Contacts of the strand formed by residues 1036 - 1040 (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 TYR1036 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1035B  VAL*     1.3    75.2    -      -       -      +
   1037B  VAL*     1.3    57.3    +      -       -      +
   1038B  ALA*     3.7    21.1    -      -       +      -
   1052B  VAL*     4.0     6.7    -      -       -      -
   1055B  GLU*     2.7    46.9    +      -       +      +
   1056B  ALA*     3.9    26.7    -      -       +      -
   1059B  PHE*     3.7    15.9    -      -       +      -
   1062B  PRO      3.0     7.1    +      -       -      -
   1063B  SER*     3.3    18.5    -      -       -      +
   1064B  LEU      2.8    32.8    +      -       -      -
   1065B  VAL*     5.0     0.2    -      -       +      -
   1100B  ARG*     3.4    22.0    -      -       +      +
   1101B  TYR      3.4    13.9    -      -       -      -
   1102B  ASP*     3.7    34.1    -      -       +      -
   1103B  PRO*     3.9     2.5    -      -       +      -
   1104B  ARG*     3.9     8.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1037 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026B  ALA*     3.9    34.1    -      -       +      +
   1029B  VAL*     3.2    33.2    -      -       +      -
   1030B  MET*     3.9    23.8    -      -       +      -
   1035B  VAL      3.7     9.9    -      -       -      +
   1036B  TYR*     1.3    79.8    -      -       -      +
   1038B  ALA*     1.3    66.9    +      -       -      +
   1064B  LEU*     3.2    16.2    -      -       +      +
   1066B  ILE*     5.4     1.1    -      -       +      -
   1099B  PHE*     4.3     5.7    -      -       +      +
   1100B  ARG      3.4     0.3    -      -       -      -
   1101B  TYR*     2.7    39.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA1038 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1036B  TYR*     3.7     8.0    -      -       +      -
   1037B  VAL*     1.3    79.5    -      -       -      +
   1039B  THR*     1.3    68.9    +      -       -      +
   1052B  VAL*     3.6    30.5    -      -       +      -
   1064B  LEU      3.0     7.8    +      -       -      +
   1065B  VAL*     3.3     4.5    -      -       +      -
   1066B  ILE*     3.0    25.0    +      -       -      +
   1099B  PHE*     3.3    14.6    -      -       -      +
   1100B  ARG*     3.7    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR1039 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026B  ALA*     4.5     9.0    -      -       +      -
   1038B  ALA*     1.3    79.0    -      -       -      +
   1040B  VAL*     1.3    65.1    -      -       -      +
   1048B  GLN*     3.1    21.7    +      -       -      +
   1066B  ILE*     3.2    21.3    -      -       +      +
   1096B  TRP*     4.2    13.2    -      -       +      +
   1097B  PRO      3.0    24.4    +      -       -      +
   1098B  LEU*     3.2     4.6    -      -       -      +
   1099B  PHE*     3.1    44.3    +      -       +      +
   1159B  ARG*     5.7     1.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1040 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    820B  TYR*     4.0    10.1    -      -       +      -
   1039B  THR*     1.3    79.3    -      -       -      +
   1041B  SER*     1.3    61.0    +      -       -      +
   1048B  GLN*     3.4    18.6    -      -       -      +
   1049B  PHE*     4.0    23.8    -      -       +      -
   1052B  VAL*     3.8    29.8    -      -       +      -
   1065B  VAL*     4.1    11.4    -      -       +      -
   1066B  ILE      2.9     8.5    +      -       -      +
   1067B  ALA*     3.5    28.3    -      -       +      -
   1068B  TYR      3.1    24.3    +      -       -      -
   1096B  TRP*     3.1     7.8    +      -       -      -
   1098B  LEU*     3.6     8.1    -      -       -      -
----------------------------------------------------------
 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