Contacts of the strand formed by residues 680 - 684 (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 ASN 680 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1216A  ARG      3.2     1.8    +      -       -      -
   1217A  ALA*     2.9    39.4    +      -       -      +
   1222A  GLN      6.2     0.2    -      -       -      -
   1223A  GLN*     4.7     4.4    -      -       -      +
   1226A  LEU*     3.4    28.1    -      -       -      +
    678B  ALA*     3.5     1.2    -      -       -      +
    679B  ILE*     1.3    91.2    -      -       -      +
    681B  VAL*     1.3    66.6    +      -       -      +
    747B  GLY*     3.1    27.4    -      -       -      -
    764B  MET*     3.6    18.1    -      -       +      +
    765B  GLN      3.1     7.9    -      -       -      +
    766B  PRO*     3.3    19.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 681 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678B  ALA*     3.6    20.0    -      -       +      -
    680B  ASN*     1.3    78.8    -      -       -      +
    682B  PRO*     1.3    79.8    -      -       +      +
    683B  GLN      3.7     0.2    +      -       -      -
    740B  ILE*     4.9     0.2    -      -       +      -
    742B  THR*     3.9    20.2    -      -       +      +
    745B  CYS*     3.7    16.6    -      -       +      -
    764B  MET*     3.9     5.8    -      -       -      -
    765B  GLN*     2.8    32.9    +      -       -      +
    767B  LEU*     3.9    23.8    -      -       +      -
    770B  GLN*     3.8    27.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 682 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681B  VAL*     1.3    97.1    -      -       +      +
    683B  GLN*     1.3    59.2    +      -       -      +
    684B  TRP      4.2     0.2    -      -       -      -
    740B  ILE*     3.6    39.4    -      -       +      +
    742B  THR*     5.0     0.3    -      -       -      +
    745B  CYS*     3.7    15.5    -      -       -      -
    751B  CYS*     3.7    28.3    -      -       -      -
    762B  LEU*     4.1    20.0    -      -       +      -
    763B  VAL      3.6     5.8    -      -       -      +
    764B  MET*     3.8     9.6    -      -       -      -
    770B  GLN*     4.5     2.3    -      -       -      +
    774B  GLN*     6.1     0.7    -      -       -      +
   3234B  SF4      3.9    15.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 683 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  PRO*     1.3    74.5    -      -       -      +
    684B  TRP*     1.3    73.4    +      -       -      +
    685B  VAL*     3.7    13.0    +      -       -      +
    740B  ILE*     4.9     0.2    -      -       -      -
    762B  LEU*     3.4     4.9    -      -       -      -
    763B  VAL*     2.8    36.6    +      -       +      +
    765B  GLN*     3.7    25.2    +      -       +      +
    770B  GLN*     2.8    42.4    +      -       -      +
    774B  GLN*     6.1     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 684 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  PRO      4.2     1.2    +      -       -      -
    683B  GLN*     1.3    85.6    +      -       -      +
    685B  VAL*     1.3    60.2    +      -       -      +
    686B  PRO*     3.4    45.3    -      -       +      +
    689B  CYS*     3.5    39.7    -      -       +      +
    722B  THR      3.3    24.2    -      -       -      -
    724B  LEU*     3.9    10.1    -      -       +      -
    736B  PHE*     3.8    11.0    -      +       -      -
    737B  ARG*     3.6    23.3    -      -       +      +
    738B  ILE*     3.5    55.6    -      -       +      +
    740B  ILE*     4.5     7.6    -      -       +      +
    761B  ALA      3.2    17.3    -      -       -      -
    762B  LEU*     3.9     8.2    -      -       +      +
   3233B  SF4      3.5    13.3    -      -       -      -
----------------------------------------------------------
 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