Contacts of the strand formed by residues 132 - 135 (chain B) in PDB entry 3IKH


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 132 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -1B  LEU*     4.2    12.1    -      -       +      -
      2B  ARG      3.0     7.5    +      -       -      -
      3B  VAL*     4.1    18.6    -      -       +      -
      4B  TYR      2.7    31.5    +      -       -      -
    130B  GLY      4.2     4.5    -      -       -      +
    131B  ASP*     1.3    76.0    -      -       -      +
    133B  LEU*     1.3    69.9    +      -       -      +
    134B  LEU*     4.1     3.4    -      -       +      +
    156B  MSE      3.5     9.0    -      -       -      +
    157B  THR*     3.2    30.7    -      -       +      +
    159B  VAL*     3.7    17.9    -      -       +      -
    178B  ILE*     5.9     1.3    -      -       +      -
    239B  LEU*     4.4    12.3    -      -       +      -
    243B  LEU*     3.7    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  TYR*     3.6    11.0    -      -       +      +
      6B  THR*     3.8    32.1    -      -       +      +
    124B  MSE      3.9    19.7    -      -       +      -
    132B  ILE*     1.3    73.6    -      -       -      +
    134B  LEU*     1.3    63.0    +      -       -      +
    135B  GLN*     4.1    11.7    -      -       +      +
    147B  LEU*     3.4    37.0    -      -       +      +
    148B  PHE*     3.8    14.7    -      -       +      -
    151B  ALA*     3.6    25.1    -      -       +      -
    156B  MSE      3.9     1.0    -      -       +      +
    157B  THR      2.9     8.1    +      -       -      +
    158B  THR*     3.5     3.5    -      -       +      -
    159B  VAL      2.9    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  VAL*     4.6     7.0    -      -       +      -
      4B  TYR      2.8    11.5    +      -       -      +
      5B  VAL*     3.3    15.0    -      -       +      +
      6B  THR      3.2    24.4    +      -       -      -
     43B  GLN*     3.4    29.8    -      -       +      +
     47B  LEU*     3.9    26.0    -      -       +      -
    132B  ILE*     4.0     2.4    -      -       +      -
    133B  LEU*     1.3    73.5    -      -       -      +
    135B  GLN*     1.3    74.7    +      -       -      +
    136B  GLN*     3.6     9.4    -      -       -      +
    159B  VAL*     3.5    34.5    -      -       +      +
    160B  PHE      4.8     0.2    -      -       -      +
    161B  ASN      5.1     0.7    -      -       -      +
    235B  LEU*     4.0    18.8    -      -       +      -
    239B  LEU*     4.8     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  THR*     3.0    24.6    +      -       -      +
    133B  LEU*     4.2     5.6    -      -       +      -
    134B  LEU*     1.3    77.8    -      -       -      +
    136B  GLN*     1.3    74.5    +      -       -      +
    139B  PHE*     4.0    12.1    -      -       -      -
    144B  THR*     3.0    35.6    -      -       -      +
    147B  LEU*     3.1    36.9    -      -       -      +
    148B  PHE*     3.3    37.9    -      -       +      -
    159B  VAL      3.1     6.1    +      -       -      -
    160B  PHE*     3.6     3.0    -      -       -      -
    161B  ASN*     3.0    23.7    +      -       -      +
----------------------------------------------------------
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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