Contacts of the strand formed by residues 261 - 264 (chain A) in PDB entry 6DWZ


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 ILE 261 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  ASP*     5.7     0.4    -      -       -      +
    241A  SER      3.2    26.2    -      -       -      +
    242A  SER*     3.7    18.4    -      -       -      +
    243A  ILE      3.5    13.2    -      -       -      +
    244A  LYS*     3.7    18.8    -      -       +      -
    245A  PHE*     3.0    33.0    +      -       -      +
    260A  ASN*     1.3    72.5    -      -       -      +
    262A  ARG*     1.3    60.6    +      -       -      +
    263A  ILE*     5.0     1.3    -      -       +      -
    428A  TRP*     3.6    40.8    -      -       +      +
    457A  LYS*     5.7     2.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  PHE      3.5     4.9    -      -       -      -
    247A  THR*     3.2    31.8    -      -       -      +
    248A  ASP      4.3     0.6    +      -       -      -
    249A  ARG*     4.6     0.8    -      -       -      +
    253A  VAL      5.3     0.2    -      -       -      -
    254A  VAL*     3.2    52.9    +      -       -      +
    257A  LEU*     3.5    39.3    -      -       +      +
    258A  ALA*     5.7     0.2    -      -       -      -
    260A  ASN      3.4     7.0    +      -       -      +
    261A  ILE*     1.3    77.5    -      -       -      +
    263A  ILE*     1.3    67.0    +      -       -      +
    264A  ASN*     2.5    31.6    +      -       -      +
    426A  SER*     5.2     6.6    +      -       -      -
    428A  TRP*     5.7     1.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  LYS*     3.6    30.7    -      -       +      -
    245A  PHE      2.6    19.6    +      -       -      +
    246A  VAL*     3.2    26.2    -      -       +      -
    247A  THR      3.2     6.6    +      -       -      +
    261A  ILE      5.0     0.2    -      -       -      -
    262A  ARG*     1.3    83.9    +      -       -      +
    264A  ASN*     1.3    70.6    +      -       -      +
    382A  LEU*     5.2     6.1    -      -       +      -
    426A  SER*     4.7    10.5    -      -       -      +
    428A  TRP*     4.3    25.1    -      -       +      +
    429A  HIS*     3.8    25.4    -      -       +      +
    564A  ILE*     4.2    27.1    -      -       +      -
    566A  ALA*     6.4     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  VAL*     5.1     1.0    -      -       -      +
    247A  THR      3.8     1.9    -      -       -      +
    249A  ARG*     3.7    19.6    -      -       +      +
    262A  ARG*     2.5    34.3    +      -       -      -
    263A  ILE*     1.3    77.1    -      -       -      +
    265A  CYS*     1.3    65.5    +      -       -      +
    266A  SER*     3.2     5.4    +      -       -      -
    269A  LEU*     3.8    15.7    -      -       +      +
    424A  ASN*     2.9    53.6    +      -       -      +
    426A  SER*     5.8     1.0    -      -       -      -
    429A  HIS*     4.2    17.6    +      -       +      -
    566A  ALA      4.5     2.4    -      -       -      +
----------------------------------------------------------
 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