Contacts of the strand formed by residues 327 - 331 (chain B) in PDB entry 1RHR


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 327 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  THR*     3.6    25.8    -      -       -      -
    263A  ASN*     5.6     0.7    -      -       -      -
    265A  PHE*     3.3    23.6    -      -       +      -
    266A  ARG*     3.5    20.6    -      -       +      -
    267A  GLY      4.4     0.9    -      -       -      -
    278A  LYS*     3.7    27.4    -      -       +      -
    280A  PHE*     4.4    10.8    -      +       -      -
    323B  VAL      3.6    17.9    -      -       -      -
    324B  GLU*     3.7    24.5    -      -       -      +
    325B  ALA      2.9    23.2    +      -       -      -
    326B  ASP*     1.3    77.9    -      -       -      +
    328B  LEU*     1.3    58.0    +      -       -      +
    329B  TYR*     3.4    36.2    -      +       +      +
    392B  SER*     4.0     0.3    -      -       -      -
    393B  MET*     3.0    33.7    +      -       +      +
    394B  LEU      3.8     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278A  LYS      3.0    10.5    +      -       -      +
    279A  LEU*     4.4    12.8    -      -       +      -
    280A  PHE*     2.7    30.0    +      -       -      +
    326B  ASP      3.7     0.4    +      -       -      -
    327B  PHE*     1.3    74.6    -      -       -      +
    329B  TYR*     1.3    67.6    +      -       -      +
    330B  ALA*     5.0     2.0    -      -       +      +
    366B  PHE*     3.1    41.1    -      -       +      -
    367B  MET*     4.0    10.8    -      -       +      -
    370B  LEU*     4.4     4.9    -      -       +      -
    389B  ILE*     4.5     6.7    -      -       +      -
    390B  VAL      2.9    28.5    -      -       -      +
    392B  SER*     3.8    15.9    -      -       -      +
    394B  LEU*     3.7    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258A  LEU*     5.3     4.0    -      -       +      -
    262A  THR*     4.1    26.0    +      -       +      -
    280A  PHE*     3.3    17.9    -      +       +      +
    282A  ILE*     4.7     6.1    -      -       +      -
    324B  GLU*     5.5     2.4    +      -       -      -
    327B  PHE*     3.4    47.8    -      +       +      +
    328B  LEU*     1.3    81.8    -      -       -      +
    330B  ALA*     1.3    59.7    +      -       -      +
    331B  TYR*     3.3    38.5    +      +       +      -
    388B  CYS      3.6     2.4    -      -       -      +
    389B  ILE*     3.9     0.3    -      -       -      -
    390B  VAL*     3.0    46.1    +      -       +      +
    393B  MET*     4.2    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  PHE      2.9    12.3    +      -       -      +
    281A  ILE*     3.9    12.9    -      -       +      -
    282A  ILE*     3.3    22.3    +      -       -      +
    328B  LEU*     4.1     3.9    +      -       +      -
    329B  TYR*     1.3    71.4    -      -       -      +
    331B  TYR*     1.3    64.4    +      -       -      +
    349B  PHE*     3.7    20.6    -      -       +      -
    353B  LEU*     5.8     0.2    -      -       +      -
    366B  PHE*     6.3     0.9    -      -       +      -
    370B  LEU*     4.4    27.6    -      -       +      -
    388B  CYS      3.6     6.1    -      -       -      +
    389B  ILE*     4.8     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  GLU*     5.4     1.8    -      -       -      -
    241A  GLY*     6.0     3.1    -      -       -      -
    258A  LEU*     3.8    24.5    -      -       +      +
    282A  ILE*     3.8    25.8    -      -       +      -
    286A  ARG*     3.3    55.9    -      -       +      +
    329B  TYR*     3.3    49.0    -      +       +      -
    330B  ALA*     1.3    74.2    -      -       -      +
    332B  SER*     1.3    58.6    +      -       -      +
    333B  THR      3.1     8.2    +      -       -      +
    349B  PHE*     3.8     4.1    -      -       -      -
    387B  PRO*     3.7     5.7    -      -       -      +
    388B  CYS      2.9    36.4    +      -       -      +
    390B  VAL*     4.2    14.6    -      -       +      -
----------------------------------------------------------
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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