Contacts of the strand formed by residues 762 - 766 (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 LEU 762 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  PRO*     4.1     9.0    -      -       +      -
    683B  GLN      3.4     4.0    -      -       -      +
    684B  TRP*     3.9    24.5    -      -       +      +
    695B  CYS*     3.5    33.0    -      -       +      -
    704B  ILE*     4.6     1.8    -      -       +      -
    738B  ILE*     4.6     1.3    -      -       +      -
    740B  ILE*     4.1    20.6    -      -       +      -
    751B  CYS*     3.8    26.2    -      -       +      +
    752B  ALA*     3.7    27.7    -      -       +      +
    755B  CYS*     4.0     3.7    -      -       +      -
    760B  LYS*     3.3    13.7    -      -       -      +
    761B  ALA*     1.3    87.2    -      -       -      +
    763B  VAL*     1.3    67.0    -      -       -      +
   3233B  SF4      3.6    14.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 763 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1225A  ASP*     5.1     1.6    -      -       -      +
   1229A  ARG*     3.3    37.9    -      -       -      +
    682B  PRO*     4.2     1.6    -      -       -      -
    683B  GLN*     2.8    39.6    +      -       +      +
    685B  VAL*     4.3    17.5    -      -       +      -
    752B  ALA*     4.9     0.7    -      -       -      -
    760B  LYS*     4.4    14.8    -      -       +      +
    762B  LEU*     1.3    81.1    -      -       -      +
    764B  MET*     1.3    59.5    +      -       -      +
    765B  GLN*     3.6    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 764 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1217A  ALA      5.5     1.1    -      -       -      +
   1218A  GLY*     4.5     3.6    -      -       -      -
   1222A  GLN*     3.5    43.1    -      -       +      +
   1225A  ASP*     5.4     1.5    +      -       -      +
   1226A  LEU*     4.0     6.9    -      -       +      +
   1229A  ARG*     2.9    30.0    +      -       -      +
    680B  ASN*     3.6    42.8    -      -       +      +
    681B  VAL*     3.4     8.1    -      -       -      -
    682B  PRO*     3.8    18.4    -      -       -      -
    747B  GLY      4.0    14.6    -      -       -      +
    749B  GLY*     3.9    22.0    -      -       -      -
    752B  ALA*     4.1    11.9    -      -       +      +
    763B  VAL*     1.3    72.1    -      -       -      +
    765B  GLN*     1.3    60.6    +      -       -      +
   3234B  SF4      4.1     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 765 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1226A  LEU*     3.9     3.7    -      -       -      +
   1229A  ARG*     3.0    30.3    +      -       -      +
   1230A  THR*     5.9     0.6    -      -       -      +
    680B  ASN*     3.1     7.4    -      -       -      -
    681B  VAL*     2.8    33.0    +      -       -      +
    683B  GLN*     3.7    30.8    +      -       +      +
    763B  VAL*     3.6    20.9    -      -       -      +
    764B  MET*     1.3    78.2    +      -       -      +
    766B  PRO*     1.3    79.3    -      -       +      +
    769B  THR*     3.7    13.0    +      -       -      +
    770B  GLN*     3.8    11.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 766 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1226A  LEU*     4.1    16.8    -      -       +      -
   1230A  THR*     5.7     4.0    -      -       +      -
    679B  ILE*     3.6     2.2    -      -       +      +
    680B  ASN*     3.3    16.6    -      -       -      +
    765B  GLN*     1.3    98.6    -      -       +      +
    767B  LEU*     1.3    65.3    +      -       -      +
    768B  ASP*     3.1    24.2    -      -       -      +
    769B  THR*     2.7    38.1    +      -       +      +
    770B  GLN*     3.7     4.0    +      -       -      +
----------------------------------------------------------
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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