Contacts of the strand formed by residues 263 - 267 (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 ILE 263 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  VAL*     4.4    10.1    -      -       +      -
    204A  SER      3.2    10.3    -      -       -      +
    205A  VAL*     4.7    11.4    -      -       +      -
    237A  LEU*     4.5    13.0    -      -       +      -
    241A  LEU*     4.3    11.4    -      -       +      -
    261A  PRO      4.2     1.1    -      -       -      +
    262A  ASP*     1.3    78.6    -      -       -      +
    264A  SER*     1.3    63.4    +      -       -      +
    265A  PHE*     3.8    28.8    -      -       +      -
    272A  TYR      3.7     1.4    -      -       -      +
    273A  THR*     3.7     0.4    -      -       -      -
    274A  LEU*     2.9    38.0    +      -       +      +
    279A  TYR*     3.5    34.8    -      -       +      +
    295A  ILE*     3.5    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  GLY      4.0     0.2    -      -       -      +
    203A  VAL*     3.3     8.7    -      -       -      +
    204A  SER*     2.8    43.7    +      -       -      -
    206A  GLY      5.7     0.5    +      -       -      -
    262A  ASP*     4.2     2.5    -      -       -      +
    263A  ILE*     1.3    76.1    +      -       -      +
    265A  PHE*     1.3    63.5    +      -       -      +
    271A  GLU*     3.1    26.1    -      -       -      +
    272A  TYR      3.4     7.0    -      -       -      -
    273A  THR*     3.2    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  MET*     3.8    26.7    -      -       -      -
    202A  GLY      3.7     3.4    -      -       -      -
    203A  VAL*     3.9    20.4    -      -       +      -
    227A  ILE*     3.7    46.4    -      -       +      -
    263A  ILE*     3.8    25.1    -      -       +      -
    264A  SER*     1.3    74.7    -      -       -      +
    266A  HIS*     1.3    60.2    +      -       -      +
    267A  LEU*     3.3    12.4    +      -       +      -
    270A  LYS      3.7     0.2    -      -       -      +
    271A  GLU*     4.4     1.6    -      -       -      -
    272A  TYR*     3.0    37.0    +      -       -      +
    274A  LEU*     4.1    12.6    -      -       +      -
    295A  ILE*     5.3     4.7    -      -       +      -
    308A  TRP*     4.1    13.9    -      +       -      -
    310A  LEU*     4.2     6.5    -      -       +      -
    314A  PHE*     3.7    25.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with HIS 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  MET*     3.5     6.3    -      -       -      +
    201A  LYS*     2.8    53.0    +      -       +      +
    202A  GLY*     2.7    28.9    +      -       -      +
    264A  SER      4.1     0.6    -      -       -      -
    265A  PHE*     1.3    70.0    -      -       -      +
    267A  LEU*     1.3    60.7    +      -       -      +
    269A  GLY*     3.4    33.0    +      -       -      -
    270A  LYS      3.9     6.3    +      -       -      -
    271A  GLU*     2.8    26.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  ILE*     3.3    15.7    -      -       +      +
    198A  ILE*     4.0    15.3    -      -       +      -
    199A  GLN      4.6     0.2    -      -       -      -
    200A  MET*     3.4    46.4    -      -       +      -
    201A  LYS*     4.0     1.3    -      -       -      +
    218A  ALA*     4.2     4.0    -      -       +      -
    265A  PHE*     3.3    12.3    +      -       +      +
    266A  HIS*     1.3    72.8    +      -       -      +
    268A  GLY*     1.3    55.3    +      -       -      +
    269A  GLY      2.7    17.4    +      -       -      -
    270A  LYS*     3.3    16.9    +      -       -      +
    272A  TYR*     3.8    13.5    +      -       +      -
    310A  LEU*     3.8    18.8    -      -       +      -
    314A  PHE*     4.1    11.4    -      -       +      -
    331A  PHE*     3.5    31.9    -      -       +      -
----------------------------------------------------------
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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