Contacts of the strand formed by residues 594 - 601 (chain B) in PDB entry 4YZ9


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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617A  ARG*     3.4    56.2    +      -       +      +
    621A  GLU*     5.1     4.2    +      -       -      +
    628A  TYR*     3.6    37.6    +      -       -      -
    629A  PHE      5.2     3.4    +      -       -      -
    590B  MET*     3.1    29.5    -      -       -      +
    591B  PHE*     2.8    22.2    +      -       -      +
    592B  ASP*     4.0     9.3    +      -       -      +
    593B  ASN*     1.3    78.3    -      -       -      +
    595B  ASP*     1.3    64.7    +      -       -      +
    596B  VAL*     3.5    11.2    +      -       +      -
    627B  ARG*     3.9    25.6    -      -       -      +
    629B  PHE*     3.6    37.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 595 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588B  ARG*     3.4    31.7    +      -       -      +
    589B  GLY      3.9     2.5    -      -       -      -
    590B  MET*     3.6    21.4    -      -       -      +
    593B  ASN      4.3     0.4    +      -       -      -
    594B  ARG*     1.3    72.9    -      -       -      +
    596B  VAL*     1.3    61.8    +      -       -      +
    644B  LEU*     3.6    25.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 596 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588B  ARG*     4.6     0.7    -      -       -      +
    589B  GLY      2.9    37.7    +      -       -      +
    590B  MET*     3.9     3.4    -      -       -      -
    591B  PHE*     3.8    21.3    -      -       +      +
    594B  ARG*     3.8    17.7    -      -       +      -
    595B  ASP*     1.3    79.4    -      -       -      +
    597B  ALA*     1.3    62.3    +      -       -      +
    598B  VAL*     4.3     4.5    -      -       +      -
    629B  PHE*     3.7    33.0    -      -       +      -
    641B  ALA*     3.9    19.3    -      -       +      -
    642B  ILE      3.3    11.9    -      -       -      +
    644B  LEU*     3.9    13.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 597 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    577B  LEU*     4.2     9.4    -      -       +      -
    586B  VAL*     4.0     9.0    -      -       +      -
    587B  TYR      3.8     5.2    -      -       -      -
    596B  VAL*     1.3    73.1    -      -       -      +
    598B  VAL*     1.3    60.3    +      -       -      +
    641B  ALA*     3.4     2.6    -      -       -      -
    642B  ILE*     2.8    50.1    +      -       +      +
    643B  GLU      4.0     6.5    -      -       -      +
    644B  LEU*     4.0    11.2    -      -       +      +
    712B  PHE*     3.9    27.6    -      -       +      -
    714B  LEU*     6.1     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 598 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    569B  ILE*     3.9    31.6    -      -       +      -
    570B  SER      4.1     0.4    -      -       -      +
    571B  PHE*     3.9    25.4    -      -       +      -
    585B  ILE      3.9     0.5    -      -       -      +
    586B  VAL*     3.1     5.5    -      -       -      -
    587B  TYR*     2.8    42.7    +      -       +      +
    589B  GLY*     3.7    32.1    -      -       -      -
    596B  VAL*     4.3     6.7    -      -       +      -
    597B  ALA*     1.3    75.6    -      -       -      +
    599B  LYS*     1.3    62.5    +      -       -      +
    600B  ARG      4.0     0.7    +      -       -      +
    639B  TYR*     4.2    20.4    -      -       +      -
    640B  ILE      3.6     4.7    -      -       -      +
    641B  ALA*     4.5     1.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 599 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    584B  THR*     3.2    24.9    -      -       +      -
    585B  ILE      3.7     2.9    -      -       -      -
    586B  VAL*     3.9    15.0    -      -       +      -
    598B  VAL*     1.3    72.9    -      -       -      +
    600B  ARG*     1.3    59.4    +      -       -      +
    601B  ILE*     3.7     6.0    +      -       +      +
    638B  GLN      3.8     0.3    -      -       -      +
    639B  TYR*     3.4     3.5    -      -       -      -
    640B  ILE*     2.7    56.5    +      -       +      +
    642B  ILE*     3.9    26.3    -      -       +      +
    711B  ASP*     3.5    35.8    +      -       -      +
    712B  PHE*     4.9     2.5    -      -       +      -
   1001B  4K7      3.1    46.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 600 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    571B  PHE*     5.6     1.3    -      -       -      -
    583B  GLY      4.6     1.4    -      -       -      +
    584B  THR*     3.2    16.8    -      -       -      +
    585B  ILE*     2.7    54.7    +      -       -      +
    587B  TYR*     3.7    28.1    +      -       +      -
    598B  VAL      4.0     0.8    +      -       -      -
    599B  LYS*     1.3    69.7    -      -       -      +
    601B  ILE*     1.3    67.1    +      -       -      +
    602B  LEU*     4.6     7.8    -      -       -      +
    637B  PHE*     3.5    51.9    -      -       +      -
    638B  GLN      3.7     3.4    -      -       -      +
    639B  TYR*     3.7    32.6    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 601 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    584B  THR*     3.9    24.0    -      -       +      +
    599B  LYS*     4.2    13.9    -      -       +      +
    600B  ARG*     1.3    78.2    -      -       -      +
    602B  LEU*     1.3    65.8    +      -       -      +
    605B  CYS*     4.1    10.5    -      -       +      +
    606B  PHE*     3.6    16.2    -      -       +      +
    609B  ALA*     3.7    22.0    -      -       +      -
    637B  PHE*     3.3    22.0    -      -       -      -
    638B  GLN*     3.0    55.4    +      -       +      +
    640B  ILE*     4.5    14.6    -      -       +      -
   1001B  4K7      4.5    12.8    -      -       -      +
----------------------------------------------------------
 Back to top of page


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