Contacts of the strand formed by residues 197 - 206 (chain A) in PDB entry 2GP0


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 PHE 197 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  GLN*     3.9    15.3    -      -       +      -
    156A  SER      5.1     0.7    -      -       -      -
    159A  TRP*     4.0    15.3    -      -       +      -
    160A  GLU*     3.6    33.0    -      -       +      -
    163A  TRP*     3.5    38.8    -      +       +      -
    193A  THR*     3.1     6.1    -      -       -      +
    194A  TYR*     2.8    45.1    +      -       -      +
    195A  GLY      3.2     0.2    -      -       -      -
    196A  PRO*     1.3    97.1    -      -       +      +
    198A  GLN*     1.3    60.6    +      -       -      +
    199A  ILE*     4.0     7.1    +      -       +      -
    217A  ILE*     3.9    29.4    -      -       +      -
    218A  GLN      3.5     1.3    -      -       -      -
    219A  TYR*     3.8    26.5    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  GLU*     2.9    39.4    +      -       +      +
    192A  GLU      3.7     2.5    -      -       -      +
    193A  THR*     4.0    10.5    +      -       -      +
    196A  PRO      4.0     1.2    +      -       -      -
    197A  PHE*     1.3    73.9    -      -       -      +
    199A  ILE*     1.3    62.3    +      -       -      +
    200A  ARG*     3.0    39.6    +      -       +      +
    216A  THR*     3.7     1.4    +      -       -      +
    217A  ILE*     3.4     2.8    -      -       -      -
    218A  GLN*     2.9    52.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  TRP*     3.7    39.5    -      -       +      -
    188A  PRO*     3.5    22.3    -      -       +      +
    191A  GLU*     3.3     4.7    -      -       -      +
    192A  GLU      2.8    31.3    +      -       -      +
    194A  TYR*     3.3    35.2    -      -       +      -
    197A  PHE*     4.4     4.7    -      -       +      +
    198A  GLN*     1.3    74.7    -      -       -      +
    200A  ARG*     1.3    69.6    +      -       -      +
    215A  LEU*     4.4    11.7    -      -       +      -
    216A  THR      3.2     9.4    -      -       -      +
    217A  ILE*     3.6    33.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  PRO*     4.4     3.4    -      -       -      -
    190A  GLU      3.5     7.2    -      -       -      +
    191A  GLU*     3.8    23.9    +      -       +      +
    198A  GLN*     3.0    39.2    +      -       +      +
    199A  ILE*     1.3    79.7    -      -       -      +
    201A  ILE*     1.3    63.7    +      -       -      +
    202A  GLN*     3.8     3.0    +      -       +      -
    215A  LEU*     3.1     8.8    -      -       -      +
    216A  THR*     2.9    47.0    +      -       -      +
    218A  GLN*     5.6     1.8    +      -       -      -
    223A  ARG*     5.4     6.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  TRP*     5.1     0.2    -      -       +      -
    188A  PRO*     3.9    12.7    -      -       +      +
    189A  THR      3.0    34.8    -      -       -      +
    190A  GLU*     3.0    19.5    +      -       -      +
    200A  ARG*     1.3    74.6    -      -       -      +
    202A  GLN*     1.3    60.1    +      -       -      +
    203A  ASP*     3.6    18.2    -      -       -      +
    204A  MET*     4.3    13.2    -      -       +      -
    213A  ARG*     3.8    39.7    -      -       +      +
    214A  GLN      3.7     5.2    -      -       -      +
    215A  LEU*     4.0    10.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  ARG*     4.4     7.0    -      -       +      +
    201A  ILE*     1.3    75.7    -      -       -      +
    203A  ASP*     1.3    61.9    +      -       +      +
    214A  GLN*     2.8    24.4    +      -       +      +
    215A  LEU      4.4     1.6    -      -       -      -
    216A  THR*     3.7    31.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ILE*     3.6    11.8    -      -       -      +
    202A  GLN*     1.3    83.0    -      -       +      +
    204A  MET*     1.3    76.2    +      -       -      +
    205A  LYS*     4.4    15.0    -      -       -      +
    212A  VAL      4.6     0.2    -      -       -      -
    213A  ARG*     3.4     4.0    -      -       -      -
    214A  GLN*     2.9    42.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ILE*     4.3    10.8    -      -       +      -
    203A  ASP*     1.3    85.2    +      -       -      +
    205A  LYS*     1.3    61.8    +      -       -      +
    206A  GLU*     4.3    11.2    +      -       +      +
    211A  THR*     3.9    21.3    -      -       +      +
    212A  VAL      3.5     3.8    -      -       -      -
    213A  ARG*     3.2    42.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  ASP*     4.4    11.2    -      -       -      +
    204A  MET*     1.3    73.7    -      -       -      +
    206A  GLU*     1.3    65.4    +      -       -      +
    207A  CYS*     3.7    27.6    +      -       -      -
    211A  THR*     3.5     2.4    -      -       -      -
    212A  VAL*     2.8    54.3    +      -       +      +
    252A  GLU*     5.2     7.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  MET*     4.3    11.3    +      -       +      -
    205A  LYS*     1.3    74.5    -      -       -      +
    207A  CYS*     1.3    66.7    +      -       -      +
    210A  TYR      4.1     2.2    -      -       -      -
    211A  THR*     3.9    22.7    -      -       +      +
----------------------------------------------------------
 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