Contacts of the strand formed by residues 224 - 228 (chain A) in PDB entry 2WHR


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 224 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  MET      5.2     0.4    +      -       -      -
    196A  SER*     3.0    28.3    +      -       -      +
    197A  VAL      3.4     2.4    +      -       -      -
    198A  THR*     3.3    17.1    +      -       -      +
    199A  LEU      2.9    24.3    +      -       -      -
    222A  PHE*     3.8     8.3    -      -       -      -
    223A  HIS*     1.3    95.3    +      -       -      +
    225A  ALA*     1.3    63.0    +      -       -      +
    324A  LEU*     4.6     1.6    -      -       -      -
    325A  GLN*     3.2    44.0    +      -       +      +
    483A  PHE*     3.2    13.9    +      -       +      -
    484A  ALA      2.8    29.8    +      -       -      -
    485A  ARG      4.0     9.0    +      -       -      -
    486A  THR      4.9     1.6    -      -       -      -
    487A  GLY*     3.2    23.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  LEU*     3.4     4.7    -      -       +      -
    209A  VAL*     3.6    22.9    -      -       +      -
    213A  ILE*     3.7    25.4    -      -       +      -
    222A  PHE*     4.5     6.7    -      -       +      -
    224A  ARG*     1.3    78.2    -      -       -      +
    226A  VAL*     1.3    64.1    +      -       -      +
    227A  LEU*     4.0     3.4    -      -       +      -
    324A  LEU*     5.0     1.1    -      -       +      -
    325A  GLN      3.2     9.1    +      -       -      +
    326A  VAL*     3.2     8.7    -      -       +      +
    327A  LEU      2.9    23.2    +      -       -      -
    483A  PHE*     3.6     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  LEU*     5.9     1.1    -      -       +      -
    198A  THR*     4.3     5.6    -      -       +      -
    199A  LEU      2.8    11.3    +      -       -      +
    200A  PHE*     3.5    20.0    -      -       +      -
    201A  GLY      3.4    20.8    +      -       -      -
    209A  VAL*     4.0     4.3    -      -       -      +
    225A  ALA*     1.3    76.3    -      -       -      +
    227A  LEU*     1.3    69.6    +      -       -      +
    228A  GLN*     3.8    17.5    -      -       +      +
    327A  LEU*     3.2    26.9    -      -       +      +
    428A  TYR*     5.4     0.9    -      -       +      -
    480A  TRP*     3.7    29.2    -      -       +      +
    483A  PHE*     3.6    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  ALA*     3.3    28.7    -      -       +      +
    209A  VAL*     3.6    16.4    -      -       +      -
    210A  GLY*     3.7    17.9    -      -       -      -
    213A  ILE*     4.3     7.0    -      -       +      -
    225A  ALA*     4.0     6.5    -      -       +      -
    226A  VAL*     1.3    77.9    -      -       -      +
    228A  GLN*     1.3    61.7    +      -       -      +
    229A  SER      3.7     1.4    +      -       -      -
    230A  GLY      3.7    17.5    -      -       -      +
    231A  THR*     5.6     0.2    -      -       +      -
    232A  PRO*     4.2     3.4    -      -       +      -
    326A  VAL*     3.9    24.0    -      -       +      -
    327A  LEU      2.8     9.5    +      -       -      -
    328A  VAL*     3.4    12.7    -      -       +      +
    329A  GLY      3.3    22.2    +      -       -      +
    411A  VAL*     5.5     1.7    -      -       +      +
    414A  LEU*     3.8    24.0    -      -       +      -
    418A  LEU*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  TRP*     3.9     7.5    -      -       -      -
    200A  PHE*     3.6    16.6    -      -       -      -
    201A  GLY      3.0    17.4    +      -       -      +
    202A  GLU*     3.1    11.0    -      -       +      +
    203A  SER      2.9    20.1    +      -       -      -
    206A  ALA*     3.5     1.1    -      -       -      +
    226A  VAL*     3.8    13.3    -      -       +      +
    227A  LEU*     1.3    71.0    -      -       -      +
    229A  SER*     1.3    70.9    +      -       -      +
    230A  GLY      3.3     1.3    +      -       -      -
    428A  TYR*     3.4    15.5    -      -       -      +
    450A  GLU*     3.0    37.3    +      -       -      +
    451A  ILE*     4.4     5.5    -      -       -      +
    454A  ILE*     4.2     9.8    -      -       -      +
    480A  TRP*     3.0    30.4    +      -       +      -
----------------------------------------------------------
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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