Contacts of the strand formed by residues 540 - 544 (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 LYS 540 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507B  GLY*     4.2    11.0    -      -       -      +
    508B  GLY      2.9    10.3    +      -       -      +
    509B  THR*     3.4    25.2    -      -       +      +
    510B  PHE      3.0    22.8    +      -       -      -
    538B  LYS      4.8     2.5    -      -       -      +
    539B  LEU*     1.3    71.9    -      -       -      +
    541B  PHE*     1.3    59.3    +      -       -      +
    542B  TYR*     3.5    33.3    +      -       +      -
    570B  LEU*     6.0     0.6    -      -       -      +
    615B  GLU*     3.4    31.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 541 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    510B  PHE*     3.4    42.0    -      +       +      +
    512B  LEU*     4.0    12.8    -      -       +      -
    522B  MET*     3.5    32.1    -      -       +      -
    526B  LEU*     4.1     8.7    -      -       +      -
    534B  ILE*     3.9    27.8    -      -       +      -
    539B  LEU*     3.4     3.2    +      -       +      -
    540B  LYS*     1.3    74.2    -      -       -      +
    542B  TYR*     1.3    72.8    +      -       -      +
    543B  ASN*     4.7     1.3    -      -       +      -
    615B  GLU*     3.5     7.5    +      -       -      +
    616B  PHE*     2.6    70.6    +      +       +      +
    618B  TYR*     4.3     8.5    -      +       +      -
    622B  TRP*     4.0    18.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 542 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509B  THR*     4.3    10.8    -      -       +      -
    510B  PHE      3.0    10.7    +      -       -      +
    511B  VAL*     3.2    12.2    -      -       +      -
    512B  LEU      2.9    25.5    +      -       -      +
    540B  LYS*     3.5    49.2    +      -       +      -
    541B  PHE*     1.3    84.4    -      -       -      +
    543B  ASN*     1.3    60.6    +      -       -      +
    570B  LEU*     3.8    46.3    -      -       +      +
    613B  LEU*     3.9    15.0    -      -       +      -
    614B  GLN*     3.3    29.8    -      -       -      +
    615B  GLU*     3.6    27.5    -      -       +      +
    616B  PHE      4.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 543 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    512B  LEU*     3.2    24.7    -      -       -      +
    514B  SER*     2.7    44.6    +      -       -      -
    516B  TRP      4.0    11.7    +      -       -      -
    517B  SER*     4.3     9.2    +      -       -      +
    522B  MET*     3.6    21.9    -      -       +      +
    541B  PHE*     4.7     1.6    -      -       +      -
    542B  TYR*     1.3    76.2    -      -       -      +
    544B  ILE*     1.3    73.4    +      -       -      +
    545B  ASP      4.2     1.0    -      -       -      +
    612B  SER      4.9     6.8    -      -       -      +
    613B  LEU*     5.4     1.0    -      -       -      +
    614B  GLN      4.6     7.5    +      -       -      +
    616B  PHE*     4.2    17.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 544 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511B  VAL*     4.3     2.9    -      -       +      -
    512B  LEU      2.8    15.1    +      -       -      +
    513B  ASN*     3.2     1.9    -      -       -      -
    514B  SER      3.1    19.7    +      -       -      -
    543B  ASN*     1.3    77.3    -      -       -      +
    545B  ASP*     1.3    62.8    +      -       -      +
    546B  ALA      2.9     8.5    +      -       -      +
    549B  ILE*     3.8    23.8    -      -       +      -
    562B  ILE*     3.8    22.4    -      -       +      -
    563B  MET*     3.8    33.0    -      -       +      -
    566B  ALA*     5.5     0.7    -      -       +      -
    609B  ALA*     4.2     7.9    -      -       -      +
    612B  SER*     4.3     8.7    -      -       -      +
    613B  LEU*     3.3    41.5    -      -       +      +
----------------------------------------------------------
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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