Contacts of the strand formed by residues 594 - 599 (chain A) in PDB entry 5A31


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 594 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  GLN*     5.5     7.2    -      -       -      -
     78A  LYS*     5.0     0.6    -      -       -      +
     88A  ASP*     2.5    38.8    +      -       -      +
     89A  TYR*     4.2     3.6    +      -       -      +
     90A  ASP*     2.9    27.8    +      -       -      -
    106A  SER*     6.3     0.4    -      -       -      -
    482A  VAL*     4.8     0.3    -      -       -      +
    590A  PRO*     3.3     3.1    -      -       -      +
    591A  VAL*     2.9    45.9    +      -       -      +
    592A  HIS*     3.2    25.7    +      -       -      +
    593A  ASN*     1.3    83.6    +      -       -      +
    595A  VAL*     1.3    63.2    +      -       -      +
    606A  ARG*     3.3    23.7    +      -       +      +
    607A  ILE      3.1     6.3    -      -       -      +
    608A  THR*     3.4    29.6    -      -       +      +
    533O  THR*     4.5    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 595 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480A  ALA*     4.8     3.8    -      -       +      -
    482A  VAL*     4.0    22.0    -      -       +      -
    489A  LEU*     4.1    13.2    -      -       +      -
    587A  ILE*     3.3    33.4    -      -       +      -
    588A  ARG      4.1     2.7    -      -       -      +
    590A  PRO*     4.0    17.9    -      -       +      -
    594A  ARG*     1.3    79.0    -      -       -      +
    596A  THR*     1.3    66.8    +      -       -      +
    597A  LEU*     4.2     5.8    -      -       +      -
    606A  ARG*     3.3     9.0    -      -       -      +
    607A  ILE*     2.9    40.8    +      -       +      +
    609A  ILE*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 596 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.7    21.8    -      -       +      -
    587A  ILE*     3.4     3.5    -      -       -      -
    588A  ARG*     2.8    71.9    +      -       +      +
    589A  ASP*     3.7    17.9    -      -       +      +
    595A  VAL*     1.3    77.3    -      -       -      +
    597A  LEU*     1.3    67.0    +      -       -      +
    604A  MET*     3.9    12.1    -      -       -      +
    605A  VAL      3.5    12.0    +      -       -      -
    606A  ARG*     3.6    18.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 597 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497A  LEU*     4.2    15.3    -      -       +      -
    511A  ILE*     4.4    13.7    -      -       +      -
    584A  ILE*     4.1    22.9    -      -       +      -
    586A  SER      3.4     5.8    -      -       -      +
    587A  ILE*     4.0    28.7    -      -       +      -
    595A  VAL*     4.2     6.7    -      -       +      -
    596A  THR*     1.3    85.7    +      -       -      +
    598A  GLU*     1.3    59.9    +      -       -      +
    599A  LEU*     3.9    12.3    +      -       +      +
    603A  SER      3.8     0.9    -      -       -      +
    604A  MET*     3.2     6.0    -      -       -      -
    605A  VAL*     3.0    42.7    +      -       +      +
    607A  ILE*     4.1    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 598 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    584A  ILE*     3.6     2.1    -      -       -      +
    585A  HIS*     2.7    40.2    +      -       +      +
    586A  SER*     3.1    30.6    +      -       -      +
    588A  ARG*     4.3    10.6    +      -       -      +
    596A  THR      4.3     0.6    +      -       -      -
    597A  LEU*     1.3    71.2    -      -       -      +
    599A  LEU*     1.3    62.2    +      -       -      +
    602A  GLY*     5.1     8.9    -      -       -      +
    603A  SER      4.0     3.4    -      -       -      +
    604A  MET*     3.1    39.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 599 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  ILE*     5.7     8.1    -      -       +      -
    513A  ALA*     6.5     1.3    -      -       +      -
    583A  TYR*     3.7    11.4    -      -       +      +
    584A  ILE*     3.7    29.8    -      -       +      -
    585A  HIS*     3.8     6.9    -      -       -      +
    597A  LEU*     4.4    17.0    -      -       +      +
    598A  GLU*     1.3    81.3    -      -       -      +
    600A  SER*     1.3    57.3    +      -       -      +
    601A  ASN*     3.1    16.4    -      -       +      +
    602A  GLY*     2.7    24.4    +      -       -      -
    603A  SER*     3.1    28.2    +      -       -      +
    605A  VAL*     4.7    21.3    -      -       +      -
----------------------------------------------------------
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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