Contacts of the strand formed by residues 631 - 637 (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 ARG 631 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    625A  LEU*     3.6    36.8    -      -       +      +
    629A  GLN*     5.4     6.2    +      -       +      +
    630A  GLY*     1.3    75.1    -      -       -      +
    632A  ILE*     1.3    60.4    +      -       -      +
    633A  ILE*     3.9    19.3    -      -       +      +
    657A  PHE      3.2     5.6    -      -       -      +
    658A  GLU*     3.8    22.8    +      -       +      -
    701A  GLU*     3.5    28.1    +      -       -      +
    702A  VAL      3.8     1.4    -      -       -      -
    703A  SER*     2.9    34.3    +      -       -      -
    777A  PHE*     4.2     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 632 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    631A  ARG*     1.3    76.2    -      -       -      +
    633A  ILE*     1.3    60.7    +      -       -      +
    634A  LEU*     4.0    26.0    -      -       +      -
    655A  VAL*     3.8     1.5    -      -       +      +
    656A  TYR*     3.5     4.2    +      -       -      -
    657A  PHE*     2.8    56.3    +      -       +      +
    682A  THR*     5.0     0.4    -      -       +      -
    686A  VAL*     3.9    28.3    -      -       +      -
    701A  GLU      3.2     6.7    -      -       -      +
    702A  VAL*     4.4     2.5    -      -       +      -
    703A  SER      3.9    15.0    -      -       -      +
    705A  VAL*     4.3    14.1    -      -       +      -
    744A  LEU*     5.3     2.5    -      -       +      -
    777A  PHE*     3.7    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 633 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    631A  ARG*     3.9    14.8    -      -       +      -
    632A  ILE*     1.3    77.6    -      -       -      +
    634A  LEU*     1.3    65.3    +      -       -      +
    635A  LYS*     4.9    10.3    -      -       +      +
    655A  VAL      3.6     7.9    -      -       -      +
    656A  TYR*     4.3    25.4    -      -       +      -
    657A  PHE      4.6     3.4    -      -       -      +
    658A  GLU*     3.8    21.8    -      -       -      +
    699A  SER      3.8     2.1    -      -       -      +
    700A  ALA*     3.5     2.9    -      -       -      -
    701A  GLU*     2.8    65.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 634 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    632A  ILE*     4.0    11.2    -      -       +      -
    633A  ILE*     1.3    79.9    -      -       -      +
    635A  LYS*     1.3    60.8    +      -       -      +
    636A  ALA      3.7     0.6    +      -       -      -
    637A  SER*     4.1     9.4    -      -       -      -
    653A  ASN      4.0     1.0    -      -       -      +
    654A  ASP*     3.4     7.3    -      -       -      +
    655A  VAL*     2.9    64.3    +      -       +      +
    682A  THR*     4.0    19.7    -      -       +      +
    685A  ILE*     3.8    42.8    -      -       +      -
    686A  VAL*     5.3     0.9    -      -       +      -
    697A  CYS*     4.5     3.8    -      -       -      -
    699A  SER      4.0     2.2    -      -       -      -
    700A  ALA*     3.9    16.4    -      -       +      +
    702A  VAL*     3.9    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 635 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    633A  ILE*     3.9    10.5    -      -       +      -
    634A  LEU*     1.3    69.8    -      -       -      +
    636A  ALA*     1.3    73.9    +      -       +      +
    654A  ASP*     4.0    18.1    +      -       +      +
    697A  CYS*     3.7     1.9    -      -       -      +
    698A  GLU*     3.4    20.9    +      -       +      +
    699A  SER*     3.1    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 636 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    635A  LYS*     1.3    79.0    -      -       +      +
    637A  SER*     1.3    62.7    +      -       -      +
    638A  ARG*     4.4     6.5    +      -       -      +
    652A  PRO*     4.1    20.4    -      -       +      +
    653A  ASN      3.6     4.2    +      -       -      -
    654A  ASP*     3.0    17.3    +      -       -      +
    696A  PRO      3.8     1.6    -      -       -      +
    697A  CYS*     3.4    16.1    -      -       -      -
    698A  GLU*     3.9    30.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 637 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    634A  LEU*     4.1    13.5    -      -       -      -
    636A  ALA*     1.3    74.2    -      -       -      +
    638A  ARG*     1.3    62.4    +      -       -      +
    650A  PHE*     3.9     0.9    -      -       -      -
    652A  PRO*     3.3     8.0    -      -       -      +
    653A  ASN      2.7    44.7    +      -       -      -
    655A  VAL*     3.8    11.0    -      -       -      +
    681A  GLN*     3.3    20.6    +      -       -      -
    685A  ILE*     3.7    21.1    -      -       -      -
    697A  CYS*     3.6    12.3    -      -       -      -
----------------------------------------------------------
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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