Contacts of the strand formed by residues 157 - 162 (chain V) in PDB entry 5GJQ


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 157 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174U  HIS*     5.7     5.2    -      -       +      +
     33V  ILE*     4.8     8.5    -      -       +      -
     38V  LEU*     4.5    19.7    -      -       +      -
     41V  MET*     4.8     1.8    -      -       +      -
    120V  CYS*     4.3     2.6    -      -       -      -
    143V  VAL*     4.0    12.3    -      -       +      -
    144V  VAL      3.7     9.4    -      -       -      +
    145V  VAL*     3.4    38.6    -      -       +      -
    155V  VAL*     4.3    19.5    -      -       +      +
    156V  VAL*     1.3    79.0    -      -       -      +
    158V  ASP*     1.3    65.7    +      -       -      +
    205V  ILE*     3.7    32.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 158 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120V  CYS*     3.5    33.8    -      -       +      +
    143V  VAL*     3.3     5.0    -      -       -      +
    144V  VAL*     2.7    39.1    +      -       +      +
    157V  ILE*     1.3    79.2    -      -       -      +
    159V  ALA*     1.3    79.8    +      -       -      +
    160V  PHE*     3.2    30.6    -      -       +      +
    196V  LEU*     5.7     3.5    -      -       -      +
    202V  SER*     5.2     5.5    -      -       -      -
    203V  ILE      4.4     8.0    +      -       -      +
    205V  ILE*     4.0     5.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 159 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31V  VAL*     4.5    13.7    -      -       +      -
     33V  ILE*     5.4     0.4    -      -       +      -
    141V  VAL*     5.2     4.3    -      -       +      -
    142V  ALA      3.0     6.5    -      -       -      +
    143V  VAL*     3.6    22.0    -      -       +      -
    158V  ASP*     1.3    82.8    +      -       -      +
    160V  PHE*     1.3    68.2    +      -       -      +
    203V  ILE*     3.0    26.6    +      -       +      +
    205V  ILE*     3.8    24.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 160 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120V  CYS      4.9     0.2    -      -       -      -
    121V  TRP*     4.1    19.1    -      -       -      -
    122V  LEU*     3.4    36.6    -      -       +      -
    141V  VAL*     4.8     0.6    -      -       -      +
    142V  ALA*     2.8    39.2    +      -       -      +
    144V  VAL*     4.5     9.4    -      -       +      -
    158V  ASP*     3.2    38.6    -      -       +      -
    159V  ALA*     1.3    79.9    -      -       -      +
    161V  ARG*     1.3    60.7    +      -       -      +
    196V  LEU*     5.3     2.2    -      -       +      -
    200V  TYR*     3.3    38.4    -      +       -      -
    201V  TYR      2.9    17.0    -      -       -      +
    202V  SER*     3.3    14.6    -      -       -      -
    203V  ILE*     3.6    14.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 161 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29V  GLU*     4.8     7.8    +      -       -      -
    122V  LEU*     5.6     1.8    -      -       -      -
    130V  GLN*     4.7     5.6    -      -       -      +
    134V  GLU*     3.0    20.6    +      -       -      +
    138V  GLU      2.2    32.8    +      -       -      -
    139V  ARG*     4.1    10.3    -      -       -      +
    140V  ALA      3.5    24.5    +      -       -      +
    141V  VAL*     4.2     9.0    -      -       -      -
    142V  ALA      4.9     0.2    -      -       -      +
    160V  PHE*     1.3    79.2    -      -       -      +
    162V  LEU*     1.3    66.1    +      -       -      +
    200V  TYR*     3.9     4.7    -      -       -      -
    201V  TYR*     2.9    73.5    +      -       +      +
    203V  ILE*     3.9    16.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 162 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122V  LEU*     5.9     2.0    -      -       +      +
    127V  ILE*     4.4    11.2    -      -       +      +
    130V  GLN*     3.6    22.9    -      -       +      +
    131V  GLN*     3.7    28.0    -      -       +      +
    134V  GLU*     3.6    37.9    +      -       +      +
    161V  ARG*     1.3    87.7    +      -       -      +
    163V  ILE*     1.3    92.7    +      -       -      +
    199V  HIS      3.6     7.0    -      -       -      +
    200V  TYR*     3.4    13.5    -      -       +      -
    201V  TYR*     3.2    17.5    -      -       -      -
----------------------------------------------------------
 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