Contacts of the strand formed by residues 414 - 421 (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 ARG 414 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364A  GLY*     3.5     4.3    -      -       -      -
    367A  GLU*     3.2    35.4    +      -       +      +
    370A  ARG*     3.5    29.8    -      -       +      +
    372A  VAL*     4.5     2.7    -      -       +      -
    412A  PRO*     3.2    26.0    -      -       -      +
    413A  ARG*     1.3    79.5    -      -       -      +
    415A  THR*     1.3    67.2    +      -       -      +
    416A  ILE      3.6     0.2    +      -       -      -
    447A  VAL*     4.1     8.9    -      -       -      +
    586A  GLU      4.6     0.2    +      -       -      -
    587A  LEU      3.0    26.8    +      -       -      -
    588A  ALA*     2.8    26.7    +      -       -      +
    590A  SER*     2.8    30.7    +      -       -      +
    591A  ILE      3.1    17.6    +      -       -      -
    593A  LEU*     3.5    26.6    -      -       -      +
    665A  ASN*     3.4    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361A  THR*     4.1    11.0    -      -       +      -
    362A  LEU      3.4    11.9    -      -       -      +
    363A  ARG*     3.6     3.8    -      -       -      +
    364A  GLY*     3.0    17.6    +      -       -      +
    367A  GLU      3.7     1.2    +      -       -      -
    368A  PRO*     2.8    28.9    +      -       -      +
    370A  ARG      2.9    11.7    +      -       -      +
    371A  TYR*     3.5    20.0    -      -       +      -
    372A  VAL*     2.9    28.1    +      -       -      +
    414A  ARG*     1.3    72.9    -      -       -      +
    416A  ILE*     1.3    63.1    +      -       -      +
    417A  LEU*     3.8    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  GLY      3.9     0.5    -      -       -      +
    361A  THR*     3.6     2.3    -      -       -      -
    362A  LEU*     2.9    39.6    +      -       +      +
    372A  VAL*     3.2    10.8    -      -       +      +
    374A  LEU      5.1     1.3    -      -       -      +
    402A  PHE*     3.8    39.0    -      -       +      -
    412A  PRO*     4.0    15.3    -      -       +      -
    414A  ARG      4.2     2.9    -      -       -      +
    415A  THR*     1.3    73.9    -      -       -      +
    417A  LEU*     1.3    68.8    +      -       -      +
    418A  PHE*     3.4    33.3    -      -       +      -
    584A  VAL*     3.9    14.1    -      -       +      -
    588A  ALA*     3.5    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359A  ILE*     5.2     9.0    -      -       +      -
    360A  GLY      3.3     4.0    -      -       -      +
    361A  THR*     3.5    26.7    -      -       +      +
    371A  TYR*     4.0    37.5    -      -       +      -
    372A  VAL      2.9     6.7    +      -       -      +
    373A  ILE*     3.3    20.6    -      -       +      +
    374A  LEU      2.8    31.2    +      -       -      +
    415A  THR*     3.8    20.0    -      -       +      -
    416A  ILE*     1.3    81.3    -      -       -      +
    418A  PHE*     1.3    58.5    +      -       -      +
    434A  TRP*     4.2    27.4    -      -       +      -
    442A  LEU*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  TRP*     3.5    23.1    -      -       +      -
    105A  LEU*     3.7    37.0    -      -       +      -
    359A  ILE*     3.5     5.5    -      -       -      +
    360A  GLY      2.9    35.7    +      -       -      +
    362A  LEU*     4.2     8.1    -      -       +      -
    374A  LEU*     3.3    32.8    -      -       +      +
    395A  VAL*     4.8     2.0    -      -       +      -
    398A  ILE*     4.2     1.1    -      -       +      -
    399A  VAL*     3.5    24.9    -      -       +      -
    402A  PHE*     3.7    34.5    -      +       +      -
    416A  ILE*     3.4    32.8    -      -       +      -
    417A  LEU*     1.3    75.1    -      -       -      +
    419A  ALA*     1.3    62.6    +      -       -      +
    584A  VAL*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  TRP*     3.9     6.5    -      -       -      -
    358A  VAL      3.3     3.6    -      -       -      -
    359A  ILE*     3.9     8.3    -      -       +      -
    373A  ILE*     5.0     4.5    -      -       +      -
    374A  LEU      3.0     8.3    +      -       -      +
    375A  GLY*     3.4     5.1    -      -       -      -
    376A  GLY      3.1    24.1    +      -       -      +
    395A  VAL*     4.9     5.4    -      -       -      +
    418A  PHE*     1.3    76.7    -      -       -      +
    420A  SER*     1.3    59.5    +      -       -      +
    421A  TRP*     3.5    47.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 420 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ILE*     4.4     8.0    -      -       -      +
    100A  TRP*     3.8    12.3    -      -       -      -
    357A  ASN*     3.3     3.0    -      -       -      -
    358A  VAL*     3.0    48.4    +      -       -      -
    376A  GLY      3.4     5.6    -      -       -      -
    377A  HIS      5.0     0.4    -      -       -      -
    378A  ARG*     3.1    43.1    +      -       -      +
    392A  ALA*     6.0     1.2    -      -       -      +
    419A  ALA*     1.3    70.6    -      -       -      +
    421A  TRP*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  ASN*     3.5    24.9    -      -       +      +
    359A  ILE*     3.7    20.0    -      -       +      -
    373A  ILE*     4.8     2.9    -      -       +      -
    375A  GLY*     3.8     0.2    -      -       -      -
    376A  GLY      2.9    31.5    +      -       -      +
    377A  HIS*     3.2     5.7    -      -       +      +
    378A  ARG*     2.8    34.1    +      -       -      +
    419A  ALA*     3.5    22.4    -      -       +      -
    420A  SER*     1.3    74.9    -      -       -      +
    422A  ASP*     1.3    65.5    +      -       -      +
    424A  GLU*     5.4     0.2    -      -       +      -
    431A  SER*     3.7    19.7    -      -       -      +
    434A  TRP*     3.4    44.6    -      +       +      -
    449A  TYR*     2.9    27.5    +      +       -      -
    520A  ASP*     3.2    34.9    -      -       +      +
    524A  PHE*     3.6    22.4    -      +       -      -
----------------------------------------------------------
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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