Contacts of the strand formed by residues 578 - 582 (chain B) in PDB entry 1KT8


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 MET 578 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    577B  GLY*     1.3    77.2    -      -       -      +
    579B  LYS*     1.3    67.0    +      -       -      +
    590B  LEU*     4.2    12.8    -      -       +      -
    591B  PHE      5.0     4.7    -      -       -      +
    593B  PRO*     3.9    25.6    -      -       +      +
    596B  ASN*     3.6    38.1    -      -       +      +
    597B  MET*     4.0     9.6    -      -       +      -
    618B  LEU*     4.9     1.8    -      -       +      -
    621B  ILE*     3.8    41.5    -      -       +      -
    641B  TYR*     3.6     6.3    -      -       -      -
    642B  VAL*     2.8    45.1    +      -       +      +
    644B  PRO*     5.0     4.7    -      -       +      -
    813B  THR*     4.0     7.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 579 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530B  PHE*     6.4     0.4    -      -       -      -
    578B  MET*     1.3    79.0    -      -       -      +
    580B  ALA*     1.3    60.4    +      -       -      +
    581B  PHE*     3.7    28.8    -      -       +      -
    590B  LEU*     3.5     9.8    -      -       -      +
    591B  PHE*     3.2    28.1    +      -       +      +
    639B  SER*     3.3    27.0    +      -       -      +
    640B  LEU      3.4     6.5    -      -       -      +
    641B  TYR*     4.2    14.8    -      -       +      -
    642B  VAL*     4.9     0.2    -      -       -      -
    670B  VAL*     4.9    17.0    -      -       -      +
    671B  GLY      5.6     1.0    +      -       -      -
    673B  TYR*     5.6     1.4    -      -       -      +
    813B  THR*     2.9    43.7    +      -       +      +
    814B  ALA*     3.3    18.6    +      -       -      +
    816B  GLN*     5.2     5.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 580 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    579B  LYS*     1.3    72.6    -      -       -      +
    581B  PHE*     1.3    61.1    +      -       -      +
    588B  VAL*     3.9    21.8    -      -       +      -
    589B  ARG      3.3     6.1    -      -       -      +
    590B  LEU*     3.7    17.2    -      -       +      +
    625B  ILE*     4.2    12.3    -      -       +      -
    632B  VAL*     4.1     2.7    -      -       -      +
    639B  SER*     3.3     5.5    -      -       -      -
    640B  LEU*     2.9    47.1    +      -       +      +
    642B  VAL*     4.8     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 581 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    579B  LYS*     3.7    38.8    -      -       +      -
    580B  ALA*     1.3    75.3    -      -       -      +
    582B  LYS*     1.3    60.4    +      -       -      +
    583B  GLY      4.0     1.0    +      -       -      -
    587B  GLN      3.7     1.4    -      -       -      +
    588B  VAL*     3.2     2.2    -      -       -      -
    589B  ARG*     2.7    42.7    +      -       -      +
    591B  PHE*     3.9    11.7    -      -       +      -
    632B  VAL*     4.5     2.2    -      -       -      -
    639B  SER*     3.9    17.5    -      -       -      +
    816B  GLN*     4.3     7.6    -      -       +      -
    853B  GLN*     3.4    64.1    -      -       +      +
    854B  TYR*     3.4    39.7    -      +       +      -
    862B  MET*     4.3     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 582 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    581B  PHE*     1.3    73.1    -      -       -      +
    583B  GLY*     1.3    59.1    +      -       -      +
    586B  GLN*     3.1    58.5    -      -       -      +
    587B  GLN      3.2     4.3    -      -       -      -
    588B  VAL*     3.7    17.0    -      -       +      -
    629B  LYS*     2.8    34.1    +      -       -      +
    630B  ASP*     3.9     6.3    +      -       -      +
    632B  VAL*     3.0    29.8    +      -       +      +
    633B  PRO      3.6    13.4    +      -       -      +
    634B  ASP*     3.9    36.0    +      -       +      +
    638B  THR      5.5     0.6    +      -       -      -
    854B  TYR*     4.0    13.1    -      -       -      -
----------------------------------------------------------
 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