Contacts of the strand formed by residues 167 - 172 (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 PHE 167 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  GLY      2.8    11.3    +      -       -      +
    108A  VAL*     3.2     6.8    -      -       +      +
    109A  PHE      2.9    25.5    +      -       -      +
    138A  PHE*     3.5     7.8    -      -       -      -
    139A  ALA*     3.5    29.2    -      -       +      -
    141A  LEU*     4.5    15.9    -      -       +      -
    156A  ALA*     3.8    37.5    -      -       +      +
    159A  ALA*     3.6    13.0    -      -       +      -
    160A  ALA*     3.8    19.5    -      -       +      -
    163A  SER*     4.0     6.3    -      -       -      -
    165A  VAL*     3.2    27.4    -      -       +      -
    166A  PRO*     1.3    76.6    -      -       -      +
    168A  MET*     1.3    58.2    +      -       -      +
    169A  HIS      4.0     0.4    -      -       -      -
    239A  VAL*     4.3     6.5    -      -       +      -
    243A  VAL*     3.5    33.4    -      -       +      -
    304A  LEU*     4.3     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  LEU*     3.2    41.7    -      -       +      -
     97A  MET*     3.4    20.0    -      -       +      -
    109A  PHE*     3.5     8.5    -      -       +      +
    111A  VAL*     3.6    25.4    -      -       +      -
    130A  ILE*     4.0    29.2    -      -       -      +
    133A  ALA*     4.3     4.0    -      -       +      -
    138A  PHE*     3.7    10.3    -      -       +      -
    139A  ALA      2.7    14.8    +      -       -      +
    140A  MET*     3.4    19.3    -      -       +      -
    141A  LEU*     2.8    27.6    +      -       -      +
    167A  PHE*     1.3    74.9    -      -       -      +
    169A  HIS*     1.3    60.4    +      -       -      +
    170A  PHE*     3.8     4.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  THR*     3.8     7.2    -      -       -      +
    108A  VAL*     4.9     0.6    -      -       +      +
    109A  PHE      2.9     6.1    +      -       -      +
    110A  HIS*     3.1    36.8    -      +       +      +
    111A  VAL*     2.8    25.3    +      -       -      +
    141A  LEU*     3.3    11.7    +      -       +      +
    143A  SER*     2.9    38.0    +      -       -      -
    149A  ALA      3.3    15.7    +      -       -      -
    152A  MET*     3.7    17.8    +      -       +      +
    153A  ALA*     3.7    13.0    -      -       +      -
    156A  ALA*     4.1    19.7    -      -       +      -
    167A  PHE*     4.0     2.0    -      -       -      +
    168A  MET*     1.3    72.0    -      -       -      +
    170A  PHE*     1.3    63.2    +      -       -      +
    171A  PHE*     3.7    17.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  VAL*     3.3    15.5    -      -       +      +
    113A  ALA*     4.4     7.6    -      -       +      -
    127A  HIS*     4.3    14.1    -      +       -      -
    130A  ILE*     3.6    57.7    -      -       +      -
    140A  MET*     4.1    14.1    -      -       +      -
    141A  LEU      3.0    32.0    +      -       -      -
    142A  ALA*     3.4    24.5    -      -       +      +
    143A  SER*     2.9    26.7    +      -       -      +
    168A  MET*     4.0    14.8    -      -       +      -
    169A  HIS*     1.3    76.0    +      -       -      +
    171A  PHE*     1.3    69.2    +      -       -      +
    172A  ASP*     5.4     0.2    -      -       -      -
    276A  MET*     3.9    21.1    -      -       +      -
    277A  GLY*     5.9     0.9    -      -       -      -
    305A  TYR*     4.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLY*     3.8     7.9    -      -       -      -
     11A  ASN*     3.8    10.3    -      -       -      -
     14A  THR*     3.2    34.1    -      -       +      -
     36A  MET*     4.0     8.7    -      -       +      -
    110A  HIS*     5.1     0.2    -      -       +      -
    111A  VAL      3.2    10.2    +      -       -      -
    112A  THR*     3.4    22.0    -      -       +      -
    113A  ALA*     2.8    25.5    +      -       -      -
    143A  SER*     3.2    27.1    -      -       -      +
    149A  ALA*     4.5     0.7    -      -       +      -
    169A  HIS*     3.7    19.3    -      +       -      -
    170A  PHE*     1.3    77.7    -      -       -      +
    172A  ASP*     1.3    67.1    +      -       -      +
    176A  THR*     3.8    16.6    -      -       +      -
    177A  SER*     3.5    43.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ALA*     4.3     3.1    -      -       -      -
    125A  GLY*     5.4     2.9    -      -       -      -
    127A  HIS*     2.7    32.1    +      -       -      -
    143A  SER      4.7     0.6    +      -       -      -
    171A  PHE*     1.3    76.2    -      -       -      +
    173A  GLY*     1.3    66.0    +      -       -      +
    175A  ARG*     4.3     7.2    -      -       +      -
    176A  THR*     3.0    29.0    +      -       -      +
    177A  SER*     3.1     9.5    +      -       -      -
    276A  MET      4.8     0.5    -      -       -      +
    277A  GLY*     3.8     4.2    -      -       -      -
    278A  SER*     2.7    45.5    +      -       -      +
    329A  ARG*     3.5    19.9    +      -       -      +
----------------------------------------------------------
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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