Contacts of the strand formed by residues 180 - 186 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1206A  PRO*     6.6     0.7    -      -       +      -
      7B  THR*     3.3    23.8    -      -       -      +
      8B  THR*     3.2    38.4    -      -       -      +
      9B  ASP*     4.6     6.3    -      -       +      +
    178B  HIS      4.2     6.1    -      -       -      +
    179B  GLU*     1.3    74.4    -      -       -      +
    181B  GLN*     1.3    62.1    +      -       -      +
    435B  LYS*     5.2    10.3    -      -       +      -
    438B  ILE*     3.9    29.6    -      -       +      -
    439B  LYS*     3.9    11.7    -      -       -      +
    450B  GLN*     3.1     7.3    -      -       -      +
    451B  GLY      2.8    38.5    +      -       -      +
    453B  PHE*     4.2    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  MET      3.5     0.2    -      -       -      +
      7B  THR*     3.3     3.3    -      -       -      -
      8B  THR      2.9    30.4    +      -       -      +
    145B  SER*     6.6     0.2    -      -       -      -
    146B  VAL*     3.9    16.6    -      -       +      +
    179B  GLU*     2.9    27.2    +      -       -      +
    180B  ILE*     1.3    79.2    -      -       -      +
    182B  LYS*     1.3    68.0    +      -       -      +
    183B  ILE*     3.5    22.8    +      -       +      +
    448B  PHE*     5.4     4.9    -      -       -      +
    449B  ALA      3.2    23.8    +      -       -      +
    450B  GLN*     3.7    16.4    +      -       -      +
    475B  ILE*     3.0    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  MET*     4.6    26.7    -      -       +      -
      6B  MET      3.4     9.2    -      -       -      +
      7B  THR*     3.6    18.3    -      -       +      +
    181B  GLN*     1.3    79.7    +      -       -      +
    183B  ILE*     1.3    67.4    +      -       -      +
    442B  GLY*     2.7    38.9    +      -       -      +
    445B  THR      2.9    20.0    +      -       -      -
    446B  ASP*     4.0     5.4    +      -       -      +
    447B  LEU      3.0    23.4    +      -       -      +
    448B  PHE*     4.7    17.9    -      -       +      +
    449B  ALA*     3.2    21.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  MET*     3.3    13.0    -      -       -      +
      6B  MET*     2.9    39.0    +      -       +      +
      8B  THR*     4.1     9.0    -      -       -      +
     13B  ALA*     3.7    30.3    -      -       +      -
    146B  VAL*     4.1    11.4    -      -       +      +
    147B  GLN*     3.4    45.1    -      -       +      +
    150B  HIS*     4.4     2.2    -      -       +      -
    181B  GLN*     3.9    21.3    -      -       +      +
    182B  LYS*     1.3    79.9    -      -       -      +
    184B  GLU*     1.3    59.7    +      -       -      +
    185B  VAL*     3.8    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  LYS*     3.3    45.6    -      -       +      +
      4B  LYS      3.4     5.6    -      -       -      +
      5B  MET*     3.2    23.4    -      -       +      +
    147B  GLN*     2.9    25.4    -      -       -      +
    150B  HIS*     4.2     2.4    +      -       -      -
    183B  ILE*     1.3    75.4    -      -       -      +
    185B  VAL*     1.3    84.1    +      -       -      +
    186B  LEU*     3.9     2.6    -      -       -      +
    254B  THR*     3.6    16.3    -      -       -      +
    256B  ARG*     2.9    45.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  LYS*     3.3     5.5    -      -       -      -
      4B  LYS*     2.8    54.8    +      -       +      +
      6B  MET*     3.5    41.5    -      -       +      -
     13B  ALA*     5.2     0.7    -      -       -      -
     16B  HIS*     3.8    22.4    -      -       +      +
    150B  HIS*     3.4    25.8    -      -       +      -
    183B  ILE*     3.8    13.9    -      -       +      -
    184B  GLU*     1.3    82.3    -      -       -      +
    186B  LEU*     1.3    61.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  GLY      3.8    13.2    -      -       -      +
      3B  LYS*     3.9    14.1    -      -       +      -
      4B  LYS*     6.0     0.4    -      -       -      -
     16B  HIS*     3.0    25.1    +      -       -      -
    150B  HIS*     3.1    17.8    +      -       +      +
    154B  LEU*     3.8    26.2    -      -       +      -
    184B  GLU*     3.9    19.1    -      -       -      +
    185B  VAL*     1.3    74.1    -      -       -      +
    187B  ASP*     1.4    72.4    +      -       -      +
    190B  ASP*     4.3    15.5    -      -       +      +
    191B  MET*     3.4    10.0    -      -       +      +
    194B  LEU*     5.2     0.2    -      -       +      -
    250B  VAL*     4.8     1.6    -      -       +      -
    253B  LEU*     4.2    24.9    -      -       +      -
    254B  THR*     3.8    21.1    -      -       +      -
----------------------------------------------------------
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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