Contacts of the strand formed by residues 531 - 533 (chain C) in PDB entry 6OY5


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 PHE 531 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471C  TYR*     4.1    18.6    -      -       +      -
    472C  ARG      3.1    21.3    -      -       -      +
    473C  ARG*     3.6    52.3    -      -       +      -
    474C  VAL*     3.9     4.3    -      -       -      +
    484C  VAL*     4.0    13.0    -      -       +      -
    486C  MET*     3.4    32.3    -      -       +      -
    494C  TYR*     3.4    41.7    -      +       +      -
    495C  THR      3.3     3.8    +      -       -      -
    496C  ILE*     3.5    17.2    -      -       +      -
    497C  ALA      2.9    19.2    +      -       -      -
    529C  VAL*     3.4     9.7    -      -       -      +
    530C  GLU*     1.3    81.4    -      -       +      +
    532C  MET*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 532 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471C  TYR*     3.5     7.5    -      -       -      -
    472C  ARG*     2.8    68.2    +      -       +      +
    474C  VAL*     4.0    13.2    -      -       +      -
    479C  VAL*     4.1    19.5    -      -       +      -
    496C  ILE*     3.9     0.6    -      -       -      +
    497C  ALA*     3.3    11.4    -      -       +      +
    498C  GLN      3.3    24.9    -      -       -      +
    499C  ALA*     4.2    11.2    -      -       -      +
    501C  THR*     3.6    13.7    -      -       -      +
    503C  LEU*     4.2    19.1    -      -       +      -
    508C  ILE*     6.0     2.7    -      -       -      -
    531C  PHE*     1.3    78.9    -      -       -      +
    533C  ASP*     1.3    77.3    +      -       -      +
    534C  VAL      3.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 533 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435C  TYR*     2.2    35.5    +      -       -      -
    471C  TYR*     3.7    13.0    -      -       -      -
    472C  ARG*     5.2     1.2    -      -       -      +
    496C  ILE*     3.4    15.6    -      -       -      +
    497C  ALA      2.9    17.8    +      -       -      +
    498C  GLN*     3.9     7.9    +      -       -      +
    499C  ALA*     3.5    29.4    -      -       +      +
    516C  ARG*     4.1     4.3    +      -       -      -
    532C  MET*     1.3    90.0    -      -       -      +
    534C  VAL*     1.3    63.5    +      -       -      +
    535C  SER      3.4     3.8    -      -       -      +
    538C  GLN*     3.4    13.4    -      -       -      +
    539C  VAL*     5.0     0.5    -      -       -      +
   1067D  VAL*     5.1     0.5    -      -       -      +
----------------------------------------------------------
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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