Contacts of the strand formed by residues 319 - 323 (chain A) in PDB entry 3V9G


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 ASN 319 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  GLY*     3.8    10.1    +      -       -      -
    318A  LYS*     1.3    73.1    +      -       -      +
    320A  PHE*     1.3    61.3    +      -       -      +
    347A  LYS      4.8     0.2    +      -       -      -
    348A  CYS      2.7    27.4    +      -       -      -
    349A  SER      3.2     5.7    -      -       -      +
    350A  ALA      3.0    27.1    +      -       -      +
    351A  CYS*     4.3     2.2    -      -       -      -
    352A  SER*     3.1    26.1    +      -       -      -
    353A  ARG*     3.2    10.2    +      -       -      +
    478A  LEU*     3.4    12.0    +      -       -      +
    479A  THR*     2.8    51.5    +      -       -      +
    510A  SER*     4.5     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  LYS      5.0     0.2    -      -       -      -
    319A  ASN*     1.3    77.9    -      -       -      +
    321A  HIS*     1.3    68.8    +      -       -      +
    322A  PHE*     3.9     9.0    -      -       +      -
    351A  CYS*     4.3     0.7    -      -       -      -
    353A  ARG*     3.1    42.0    -      -       -      +
    355A  TYR*     4.2     8.7    -      -       +      -
    470A  VAL*     3.5    16.6    -      -       +      -
    479A  THR      3.7     3.8    +      -       -      -
    480A  GLY*     3.3    21.1    -      -       -      -
    481A  ALA      2.9    49.7    +      -       -      -
    497A  LEU*     3.9    31.4    -      -       +      -
    500A  ALA*     3.9    26.9    -      -       +      -
    501A  ALA*     4.2     4.3    -      -       +      -
    504A  PHE*     4.2     6.7    -      +       -      -
    510A  SER*     4.3     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  PHE*     1.3    84.5    -      -       -      +
    322A  PHE*     1.3    59.9    +      -       -      +
    335A  GLY      3.6    25.8    -      -       -      -
    336A  THR*     3.1    23.0    +      -       -      -
    339A  SER*     3.7     6.6    +      -       -      -
    351A  CYS*     3.6    17.0    -      -       +      -
    353A  ARG      3.0     8.5    +      -       -      +
    354A  LEU*     3.3    22.5    -      -       +      +
    355A  TYR*     2.9    24.8    +      -       -      -
    481A  ALA*     3.6    12.8    -      -       +      -
    483A  PHE*     3.5    22.1    -      +       +      -
    509A  LYS*     3.7    14.1    -      -       -      -
    510A  SER*     3.1    27.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  PHE*     3.9    13.3    -      -       +      -
    321A  HIS*     1.3    72.7    -      -       -      +
    323A  VAL*     1.3    68.3    +      -       -      +
    324A  HIS*     4.2     9.4    -      -       +      -
    355A  TYR*     3.8    16.8    -      -       +      -
    458A  TYR*     3.4    31.0    -      +       -      -
    463A  TYR*     4.2    16.4    -      +       -      -
    466A  THR*     3.8    25.4    -      -       +      -
    467A  LEU*     3.4    33.4    -      -       +      -
    470A  VAL*     3.9    16.6    -      -       +      -
    481A  ALA      2.7    15.8    +      -       -      +
    482A  VAL*     3.4    20.4    -      -       +      -
    483A  PHE*     2.9    26.0    +      -       -      +
    489A  VAL*     5.6     2.9    -      -       +      -
    493A  ALA*     5.8     0.4    -      -       +      -
    497A  LEU*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  HIS      4.4     0.2    -      -       -      +
    322A  PHE*     1.3    81.9    -      -       -      +
    324A  HIS*     1.3    66.4    +      -       -      +
    327A  ALA*     3.5    20.2    -      -       +      -
    332A  VAL*     3.8    24.9    -      -       +      -
    354A  LEU*     3.8    22.2    -      -       +      -
    355A  TYR      2.9    19.0    +      -       -      +
    356A  VAL*     4.5     3.4    -      -       +      -
    357A  PRO*     3.2    22.5    -      -       +      +
    360A  LEU*     4.5     5.4    -      -       +      -
    364A  ILE*     4.5     7.6    -      -       +      -
    458A  TYR*     2.6    27.7    +      -       -      -
    483A  PHE*     3.8     8.1    -      -       +      +
----------------------------------------------------------
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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