +      +
    116B  PHE*     4.4     5.2    -      -       +      -
    129B  ASN*     4.0    31.0    -      -       +      +
    130B  LEU      3.2     5.2    -      -       -      +
    131B  VAL*     4.2    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  PHE*     3.3    44.4    -      -       +      -
     69B  VAL      3.8     3.4    -      -       -      +
     70B  VAL*     4.3    15.3    -      -       +      +
     83B  ALA      4.0     0.8    -      -       -      -
     84B  ILE*     1.3    72.2    -      -       -      +
     86B  LYS*     1.3    59.7    +      -       -      +
     87B  VAL*     4.2    11.2    -      -       +      -
     97B  GLU*     2.8    40.9    +      -       -      +
    128B  LEU      3.3     2.4    -      -       -      +
    129B  ASN*     3.2     3.5    -      -       -      -
    130B  LEU*     2.7    52.7    +      -       +      +
    132B  LEU*     4.7    13.4    -      -       +      +
    200B  ASP*     3.3    25.2    +      -       -      +
    202B  GLY*     3.8     5.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  GLY*     3.8     2.9    -      -       -      -
     69B  VAL*     3.1    34.0    +      -       +      +
     71B  TYR*     4.4    28.3    +      -       +      +
     84B  ILE*     3.7     1.7    +      -       +      +
     85B  LYS*     1.3    71.4    -      -       -      +
     87B  VAL*     1.3    65.6    +      -       -      +
    118B  SER*     4.2    12.8    +      -       -      -
    127B  TYR*     3.5    50.7    -      -       +      -
    128B  LEU      3.3     3.4    -      -       -      -
    129B  ASN*     3.1    23.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  PHE*     3.5    25.4    -      -       +      +
     85B  LYS*     4.2    30.1    -      -       +      +
     86B  LYS*     1.3    79.2    -      -       -      +
     88B  LEU*     1.3    77.4    +      -       -      +
     89B  GLN*     3.2     1.5    +      -       -      +
     95B  ASN*     4.4    20.9    -      -       -      +
     97B  GLU*     4.9     6.7    -      -       -      +
    127B  TYR*     3.2     8.3    -      -       -      -
    128B  LEU*     2.8    45.6    +      -       +      +
    130B  LEU*     4.9     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  PHE      4.3     5.2    +      -       -      +
     68B  GLY*     5.6     0.4    -      -       -      -
     87B  VAL*     1.3    83.6    -      -       -      +
     89B  GLN*     1.3    60.1    +      -       -      +
    120B  GLY*     5.1     1.6    -      -       -      -
    121B  GLU*     5.7     0.9    -      -       -      +
    125B  GLU*     3.4    53.8    -      -       +      +
    126B  VAL      3.5     7.6    -      -       -      +
    127B  TYR*     3.4    39.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  VAL*     3.2     6.2    +      -       -      +
     88B  LEU*     1.3    77.8    -      -       -      +
     90B  ASP*     1.3    91.3    +      -       -      +
     91B  LYS*     3.9     0.7    -      -       -      -
     93B  PHE*     3.5    14.6    +      -       -      +
     94B  LYS      3.8     8.9    +      -       -      -
     95B  ASN*     2.7    46.9    +      -       +      +
    117B  TYR*     5.7     3.4    -      -       +      -
    125B  GLU*     3.2     7.8    -      -       -      +
    126B  VAL*     2.6    49.4    +      -       +      +
    128B  LEU*     4.6    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  GLN*     1.3    86.3    +      -       -      +
     91B  LYS*     1.3    59.2    +      -       -      +
     92B  ARG*     2.9    47.0    +      -       -      -
     93B  PHE*     2.7    59.5    +      -       +      +
    124B  ASP*     3.5    10.6    -      -       -      +
    125B  GLU*     4.6     4.0    -      -       +      +
----------------------------------------------------------
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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