Contacts of the strand formed by residues 108 - 113 (chain A) in PDB entry 1KEK


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 VAL 108 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  THR      3.5     8.5    +      -       -      +
     82A  THR*     2.8    32.9    -      -       -      +
     83A  THR      3.3     1.6    +      -       -      -
    106A  PRO      3.9     3.6    +      -       -      +
    107A  GLY*     1.3    79.6    -      -       -      +
    109A  PHE*     1.3    67.3    +      -       -      +
    110A  HIS*     3.4    31.4    -      -       +      +
    156A  ALA*     3.9    14.6    -      -       +      +
    157A  HIS*     3.7    37.7    -      -       +      +
    160A  ALA*     3.6    22.7    -      -       +      -
    167A  PHE*     3.2     9.2    -      -       +      +
    169A  HIS*     4.9     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ALA*     4.9     4.9    -      -       +      -
     71A  VAL*     4.0    21.3    -      -       +      -
     83A  THR*     3.6    23.6    -      -       +      -
     85A  THR*     5.1     2.0    -      -       +      -
     90A  LEU*     4.3     8.1    -      -       +      -
     93A  MET*     3.5    31.9    -      -       +      -
     97A  MET*     3.6    33.4    -      -       +      -
    100A  ILE*     3.9    16.4    -      -       +      -
    107A  GLY*     5.5     0.7    -      -       -      -
    108A  VAL*     1.3    81.0    -      -       -      +
    110A  HIS*     1.3    62.4    +      -       -      +
    111A  VAL*     3.9    11.3    +      -       +      -
    138A  PHE*     3.7    29.8    -      +       +      -
    167A  PHE      2.9     9.4    +      -       -      +
    168A  MET*     3.5     5.1    -      -       +      +
    169A  HIS*     2.9    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  THR*     3.5    15.9    -      -       -      +
     18A  ALA*     3.5    16.1    -      -       +      +
     36A  MET*     3.9     9.1    -      -       -      +
     82A  THR*     3.2    26.7    -      -       +      +
     83A  THR      2.9     7.1    +      -       -      -
     84A  PHE*     3.2    21.4    -      +       +      -
     85A  THR*     3.0    22.9    +      -       -      +
    108A  VAL*     3.4    14.1    -      -       +      +
    109A  PHE*     1.3    69.0    -      -       -      +
    111A  VAL*     1.3    61.1    +      -       -      +
    153A  ALA*     4.0     9.5    -      -       -      +
    157A  HIS*     2.9    35.4    +      -       -      -
    169A  HIS*     3.1    40.7    -      +       +      +
    171A  PHE*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  THR*     3.1    18.4    -      -       +      +
     86A  ALA*     4.2     3.1    -      -       -      -
     90A  LEU*     4.3    11.4    -      -       +      -
    109A  PHE*     4.3     9.4    -      -       +      -
    110A  HIS*     1.3    77.4    -      -       -      +
    112A  THR*     1.3    74.1    +      -       -      +
    113A  ALA      3.9     0.7    -      -       -      +
    129A  ASP*     4.0     9.0    -      -       -      +
    130A  ILE*     3.8    24.2    -      -       +      -
    168A  MET*     3.6    40.8    -      -       +      -
    169A  HIS      2.8    12.9    +      -       -      +
    170A  PHE*     3.3     6.2    -      -       +      +
    171A  PHE*     3.2    27.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ASN*     3.3    29.8    -      -       -      +
     32A  PRO*     3.2    30.1    -      -       -      +
     33A  SER*     3.3    18.5    -      -       -      -
     36A  MET*     3.7    11.9    -      -       +      -
     85A  THR      3.1     3.6    +      -       -      -
     86A  ALA*     3.1    18.7    -      -       -      +
    110A  HIS      4.3     0.2    +      -       -      -
    111A  VAL*     1.3    71.1    -      -       -      +
    113A  ALA*     1.3    64.0    +      -       -      +
    114A  ARG*     3.9     1.2    -      -       -      +
    129A  ASP*     3.6     0.9    -      -       -      +
    171A  PHE*     3.4    21.5    -      -       +      -
    173A  GLY*     4.1     5.8    -      -       -      -
    177A  SER*     3.8     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  VAL*     3.5     3.3    +      -       -      -
    112A  THR*     1.3    69.4    -      -       -      +
    114A  ARG*     1.3    57.6    +      -       -      +
    125A  GLY*     3.2    10.4    -      -       -      -
    126A  ASP      3.1    18.0    +      -       -      +
    127A  HIS*     3.9    17.0    -      -       +      -
    129A  ASP*     3.3    14.4    -      -       -      +
    130A  ILE*     3.8    16.4    -      -       +      -
    170A  PHE*     4.4     5.4    -      -       +      -
    171A  PHE      2.8    18.1    +      -       -      +
    172A  ASP*     4.3     0.6    -      -       -      -
    173A  GLY*     2.8    25.2    +      -       -      +
----------------------------------------------------------
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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