Contacts of the strand formed by residues 802 - 808 (chain A) in PDB entry 2G30


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 802 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    760A  ASN*     4.1     6.4    -      -       -      +
    797A  MET*     3.5    39.7    -      -       +      +
    798A  GLU      4.1     9.9    +      -       -      +
    799A  PRO*     3.0    31.6    +      -       +      +
    800A  LEU      3.3     1.1    -      -       -      +
    801A  ASN*     1.3    79.9    +      -       -      +
    803A  LEU*     1.3    64.0    +      -       -      +
    804A  GLN*     4.2    16.4    -      -       -      +
    817A  SER*     3.6    21.5    +      -       -      -
    818A  CYS      3.4    10.8    +      -       -      +
    819A  LEU*     3.9    10.5    -      -       +      +
    820A  ILE*     5.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 803 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    729A  PHE*     4.3     5.6    -      -       +      -
    738A  MET*     3.9    20.4    -      -       +      -
    757A  PHE*     3.7    42.0    -      -       +      -
    758A  ASN      4.2     1.3    -      -       -      +
    760A  ASN*     3.4    36.8    -      -       +      +
    764A  VAL*     4.9     1.3    -      -       +      -
    802A  ASN*     1.3    75.3    +      -       -      +
    804A  GLN*     1.3    63.5    +      -       -      +
    805A  VAL*     3.9    12.1    +      -       +      +
    816A  PHE      4.0     0.2    -      -       -      +
    817A  SER*     3.2     5.5    -      -       -      -
    818A  CYS*     2.8    42.5    +      -       -      +
    820A  ILE*     4.0    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 804 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    757A  PHE*     3.5     5.4    -      -       -      +
    758A  ASN*     2.9    61.5    +      -       +      +
    759A  LYS      5.7     0.8    +      -       -      -
    797A  MET*     4.0    23.9    -      -       +      +
    802A  ASN*     4.2    12.5    +      -       -      +
    803A  LEU*     1.3    77.1    -      -       -      +
    805A  VAL*     1.3    61.2    +      -       -      +
    816A  PHE      3.7     5.2    -      -       -      +
    817A  SER*     4.5     7.5    -      -       -      -
      8S  PHE*     3.9    13.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 805 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    738A  MET*     4.4     4.9    -      -       +      -
    755A  ILE*     3.6    36.3    -      -       +      -
    756A  GLN      3.5     5.6    -      -       -      +
    757A  PHE*     4.0     9.4    -      -       +      -
    803A  LEU*     3.9    31.2    -      -       +      +
    804A  GLN*     1.3    80.8    -      -       -      +
    806A  ALA*     1.3    65.2    +      -       -      +
    814A  PHE      3.9     0.3    -      -       -      +
    815A  TYR*     3.3     6.1    -      -       -      +
    816A  PHE*     2.9    67.5    +      -       +      +
    818A  CYS*     4.5     2.0    -      -       -      -
      8S  PHE*     3.9     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 806 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    754A  ALA      4.0     0.3    -      -       -      +
    755A  ILE*     3.3     4.5    -      -       -      +
    756A  GLN*     2.9    34.6    +      -       +      +
    805A  VAL*     1.3    74.8    -      -       -      +
    807A  VAL*     1.3    62.8    +      -       -      +
    808A  LYS      4.4     0.2    +      -       -      -
    813A  VAL*     4.1    10.5    -      -       +      -
    814A  PHE      3.4     4.7    -      -       -      -
    815A  TYR*     3.8    19.7    -      -       +      -
      7S  ALA*     3.6    31.0    -      -       +      -
      8S  PHE*     4.0     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 807 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    715A  LEU*     5.4     0.2    -      -       +      -
    723A  LEU*     4.4    13.5    -      -       +      -
    725A  ILE*     4.1    23.1    -      -       +      -
    740A  MET*     6.0     0.2    -      -       -      -
    742A  PHE*     4.4    14.8    -      -       +      -
    753A  PHE*     4.5     2.5    -      -       +      -
    754A  ALA      3.4     9.9    -      -       -      +
    755A  ILE*     3.6    31.2    -      -       +      -
    770A  LEU*     4.9     1.3    -      -       +      -
    805A  VAL*     4.1     0.6    -      -       +      -
    806A  ALA*     1.3    73.5    -      -       -      +
    808A  LYS*     1.3    72.0    +      -       -      +
    813A  VAL*     4.1     1.1    -      -       -      -
    814A  PHE*     2.9    40.9    +      -       +      +
    816A  PHE*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 808 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    752A  ASP*     3.1    32.4    +      -       -      +
    753A  PHE*     3.2    10.2    -      -       -      -
    754A  ALA*     2.9    50.4    +      -       +      +
    806A  ALA      4.2     0.2    -      -       -      -
    807A  VAL*     1.3    77.9    -      -       -      +
    809A  ASN*     1.3    72.5    +      -       -      +
    810A  ASN*     5.7     0.2    -      -       -      +
    812A  ASP      3.3    12.3    -      -       -      +
    813A  VAL*     3.9    17.7    -      -       +      -
    814A  PHE*     4.8     0.7    -      -       -      -
----------------------------------------------------------
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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