Contacts of the strand formed by residues 475 - 476 (chain H) in PDB entry 6GYS


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 VAL 475 (chain H). 
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    405H  LEU*     6.3     1.6    -      -       +      -
    408H  THR*     3.7    24.9    -      -       +      +
    409H  ARG      2.6    17.9    +      -       -      +
    410H  ILE*     3.7    17.0    -      -       +      -
    411H  LYS*     2.6    33.9    +      -       -      -
    452H  ILE*     3.6    36.6    -      -       +      +
    454H  VAL*     5.0     9.4    -      -       +      -
    459H  PHE*     5.6     6.7    -      -       +      -
    466H  ILE*     6.3     1.6    -      -       +      -
    474H  GLN*     1.3    71.9    -      -       -      +
    476H  LEU*     1.3    56.4    +      -       -      +
    477H  VAL*     3.6    18.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 476 (chain H). Click here for Legend to table. 
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376H  ILE*     5.1     0.2    -      -       +      -
    387H  PHE*     4.0    27.4    -      -       +      +
    388H  LYS*     6.3     1.1    -      -       -      -
    392H  ILE*     4.2    15.0    -      -       +      -
    411H  LYS*     3.8    16.2    -      -       +      +
    413H  LEU*     4.4     3.8    -      -       +      -
    451H  ASN*     3.4    28.0    -      -       +      +
    452H  ILE      2.8    27.3    +      -       -      +
    453H  ILE*     3.4    26.0    -      -       +      -
    474H  GLN*     3.3    23.3    +      -       -      +
    475H  VAL*     1.3    70.3    -      -       -      +
    477H  VAL*     1.3    59.6    +      -       -      +
    478H  ILE*     3.0    26.4    +      -       +      -
----------------------------------------------------------
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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