Contacts of the strand formed by residues 633 - 637 (chain C) in PDB entry 7C97


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 LEU 633 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    631C  GLU*     3.1    25.3    -      -       +      +
    632C  ASP*     1.3   111.9    -      -       -      +
    634C  VAL*     1.3    62.2    +      -       -      +
    644C  LEU*     3.5    30.2    -      -       +      +
    645C  PHE      3.1    15.7    -      -       -      +
    646C  SER*     5.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 634 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617C  ALA*     5.1     2.7    -      -       +      -
    621C  SER*     4.4    16.6    -      -       -      +
    629C  PHE*     3.5    39.9    -      -       +      -
    631C  GLU*     4.4     6.7    -      -       +      +
    633C  LEU*     1.3    78.6    -      -       -      +
    635C  THR*     1.3    64.7    +      -       -      +
    636C  CYS*     3.8     5.1    -      -       -      -
    644C  LEU*     3.0    22.0    -      -       -      +
    645C  PHE      3.2    24.2    +      -       -      +
    646C  SER      4.3     5.6    -      -       -      +
    647C  ARG*     4.8     0.2    -      -       -      -
    650C  VAL*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 635 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617C  ALA*     3.4    16.8    -      -       -      +
    618C  GLN*     3.6    22.1    +      -       +      +
    621C  SER*     5.1     4.3    +      -       -      -
    634C  VAL*     1.3    75.1    -      -       -      +
    636C  CYS*     1.3    69.1    +      -       -      +
    642C  SER*     5.3     1.1    -      -       -      -
    643C  SER      3.7    12.3    -      -       -      +
    644C  LEU*     4.5    11.2    -      -       +      +
    768D  ASN*     6.2     1.8    -      -       -      +
    770D  LEU*     4.3    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 636 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615C  VAL*     3.8     5.2    -      -       +      -
    616C  ILE      3.0    16.2    -      -       -      +
    617C  ALA*     4.2     2.5    -      -       -      +
    618C  GLN*     5.3     2.5    -      -       -      -
    634C  VAL*     3.8    11.9    -      -       -      -
    635C  THR*     1.3    82.1    -      -       -      +
    637C  ARG*     1.3    63.1    +      -       -      +
    638C  SER      4.3     0.2    -      -       -      -
    642C  SER*     3.4     8.0    -      -       -      -
    643C  SER*     3.3    26.6    +      -       -      -
    645C  PHE*     3.3    35.4    -      -       +      -
    650C  VAL*     3.4    33.2    -      -       -      -
    770D  LEU*     4.3     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 637 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552C  PRO      6.0     1.5    +      -       -      -
    555C  TYR*     3.3    39.9    -      -       -      +
    591C  TYR*     2.5    40.4    +      -       -      -
    611C  GLU*     4.2    18.6    +      -       -      +
    614C  TYR      4.1     1.9    -      -       -      +
    616C  ILE*     3.0    35.3    +      -       +      +
    617C  ALA      4.3     0.8    +      -       -      -
    618C  GLN*     3.8    11.7    +      -       -      +
    636C  CYS*     1.3    77.4    -      -       -      +
    638C  SER*     1.3    62.1    +      -       -      +
    640C  GLY*     4.9     6.3    -      -       -      +
    641C  GLU      3.0    17.7    -      -       -      +
    642C  SER*     4.7     1.3    -      -       -      -
    654C  ASP*     3.2    23.6    +      -       -      -
    770D  LEU*     4.9    17.7    -      -       +      -
----------------------------------------------------------
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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