Contacts of the strand formed by residues 166 - 168 (chain B) in PDB entry 6J7Z


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 166 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  HIS*     3.8    33.8    -      -       +      +
    166A  ILE*     4.8     1.8    -      -       +      -
    168A  ASP*     3.7    15.9    -      -       -      +
    170A  SER*     4.7     3.0    -      -       -      +
    171A  THR*     3.3    19.1    +      -       -      +
    174A  GLU*     4.8     1.8    -      -       -      +
    138B  PRO*     4.4     0.9    -      -       -      -
    139B  LEU*     3.4    14.1    -      -       +      -
    144B  VAL*     3.8    29.6    -      -       +      -
    145B  HIS*     4.3    12.8    -      -       +      -
    148B  LYS*     3.8    28.5    -      -       +      -
    163B  HIS      6.0     0.2    -      -       -      +
    164B  TYR      3.8     3.6    +      -       -      +
    165B  ARG*     1.3    81.3    -      -       -      +
    167B  ILE*     1.3    67.6    +      -       -      +
    168B  ASP*     4.1    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  THR*     3.7    10.8    -      -       +      +
    174A  GLU*     4.4    13.0    -      -       +      -
    175A  LEU*     4.1    24.2    -      -       +      -
    178A  ARG*     4.0    12.3    -      -       -      +
     43B  MET*     3.6    34.5    -      -       +      -
     45B  TRP*     5.2     0.9    -      -       +      -
    138B  PRO*     3.9    25.6    -      -       +      -
    139B  LEU      2.9    12.3    +      -       -      +
    140B  ALA*     3.4     9.7    -      -       +      +
    141B  GLY      3.3    24.4    +      -       -      +
    144B  VAL*     4.3     1.2    -      -       -      +
    166B  ILE*     1.3    77.6    -      -       -      +
    168B  ASP*     1.3    59.2    +      -       -      +
    169B  VAL*     3.5     1.4    +      -       -      +
    207B  LEU*     4.4    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE*     3.6    14.6    +      -       -      +
    168A  ASP*     5.0     1.6    -      -       +      -
    171A  THR*     2.9    34.4    +      -       -      +
    141B  GLY      3.6     2.7    -      -       -      -
    143B  SER*     2.8    32.8    +      -       -      -
    144B  VAL*     4.2     4.5    -      -       +      -
    145B  HIS*     3.4    22.8    +      -       -      -
    166B  ILE*     4.1    14.4    -      -       +      -
    167B  ILE*     1.3    70.5    -      -       -      +
    169B  VAL*     1.3    63.2    +      -       -      +
    170B  SER*     2.9    19.1    +      -       -      -
    171B  THR*     3.2    21.6    +      -       -      +
    172B  VAL*     3.8     2.3    +      -       -      +
----------------------------------------------------------
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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