Contacts of the strand formed by residues 653 - 658 (chain A) in PDB entry 2O8C


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 653 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    637A  SER*     2.7    44.2    +      -       -      -
    651A  ILE      3.9     5.4    +      -       -      -
    652A  PRO*     1.3    81.2    -      -       -      +
    654A  ASP*     1.3    65.7    +      -       -      +
    674A  GLY      5.6     1.0    +      -       -      -
    678A  TYR*     3.8    25.8    -      -       +      +
    681A  GLN*     4.1     7.5    -      -       -      +
    815A  TYR      3.2    18.8    +      -       -      +
    816A  GLN*     3.2    25.4    -      -       -      +
    817A  VAL*     3.4    29.5    +      -       +      +
    936A  ADP      4.3     5.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 654 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    634A  LEU      3.4     5.8    -      -       -      +
    635A  LYS*     4.3    17.7    +      -       -      +
    636A  ALA*     3.0    26.0    +      -       -      +
    652A  PRO      5.3     0.2    -      -       -      -
    653A  ASN*     1.3    77.0    -      -       -      +
    655A  VAL*     1.3    57.7    +      -       -      +
    656A  TYR      4.4     0.2    +      -       -      -
    678A  TYR*     2.6    24.6    +      -       -      -
    800A  LEU*     5.4     0.7    -      -       -      +
    817A  VAL*     4.5     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 655 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    632A  ILE      4.2     0.9    -      -       -      +
    633A  ILE*     3.6     6.8    -      -       -      +
    634A  LEU*     2.9    53.3    +      -       +      +
    637A  SER*     3.8    14.4    -      -       -      +
    654A  ASP*     1.3    78.2    -      -       -      +
    656A  TYR*     1.3    65.0    +      -       -      +
    657A  PHE*     3.5    32.1    -      -       +      -
    665A  HIS*     5.9     0.7    -      -       +      +
    678A  TYR*     3.6    26.7    -      -       +      +
    681A  GLN*     5.3     0.9    -      -       +      +
    682A  THR*     3.7    26.0    -      -       +      +
    779A  MET*     4.9     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 656 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    632A  ILE      3.5     2.0    -      -       -      -
    633A  ILE*     4.3    29.6    -      -       +      -
    654A  ASP      4.4     0.4    +      -       -      -
    655A  VAL*     1.3    76.6    -      -       -      +
    657A  PHE*     1.3    67.3    +      -       -      +
    658A  GLU*     3.3    42.2    +      -       +      -
    661A  LYS*     4.6     8.7    -      -       +      +
    662A  GLN*     3.6    31.6    -      -       +      +
    665A  HIS*     2.8    38.1    +      -       +      -
    678A  TYR*     4.9     0.6    +      -       -      -
    819A  LYS*     6.0     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 657 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    630A  GLY      4.2     1.6    -      -       -      -
    631A  ARG*     3.2     7.1    -      -       -      -
    632A  ILE*     2.8    51.5    +      -       +      +
    633A  ILE*     4.6     0.5    -      -       -      +
    655A  VAL*     3.5    23.6    -      -       +      -
    656A  TYR*     1.3    84.8    -      -       -      +
    658A  GLU*     1.3    65.2    +      -       -      +
    662A  GLN      3.3     6.7    -      -       -      -
    663A  MET*     3.4    26.7    -      -       -      -
    665A  HIS*     3.5    17.9    -      +       -      -
    682A  THR*     4.2    13.0    -      -       +      -
    744A  LEU*     4.8     4.5    -      -       +      -
    777A  PHE*     3.6    38.4    -      +       +      -
    778A  CYS      4.0    10.3    -      -       -      -
    779A  MET*     3.6    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 658 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    630A  GLY      3.4     7.2    -      -       -      +
    631A  ARG*     3.8    31.3    +      -       +      -
    633A  ILE*     3.8    10.7    -      -       +      +
    656A  TYR*     3.3    37.0    +      -       +      +
    657A  PHE*     1.3    80.5    -      -       -      +
    659A  LYS*     1.3    69.6    +      -       -      +
    661A  LYS*     4.1    20.9    +      -       +      +
    662A  GLN      2.8    30.2    +      -       -      +
    663A  MET*     3.3    11.0    -      -       -      +
----------------------------------------------------------
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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