Contacts of the strand formed by residues 593 - 597 (chain A) in PDB entry 6N8P


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 SER 593 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509A  LYS*     4.1     8.2    -      -       -      +
    591A  VAL*     3.6     6.4    -      -       -      +
    592A  THR*     1.3    78.9    -      -       -      +
    594A  LEU*     1.3    64.2    +      -       -      +
    605A  PHE*     3.6     2.8    -      -       -      -
    606A  GLY*     3.1    28.9    +      -       -      -
    713A  VAL*     3.4    18.0    +      -       -      +
    714A  ARG      3.5    23.6    -      -       -      -
    715A  THR*     4.1     0.9    -      -       -      -
    716A  LEU*     3.3    28.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 594 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509A  LYS*     3.7    35.6    -      -       +      +
    510A  ILE      4.5     1.3    -      -       -      +
    511A  PHE*     4.6    12.9    -      -       +      +
    520A  ALA*     3.4    38.4    -      -       +      +
    521A  VAL      4.3     0.9    -      -       -      -
    522A  ALA*     4.1    11.0    -      -       +      -
    528A  VAL*     4.3     8.1    -      -       +      -
    593A  SER*     1.3    76.7    -      -       -      +
    595A  ALA*     1.3    64.2    +      -       -      +
    603A  VAL*     3.8    21.5    -      -       +      -
    604A  ALA      3.3    19.1    -      -       -      +
    605A  PHE*     4.2    11.9    -      -       +      -
    716A  LEU*     4.0     8.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 595 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  PHE*     5.1     6.1    -      -       -      -
    594A  LEU*     1.3    78.2    -      -       -      +
    596A  LEU*     1.3    61.4    +      -       -      +
    603A  VAL*     3.3     5.5    -      -       -      +
    604A  ALA*     2.7    39.3    +      -       +      +
    716A  LEU*     3.9    30.7    -      -       +      +
    717A  TYR*     4.4     1.6    -      -       -      +
    718A  PHE*     3.6    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 596 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  PHE*     3.3    49.2    -      -       +      -
    513A  CYS*     5.0     0.2    -      -       +      -
    518A  TYR*     3.7    35.9    -      -       +      +
    519A  LEU      4.3     0.9    -      -       -      -
    520A  ALA*     3.7    31.2    -      -       +      +
    530A  VAL*     4.6     6.1    -      -       +      -
    595A  ALA*     1.3    74.6    -      -       -      +
    597A  HIS*     1.3    63.0    +      -       -      +
    598A  SER*     3.8     7.2    +      -       -      +
    602A  LEU      3.6    15.3    -      -       -      +
    603A  VAL*     4.0     9.4    -      -       +      -
    616A  HIS*     3.7    26.2    -      -       +      +
    718A  PHE*     4.3     3.1    -      -       -      -
    792A  PRO*     4.1     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 597 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    596A  LEU*     1.3    71.4    -      -       -      +
    598A  SER*     1.3    60.1    +      -       -      +
    599A  GLU*     3.5    15.7    +      -       +      -
    600A  TRP*     3.1    86.1    +      +       +      -
    601A  ARG*     3.1    19.6    +      -       -      -
    602A  LEU*     2.8    22.0    +      -       +      +
    616A  HIS*     4.0     2.3    +      -       -      -
    718A  PHE*     3.7    30.2    -      -       +      -
    792A  PRO*     3.6    30.2    -      -       +      +
----------------------------------------------------------
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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