Contacts of the strand formed by residues 197 - 205 (chain A) in PDB entry 2G1O


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 GLN 197 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  LEU*     3.5     7.2    -      -       -      +
    191A  ILE*     3.0    32.2    +      -       +      +
    192A  LYS      4.6     0.5    +      -       -      -
    195A  VAL*     2.8    31.5    +      -       +      +
    196A  TRP*     1.3    73.9    -      -       -      +
    198A  ILE*     1.3    63.5    +      -       -      +
    217A  LEU*     3.1    25.6    -      -       +      +
    218A  ALA      3.3    22.9    -      -       -      +
    219A  LEU*     3.6     4.0    -      -       +      -
    303A  PRO      5.2     1.4    +      -       -      -
    304A  THR*     2.8    35.1    +      -       -      +
    307A  THR*     3.0    23.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  ILE*     3.4    44.6    -      -       +      +
    189A  ASN      3.8    15.7    -      -       -      +
    190A  LEU*     4.1     6.3    -      -       +      -
    191A  ILE*     3.7    12.0    -      -       -      +
    197A  GLN*     1.3    78.8    -      -       -      +
    199A  GLN*     1.3    64.4    +      -       -      +
    218A  ALA*     2.8    47.1    +      -       +      +
    220A  VAL*     4.3    11.0    -      -       +      -
    267A  LEU*     4.0    19.5    -      -       +      -
    329A  ILE*     3.7    24.5    -      -       +      -
    331A  PHE*     4.1     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  ILE*     4.4     6.7    -      -       +      +
    189A  ASN      4.5     4.8    +      -       -      +
    191A  ILE*     3.7    26.8    -      -       +      +
    198A  ILE*     1.3    75.8    -      -       -      +
    200A  MET*     1.3    62.6    +      -       -      +
    201A  LYS*     3.0    29.3    +      -       +      +
    214A  ASP      5.3     0.3    -      -       -      +
    215A  GLY*     4.2     7.4    -      -       -      -
    216A  CYS*     3.4    28.4    +      -       -      +
    217A  LEU*     4.4     6.3    -      -       -      +
    267A  LEU*     4.3     6.1    -      -       -      +
    268A  GLY      4.3     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  ILE      3.5     0.6    +      -       -      -
    199A  GLN*     1.3    73.4    -      -       -      +
    201A  LYS*     1.3    62.3    +      -       -      +
    202A  GLY      3.3    10.7    +      -       -      +
    203A  VAL*     3.5    19.5    -      -       +      -
    212A  CYS*     3.4     1.2    -      -       -      -
    215A  GLY*     3.8     0.3    -      -       -      -
    216A  CYS*     3.1    39.5    +      -       -      +
    217A  LEU      4.2     1.3    -      -       -      +
    218A  ALA*     3.7    15.3    -      -       +      -
    265A  PHE*     3.8    26.9    -      -       +      -
    266A  HIS      3.6     9.2    -      -       -      +
    267A  LEU*     3.4    26.5    -      -       +      -
    308A  TRP*     3.3    47.1    -      -       +      -
    310A  LEU*     5.2     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  ILE*     5.3     1.4    -      -       -      +
    199A  GLN*     3.0    40.8    +      -       +      +
    200A  MET*     1.3    71.2    -      -       -      +
    202A  GLY*     1.3    54.5    +      -       -      +
    212A  CYS*     3.3    11.0    -      -       -      +
    213A  GLU*     4.8     1.9    -      -       -      -
    214A  ASP      4.9     0.9    +      -       -      -
    215A  GLY*     3.9    13.0    +      -       -      -
    266A  HIS*     2.8    39.0    +      -       +      +
    267A  LEU      3.7     2.7    -      -       -      -
    268A  GLY*     3.0    36.2    -      -       -      +
    269A  GLY*     3.5     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  MET*     3.3     5.0    -      -       -      +
    201A  LYS*     1.3    80.1    -      -       -      +
    203A  VAL*     1.3    65.0    +      -       -      +
    209A  THR*     4.7     8.1    -      -       -      -
    211A  LEU      4.2     0.7    -      -       -      -
    212A  CYS*     3.3    17.0    -      -       -      -
    264A  SER      4.0     0.2    -      -       -      +
    265A  PHE      3.6     0.2    -      -       -      -
    266A  HIS*     2.7    40.2    +      -       -      +
    271A  GLU*     5.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  MET*     3.5    32.8    -      -       +      -
    202A  GLY*     1.3    77.9    -      -       -      +
    204A  SER*     1.3    64.8    +      -       -      +
    205A  VAL*     5.4     0.7    -      -       +      -
    209A  THR*     3.3    10.1    -      -       -      +
    211A  LEU*     3.1    44.6    +      -       +      +
    212A  CYS*     3.6    13.0    -      -       +      -
    237A  LEU*     5.1     1.3    -      -       +      -
    263A  ILE*     4.4    11.7    -      -       +      -
    264A  SER      3.3    11.4    -      -       -      +
    265A  PHE*     3.9    18.8    -      -       +      -
    308A  TRP*     3.8    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  VAL*     1.3    77.0    -      -       -      +
    205A  VAL*     1.3    64.4    +      -       -      +
    206A  GLY      3.8    14.2    +      -       -      -
    208A  SER      5.0     0.4    -      -       -      -
    209A  THR*     3.8    28.0    -      -       -      +
    210A  LEU      4.8     0.2    -      -       -      +
    262A  ASP      3.8     0.3    -      -       -      +
    263A  ILE*     3.2     7.4    -      -       -      +
    264A  SER*     2.8    60.5    +      -       -      +
    271A  GLU*     3.8     6.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  VAL*     5.4     0.9    -      -       +      -
    204A  SER*     1.3    76.5    -      -       -      +
    206A  GLY*     1.3    61.2    +      -       -      +
    207A  SER      3.9     0.2    +      -       -      -
    208A  SER*     3.5    21.5    +      -       -      -
    210A  LEU*     3.9    18.5    -      -       +      +
    211A  LEU*     4.4    14.1    -      -       +      -
    237A  LEU*     3.9    28.0    -      -       +      -
    240A  ALA*     4.3    15.5    -      -       +      +
    241A  LEU*     3.9    28.9    -      -       +      -
    261A  PRO*     4.1    10.6    -      -       +      +
    262A  ASP      3.6     4.9    -      -       -      +
    263A  ILE*     4.7     7.9    -      -       +      -
----------------------------------------------------------
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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