Contacts of the strand formed by residues 3 - 8 (chain B) in PDB entry 4R54


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 TYR 3 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  GLY*     1.3    77.7    -      -       -      -
      4B  THR*     1.3    61.7    +      -       -      +
      5B  VAL*     3.8    16.7    +      -       +      -
     27B  LEU*     4.3     8.1    -      -       +      -
     28B  PRO*     2.7    41.7    +      -       +      +
     29B  ILE*     3.6     2.9    -      -       -      +
     30B  ASP*     2.7    28.7    +      -       -      +
     31B  LYS      3.2     7.4    +      -       -      +
     66B  ASP*     3.3    26.2    -      -       +      +
     67B  ILE*     4.3    10.8    -      -       +      -
    342B  HIS*     2.7    43.0    +      +       +      -
    347B  VAL*     3.4    35.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 4 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  TYR*     1.3    71.7    -      -       -      +
      5B  VAL*     1.3    62.2    +      -       -      +
     30B  ASP*     5.3     1.7    -      -       -      +
     31B  LYS*     3.3    29.8    -      -       +      +
     33B  ARG*     4.5    15.5    -      -       -      +
     64B  GLY      3.4    27.7    +      -       -      +
     65B  VAL*     3.7    17.7    -      -       +      +
     66B  ASP*     2.7    38.7    +      -       -      +
     67B  ILE      3.2     7.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 5 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  TYR*     4.0    19.3    -      -       +      +
      4B  THR*     1.3    78.4    -      -       -      +
      6B  ALA*     1.3    69.6    +      -       -      +
     22B  LEU*     4.2    27.1    -      -       +      -
     27B  LEU*     4.9     7.0    -      -       +      -
     29B  ILE*     4.2    20.4    -      -       +      -
     31B  LYS      2.9    10.6    +      -       -      +
     32B  ILE*     3.4    16.4    -      -       +      +
     33B  ARG      2.9    24.1    +      -       -      -
     65B  VAL*     4.8     0.2    -      -       -      -
     67B  ILE*     3.2    25.8    -      -       +      +
     69B  LEU*     4.3    10.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 6 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  VAL*     1.3    75.1    -      -       -      +
      7B  VAL*     1.3    63.5    +      -       -      +
      8B  VAL*     3.9     1.1    -      -       +      -
     33B  ARG*     3.2    16.4    -      -       +      +
     35B  LEU*     4.6    11.9    -      -       +      -
     62B  PHE*     5.0     7.9    -      -       +      -
     65B  VAL*     4.0    26.9    -      -       +      +
     67B  ILE      2.8     7.7    +      -       -      +
     68B  ALA*     3.2     9.5    -      -       +      +
     69B  LEU*     2.8    27.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 7 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ALA*     1.3    74.5    -      -       -      +
      8B  VAL*     1.3    62.6    +      -       -      +
      9B  GLY      4.5     1.3    -      -       -      -
     10B  ALA*     3.9    22.4    -      -       +      +
     15B  GLY*     4.6     4.0    -      -       -      +
     18B  MET*     4.2    27.6    -      -       +      -
     19B  ILE*     4.9     2.9    -      -       +      -
     22B  LEU*     3.5    32.3    -      -       +      -
     32B  ILE*     4.6     2.9    -      -       +      -
     33B  ARG      3.0     5.3    +      -       -      -
     34B  TYR*     3.8    25.6    -      -       +      -
     35B  LEU*     2.8    29.4    +      -       -      +
     69B  LEU*     3.6    11.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ALA      4.8     1.8    -      -       -      +
      7B  VAL*     1.3    76.1    -      -       -      +
      9B  GLY*     1.3    61.4    +      -       -      +
     35B  LEU*     3.6    11.0    -      -       +      -
     57B  THR*     3.7    26.7    -      -       +      +
     62B  PHE*     4.0    16.6    -      -       +      -
     68B  ALA*     4.7     3.6    -      -       +      -
     69B  LEU      2.9    11.9    +      -       -      +
     70B  PHE*     3.8    40.8    -      -       +      -
     71B  SER*     2.8    32.2    +      -       -      -
     72B  ALA*     4.0    16.6    -      -       +      -
     76B  THR*     4.1    10.5    -      -       +      -
    403B  NAP      4.9     0.4    -      -       +      -
----------------------------------------------------------
 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