Contacts of the strand formed by residues 641 - 646 (chain B) in PDB entry 1D0N


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 641 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361B  LEU*     3.5    35.5    -      -       -      +
    364B  GLN*     4.3    13.3    +      -       -      +
    386B  HIS*     4.9     6.7    -      -       +      +
    639B  PRO*     3.5    16.8    -      -       +      +
    640B  PRO*     1.3    81.2    -      -       -      +
    642B  LEU*     1.3    59.3    +      -       -      +
    643B  PHE*     3.5    31.8    -      -       +      -
    656B  GLU*     3.1    40.8    +      -       -      +
    661B  PHE*     4.1     6.3    -      -       -      -
    673B  LEU      3.5     1.9    -      -       -      +
    674B  LEU*     3.7     2.0    -      -       -      -
    675B  ASP*     2.8    41.7    +      -       +      +
    703B  TYR*     5.4     4.0    +      -       -      -
    707B  ASP*     5.9     1.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 642 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641B  ARG*     1.3    72.7    -      -       -      +
    643B  PHE*     1.3    63.7    +      -       -      +
    656B  GLU*     3.5     8.4    -      -       -      +
    657B  VAL*     2.9    55.3    +      -       +      +
    661B  PHE*     3.9    32.0    -      -       +      -
    662B  MET      5.2     0.2    -      -       -      +
    665B  ASP*     4.8     5.6    -      -       +      -
    666B  LEU*     4.3    22.7    -      -       +      -
    672B  MET*     4.2    20.2    -      -       +      -
    673B  LEU      3.3    19.3    -      -       -      +
    674B  LEU*     4.2    15.3    -      -       +      -
    729B  PHE*     5.8     2.0    -      -       +      -
    733B  PHE*     4.5    13.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 643 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641B  ARG*     3.5    57.2    -      -       +      -
    642B  LEU*     1.3    77.2    -      -       -      +
    644B  ALA*     1.3    66.8    +      -       -      +
    654B  ILE*     4.0    28.3    -      -       +      -
    655B  GLU      3.2     8.7    -      -       -      +
    656B  GLU*     3.5    36.3    -      -       +      -
    657B  VAL*     4.2     1.3    -      -       -      -
    672B  MET*     3.2    15.9    -      -       -      +
    673B  LEU*     2.9    44.0    +      -       +      +
    675B  ASP*     5.0     0.4    -      -       +      -
    703B  TYR*     3.5    32.3    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 644 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  ARG*     3.3    40.4    -      -       -      +
    643B  PHE*     1.3    75.0    -      -       -      +
    645B  CYS*     1.3    64.3    +      -       -      +
    653B  VAL      3.7     0.3    -      -       -      +
    654B  ILE*     3.2     9.0    -      -       -      +
    655B  GLU*     2.7    38.1    +      -       +      +
    670B  ASP*     4.8     2.0    -      -       -      +
    671B  VAL      3.7     5.4    -      -       -      +
    672B  MET*     4.1    11.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 645 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644B  ALA*     1.3    78.2    -      -       -      +
    646B  SER*     1.3    66.8    +      -       -      +
    647B  ASN*     5.6     0.4    -      -       -      +
    652B  PHE*     4.0    22.0    -      -       +      -
    653B  VAL      3.5     4.9    -      -       -      -
    654B  ILE*     4.5     1.1    -      -       -      -
    670B  ASP*     3.9    15.8    -      -       -      +
    671B  VAL*     2.8    32.1    +      -       +      +
    673B  LEU*     3.4    44.0    -      -       -      -
    692B  GLU*     4.4     8.2    -      -       -      +
    699B  SER*     4.5    10.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 646 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    645B  CYS*     1.3    81.5    -      -       -      +
    647B  ASN*     1.3    80.2    +      -       -      +
    648B  LYS*     3.4    16.4    +      -       -      +
    652B  PHE*     3.6     4.3    -      -       -      -
    653B  VAL*     3.0    44.3    +      -       -      +
    692B  GLU*     4.3     7.0    -      -       -      -
----------------------------------------------------------
 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