Contacts of the strand formed by residues 253 - 257 (chain W) in PDB entry 1G3I


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 ILE 253 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31W  LEU*     5.7     2.5    -      -       +      -
     34W  ARG*     4.2    15.9    -      -       -      +
     67W  ALA      4.5     1.1    -      -       -      +
     70W  LEU*     3.1    45.8    -      -       +      +
     71W  ALA*     4.7     2.9    -      -       -      -
     74W  ALA*     5.8     0.2    -      -       +      -
     76W  ALA*     4.6    11.9    -      -       +      -
     77W  PRO      3.0    16.0    +      -       -      +
     78W  PHE*     3.5    28.3    -      -       +      -
     79W  ILE      3.4    22.0    +      -       -      -
    103W  LEU*     3.8     4.5    -      -       -      +
    252W  GLY*     1.3    78.8    -      -       -      +
    254W  VAL*     1.3    64.8    +      -       -      +
    304W  LEU*     3.2    23.3    -      -       +      +
    306W  ILE*     4.4    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 254 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79W  ILE*     3.8     9.9    -      -       +      +
     81W  VAL*     4.7     7.2    -      -       +      -
     99W  ILE*     3.4    33.4    -      -       +      -
    100W  ILE*     5.2     2.5    -      -       +      -
    103W  LEU*     4.3    11.7    -      -       +      -
    253W  ILE*     1.3    76.0    -      -       -      +
    255W  PHE*     1.3    60.5    +      -       -      +
    256W  ILE*     4.2     4.7    -      -       +      +
    303W  ILE*     3.7    21.1    -      -       +      -
    304W  LEU      2.7     9.5    +      -       -      +
    305W  PHE*     3.3    39.1    -      -       +      +
    306W  ILE*     2.7    34.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 255 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55W  MET*     3.4     3.6    -      -       +      -
     63W  LYS      2.9    33.2    -      -       -      -
     64W  THR*     2.9    29.4    -      -       +      -
     67W  ALA*     3.5    15.5    -      -       +      -
     78W  PHE*     4.0    16.4    -      +       +      -
     79W  ILE      2.9    15.5    +      -       -      +
     80W  LYS*     3.3    27.4    -      -       +      -
     81W  VAL*     2.7    35.0    +      -       -      +
    254W  VAL*     1.3    75.2    -      -       -      +
    256W  ILE*     1.3    57.3    +      -       -      +
    257W  ASP*     3.8     3.5    +      -       +      -
    306W  ILE*     3.0    44.0    -      -       +      -
    308W  SER*     3.8    24.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 256 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81W  VAL*     3.5    21.3    -      -       +      +
     83W  ALA*     4.7    13.0    -      -       +      +
     99W  ILE*     5.7     1.8    -      -       +      -
    254W  VAL*     4.8     8.7    -      -       +      +
    255W  PHE*     1.3    75.0    -      -       -      +
    257W  ASP*     1.3    69.2    +      -       -      +
    259W  ILE*     4.4    23.0    +      -       +      -
    262W  ILE*     6.1     0.2    -      -       +      -
    282W  LEU*     3.5    31.4    -      -       +      -
    286W  VAL*     5.6     5.2    -      -       +      -
    305W  PHE*     5.0    17.3    -      -       +      -
    306W  ILE      2.9    10.6    +      -       -      +
    307W  ALA*     3.3    15.5    -      -       +      +
    308W  SER*     2.9    25.5    +      -       -      +
    323W  LEU*     6.5     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 257 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283V  LEU*     5.3     4.0    -      -       -      +
    287V  GLU*     5.4     0.9    -      -       -      +
    322V  GLU*     5.2     1.0    -      -       -      +
     63W  LYS*     3.5     0.2    +      -       -      -
     64W  THR*     4.0     3.2    +      -       -      -
     80W  LYS*     4.2    24.0    +      -       +      -
     81W  VAL      2.9    18.5    +      -       -      +
     82W  GLU*     3.5    22.5    -      -       -      +
     83W  ALA      4.1     4.7    +      -       -      -
    255W  PHE*     3.8     5.2    +      -       +      -
    256W  ILE*     1.3    73.5    -      -       -      +
    258W  GLU*     1.3    82.2    +      -       -      +
    308W  SER*     2.5    25.7    +      -       -      +
    460W  ATP      2.7    44.1    +      -       -      -
----------------------------------------------------------
 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