Contacts of the strand formed by residues 633 - 637 (chain I) in PDB entry 6PSS


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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    631I  GLU*     4.3    10.8    -      -       -      +
    632I  ASP*     1.3    80.0    -      -       +      +
    634I  VAL*     1.3    61.3    +      -       -      +
    635I  THR*     4.0     0.5    +      -       -      +
    644I  LEU*     3.6    49.3    -      -       +      +
    645I  PHE      3.8     7.0    -      -       -      +
    646I  SER*     4.6     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 634 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617I  ALA*     4.4     1.6    -      -       +      -
    621I  SER*     3.8    17.0    -      -       -      +
    629I  PHE*     3.6    42.4    -      -       +      -
    631I  GLU*     3.3    25.1    -      -       +      +
    632I  ASP      4.0     4.7    -      -       -      +
    633I  LEU*     1.3    72.0    -      -       -      +
    635I  THR*     1.3    65.4    +      -       -      +
    636I  CYS*     3.2    21.7    +      -       -      -
    644I  LEU*     3.6     2.6    -      -       -      +
    645I  PHE      2.8    34.7    +      -       -      +
    646I  SER      5.0     2.0    -      -       -      +
    647I  ARG*     4.3     8.5    -      -       +      -
    650I  VAL*     5.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 635 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    618I  GLN*     3.3    24.3    +      -       +      +
    620I  ASN*     5.2    11.4    -      -       -      +
    621I  SER*     4.1    12.9    +      -       -      +
    633I  LEU      4.0     1.0    +      -       -      +
    634I  VAL*     1.3    68.7    -      -       -      +
    636I  CYS*     1.3    60.5    +      -       -      +
    642I  SER*     5.0     1.7    +      -       -      -
    643I  SER      4.1     3.4    -      -       -      -
    644I  LEU*     3.6    21.1    -      -       +      +
    770J  LEU*     3.8    20.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 636 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615I  VAL*     4.1     3.4    -      -       +      -
    616I  ILE      3.2    15.7    -      -       -      +
    617I  ALA*     3.7    10.3    -      -       -      +
    618I  GLN*     3.5     6.4    +      -       -      +
    634I  VAL*     3.2    30.9    +      -       -      -
    635I  THR*     1.3    77.0    +      -       -      +
    637I  ARG*     1.3    65.3    +      -       -      +
    642I  SER*     3.3    16.2    +      -       -      -
    643I  SER      3.3    15.9    +      -       -      +
    645I  PHE*     3.6    19.7    -      -       +      -
    650I  VAL*     3.6    28.7    -      -       -      -
    770J  LEU*     4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 637 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552I  PRO      4.8     2.4    +      -       -      -
    555I  TYR*     3.3    37.7    -      -       -      +
    591I  TYR*     2.7    40.4    +      -       -      -
    611I  GLU*     3.2    28.8    +      -       -      +
    614I  TYR      4.7     0.2    -      -       -      +
    616I  ILE*     2.8    47.9    +      -       -      +
    618I  GLN*     3.4    32.1    +      -       -      +
    636I  CYS*     1.3    76.5    -      -       -      +
    638I  SER*     1.3    63.6    +      -       -      +
    641I  GLU      3.5    15.7    -      -       -      +
    642I  SER*     3.7    11.2    -      -       -      +
    645I  PHE*     4.4     2.0    -      -       -      -
    654I  ASP*     4.0     0.4    +      -       -      -
    770J  LEU*     4.0    13.9    -      -       +      -
----------------------------------------------------------
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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