Contacts of the strand formed by residues 84 - 90 (chain A) in PDB entry 1GOG


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 ARG 84 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ILE*     3.7     4.7    -      -       -      +
     83A  GLY*     1.3    72.4    -      -       -      -
     85A  HIS*     1.3    63.8    +      -       -      +
     86A  GLU*     5.2     6.9    +      -       -      +
    103A  GLY      3.3    10.3    +      -       -      +
    104A  SER*     3.6    14.3    +      -       -      +
    129A  ILE*     2.8    56.9    +      -       +      +
    130A  THR*     2.9    34.1    +      -       -      +
    211A  THR      5.1     2.2    +      -       -      -
    212A  GLY      4.4    10.7    +      -       -      -
    213A  ILE*     4.0    41.1    -      -       -      +
    214A  VAL      5.1     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ILE*     3.8    12.8    -      -       +      -
     83A  GLY      2.9    20.0    +      -       -      -
     84A  ARG*     1.3    78.0    +      -       -      +
     86A  GLU*     1.3    70.6    +      -       -      +
     87A  VAL*     4.4     5.4    -      -       +      -
    102A  SER*     3.3     3.7    -      -       -      -
    103A  GLY      3.0    42.5    +      -       -      +
    104A  SER      3.8     1.1    -      -       -      -
    105A  TRP*     3.4    44.2    -      +       -      -
    114A  SER*     4.3     3.1    -      -       -      -
    126A  LEU*     4.0    12.6    -      -       +      -
    127A  VAL      3.1    16.4    -      -       -      +
    129A  ILE*     4.2     2.7    -      -       -      +
    166A  ASP*     2.5    40.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ARG*     5.2     6.8    +      -       -      +
     85A  HIS*     1.3    81.7    -      -       -      +
     87A  VAL*     1.3    65.8    +      -       -      +
     88A  TYR*     2.5    43.4    +      -       +      -
     99A  PRO*     4.1    12.5    -      -       +      +
    101A  ALA      3.4     6.7    -      -       -      -
    102A  SER*     4.0    10.9    -      -       -      -
    125A  ARG      3.9     0.3    -      -       -      +
    126A  LEU*     3.6     3.5    -      -       -      +
    127A  VAL*     3.0    33.4    +      -       +      +
    129A  ILE*     4.0    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  LEU*     4.1    18.8    -      -       +      -
     85A  HIS*     4.4     3.8    -      -       +      -
     86A  GLU*     1.3    78.8    -      -       -      +
     88A  TYR*     1.3    67.3    +      -       -      +
     89A  LEU*     4.8     0.7    -      -       +      -
     99A  PRO*     3.0     6.6    -      -       -      +
    100A  VAL*     2.8    40.2    +      -       +      -
    101A  ALA*     2.7    20.6    +      -       +      +
    114A  SER*     3.7    26.7    -      -       -      +
    116A  PHE*     4.1    14.6    -      -       +      -
    124A  VAL*     4.6     4.7    -      -       +      -
    125A  ARG      3.4     8.5    -      -       -      +
    126A  LEU*     4.0    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  GLU*     2.5    43.3    +      -       +      -
     87A  VAL*     1.3    74.6    -      -       -      +
     89A  LEU*     1.3    75.9    +      -       -      +
     96A  TRP*     3.5    36.1    -      +       +      -
     97A  GLY      3.3    26.2    -      -       -      -
     98A  SER      5.0     0.4    -      -       -      -
     99A  PRO*     3.6    28.4    -      -       +      +
    100A  VAL      4.7     1.8    -      -       -      +
    124A  VAL*     3.4     1.4    -      -       -      +
    125A  ARG*     2.8    43.1    +      -       +      +
    127A  VAL*     3.6    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  VAL*     4.1    12.8    -      -       +      -
     87A  VAL*     4.8     1.3    -      -       +      -
     88A  TYR*     1.3    87.7    -      -       -      +
     90A  SER*     1.3    61.8    -      -       -      +
     95A  ASN      4.2     0.2    -      -       -      +
     96A  TRP*     2.9    24.8    +      -       -      +
     98A  SER      5.3     0.4    +      -       -      -
    100A  VAL*     4.0    19.0    -      -       +      +
    116A  PHE*     4.1    24.0    -      -       +      -
    119A  ARG*     3.5    64.3    +      -       +      +
    121A  ALA*     3.8    11.9    -      -       +      -
    123A  TYR      3.4     3.8    -      -       -      +
    124A  VAL*     3.8    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  LEU*     1.3    74.7    -      -       -      +
     91A  SER*     1.3    58.5    +      -       -      +
     92A  ASP*     2.8    18.2    +      -       -      -
     93A  GLY*     2.9    14.4    +      -       -      -
     95A  ASN      2.4    30.0    +      -       -      -
     96A  TRP*     3.4    24.7    -      -       -      -
    119A  ARG*     4.8     3.8    -      -       -      +
    120A  PRO      5.4     0.2    -      -       -      -
    121A  ALA*     3.7     3.7    -      -       -      +
    122A  ARG      3.1     5.6    +      -       -      -
    123A  TYR*     2.8    37.3    +      -       -      -
----------------------------------------------------------
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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