Contacts of the strand formed by residues 180 - 186 (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 ILE 180 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  THR*     3.2    23.8    -      -       -      +
      8A  THR*     3.1    39.9    -      -       -      +
      9A  ASP*     4.5     6.7    -      -       +      +
    178A  HIS      4.3     6.7    -      -       -      +
    179A  GLU*     1.3    75.9    -      -       -      +
    181A  GLN*     1.3    72.2    +      -       -      +
    435A  LYS*     5.1     8.3    -      -       +      -
    438A  ILE*     4.0    25.8    -      -       +      -
    439A  LYS*     4.1    14.1    -      -       -      +
    450A  GLN*     3.2     8.5    -      -       -      +
    451A  GLY*     2.9    35.5    +      -       -      +
    453A  PHE*     4.5    16.8    -      -       +      -
   1206B  PRO*     6.4     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  THR*     3.2     1.3    -      -       -      -
      8A  THR      3.0    29.4    +      -       -      +
    145A  SER*     6.5     0.2    -      -       -      -
    146A  VAL*     3.9    17.3    -      -       +      +
    179A  GLU*     3.1    25.1    +      -       -      +
    180A  ILE*     1.3    82.3    -      -       -      +
    182A  LYS*     1.3    67.8    +      -       -      +
    183A  ILE*     3.4    21.7    +      -       +      +
    448A  PHE*     5.1     5.7    -      -       -      +
    449A  ALA      3.4    22.3    +      -       -      +
    450A  GLN*     3.6    14.9    +      -       -      +
    475A  ILE*     3.0    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  MET*     5.0    18.3    -      -       +      +
      6A  MET      3.6     9.0    -      -       -      +
      7A  THR*     3.5    21.2    -      -       +      +
    181A  GLN*     1.3    80.4    +      -       -      +
    183A  ILE*     1.4    65.8    +      -       -      +
    442A  GLY*     2.9    36.3    +      -       -      -
    443A  ASP*     5.8     0.2    -      -       -      -
    445A  THR      3.1    15.8    +      -       -      -
    446A  ASP*     3.9     6.9    +      -       -      +
    447A  LEU      2.9    27.5    +      -       -      +
    448A  PHE*     4.6    19.5    -      -       +      -
    449A  ALA*     3.3    23.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  MET*     3.4     9.9    -      -       -      +
      6A  MET*     2.7    43.8    +      -       +      +
      8A  THR*     4.2    11.2    -      -       -      +
     13A  ALA*     3.9    25.6    -      -       +      -
    146A  VAL*     3.7    27.1    -      -       +      +
    147A  GLN*     3.5    30.3    -      -       +      +
    150A  HIS*     4.4     2.7    -      -       +      -
    181A  GLN*     3.8    11.9    -      -       +      +
    182A  LYS*     1.4    80.1    -      -       -      +
    184A  GLU*     1.3    62.8    +      -       -      +
    185A  VAL*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LYS*     2.7    51.7    +      -       +      +
      4A  LYS      3.2     4.7    -      -       -      +
      5A  MET*     3.2    30.5    -      -       +      -
    147A  GLN*     2.9    27.0    -      -       -      +
    150A  HIS*     4.1     2.3    +      -       -      -
    183A  ILE*     1.3    77.3    -      -       -      +
    185A  VAL*     1.3    74.5    +      -       -      +
    186A  LEU*     4.2     1.7    +      -       -      +
    254A  THR*     3.8    10.7    -      -       -      +
    256A  ARG*     2.9    42.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LYS*     3.4     3.8    -      -       -      -
      4A  LYS*     2.8    55.6    +      -       +      +
      6A  MET*     3.8    30.3    -      -       +      -
     13A  ALA*     5.3     1.3    -      -       -      -
     16A  HIS*     3.6    31.0    -      -       +      +
    150A  HIS*     3.4    16.4    -      -       +      -
    183A  ILE*     3.6    25.4    -      -       +      -
    184A  GLU*     1.3    80.1    -      -       -      +
    186A  LEU*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  GLY      3.5     9.9    -      -       -      +
      3A  LYS*     4.7     1.6    -      -       +      -
      4A  LYS*     5.8     0.7    -      -       -      -
     16A  HIS*     2.8    27.5    +      -       -      -
    150A  HIS*     3.0    21.1    +      -       +      +
    154A  LEU*     3.8    28.5    -      -       +      -
    184A  GLU*     4.3     4.7    -      -       -      +
    185A  VAL*     1.3    75.7    -      -       -      +
    187A  ASP*     1.3    68.1    +      -       -      +
    190A  ASP*     3.6    25.4    -      -       +      +
    191A  MET*     3.4     9.3    -      -       +      +
    194A  LEU*     5.5     0.4    -      -       +      -
    250A  VAL*     4.8     3.1    -      -       +      -
    253A  LEU*     4.2    26.7    -      -       +      +
    254A  THR*     3.9    29.4    -      -       +      -
----------------------------------------------------------
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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