Contacts of the strand formed by residues 677 - 684 (chain A) in PDB entry 5ZR1


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 VAL 677 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    649A  TYR*     4.0    25.6    -      -       +      -
    650A  VAL      3.4    19.3    -      -       -      +
    651A  ASP*     3.8    20.4    -      -       +      +
    676A  ASP*     1.3    88.2    +      -       +      +
    678A  ARG*     1.3    73.2    +      -       -      +
    679A  LYS      4.2     0.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 678 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    648A  PHE      3.9     0.7    -      -       -      +
    649A  TYR*     5.3     0.4    -      -       -      -
    650A  VAL*     3.0    34.2    +      -       +      +
    652A  THR*     3.4    31.6    -      -       +      +
    676A  ASP      4.3     0.6    +      -       -      -
    677A  VAL*     1.3    80.0    -      -       -      +
    679A  LYS*     1.3    59.7    +      -       -      +
    680A  VAL*     3.3    12.2    +      -       +      +
    725A  HIS*     5.8     5.9    -      -       -      -
    769A  GLY*     6.0     7.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 679 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    647A  PHE*     3.7    47.1    -      -       +      -
    648A  PHE      3.7    11.0    -      -       -      +
    649A  TYR*     4.7    27.3    +      -       +      +
    660A  ILE*     5.1     4.7    -      -       -      -
    677A  VAL      4.2     0.4    +      -       -      -
    678A  ARG*     1.3    70.6    -      -       -      +
    680A  VAL*     1.3    59.9    +      -       -      +
    681A  ARG*     4.1     0.9    +      -       -      +
    769A  GLY      4.8     2.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 680 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  ILE*     3.7    14.1    -      -       +      -
    647A  PHE*     3.6     3.3    -      -       -      -
    648A  PHE*     2.9    36.0    +      -       +      +
    650A  VAL*     3.7    31.4    -      -       +      -
    678A  ARG*     3.3     9.9    +      -       +      +
    679A  LYS*     1.3    77.9    -      -       -      +
    681A  ARG*     1.3    75.2    +      -       -      +
    769A  GLY*     3.4    31.0    -      -       -      +
    770A  VAL*     4.0     3.1    -      -       -      +
    771A  GLN*     4.3    14.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 681 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  ILE*     5.6     0.4    -      -       -      +
    645A  ASP*     3.6    35.4    +      -       -      +
    646A  SER      3.3    15.0    +      -       -      +
    647A  PHE*     3.6    38.0    -      -       +      +
    648A  PHE*     4.6     1.6    -      -       -      +
    679A  LYS      5.6     0.7    -      -       -      +
    680A  VAL*     1.3    83.5    -      -       -      +
    682A  LEU*     1.3    63.2    +      -       -      +
    683A  ARG*     3.0    47.6    -      -       -      +
    769A  GLY      4.1     3.0    +      -       -      +
    770A  VAL*     3.5    23.1    -      -       +      +
    771A  GLN*     3.2    25.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 682 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  ILE*     3.7    31.2    -      -       +      -
    423A  PHE*     4.4    12.8    -      -       +      -
    426A  VAL*     3.7    30.1    -      -       +      -
    643A  LEU*     3.7    15.8    -      -       +      +
    644A  ASN*     3.7     1.5    -      -       -      +
    645A  ASP*     2.8    26.2    +      -       -      -
    646A  SER      3.1    10.3    +      -       -      +
    648A  PHE*     4.3    12.8    -      -       +      -
    681A  ARG*     1.3    81.0    -      -       -      +
    683A  ARG*     1.3    65.3    +      -       -      +
    684A  MET*     5.1    11.0    -      -       +      -
    770A  VAL*     5.2     0.2    -      -       -      -
    771A  GLN*     3.4    27.1    -      -       +      +
    772A  THR*     4.3     2.7    -      -       -      +
    773A  VAL*     5.4     0.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 683 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644A  ASN*     3.3     4.7    -      -       -      +
    645A  ASP*     3.3    32.5    +      -       -      +
    681A  ARG*     3.0    41.5    -      -       -      +
    682A  LEU*     1.3    74.4    -      -       -      +
    684A  MET*     1.3    65.4    +      -       -      +
    770A  VAL*     4.5    11.7    -      -       +      +
    771A  GLN      3.5     3.4    +      -       -      +
    772A  THR*     2.9    37.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 684 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426A  VAL*     4.0    26.2    -      -       +      -
    430A  LEU*     5.4     0.7    -      -       +      -
    640A  LEU*     3.7    29.4    -      -       +      -
    644A  ASN*     3.2    28.6    +      -       +      +
    682A  LEU*     5.1    10.5    -      -       +      -
    683A  ARG*     1.3    80.2    -      -       -      +
    685A  SER*     1.3    66.9    +      -       -      +
    686A  ALA*     3.5     3.3    +      -       -      +
    688A  ALA*     6.4     1.8    -      -       +      -
    689A  ILE*     4.9    15.6    -      -       +      +
    710A  CYS*     5.0    20.4    -      -       +      +
    713A  ALA*     6.2     0.4    -      -       +      -
    714A  ALA*     5.5     0.7    -      -       +      -
    772A  THR*     4.3     1.8    -      -       -      -
    773A  VAL*     4.0    40.4    -      -       +      +
    778A  VAL*     6.0     2.9    -      -       +      -
----------------------------------------------------------
 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