Contacts of the strand formed by residues 688 - 701 (chain A) in PDB entry 3BJY


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 CYS 688 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    669A  MET*     4.0    11.0    -      -       +      +
    670A  ARG      3.1    30.3    -      -       -      +
    671A  ARG*     3.8     3.4    -      -       -      -
    672A  CYS*     3.6    11.7    -      -       -      -
    685A  MET*     3.2    48.0    -      -       +      +
    686A  GLY      3.4     4.0    +      -       -      -
    687A  ARG*     1.3    78.5    -      -       -      +
    689A  ASP*     1.3    64.2    +      -       -      +
    690A  SER      4.3     0.3    +      -       -      -
    726A  ARG*     3.7    15.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 689 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    668A  LEU      3.6     0.5    -      -       -      +
    669A  MET*     3.6     3.8    -      -       -      -
    670A  ARG*     2.8    32.4    +      -       +      +
    671A  ARG      4.8     0.9    -      -       -      +
    672A  CYS*     3.7    29.6    -      -       -      +
    673A  LYS      4.7     1.9    +      -       -      -
    688A  CYS*     1.3    75.8    -      -       -      +
    690A  SER*     1.3    63.7    +      -       -      +
    691A  PHE*     3.8    23.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 690 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    667A  LYS*     3.8    13.7    +      -       -      -
    668A  LEU      3.5     4.9    -      -       -      -
    669A  MET*     3.1    25.3    -      -       -      +
    688A  CYS      4.3     0.4    +      -       -      -
    689A  ASP*     1.3    71.0    -      -       -      +
    691A  PHE*     1.3    72.8    +      -       -      +
      7P    C      3.9    25.0    +      -       -      -
      8P    C      3.5    29.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 691 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    667A  LYS*     3.4     2.9    -      -       -      +
    668A  LEU*     2.8    55.1    +      -       +      -
    670A  ARG*     4.3    27.4    -      -       +      -
    689A  ASP*     3.8    31.9    -      -       +      -
    690A  SER*     1.3    87.6    -      -       -      +
    692A  SER*     1.3    61.8    +      -       -      +
    718A  LEU*     3.9    35.6    -      -       +      +
    720A  CYS*     6.3     0.7    -      -       +      -
      7P    C      3.7     7.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 692 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    665A  THR*     3.5    21.1    -      -       -      +
    666A  LEU      3.6     4.4    +      -       -      -
    667A  LYS*     4.0    12.0    -      -       -      +
    691A  PHE*     1.3    76.6    -      -       -      +
    693A  ARG*     1.3    66.9    +      -       -      +
    718A  LEU*     3.9     8.1    -      -       -      +
      6P    C      3.7    23.7    +      -       -      +
      7P    C      3.1    46.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 693 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    665A  THR*     3.4     3.4    -      -       -      -
    666A  LEU      3.0    31.2    +      -       -      +
    692A  SER*     1.3    77.9    +      -       -      +
    694A  SER*     1.3    72.7    +      -       -      +
    695A  SER*     6.1     0.6    -      -       -      -
    714A  LEU*     3.6    30.2    -      -       +      +
    717A  THR*     3.4    37.6    +      -       -      +
    718A  LEU*     3.9    16.7    -      -       +      +
      6P    C      3.7    21.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 694 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    663A  GLN*     4.1    17.2    +      -       -      -
    664A  ILE      3.1     6.5    -      -       -      -
    665A  THR*     3.1    24.7    -      -       -      -
    693A  ARG*     1.3    88.4    +      -       -      +
    695A  SER*     1.3    65.5    +      -       -      +
    714A  LEU*     4.3     3.1    -      -       -      +
    733A  ASN*     4.7     0.2    -      -       -      -
      5P    T      3.9    15.1    +      -       -      +
      6P    C      2.7    24.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 695 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    663A  GLN*     3.4     6.7    -      -       -      +
    664A  ILE*     2.8    34.4    +      -       -      +
    693A  ARG*     6.1     0.9    -      -       -      -
    694A  SER*     1.3    77.9    -      -       -      +
    696A  ARG*     1.3    70.6    +      -       -      +
    697A  LEU*     3.8     1.6    +      -       -      +
    710A  GLU*     2.7    41.9    +      -       -      +
    714A  LEU*     3.8     8.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 696 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    662A  SER      3.5     8.3    -      -       -      +
    663A  GLN*     3.5    14.8    -      -       -      +
    695A  SER*     1.3    80.0    -      -       -      +
    697A  LEU*     1.3    68.0    +      -       -      +
    698A  GLY      3.9     0.5    +      -       -      -
    734A  LYS*     2.7    49.5    -      -       -      +
      4P    C      3.7    24.7    +      -       -      +
      5P    T      2.8    42.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 697 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    661A  THR*     3.5    24.2    -      -       -      +
    662A  SER*     2.7    25.7    +      -       -      +
    663A  GLN*     4.3     1.8    -      -       -      +
    664A  ILE*     4.2    33.0    -      -       +      -
    695A  SER*     4.5     2.7    -      -       -      +
    696A  ARG*     1.3    81.0    -      -       -      +
    698A  GLY*     1.3    68.4    +      -       -      +
    699A  ILE*     3.2    13.9    +      -       -      +
    700A  PRO*     5.1     0.5    -      -       -      +
    701A  THR*     3.6    19.3    -      -       +      -
    706A  ILE*     4.3    17.0    -      -       +      -
    707A  ILE*     4.2    15.3    -      -       +      -
    710A  GLU*     4.5    12.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 698 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    696A  ARG      3.9     1.6    +      -       -      -
    697A  LEU*     1.3    74.0    -      -       -      +
    699A  ILE*     1.3    68.9    +      -       -      +
    700A  PRO*     4.5     2.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 699 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    661A  THR      4.6     0.2    -      -       -      -
    697A  LEU*     4.0     7.1    -      -       -      +
    698A  GLY*     1.3    83.3    -      -       -      +
    700A  PRO*     1.4    89.4    -      -       +      +
    701A  THR*     3.1    17.1    +      -       -      +
    706A  ILE*     5.8     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 700 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    660A  THR*     3.1    25.5    -      -       -      +
    661A  THR      3.3    10.3    -      -       -      +
    662A  SER*     3.8    14.4    -      -       -      -
    697A  LEU      5.1     0.2    -      -       -      +
    698A  GLY      4.5     2.9    -      -       -      +
    699A  ILE*     1.4    99.0    -      -       +      +
    701A  THR*     1.3    57.0    +      -       -      +
    736A  VAL*     3.6    35.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 701 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    660A  THR*     3.4     9.3    -      -       -      -
    661A  THR*     2.9    28.3    +      -       -      +
    697A  LEU*     3.6    26.0    -      -       +      -
    699A  ILE*     3.4    13.5    -      -       -      +
    700A  PRO*     1.3    76.6    -      -       -      +
    702A  ASN*     1.3    69.4    +      -       -      +
    703A  GLU*     2.6    29.9    +      -       -      +
    706A  ILE*     4.1    25.6    -      -       +      +
    707A  ILE*     4.0     7.7    -      -       +      +
----------------------------------------------------------
 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