Contacts of the strand formed by residues 117 - 121 (chain A) in PDB entry 2GER


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 117 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ILE*     4.3     1.7    -      -       -      +
     92A  VAL*     3.0    42.0    -      -       +      +
     94A  SER*     4.9     5.6    -      -       -      +
    101A  ILE*     3.3    31.2    -      -       +      -
    104A  ILE*     4.2    20.0    -      -       +      -
    105A  GLU*     3.6    21.5    +      -       +      +
    108A  LEU*     5.4     4.7    -      -       +      -
    115A  PRO*     3.9     3.8    +      -       +      +
    116A  ARG*     1.3    73.0    -      -       -      +
    118A  ILE*     1.3    61.9    +      -       -      +
    138A  GLY*     2.9    31.2    +      -       -      -
    140A  HIS      4.4     3.0    +      -       -      -
    141A  ALA*     4.4     3.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ILE*     4.3    15.9    -      -       +      -
     92A  VAL      2.6    19.9    +      -       -      +
     93A  VAL*     3.2    20.6    -      -       +      +
     94A  SER*     2.9    27.1    +      -       -      -
    101A  ILE*     5.3     0.7    -      -       -      -
    117A  VAL*     1.3    77.8    -      -       -      +
    119A  ARG*     1.3    64.2    +      -       -      +
    135A  TYR*     4.9     7.0    -      -       +      -
    136A  ALA      3.3    16.2    -      -       -      +
    137A  THR*     3.8    21.5    -      -       +      -
    138A  GLY      4.4     0.2    -      -       -      +
    141A  ALA*     5.2     4.5    -      -       +      -
    145A  ASP*     4.8     6.5    -      -       +      +
    146A  GLY*     5.5     5.2    -      -       -      +
    149A  MET*     3.1    44.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  SER*     3.6    12.1    -      -       -      +
     96A  ALA      4.8     5.2    +      -       -      +
     98A  GLY*     3.0    42.6    +      -       -      +
     99A  VAL      3.4    21.7    +      -       -      +
    100A  THR*     4.3     3.4    +      -       -      +
    101A  ILE*     3.9    19.6    -      -       +      +
    118A  ILE*     1.3    72.9    -      -       -      +
    120A  CYS*     1.3    64.4    +      -       -      +
    135A  TYR*     3.0     8.9    -      -       -      +
    136A  ALA*     2.9    32.6    +      -       +      +
    164A  GLU*     3.2    47.0    +      -       -      +
    165A  ASP*     5.8     0.2    -      -       -      +
    167A  ILE*     3.9    36.4    +      -       +      +
    168A  ASP*     3.1    17.8    +      -       -      -
    171A  THR*     5.6     0.6    -      -       -      +
    265A  THR*     4.7     0.2    -      -       -      +
    269A  GLN*     4.3     1.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     5.9     0.9    -      -       -      -
     67A  PHE*     5.5     1.1    -      -       -      -
     93A  VAL*     3.4    20.2    -      -       +      -
     94A  SER      2.8     6.5    +      -       -      +
     95A  CYS*     2.1    63.8    -      -       -      +
     96A  ALA      4.7     1.4    -      -       -      +
    119A  ARG*     1.3    83.1    +      -       -      +
    121A  MET*     1.3    68.3    +      -       -      +
    122A  THR*     4.3    16.2    -      -       -      -
    133A  THR*     5.1     2.9    -      -       +      -
    134A  VAL      3.4     7.0    -      -       -      +
    135A  TYR*     4.8     3.6    -      -       +      -
    149A  MET*     5.2     1.6    -      -       -      -
    153A  LEU*     5.6     3.6    -      -       +      -
    167A  ILE*     5.2     2.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     5.9     3.8    -      -       +      -
     95A  CYS      3.9    19.5    -      -       -      +
     97A  ALA*     4.5    12.8    -      -       +      -
    120A  CYS*     1.3    75.5    -      -       -      +
    122A  THR*     1.3   100.6    +      -       -      +
    132A  ALA      3.4     2.8    -      -       -      +
    133A  THR*     3.2     3.1    -      -       -      -
    134A  VAL*     2.8    46.2    +      -       +      +
    167A  ILE*     3.8    19.1    -      -       +      -
    170A  VAL*     4.8     5.6    -      -       +      -
    171A  THR*     2.9    51.1    -      -       +      +
    174A  SER*     5.1     2.8    +      -       -      +
    175A  GLY*     4.3    13.2    -      -       -      -
----------------------------------------------------------
 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