Contacts of the strand formed by residues 297 - 302 (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 297 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  GLY*     3.5     3.1    -      -       -      -
    266A  ALA*     3.0    23.7    +      -       -      +
    269A  ALA*     3.5     7.3    -      -       -      +
    271A  ARG*     3.3    32.8    -      -       -      +
    287A  ILE*     4.0    20.6    -      -       +      +
    290A  LEU*     3.5    41.7    -      -       +      -
    291A  ALA*     4.6     3.5    -      -       +      +
    295A  GLU*     3.0    16.3    +      -       +      +
    296A  LYS*     1.3    79.5    -      -       -      +
    298A  GLY*     1.3    60.3    +      -       -      +
    379A  TYR*     3.7    39.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  TYR*     3.1    21.5    -      -       -      -
    264A  VAL      3.2     7.6    -      -       -      -
    269A  ALA*     3.7     2.3    -      -       -      +
    271A  ARG      3.1     7.5    +      -       -      -
    272A  VAL*     3.4     6.1    -      -       -      -
    273A  ILE      3.1    14.2    +      -       -      -
    287A  ILE*     3.6     3.4    -      -       -      -
    297A  ILE*     1.3    77.0    -      -       -      +
    299A  LEU*     1.3    60.6    +      -       -      -
    379A  TYR*     2.7    24.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  ASP      3.8     0.5    -      -       -      +
    263A  TYR*     3.2    12.4    -      -       -      -
    264A  VAL*     2.9    38.9    +      -       +      +
    273A  ILE*     3.3    25.1    -      -       +      +
    275A  SER*     4.1     7.6    -      -       -      +
    280A  CYS*     3.6    26.0    -      -       -      +
    283A  ILE*     3.8    35.9    -      -       +      -
    284A  GLU      4.3     1.3    -      -       -      +
    287A  ILE*     3.4    14.8    -      -       +      -
    298A  GLY*     1.3    75.4    -      -       -      +
    300A  ILE*     1.3    73.5    +      -       -      +
    301A  LYS*     3.5    27.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  PHE*     3.9    38.1    -      -       +      -
    262A  ASP      3.4     4.5    -      -       -      +
    263A  TYR*     4.0     5.2    -      -       +      -
    272A  VAL*     4.1     9.6    -      -       +      -
    273A  ILE      2.8    12.7    +      -       -      +
    274A  VAL*     3.4    10.7    -      -       +      +
    275A  SER      3.1    25.8    +      -       -      -
    299A  LEU*     1.3    77.6    -      -       -      +
    301A  LYS*     1.3    62.8    +      -       -      +
    302A  VAL      3.7     0.3    +      -       -      -
    313A  PHE*     3.9    27.8    -      -       +      +
    316A  ALA*     3.7    30.3    -      -       +      +
    317A  LEU*     3.9    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  SER*     5.1     1.1    +      -       -      +
    148A  GLU*     4.9     4.0    +      -       -      -
    261A  PHE*     3.4     5.7    -      -       -      +
    262A  ASP*     2.8    37.1    +      -       +      +
    264A  VAL*     4.2    16.2    -      -       +      +
    275A  SER      3.7     5.2    -      -       -      -
    280A  CYS*     3.8    24.4    -      -       +      +
    281A  GLU*     4.2    12.7    +      -       -      -
    284A  GLU*     2.7    28.3    +      -       -      -
    299A  LEU*     3.5    32.1    -      -       +      +
    300A  ILE*     1.3    73.6    -      -       -      +
    302A  VAL*     1.3    63.5    +      -       -      +
    303A  ARG*     3.6    39.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  ALA*     3.9     4.9    -      -       -      +
    261A  PHE*     3.7    22.2    -      -       +      -
    274A  VAL*     3.9    24.7    -      -       +      -
    275A  SER      3.0    18.2    +      -       -      +
    276A  MET*     3.6    38.4    -      -       +      +
    277A  GLY      4.9     1.0    +      -       -      -
    280A  CYS*     5.6     0.5    -      -       -      -
    301A  LYS*     1.3    73.8    -      -       -      +
    303A  ARG*     1.3    63.2    +      -       -      +
    304A  LEU      3.9    18.6    -      -       -      +
    305A  TYR*     3.9    15.9    -      -       +      +
    308A  PHE*     5.1     0.2    -      -       +      -
    340A  LEU*     4.0    18.6    -      -       +      -
----------------------------------------------------------
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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