Contacts of the strand formed by residues 102 - 106 (chain B) in PDB entry 4IJ3


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 THR 102 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLN*     3.1    19.7    +      -       -      +
      8B  HIS*     2.7    26.8    +      -       -      +
      9B  LYS      3.4     2.7    -      -       -      +
     11B  MET*     3.6    38.5    -      -       +      +
     21B  ILE*     3.3    26.5    -      -       +      +
     22B  THR      5.1     0.2    +      -       -      -
     84B  ALA      3.6     1.4    -      -       -      +
     85B  VAL*     3.3     5.0    -      -       -      +
     86B  TYR*     2.8    33.4    +      -       -      +
    101B  GLY*     1.3    72.6    +      -       -      -
    103B  LYS*     1.3    63.6    +      -       -      +
    104B  LEU      4.1     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  LYS      2.7    11.1    +      -       -      +
     10B  PHE*     3.4    35.3    -      -       +      +
     11B  MET      3.1    26.3    +      -       -      +
     40B  SER*     5.7     6.5    -      -       -      -
     84B  ALA*     3.5    10.5    -      -       -      +
     85B  VAL*     3.5    27.3    -      -       +      +
    102B  THR*     1.3    75.6    -      -       -      +
    104B  LEU*     1.3    76.4    +      -       -      +
    105B  GLU*     3.9     5.4    +      -       +      +
    165B  ASP*     3.7    25.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  MET*     3.4    31.2    -      -       +      +
     13B  THR*     4.3    12.6    -      -       -      +
     19B  VAL*     4.0    23.6    -      -       +      -
     21B  ILE*     4.8     7.4    -      -       +      -
     75B  ILE*     3.8    19.3    -      -       +      -
     78B  VAL*     4.9     3.6    -      -       +      -
     82B  ASP      3.6    11.2    -      -       -      +
     83B  LEU*     3.8    22.1    -      -       +      +
     84B  ALA      2.9    22.8    +      -       -      +
     86B  TYR*     3.5    32.3    -      -       +      -
    103B  LYS*     1.3    84.1    -      -       -      +
    105B  GLU*     1.3    60.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  PHE*     4.5    17.1    -      -       +      +
     11B  MET*     3.3     7.3    +      -       -      +
     12B  SER*     3.2    23.7    +      -       -      +
     13B  THR*     2.8    28.1    +      -       -      +
     83B  LEU*     3.9     7.4    -      -       -      -
    103B  LYS*     4.9     8.3    -      -       +      +
    104B  LEU*     1.3    75.5    -      -       -      +
    106B  LEU*     1.3    59.2    +      -       -      +
    140B  TYR*     3.3    24.9    +      -       -      -
    141B  PRO*     5.7     1.1    -      -       -      +
    142B  LYS*     4.5    13.2    +      -       -      +
    166B  GLN*     3.4    20.7    +      -       +      +
    173B  TYR*     3.0    26.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  SER*     4.6     0.2    -      -       -      -
     13B  THR      3.3    10.8    -      -       -      +
     14B  SER*     4.1    14.4    -      -       -      -
     15B  VAL*     4.2    20.0    -      -       +      +
     78B  VAL*     6.0     0.9    -      -       +      -
     80B  ALA*     6.3     0.9    -      -       -      -
     83B  LEU*     3.4    30.9    -      -       +      +
    105B  GLU*     1.3    74.4    -      -       -      +
    107B  LYS*     1.3    65.9    +      -       -      +
    108B  ARG*     4.6     0.7    -      -       -      +
    140B  TYR*     3.2    11.5    +      -       -      -
    166B  GLN*     2.9    27.9    +      -       -      +
    168B  SER      6.0     1.6    -      -       -      +
    171B  SER*     3.7    25.1    -      -       -      +
----------------------------------------------------------
 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