Contacts of the strand formed by residues 200 - 204 (chain A) in PDB entry 2OR4


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 200 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  PRO*     3.8    16.4    -      -       +      +
    171A  GLU      4.1     0.9    -      -       -      -
    172A  GLY*     3.7    16.4    -      -       -      +
    173A  ASP      2.9    12.0    +      -       -      +
    174A  LEU*     3.2    24.8    -      -       +      +
    175A  VAL      2.9    23.6    +      -       -      -
    198A  GLY      4.2     0.2    +      -       -      -
    199A  LYS*     1.3    72.0    -      -       -      +
    201A  VAL*     1.3    67.0    +      -       -      +
    223A  LYS*     4.2    15.0    -      -       +      -
    224A  GLY*     3.7    16.2    -      -       -      +
    226A  ILE*     3.8    21.5    -      -       +      -
    342A  VAL*     3.4    31.6    -      -       +      +
    344A  MET*     4.2    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  VAL*     3.2    10.3    -      -       +      +
    177A  VAL*     4.2    24.5    -      -       +      -
    180A  ALA*     6.2     0.2    -      -       +      -
    185A  PHE*     4.9     1.8    -      -       +      -
    196A  CYS*     4.3    20.4    -      -       +      -
    199A  LYS*     4.4     2.5    -      -       +      +
    200A  ILE*     1.3    80.1    -      -       -      +
    202A  ILE*     1.3    59.2    +      -       -      +
    203A  ALA*     5.7     0.2    -      -       +      -
    217A  ALA*     3.6    27.8    -      -       +      -
    222A  ALA*     3.4    21.5    -      -       +      -
    224A  GLY      3.0    15.0    +      -       -      +
    225A  VAL*     3.4    12.6    -      -       +      -
    226A  ILE      2.9    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  LEU*     3.4    30.3    -      -       +      -
    175A  VAL      2.8    14.3    +      -       -      +
    176A  TYR*     3.4    19.7    -      -       +      -
    177A  VAL*     3.0    25.1    +      -       -      +
    201A  VAL*     1.3    73.9    -      -       -      +
    203A  ALA*     1.3    63.2    +      -       -      +
    226A  ILE*     3.3    28.3    -      -       +      +
    228A  TYR*     3.8    23.1    -      -       +      -
    297A  ILE*     4.7     3.6    -      -       +      -
    302A  ALA*     4.9     1.1    -      -       +      +
    305A  LEU*     4.2    24.7    -      -       +      -
    306A  LEU*     3.9    24.5    -      -       +      -
    309A  MET*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  TYR*     4.9     0.7    -      -       -      -
    177A  VAL*     3.5    18.8    -      -       +      -
    178A  ASN      3.2     9.9    -      -       -      +
    179A  TYR      4.5     0.2    -      -       -      -
    180A  ALA*     3.6    17.7    -      -       +      -
    202A  ILE*     1.3    75.8    -      -       -      +
    204A  ARG*     1.3    63.0    +      -       -      +
    213A  LYS*     4.9     0.4    -      -       +      -
    225A  VAL*     5.0     5.8    -      -       +      -
    226A  ILE      3.0     5.8    +      -       -      +
    227A  LEU*     3.4    21.2    -      -       +      +
    228A  TYR*     3.1    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  TYR*     3.4    14.3    +      -       +      +
    178A  ASN*     2.9    48.1    +      -       -      +
    179A  TYR*     3.1    33.2    +      -       +      +
    203A  ALA*     1.3    74.3    -      -       -      +
    205A  TYR*     1.3    56.3    +      -       -      +
    213A  LYS*     2.8    29.4    +      -       -      +
    228A  TYR*     3.3    28.3    -      -       +      +
    230A  ASP*     4.0    12.1    -      -       +      +
    232A  ALA*     3.8    19.0    -      -       -      +
    233A  ASP*     3.0    24.7    +      -       -      -
    318A  SER      3.1    19.6    +      -       -      -
    319A  TRP      3.9     9.5    -      -       -      -
    320A  ARG      4.0     5.7    +      -       -      -
    321A  GLY*     3.8    10.5    -      -       -      -
----------------------------------------------------------
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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