Contacts of the strand formed by residues 164 - 168 (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 LEU 164 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  VAL      3.8     0.9    -      -       -      +
     35B  VAL*     3.5     1.0    -      -       -      -
     36B  ARG*     2.6    46.8    +      -       +      +
     39B  PHE*     3.8    34.3    -      -       +      +
     92B  VAL*     4.0    22.7    -      -       +      +
     95B  ALA*     4.1    25.8    -      -       +      -
     96B  ALA*     5.0     0.7    -      -       +      -
    133B  ALA*     4.3     2.7    -      -       +      -
    134B  GLY      3.5    15.3    -      -       -      +
    135B  LEU*     3.9    20.6    -      -       +      -
    163B  SER*     1.3    74.8    -      -       -      +
    165B  TYR*     1.3    68.2    +      -       -      +
    166B  ILE*     4.2    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  VAL      3.1    10.1    -      -       -      +
     35B  VAL*     4.3     5.2    -      -       +      +
    132B  ILE*     4.6    13.9    -      -       +      +
    133B  ALA*     3.3     4.3    -      -       -      -
    134B  GLY*     2.8    72.2    +      -       -      -
    135B  LEU      5.5     0.2    -      -       -      -
    136B  SER*     4.7     2.2    -      -       -      -
    143B  MSE      3.4    25.2    -      -       +      +
    157B  LEU*     4.7     5.8    -      -       +      -
    159B  LEU*     3.7    37.2    -      -       +      -
    163B  SER*     4.2     1.4    +      -       -      -
    164B  LEU*     1.3    75.8    -      -       -      +
    166B  ILE*     1.3    64.8    +      -       -      +
    167B  LEU*     3.9    25.6    -      -       +      -
    177B  HIS*     6.3     0.2    -      +       -      -
    197B  ARG*     4.2     3.8    -      -       -      -
    199B  SER*     5.9     0.2    -      -       -      -
    201B  ILE*     4.3     4.9    -      -       -      +
    302B  AKG      2.2    44.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  ALA      3.3     4.7    -      -       -      +
     33B  ALA*     3.4     1.6    -      -       -      -
     34B  VAL*     2.7    54.8    +      -       +      +
     36B  ARG*     5.0     7.2    -      -       -      -
     95B  ALA      3.9     9.0    -      -       -      +
     96B  ALA*     3.8    31.2    -      -       +      -
    131B  THR*     4.0    14.8    -      -       +      -
    132B  ILE      3.5     9.6    -      -       -      +
    133B  ALA*     4.6     0.4    -      -       +      -
    164B  LEU*     4.2    18.2    -      -       +      +
    165B  TYR*     1.3    79.3    -      -       -      +
    167B  LEU*     1.3    69.2    +      -       -      +
    168B  ARG*     3.9    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  ALA      3.5     2.0    -      -       -      -
     33B  ALA*     4.2     7.2    -      -       +      -
    130B  ALA      3.8     0.5    -      -       -      +
    131B  THR*     3.6     1.7    -      -       -      +
    132B  ILE*     2.9    44.5    +      -       +      +
    143B  MSE      4.1     9.0    -      -       -      -
    145B  LEU*     3.9    36.1    -      -       +      -
    157B  LEU*     4.1    15.3    -      -       +      -
    165B  TYR*     3.9    18.1    -      -       +      -
    166B  ILE*     1.3    81.1    -      -       -      +
    168B  ARG*     1.3    62.1    +      -       -      +
    171B  ALA*     4.3    13.0    -      -       +      +
    172B  ARG*     4.0     7.4    -      -       +      +
    177B  HIS*     3.4    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  ASP*     3.0    25.7    +      -       -      +
     32B  ALA*     2.9    33.1    +      -       +      +
     34B  VAL*     4.5     8.9    -      -       -      +
     95B  ALA      4.6     4.6    +      -       -      -
     96B  ALA*     3.1    30.9    +      -       -      +
    101B  GLN*     6.1     0.8    -      -       -      +
    130B  ALA      3.2    13.7    -      -       -      +
    131B  THR*     4.3    11.8    +      -       +      +
    166B  ILE*     3.9    21.9    -      -       +      +
    167B  LEU*     1.3    74.5    -      -       -      +
    169B  GLY*     1.3    69.0    +      -       -      +
    170B  SER      3.2     1.0    +      -       -      -
    171B  ALA*     3.2    17.0    +      -       -      +
    172B  ARG*     4.0     2.5    -      -       -      -
----------------------------------------------------------
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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