Contacts of the strand formed by residues 131 - 137 (chain B) in PDB entry 4QKB


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 THR 131 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ALA*     3.8    18.9    +      -       +      +
     97B  PHE*     3.6    27.9    -      -       +      -
    101B  GLN*     3.1    24.0    +      -       -      -
    128B  CYS*     4.3     1.6    -      -       -      -
    129B  GLY      3.4     1.2    -      -       -      -
    130B  ALA*     1.3    82.4    +      -       -      +
    132B  ILE*     1.3    76.8    +      -       -      +
    166B  ILE*     4.0    15.3    -      -       +      -
    167B  LEU      3.6     2.7    -      -       -      +
    168B  ARG*     4.3    10.0    +      -       +      +
    203B  ARG*     3.6     4.2    -      -       -      +
    204B  SER*     3.1    29.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  ASP*     3.3    31.6    -      -       +      +
    128B  CYS*     4.0    15.0    -      -       -      -
    131B  THR*     1.3    81.7    -      -       -      +
    133B  ALA*     1.3    65.0    +      -       -      +
    165B  TYR*     4.6    15.7    -      -       +      +
    166B  ILE*     3.5     2.9    -      -       -      -
    167B  LEU*     2.9    43.1    +      -       +      +
    172B  ARG*     3.9    24.7    -      -       +      +
    177B  HIS*     3.7    21.3    -      -       +      +
    201B  ILE*     3.6    26.5    -      -       +      -
    202B  CYS      3.5     3.8    -      -       -      +
    203B  ARG*     4.3     2.0    -      -       +      +
    302B  AKG      6.4     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  VAL*     4.1    11.6    -      -       +      +
     96B  ALA*     3.6    30.5    -      -       +      -
     97B  PHE*     3.7    15.5    -      -       +      -
    132B  ILE*     1.3    76.9    -      -       -      +
    134B  GLY*     1.3    57.1    +      -       -      +
    135B  LEU      4.3     0.2    +      -       -      -
    164B  LEU*     4.3     5.7    -      -       +      +
    165B  TYR      3.3     9.9    -      -       -      +
    166B  ILE*     4.6     0.9    -      -       +      -
    200B  VAL      3.6     2.1    -      -       -      +
    201B  ILE*     3.5     2.2    -      -       -      -
    202B  CYS*     2.9    39.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  ALA*     1.3    74.2    -      -       -      +
    135B  LEU*     1.3    62.2    +      -       -      -
    136B  SER      4.0     0.3    +      -       -      -
    163B  SER      3.7     1.0    -      -       -      +
    164B  LEU*     3.5     5.2    -      -       -      +
    165B  TYR*     2.8    72.8    +      -       -      -
    199B  SER*     6.0     0.2    -      -       -      -
    200B  VAL      3.6     6.3    -      -       -      -
    201B  ILE*     4.5     4.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  PHE*     3.8    20.4    -      -       +      -
     40B  LEU*     3.8    29.2    -      -       +      -
     48B  LEU*     4.2    19.5    -      -       +      -
     88B  ILE*     4.4     9.0    -      -       +      -
     89B  MSE      4.4     9.2    -      -       +      -
     92B  VAL*     3.7    20.2    -      -       +      -
    133B  ALA      5.9     0.2    -      -       -      +
    134B  GLY*     1.3    72.2    -      -       -      -
    136B  SER*     1.3    60.9    +      -       -      +
    137B  LEU*     5.0     2.7    -      -       +      -
    163B  SER      3.3    16.6    -      -       -      +
    164B  LEU*     3.9    15.3    -      -       +      -
    198B  ILE      4.1     0.2    -      -       -      +
    199B  SER*     3.2     8.7    -      -       -      -
    200B  VAL*     2.9    50.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  LEU*     4.9     0.2    -      -       -      +
    135B  LEU*     1.3    71.8    -      -       -      +
    137B  LEU*     1.3    66.4    +      -       -      +
    139B  SER      5.0     2.0    -      -       -      -
    159B  LEU*     3.9    18.0    -      -       -      +
    160B  GLU      3.8    19.7    -      -       -      -
    161B  PRO*     4.2     1.6    -      -       -      -
    162B  GLY*     2.8    28.2    +      -       -      -
    163B  SER*     3.2    12.6    +      -       -      -
    165B  TYR*     4.7     2.9    -      -       -      -
    197B  ARG*     2.9    35.7    +      -       -      +
    198B  ILE      3.8     3.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  LEU*     3.8    26.5    -      -       +      -
     45B  GLU*     4.6    18.2    -      -       +      +
     48B  LEU*     3.7    35.9    -      -       +      -
     49B  SER*     4.5    12.6    -      -       -      +
     52B  LEU*     4.6     1.3    -      -       +      -
    135B  LEU*     5.0     1.8    -      -       +      -
    136B  SER*     1.3    88.5    -      -       -      +
    138B  LEU*     1.3    71.5    +      -       +      +
    139B  SER      3.0    12.0    +      -       -      +
    161B  PRO*     4.5     4.3    -      -       -      -
    197B  ARG*     3.8     6.8    -      -       -      +
    198B  ILE*     2.8    52.6    +      -       +      +
    200B  VAL*     4.6     8.1    -      -       +      -
----------------------------------------------------------
 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