Contacts of the strand formed by residues 202 - 205 (chain A) in PDB entry 3GBN


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 202 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  VAL*     4.3    17.5    -      -       +      -
    201A  TYR*     1.3    76.9    -      -       -      +
    203A  SER*     1.3    65.6    +      -       -      +
    204A  VAL*     4.2    15.3    -      -       +      -
    212A  ARG*     3.3     3.6    -      -       -      +
    213A  PHE*     2.6    50.8    +      -       +      +
    245A  PHE*     4.9     0.9    -      -       +      -
    246A  GLU      3.4     9.4    -      -       -      +
    247A  ALA*     3.7     5.4    -      -       +      -
    249A  GLY      3.4    24.7    -      -       -      +
    250A  ASN*     4.0    18.6    -      -       +      +
    251A  LEU*     3.6    26.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  TYR*     4.2    15.7    -      -       -      -
    202A  VAL*     1.3    77.1    -      -       -      +
    204A  VAL*     1.3    69.3    +      -       -      +
    205A  GLY*     4.9     0.5    +      -       -      -
    210A  ASN*     4.7     6.1    +      -       -      -
    211A  ARG      3.6     9.3    +      -       -      -
    212A  ARG*     4.6     6.8    -      -       -      +
    213A  PHE*     5.4     0.2    -      -       -      -
    244A  THR      3.6     1.1    -      -       -      +
    245A  PHE*     3.5     2.4    -      -       -      -
    246A  GLU*     2.6    53.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TRP*     3.8    38.4    -      -       +      +
    202A  VAL*     4.2     8.1    -      -       +      -
    203A  SER*     1.3    80.6    +      -       -      +
    205A  GLY*     1.3    61.7    +      -       -      +
    209A  TYR*     4.0    10.7    -      -       +      -
    210A  ASN*     3.5     4.2    -      -       -      +
    211A  ARG      3.1    31.0    +      -       -      +
    213A  PHE*     4.7     3.6    -      -       +      -
    243A  ILE*     3.8    31.0    -      -       +      -
    244A  THR      3.4     3.6    -      -       -      +
    245A  PHE*     3.4    33.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  SER*     4.9     0.6    +      -       -      -
    204A  VAL*     1.3    77.4    -      -       -      +
    206A  SER*     1.3    62.9    +      -       -      -
    209A  TYR*     3.6     5.4    -      -       -      -
    210A  ASN*     4.5     9.2    -      -       -      -
    242A  THR      3.7     0.9    -      -       -      +
    243A  ILE*     3.4     4.7    -      -       -      +
    244A  THR*     2.9    41.0    +      -       -      -
----------------------------------------------------------
 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