Contacts of the strand formed by residues 126 - 130 (chain A) in PDB entry 2GC3


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 126 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  TYR      3.7     1.4    -      -       -      +
    100A  VAL*     3.6     1.0    -      -       -      -
    101A  ALA*     2.8    32.2    +      -       -      +
    121A  SER      3.7    20.3    +      -       -      +
    122A  MET*     3.9     5.3    -      -       +      +
    123A  GLU*     2.9    36.9    +      -       -      +
    124A  PRO      3.4     0.6    +      -       -      -
    125A  GLY*     1.3    74.2    -      -       -      +
    127A  VAL*     1.3    62.7    +      -       -      +
    128A  VAL*     3.9    20.1    +      -       +      -
      7B  GLY*     4.4     3.6    -      -       -      -
      8B  VAL      3.4    17.3    -      -       -      +
      9B  LYS*     4.4    12.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  VAL*     3.7    22.7    -      -       +      -
     99A  TYR      3.2     8.5    -      -       -      +
    100A  VAL*     4.2    22.4    -      -       +      -
    125A  GLY      4.2     2.2    -      -       -      +
    126A  THR*     1.3    74.6    -      -       -      +
    128A  VAL*     1.3    64.2    +      -       -      +
    129A  TYR      4.1     0.3    +      -       -      -
      6B  PHE*     4.0     0.5    -      -       -      +
      7B  GLY*     3.2     2.1    -      -       -      -
      8B  VAL*     2.7    51.6    +      -       +      +
     10B  VAL*     3.4    25.8    -      -       +      -
     12B  PHE*     5.8     0.2    -      -       +      -
     68B  PHE*     3.7    28.6    -      -       +      -
    149B  LEU*     4.3     9.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLU      4.5     0.2    -      -       -      -
     98A  VAL*     3.5     6.2    -      -       -      +
     99A  TYR*     2.8    37.2    +      -       +      +
    108A  MET*     3.7    32.3    -      -       +      -
    110A  LEU*     5.1     2.2    -      -       +      -
    120A  ILE*     4.0    21.3    -      -       +      -
    122A  MET*     3.7    38.4    -      -       +      -
    126A  THR*     3.9     9.6    -      -       +      -
    127A  VAL*     1.3    79.7    -      -       -      +
    129A  TYR*     1.3    71.1    +      -       -      +
    130A  VAL*     3.7     1.4    +      -       +      -
      6B  PHE      3.4    11.9    -      -       -      +
      7B  GLY*     4.3     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ALA*     4.2     9.9    -      -       +      -
     97A  GLU      3.8     6.1    -      -       -      -
     98A  VAL*     4.7     9.9    -      -       +      +
    127A  VAL*     4.1     1.2    +      -       -      +
    128A  VAL*     1.3    72.0    -      -       -      +
    130A  VAL*     1.3    61.9    +      -       -      +
    131A  PRO*     3.4    35.5    -      -       +      +
    132A  PRO*     3.5     5.4    -      -       -      +
      3B  LYS*     3.0    25.1    +      -       +      -
      4B  GLU      4.5     3.4    -      -       -      -
      5B  PRO*     3.6     3.1    -      -       -      +
      6B  PHE*     2.9    64.4    +      +       +      +
     59B  GLN*     3.5    21.0    -      -       +      +
     65B  ASP*     2.7    30.4    +      -       -      -
     66B  LEU*     3.7    15.9    -      -       +      -
     68B  PHE*     4.4    10.1    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  HIS*     5.4     0.4    -      -       +      -
     95A  ARG      5.8     0.2    -      -       -      +
     96A  ALA*     3.3     5.7    -      -       -      +
     97A  GLU*     2.8    46.3    +      -       +      +
     99A  TYR*     3.7    26.9    -      -       +      -
    108A  MET*     3.5    31.4    -      -       +      -
    110A  LEU*     3.9    11.2    -      -       +      -
    128A  VAL*     4.5     1.3    -      -       +      -
    129A  TYR*     1.3    73.8    -      -       -      +
    131A  PRO*     1.3    67.8    -      -       +      +
    134A  TRP      3.8     9.4    -      -       -      +
    136A  HIS*     3.4    32.5    -      -       +      +
----------------------------------------------------------
 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