Contacts of the helix formed by residues 733 - 738 (chain B) in PDB entry 6WCZ


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 GLN 733 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333B  TRP*     3.5    23.2    -      -       -      +
    731B  ARG      3.4     4.5    +      -       -      -
    732B  HIS*     1.3    71.7    -      -       -      +
    734B  ASP*     1.3    62.2    +      -       -      +
    736B  LEU*     3.4    11.3    +      -       -      +
    737B  ILE*     3.2    28.5    +      -       +      +
    771B  ARG*     3.7    15.6    +      -       -      +
    773B  ASP*     2.7    44.6    +      -       -      +
    774B  LEU*     4.1    20.7    -      -       +      +
    846B  ASP*     4.6     0.3    -      -       -      +
    849B  CYS      2.9    16.9    +      -       -      +
    850B  GLY      2.9    23.0    -      -       -      +
    851B  SER*     3.3     7.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 734 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  ARG*     5.1     6.4    +      -       -      +
    198A  ILE*     5.6     6.3    -      -       +      +
    333B  TRP*     5.7     2.5    -      -       -      +
    336B  VAL*     3.9    14.5    -      -       -      +
    338B  GLY*     3.2    26.1    +      -       -      -
    339B  VAL*     3.2    30.1    +      -       -      +
    342B  ILE*     4.4     1.4    -      -       -      +
    732B  HIS*     3.1    24.7    +      -       +      +
    733B  GLN*     1.3    78.9    -      -       -      +
    735B  GLU*     1.3    60.6    +      -       +      +
    737B  ILE*     3.8     5.8    -      -       -      -
    738B  GLY*     3.0    28.9    +      -       -      -
    850B  GLY      5.1     0.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 735 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  LYS*     5.7     4.2    +      -       -      +
    198A  ILE*     5.8     5.9    -      -       +      +
    342B  ILE*     3.7    30.7    -      -       +      +
    712B  SER*     5.6     0.7    -      -       -      -
    731B  ARG*     3.4    35.4    +      -       -      +
    732B  HIS*     3.2    20.2    +      -       -      +
    734B  ASP*     1.3    80.3    -      -       +      +
    736B  LEU*     1.3    57.0    +      -       -      +
    739B  ARG*     3.8    12.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 736 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    731B  ARG*     3.8    34.3    -      -       +      +
    732B  HIS      4.1     2.8    +      -       -      +
    733B  GLN*     3.4    14.4    -      -       -      +
    734B  ASP      3.1     0.6    -      -       -      -
    735B  GLU*     1.3    78.3    -      -       -      +
    737B  ILE*     1.3    68.9    +      -       -      +
    738B  GLY      3.1     1.6    -      -       -      -
    739B  ARG*     2.7    29.5    +      -       -      +
    740B  ALA      3.4     5.2    +      -       -      -
    763B  MET*     6.2     1.1    -      -       +      -
    764B  TRP*     3.5    29.0    +      -       +      +
    768B  TYR*     3.6    31.2    -      -       +      -
    771B  ARG*     5.4     3.4    -      -       -      +
    774B  LEU*     3.8    38.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 737 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  VAL*     6.0     3.1    -      -       +      +
    330B  SER*     5.5     1.1    -      -       -      -
    333B  TRP*     3.8    45.3    -      -       +      +
    339B  VAL*     4.0     5.8    -      -       +      +
    733B  GLN*     3.2    24.3    +      -       +      +
    734B  ASP*     3.4    12.6    -      -       -      +
    736B  LEU*     1.3    80.0    -      -       +      +
    738B  GLY*     1.3    63.0    +      -       -      +
    739B  ARG      3.5     0.3    +      -       -      -
    740B  ALA*     3.9     3.2    +      -       +      +
    741B  ARG*     3.7    23.9    +      -       -      +
    764B  TRP*     3.6    32.3    -      -       +      -
    774B  LEU*     4.0    11.0    -      -       +      -
    777B  MET*     3.8    23.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 738 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339B  VAL*     4.3    15.6    -      -       -      +
    342B  ILE*     3.3    34.7    -      -       -      +
    734B  ASP      3.0    13.4    +      -       -      -
    737B  ILE*     1.3    78.4    -      -       -      +
    739B  ARG*     1.3    58.6    +      -       -      +
    741B  ARG*     4.0    12.9    -      -       -      +
    742B  VAL*     3.8    14.6    -      -       -      +
----------------------------------------------------------
 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