Contacts of the strand formed by residues 19 - 25 (chain I) in PDB entry 2BX5


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 VAL 19 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8H  PRO*     3.9     6.5    -      -       +      -
     11I  LEU*     3.5    26.0    -      -       +      +
     13I  ALA*     4.6    15.5    -      -       +      +
     17I  ASP*     3.6     4.7    +      -       +      -
     18I  ARG*     1.3    73.6    -      -       -      +
     20I  THR*     1.3    64.0    +      -       -      +
     21I  ILE*     3.7    20.4    -      -       +      -
     74I  THR*     3.6     2.3    -      -       -      -
     75I  ILE*     3.0    52.7    +      -       +      +
     78I  LEU*     3.7    32.1    -      -       +      -
    104I  VAL*     5.0     7.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 20 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8H  PRO*     3.8    13.7    -      -       -      +
     20H  THR*     4.2    29.9    -      -       +      +
     22H  THR*     3.0    24.4    +      -       +      +
     72H  THR*     6.1     0.2    -      -       +      -
      8I  PRO*     5.1     4.3    -      -       -      +
     11I  LEU*     4.5     3.6    -      -       -      +
     18I  ARG*     3.5    16.3    +      -       -      +
     19I  VAL*     1.3    77.4    +      -       -      +
     21I  ILE*     1.3    61.3    +      -       -      +
     22I  THR*     3.8     7.6    +      -       +      +
     72I  THR*     3.8    22.4    -      -       +      -
     73I  LEU      3.5     2.2    -      -       -      -
     74I  THR*     4.4     7.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 21 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6I  GLN*     4.1    13.7    -      -       -      +
      7I  SER      3.8     8.1    -      -       -      +
      8I  PRO*     4.7     1.6    -      -       +      -
     11I  LEU*     4.4     2.0    -      -       +      -
     19I  VAL*     3.7    23.3    -      -       +      -
     20I  THR*     1.3    71.5    -      -       -      +
     22I  THR*     1.3    68.6    +      -       -      +
     35I  TRP*     4.1     5.9    -      -       +      -
     72I  THR*     3.4     4.6    -      -       -      +
     73I  LEU*     2.7    62.1    +      -       +      +
     75I  ILE*     4.3     0.9    -      -       +      -
     86I  TYR*     3.7    31.6    -      -       +      -
    102I  THR*     3.4    44.4    -      -       +      +
    104I  VAL*     4.3     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 22 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18H  ARG*     3.1    23.4    +      -       -      +
     20H  THR*     3.4    32.8    -      -       -      +
      5I  THR      4.9     0.2    -      -       -      -
      6I  GLN*     3.7     3.5    -      -       -      +
      7I  SER*     2.9    46.8    +      -       -      +
      8I  PRO*     4.9     0.3    -      -       -      +
     20I  THR*     3.8     5.3    +      -       +      +
     21I  ILE*     1.3    76.9    -      -       -      +
     23I  CYS*     1.3    64.9    +      -       -      +
     35I  TRP*     4.4     0.9    -      -       -      -
     71I  PHE      3.9     6.1    -      -       -      +
     72I  THR*     4.9     7.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 23 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4I  MET*     4.2    11.0    -      -       -      -
      5I  THR      3.4     9.6    -      -       -      +
      6I  GLN*     4.4     4.0    -      -       +      -
     22I  THR*     1.3    77.3    -      -       -      +
     24I  ARG*     1.3    76.7    +      -       -      +
     33I  LEU*     3.8    12.1    -      -       -      -
     35I  TRP*     3.4    20.5    -      -       +      -
     70I  ASP*     3.8     3.1    -      -       -      +
     71I  PHE*     3.1    32.6    +      -       -      +
     88I  CYS*     2.1    49.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 24 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18H  ARG*     3.8    24.0    -      -       +      +
      4I  MET*     3.2    10.8    -      -       -      +
      5I  THR*     2.7    57.5    +      -       -      +
     23I  CYS*     1.3    81.1    -      -       -      +
     25I  ALA*     1.3    62.0    +      -       -      +
     26I  SER*     6.2     0.2    -      -       -      +
     33I  LEU*     5.0     0.6    -      -       -      +
     69I  THR*     3.1    27.8    -      -       -      +
     70I  ASP*     2.6    35.5    +      -       -      +
     71I  PHE*     5.0     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 25 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2I  ILE*     5.0     0.7    -      -       +      -
      3I  GLN      3.6     3.1    -      -       -      -
      4I  MET*     3.8    15.5    -      -       +      -
      5I  THR*     5.7     0.2    -      -       -      -
     24I  ARG*     1.3    78.4    -      -       -      +
     26I  SER*     1.3    68.6    +      -       -      +
     27I  GLN      2.5    24.3    +      -       -      +
     29I  ILE*     3.7    28.0    -      -       +      -
     68I  GLY      3.9     5.2    -      -       -      +
     69I  THR*     2.9    27.6    +      -       -      +
     71I  PHE*     4.4     1.3    -      -       +      -
----------------------------------------------------------
 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