Contacts of the strand formed by residues 695 - 698 (chain B) in PDB entry 1J1B


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 695 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607B  CYS      4.3     3.8    -      -       -      +
    608B  ASN*     4.7     0.2    -      -       -      +
    664B  GLN*     3.3     7.9    -      -       -      +
    689B  LEU*     3.4     5.6    -      -       -      +
    690B  ASP*     3.0    30.2    +      -       +      +
    693B  THR*     3.1    24.2    +      -       -      +
    694B  ALA*     1.3    78.3    -      -       -      +
    696B  LEU*     1.3    71.6    +      -       -      +
    697B  LYS*     3.9    30.9    +      -       +      +
    857B  PRO*     3.5    27.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 696 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608B  ASN*     3.0    30.2    -      -       -      +
    639B  VAL*     4.0    13.7    -      -       +      -
    661B  TYR*     3.5    33.4    -      -       +      +
    664B  GLN*     3.0    24.3    -      -       +      +
    665B  LEU*     4.1    26.0    -      -       +      +
    668B  SER*     5.3     0.2    -      -       -      +
    687B  LEU*     4.1    20.6    -      -       +      -
    688B  LEU      3.2    10.8    -      -       -      +
    689B  LEU*     3.7    14.4    -      -       +      -
    695B  VAL*     1.3    75.3    -      -       -      +
    697B  LYS*     1.3    76.2    +      -       -      +
    698B  LEU*     4.1     4.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 697 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    606B  HIS      5.1     0.2    +      -       -      -
    607B  CYS*     2.7    36.8    +      -       -      +
    608B  ASN      3.4     2.9    -      -       -      -
    609B  ILE      4.1     8.6    +      -       -      +
    610B  VAL*     3.8    25.1    -      -       +      +
    611B  ARG      5.5     0.7    -      -       -      +
    633B  ASP*     5.4    10.5    -      -       +      -
    635B  VAL*     3.9    24.5    -      -       +      -
    688B  LEU*     2.9    42.2    +      -       +      +
    695B  VAL*     3.9    17.8    +      -       +      +
    696B  LEU*     1.3    82.4    -      -       -      +
    698B  LEU*     1.3    63.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 698 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608B  ASN      2.8    17.1    +      -       -      +
    609B  ILE*     3.6    10.4    -      -       +      +
    610B  VAL*     3.0    23.9    +      -       -      +
    665B  LEU*     4.6     2.0    -      -       +      -
    668B  SER*     3.5    25.6    -      -       -      +
    669B  LEU*     4.3    15.5    -      -       +      -
    672B  ILE*     4.4     7.6    -      -       +      -
    679B  HIS*     3.7    28.0    -      -       +      +
    682B  ILE*     3.6    24.2    -      -       +      -
    686B  ASN*     3.8    12.3    -      -       +      +
    687B  LEU*     3.8    13.2    -      -       +      -
    696B  LEU*     4.1     6.2    -      -       +      +
    697B  LYS*     1.3    72.0    -      -       -      +
    699B  CYS*     1.3    62.5    +      -       -      +
    701B  PHE*     4.0    15.2    -      -       +      -
----------------------------------------------------------
 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