Contacts of the strand formed by residues 158 - 162 (chain B) in PDB entry 4IRQ


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 TYR 158 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  HIS*     4.3     7.1    -      -       +      +
     94B  ARG*     3.5    18.8    -      -       -      -
     95B  LEU*     3.4    39.0    -      -       +      +
     96B  ALA*     2.9    25.8    +      -       -      +
    124B  ILE*     3.6    11.3    -      -       -      +
    156B  THR*     3.6     1.4    -      -       -      -
    157B  ASP*     1.3    93.5    -      -       -      +
    159B  ILE*     1.3    69.3    +      -       -      +
    175B  TYR      2.8    22.9    +      -       -      -
    176B  GLY*     3.5    20.9    -      -       -      -
    177B  PHE*     3.6    24.3    +      +       +      -
    178B  PRO*     3.4    16.2    -      -       +      -
    205B  LEU*     4.0     6.5    -      -       +      -
    206B  LEU      3.3    12.8    -      -       -      +
    207B  SER*     3.6     8.1    -      -       -      -
    208B  LYS*     3.9     4.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  LEU*     3.6     3.9    -      -       -      +
     96B  ALA*     3.3    10.8    -      -       +      -
     98B  LEU*     3.6    30.3    -      -       +      -
    145B  ILE*     4.5     1.8    -      -       +      -
    149B  PHE*     4.0    20.2    -      -       +      -
    158B  TYR*     1.3    79.4    -      -       -      +
    160B  ALA*     1.3    60.2    +      -       -      +
    161B  MET*     4.0    22.4    -      -       +      +
    204B  LEU      4.5     2.0    -      -       -      +
    205B  LEU*     3.2     8.7    -      -       -      +
    206B  LEU*     2.9    42.5    +      -       +      +
    207B  SER      5.3     0.2    -      -       -      +
    208B  LYS*     4.1    16.6    -      -       +      -
    211B  TYR*     3.9    36.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  LEU*     3.6    23.6    -      -       +      -
     96B  ALA      3.0     9.0    +      -       -      +
     97B  VAL*     4.5     4.3    -      -       +      -
     98B  LEU*     2.8    26.7    +      -       -      -
    159B  ILE*     1.3    75.9    -      -       -      +
    161B  MET*     1.3    66.6    +      -       -      +
    162B  HIS*     3.2    16.0    +      -       +      +
    175B  TYR*     5.2     1.3    -      -       +      -
    204B  LEU      3.5     6.1    -      -       -      -
    205B  LEU*     3.8    20.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  LEU*     3.3     8.3    -      -       -      -
    141B  ARG*     3.9    25.6    -      -       -      +
    145B  ILE*     3.6    26.0    -      -       +      -
    159B  ILE*     4.0     7.7    -      -       +      +
    160B  ALA*     1.3    70.9    -      -       -      +
    162B  HIS*     1.3    58.1    +      -       -      +
    202B  GLY      3.5     3.1    -      -       -      +
    203B  ILE*     3.2     5.7    -      -       -      +
    204B  LEU*     3.0    57.2    +      -       +      +
    206B  LEU*     4.1     8.1    -      -       +      -
    211B  TYR*     3.9    16.4    -      -       +      -
    217B  MET*     3.7    29.6    -      -       -      +
    231B  PHE*     3.8    28.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  VAL*     3.8    18.2    -      -       +      -
     98B  LEU      2.8     9.0    +      -       -      +
     99B  VAL*     3.5    11.1    -      -       -      +
    100B  PRO*     3.4    16.8    -      -       -      +
    111B  PHE*     3.3    18.0    -      +       +      -
    115B  MET*     3.6    19.0    -      -       +      +
    160B  ALA*     3.7    12.6    -      -       +      +
    161B  MET*     1.3    74.5    -      -       -      +
    163B  ASP*     1.3    86.2    +      -       -      +
    164B  VAL      3.5     0.9    +      -       -      -
    166B  LEU      3.0    26.9    -      -       -      -
    168B  PRO*     4.4     0.4    -      -       +      -
    175B  TYR*     2.8    34.0    +      +       -      -
    202B  GLY      3.6     1.6    -      -       -      -
    203B  ILE*     3.3    28.4    -      -       +      +
----------------------------------------------------------
 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