Contacts of the strand formed by residues 6916 - 6918 (chain A) in PDB entry 6W4H


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 VAL6916 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6866A  ILE*     4.6     5.4    -      -       +      -
   6868A  PHE*     4.2    15.5    -      -       +      -
   6896A  SER*     3.7    24.2    -      -       -      +
   6909A  LEU*     3.9    27.8    -      -       +      -
   6911A  GLY      5.1     1.8    -      -       -      +
   6912A  ASP      4.2     4.3    -      -       -      +
   6913A  CYS*     2.9    22.4    +      -       -      +
   6915A  THR*     1.3    80.8    -      -       -      +
   6917A  HIS*     1.3    73.0    +      -       -      +
   6918A  THR*     4.5    11.7    -      -       +      -
   6950A  TYR*     2.8    35.5    +      -       -      +
   6954A  PHE*     5.0     0.9    -      -       -      -
   7089A  SER      3.5     4.3    -      -       -      +
   7090A  SER*     4.6     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS6917 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6914A  ALA      3.8    15.1    +      -       -      -
   6915A  THR      3.1    25.8    +      -       -      -
   6916A  VAL*     1.3    76.4    +      -       -      +
   6918A  THR*     1.3    68.7    +      -       -      +
   6950A  TYR*     6.0     1.6    -      +       -      -
   6954A  PHE*     5.8     0.9    -      -       -      -
   7088A  ILE*     3.4     0.5    -      -       -      +
   7089A  SER*     2.9    45.5    +      -       -      +
   7091A  ASP*     3.1    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR6918 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6866A  ILE*     4.4     8.3    -      -       +      -
   6916A  VAL*     4.5     4.5    -      -       +      -
   6917A  HIS*     1.3    81.1    -      -       -      +
   6919A  ALA*     1.3    53.1    +      -       -      +
   6920A  ASN*     3.1    18.4    +      -       -      -
   6922A  TRP*     3.1    26.7    +      -       +      +
   6954A  PHE*     3.9    14.1    -      -       +      -
   6958A  LYS*     2.8    45.3    +      -       -      +
   7087A  VAL      3.4     9.6    -      -       -      -
   7088A  ILE*     3.7    20.2    -      -       +      -
----------------------------------------------------------
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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