Contacts of the strand formed by residues 41 - 45 (chain B) in PDB entry 3K9O


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 GLN 41 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  LYS*     3.0    70.6    +      -       +      +
     30B  ILE*     3.5    31.1    -      -       -      +
     36B  ILE*     2.9    45.4    +      -       +      -
     37B  PRO      3.7     2.2    -      -       -      +
     38B  PRO*     3.0    17.8    +      -       -      +
     39B  ASP      3.4     0.2    -      -       -      -
     40B  GLN*     1.3    79.2    -      -       -      +
     42B  ARG*     1.3    66.7    +      -       -      +
     43B  LEU*     4.7     0.6    -      -       +      +
     69B  LEU*     3.7    16.7    -      -       +      +
     72B  ARG*     4.0     5.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  GLU*     2.7    44.8    +      -       -      -
    198A  LEU*     3.8    20.9    -      -       -      +
     27B  LYS*     4.6     2.5    -      -       -      +
     41B  GLN*     1.3    79.9    -      -       -      +
     43B  LEU*     1.3    63.0    +      -       -      +
     44B  ILE*     4.0     9.4    -      -       +      +
     49B  GLN*     3.4    38.0    -      -       -      +
     68B  HIS      3.4     0.7    -      -       -      +
     69B  LEU*     3.4     5.8    -      -       -      +
     70B  VAL*     2.9    53.2    +      -       -      +
     71B  LEU      3.0    23.2    +      -       -      -
     72B  ARG*     3.6    41.4    -      -       +      +
     73B  LEU*     5.2     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  VAL*     4.4     5.8    -      -       +      -
     23B  ILE*     4.2    15.3    -      -       +      -
     26B  VAL*     3.9    25.4    -      -       +      -
     27B  LYS*     3.8    31.8    -      -       +      +
     30B  ILE*     3.9    21.3    -      -       +      -
     41B  GLN*     4.8     1.1    -      -       -      +
     42B  ARG*     1.3    79.0    -      -       -      +
     44B  ILE*     1.3    67.0    +      -       -      +
     49B  GLN*     3.6     2.1    -      -       -      +
     50B  LEU*     2.9    46.2    +      -       +      +
     67B  LEU*     4.3    16.2    -      -       +      -
     68B  HIS      3.4    10.8    -      -       -      +
     69B  LEU*     4.0    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  MET*     3.7    30.5    -      -       +      +
    174A  PHE*     4.1    15.9    -      -       +      -
    198A  LEU*     3.6    33.4    -      -       +      -
     42B  ARG*     4.0    22.9    -      -       +      +
     43B  LEU*     1.3    83.2    -      -       -      +
     45B  PHE*     1.3    64.5    +      -       -      +
     48B  LYS      3.3    19.7    -      -       -      +
     49B  GLN*     4.0     5.6    -      -       +      -
     50B  LEU*     4.5     1.6    -      -       -      -
     67B  LEU*     3.7     3.5    -      -       -      -
     68B  HIS*     2.9    43.8    +      -       +      +
     70B  VAL*     4.0    16.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  MET      4.6     0.9    -      -       -      -
     44B  ILE*     1.3    76.1    -      -       -      +
     46B  ALA*     1.3    84.6    +      -       +      +
     47B  GLY      3.2     2.0    -      -       -      -
     48B  LYS*     3.0    22.1    +      -       -      +
     50B  LEU*     3.9    25.6    -      -       +      +
     59B  TYR*     3.7    19.1    -      +       +      -
     60B  ASN*     4.1    11.4    -      -       +      -
     61B  ILE*     3.5    25.4    -      -       +      -
     65B  SER*     4.2    22.2    -      -       -      -
     66B  THR      3.4    26.7    -      -       -      -
     67B  LEU*     3.7     8.7    -      -       +      -
     68B  HIS*     5.2     2.0    -      +       -      -
----------------------------------------------------------
 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