Contacts of the strand formed by residues 107 - 111 (chain A) in PDB entry 1K3X


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 ASP 107 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  TYR*     3.5    25.5    +      -       -      -
     66A  SER*     3.3     4.3    -      -       -      -
     67A  HIS*     3.0    50.2    +      -       +      +
     69A  GLN*     6.2     2.5    -      -       +      -
    105A  ALA      3.6     0.6    -      -       -      -
    106A  SER*     1.3    79.4    +      -       -      +
    108A  ILE*     1.3    61.6    +      -       -      +
    109A  GLU*     3.9    11.3    -      -       -      +
    119A  HIS*     5.1     1.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PHE*     3.9    30.6    -      -       +      -
     31A  GLN*     4.9     3.3    +      -       -      -
     32A  LEU*     3.9    14.4    -      -       +      +
     64A  LEU*     3.8    25.6    -      -       +      -
     65A  TYR      3.2     7.4    -      -       -      +
     66A  SER*     4.4     2.0    -      -       -      -
     90A  ARG*     3.6    24.7    -      -       +      +
     91A  VAL*     4.0    14.4    -      -       +      -
    102A  LEU*     3.9    21.3    -      -       +      -
    105A  ALA*     3.5    22.9    -      -       +      +
    106A  SER      3.4     3.4    +      -       -      -
    107A  ASP*     1.3    85.9    +      -       -      +
    109A  GLU*     1.3    67.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     4.3     7.9    -      -       +      -
     64A  LEU*     3.6     8.5    -      -       -      +
     65A  TYR*     2.8    42.4    +      -       +      +
    107A  ASP*     3.9    13.3    -      -       -      +
    108A  ILE*     1.3    75.6    -      -       -      +
    110A  MET*     1.3    61.8    +      -       -      +
    111A  LEU*     3.8    17.4    -      -       +      +
    115A  GLN*     4.5     6.6    +      -       -      -
    119A  HIS*     3.0    34.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  PHE*     3.7    30.1    -      -       +      -
     32A  LEU*     3.9     8.3    -      -       +      +
     35A  TYR*     3.5    55.7    +      -       +      +
     39A  LEU*     3.8    16.8    -      -       +      -
     58A  PHE*     4.0     5.6    -      -       +      -
     62A  LEU*     4.0    24.7    -      -       +      -
     63A  THR      3.7    22.2    -      -       -      +
     64A  LEU*     3.9    12.6    -      -       +      -
    109A  GLU*     1.3    77.2    -      -       -      +
    111A  LEU*     1.3    64.5    +      -       -      +
    112A  ARG*     4.2     1.0    +      -       -      +
    115A  GLN*     4.0     8.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  LEU*     4.2     3.1    -      -       +      -
     61A  ASP      4.1     0.2    -      -       -      +
     62A  LEU*     3.5     9.7    -      -       -      +
     63A  THR*     2.8    47.0    +      -       -      +
     65A  TYR*     3.8    23.8    -      -       +      -
    109A  GLU*     3.8    23.3    -      -       +      +
    110A  MET*     1.3    77.7    -      -       -      +
    112A  ARG*     1.3    70.0    +      -       -      +
    115A  GLN*     3.5    32.5    -      -       +      +
    116A  LEU*     4.1    12.3    -      -       +      -
    119A  HIS*     4.0    10.5    -      -       +      -
    122A  LEU*     3.7    30.1    -      -       +      -
----------------------------------------------------------
 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