Contacts of the strand formed by residues 509 - 513 (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 THR 509 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    485A  ASP      2.8    14.6    +      -       -      +
    486A  TYR*     3.4    25.0    -      -       +      +
    487A  VAL      2.8    26.7    +      -       -      +
    504A  ILE*     3.8     4.1    -      -       -      +
    507A  GLY      4.9     0.7    -      -       -      +
    508A  GLY*     1.3    76.2    -      -       -      -
    510A  PHE*     1.3    61.7    +      -       -      +
    511A  VAL*     4.5     1.4    -      -       -      +
    540A  LYS*     3.4    36.2    +      -       +      +
    542A  TYR*     4.3    12.1    -      -       +      -
    570A  LEU*     4.2    18.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 510 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    487A  VAL*     3.1    17.9    -      -       +      +
    489A  CYS*     4.0    20.6    -      -       +      -
    495A  VAL*     4.9     9.2    -      -       +      -
    500A  ILE*     4.2    10.1    -      -       +      -
    501A  LEU*     3.5    38.8    -      -       +      -
    504A  ILE*     4.3     6.3    -      -       +      -
    508A  GLY      4.2     0.6    +      -       -      -
    509A  THR*     1.3    73.9    -      -       -      +
    511A  VAL*     1.3    72.9    +      -       -      +
    512A  LEU*     4.2    17.7    -      -       +      -
    530A  ILE*     4.4     6.7    -      -       +      -
    534A  ILE*     3.9    18.4    -      -       +      -
    539A  LEU*     4.6     7.2    -      -       +      -
    540A  LYS      3.0    10.0    +      -       -      +
    541A  PHE*     3.4    37.4    -      +       +      -
    542A  TYR*     2.8    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 511 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    486A  TYR*     3.2    40.2    -      -       +      +
    487A  VAL      2.9     5.3    +      -       -      +
    488A  ALA*     3.3     3.6    -      -       +      -
    489A  CYS      2.8    27.4    +      -       -      +
    509A  THR*     4.5     2.5    -      -       -      +
    510A  PHE*     1.3    79.2    -      -       -      +
    512A  LEU*     1.3    64.6    +      -       -      +
    542A  TYR*     3.2    14.8    -      -       +      +
    544A  ILE*     4.5     5.8    -      -       +      -
    563A  MET*     3.4    29.8    -      -       +      -
    566A  ALA*     4.1    13.7    -      -       +      -
    570A  LEU*     4.4    15.3    -      -       +      -
    613A  LEU*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 512 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489A  CYS*     3.6    27.4    -      -       +      +
    492A  PRO*     4.3     6.5    -      -       +      -
    495A  VAL*     4.2    11.9    -      -       +      -
    510A  PHE*     4.1     6.5    -      -       +      -
    511A  VAL*     1.3    79.4    -      -       -      +
    513A  ASN*     1.3    74.9    +      -       -      +
    514A  SER*     3.8    10.3    -      -       -      +
    516A  TRP*     4.0     9.9    -      -       +      -
    522A  MET*     4.5     0.4    -      -       -      -
    526A  LEU*     3.9    27.8    -      -       +      -
    541A  PHE*     4.0    17.9    -      -       +      -
    542A  TYR      2.7    12.5    +      -       -      +
    543A  ASN*     3.4    22.9    -      -       -      +
    544A  ILE*     2.9    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 513 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489A  CYS      3.0    16.5    +      -       -      +
    490A  HIS*     2.9    23.3    -      -       -      +
    492A  PRO*     3.1    30.4    -      -       -      +
    512A  LEU*     1.3    73.7    -      -       -      +
    514A  SER*     1.3    69.7    +      -       -      +
    544A  ILE*     3.3     5.4    -      -       -      -
    545A  ASP*     4.2     1.2    +      -       -      +
    546A  ALA*     3.2    36.8    -      -       -      +
    547A  VAL*     4.0    13.8    -      -       -      +
    559A  ILE*     3.8    12.3    -      -       -      +
    563A  MET*     4.0    16.8    -      -       -      -
----------------------------------------------------------
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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