Contacts of the strand formed by residues 297 - 302 (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 297 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265B  GLY*     3.6     2.8    -      -       -      -
    266B  ALA*     3.0    23.0    +      -       -      +
    269B  ALA*     3.3     6.7    -      -       -      +
    271B  ARG*     3.2    39.9    -      -       -      +
    287B  ILE*     3.9    22.9    -      -       +      +
    290B  LEU*     3.6    37.2    -      -       +      -
    291B  ALA*     5.0     1.3    -      -       +      +
    295B  GLU*     3.1    14.6    +      -       +      +
    296B  LYS*     1.3    83.0    -      -       -      +
    298B  GLY*     1.4    59.7    +      -       -      +
    379B  TYR*     3.6    38.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 298 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263B  TYR*     3.2    16.4    -      -       -      -
    264B  VAL      3.2    12.1    -      -       -      -
    269B  ALA*     3.7     1.6    -      -       -      +
    271B  ARG      3.0     8.7    +      -       -      -
    272B  VAL*     3.3     3.1    -      -       -      -
    273B  ILE      3.0    17.0    +      -       -      -
    287B  ILE*     3.8     6.5    -      -       -      -
    297B  ILE*     1.4    77.7    -      -       -      +
    299B  LEU*     1.3    60.7    +      -       -      -
    379B  TYR*     2.7    21.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  ASP      3.6     0.9    -      -       -      +
    263B  TYR*     3.2     7.5    -      -       -      -
    264B  VAL*     2.8    39.5    +      -       +      +
    272B  VAL*     4.4     0.2    -      -       -      -
    273B  ILE*     3.2    35.2    -      -       +      +
    275B  SER*     4.0    12.1    -      -       -      +
    280B  CYS*     3.7    26.5    -      -       +      +
    283B  ILE*     3.8    18.8    -      -       +      -
    284B  GLU      4.2     0.9    -      -       -      +
    287B  ILE*     3.5    13.5    -      -       +      -
    298B  GLY*     1.3    75.8    -      -       -      +
    300B  ILE*     1.3    79.6    -      -       -      +
    301B  LYS*     3.6    27.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261B  PHE*     3.9    37.5    -      -       +      -
    262B  ASP      3.3     4.3    -      -       -      +
    263B  TYR*     4.0     4.5    -      -       +      -
    272B  VAL*     4.1    16.6    -      -       +      -
    273B  ILE      2.8    11.7    +      -       -      +
    274B  VAL*     3.5    10.6    -      -       +      +
    275B  SER      3.1    26.3    +      -       -      +
    299B  LEU*     1.3    78.1    -      -       -      +
    301B  LYS*     1.3    62.0    +      -       -      +
    302B  VAL      3.9     0.3    +      -       -      -
    313B  PHE*     3.8    33.4    -      -       +      +
    316B  ALA*     3.6    31.6    -      -       +      +
    317B  LEU*     3.8    17.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  SER*     5.2     1.5    +      -       -      +
    148B  GLU*     4.8     4.4    +      -       -      -
    261B  PHE*     3.3     6.8    -      -       -      +
    262B  ASP*     2.8    39.7    +      -       +      +
    264B  VAL*     4.1    16.0    -      -       +      +
    275B  SER      3.7     4.3    -      -       -      -
    280B  CYS*     3.9    24.0    -      -       +      +
    281B  GLU*     4.2    13.1    +      -       -      -
    284B  GLU*     2.7    29.7    +      -       -      -
    299B  LEU*     3.6    31.0    -      -       +      +
    300B  ILE*     1.3    73.2    -      -       -      +
    302B  VAL*     1.3    63.6    +      -       -      +
    303B  ARG*     3.6    38.6    +      -       -      +
    476B  GLN*     4.4     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  ALA*     3.9     5.4    -      -       -      +
    261B  PHE*     3.7    24.2    -      -       +      -
    274B  VAL*     4.0    16.4    -      -       +      -
    275B  SER      3.0    19.1    +      -       -      +
    276B  MET*     3.6    38.3    -      -       +      +
    277B  GLY      4.8     1.0    +      -       -      -
    280B  CYS*     4.7     0.2    -      -       -      -
    300B  ILE      4.7     0.2    -      -       -      +
    301B  LYS*     1.3    74.6    -      -       -      +
    303B  ARG*     1.3    63.0    +      -       -      +
    304B  LEU      4.1     4.3    -      -       -      +
    305B  TYR*     4.0    28.3    -      -       +      +
    340B  LEU*     4.0    24.9    -      -       +      -
----------------------------------------------------------
 Back to top of page


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