Contacts of the strand formed by residues 163 - 167 (chain A) in PDB entry 4HZF


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 GLY 163 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  THR*     4.7     0.5    -      -       -      -
    160A  HIS*     2.9    33.7    +      -       -      +
    162A  ASP*     1.3    80.4    -      -       -      +
    164A  MET*     1.3    70.6    +      -       -      +
    205A  VAL*     4.4     1.0    -      -       -      +
    206A  VAL      3.3    10.1    -      -       -      -
    208A  GLY*     3.9    11.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ALA*     3.4    37.0    -      -       +      +
    157A  ALA*     3.3    30.5    -      -       +      +
    158A  MET      3.3    21.8    -      -       -      +
    159A  THR*     3.5    22.4    -      -       +      +
    160A  HIS*     4.3     0.2    -      -       -      -
    163A  GLY*     1.3    84.3    -      -       -      +
    165A  GLN*     1.3    60.1    +      -       -      +
    166A  ILE*     3.9     0.6    +      -       -      -
    204A  ILE      3.7     0.7    -      -       -      +
    205A  VAL*     3.5     3.7    -      -       -      -
    206A  VAL*     2.9    34.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  ASP      4.7     0.3    -      -       -      +
    157A  ALA*     3.5     5.5    -      -       -      -
    158A  MET*     2.7    51.9    +      -       +      +
    159A  THR      5.0     0.9    -      -       -      +
    160A  HIS*     3.5    27.3    +      -       +      +
    164A  MET*     1.3    72.1    -      -       -      +
    166A  ILE*     1.3    64.0    +      -       -      +
    203A  THR*     2.9    38.6    +      -       +      +
    204A  ILE      3.5     5.6    -      -       -      +
    205A  VAL*     3.9    10.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  LEU*     3.8    34.3    -      -       +      +
    151A  LEU*     3.6    30.5    -      -       +      +
    152A  ALA*     3.6    32.5    -      -       +      -
    156A  ASP      5.7     0.9    -      -       -      -
    157A  ALA*     4.2     6.5    -      -       +      +
    164A  MET      4.6     2.0    -      -       -      +
    165A  GLN*     1.3    83.9    -      -       -      +
    167A  LYS*     1.3    61.9    +      -       -      +
    168A  ILE*     4.0    13.7    -      -       +      -
    203A  THR*     3.6     4.7    -      -       -      +
    204A  ILE*     2.9    49.3    +      -       +      +
    206A  VAL*     4.3     5.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  LEU*     6.1     0.3    -      -       -      +
    166A  ILE*     1.3    75.3    -      -       -      +
    168A  ILE*     1.3    62.6    +      -       -      +
    172A  GLU*     5.0     0.7    -      -       -      +
    202A  LYS*     3.3    10.8    -      -       +      +
    203A  THR*     5.5     1.8    -      -       +      +
----------------------------------------------------------
 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