Contacts of the strand formed by residues 514 - 518 (chain B) in PDB entry 1KWA


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 ILE 514 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505B  LEU*     3.4     6.3    -      -       -      -
    506B  LYS*     2.8    57.4    +      -       +      +
    512B  HIS*     3.1    31.2    +      -       +      +
    513B  CYS*     1.3    75.0    -      -       -      +
    515B  VAL*     1.3    76.1    +      -       -      +
    516B  ALA*     3.2     1.0    +      -       -      +
    533B  GLY*     3.9    17.7    -      -       -      +
    534B  ASP      3.4     8.7    -      -       -      +
    535B  GLU*     4.6     6.1    -      -       +      -
    571B  TYR*     3.9    31.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 515 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    503B  ILE*     4.9     5.2    -      -       +      -
    504B  THR      4.4     1.8    -      -       -      +
    505B  LEU*     3.7    20.4    -      -       +      -
    514B  ILE*     1.3    71.4    -      -       -      +
    516B  ALA*     1.3    60.3    +      -       -      +
    517B  ARG      4.0     7.4    -      -       -      +
    518B  ILE*     3.6    36.3    -      -       +      -
    530B  LEU*     4.6    14.1    -      -       +      -
    531B  HIS      3.8    11.2    -      -       -      +
    532B  VAL*     3.5     3.5    -      -       -      +
    533B  GLY*     2.7    29.3    +      -       -      -
    534B  ASP*     2.8    32.8    +      -       +      +
    536B  ILE*     4.4    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 516 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    504B  THR*     2.9    19.5    +      -       +      +
    506B  LYS*     3.2    46.4    -      -       +      +
    514B  ILE*     3.2     2.8    +      -       -      -
    515B  VAL*     1.3    73.7    -      -       -      +
    517B  ARG*     1.3    76.4    +      -       +      +
    532B  VAL*     3.4    18.9    -      -       -      +
    573B  GLU*     5.2     1.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 517 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    503B  ILE*     3.3     4.9    -      -       -      +
    504B  THR*     2.9    58.3    +      -       -      +
    515B  VAL*     3.6     1.8    -      -       -      +
    516B  ALA*     1.3    91.0    -      -       +      +
    518B  ILE*     1.3    67.7    +      -       -      +
    519B  MET*     4.2     3.8    -      -       +      +
    532B  VAL*     4.1     5.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 518 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502B  GLY      3.9     6.5    -      -       -      +
    503B  ILE*     4.3     4.9    -      -       +      -
    515B  VAL*     3.6    17.0    -      -       +      -
    517B  ARG*     1.3    80.0    -      -       -      +
    519B  MET*     1.3    65.3    +      -       -      +
    520B  HIS*     3.2    16.2    +      -       +      -
    524B  ILE*     4.3     6.1    -      -       +      -
    525B  HIS*     3.6    43.5    -      -       +      +
    530B  LEU*     3.3    41.7    -      -       +      +
    531B  HIS*     3.7    15.9    -      -       -      +
    532B  VAL*     3.9    12.9    -      -       +      +
    702B  SO4      4.7     2.5    -      -       -      +
----------------------------------------------------------
 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