Contacts of the strand formed by residues 237 - 241 (chain A) in PDB entry 2WJP


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 TYR 237 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  VAL*     3.6    25.4    -      -       +      -
    229A  SER      2.9    16.2    +      -       -      +
    230A  PHE*     3.1    13.8    -      -       +      +
    231A  GLY      2.9    24.8    +      -       -      -
    235A  GLY      3.9     1.7    -      -       -      -
    236A  ASP*     1.3    81.7    -      -       +      +
    238A  HIS*     1.3    62.5    +      -       -      +
    249A  ARG      3.5     4.7    -      -       -      -
    250A  VAL*     3.7    36.6    -      -       +      +
    251A  LYS*     5.7     2.7    -      -       -      -
    273A  LEU*     3.7    27.1    -      -       +      +
    276A  LEU*     4.0    10.3    -      -       +      -
    277A  ALA*     3.6    26.2    +      -       +      -
    280A  ASP*     2.5    39.5    +      -       -      +
    286A  ARG*     4.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  GLY      3.2    14.4    -      -       -      +
    232A  VAL      3.7     5.2    -      -       -      +
    233A  ASN      4.8     5.8    -      -       -      -
    234A  MET*     3.6    18.6    -      -       -      +
    235A  GLY      2.9    20.9    +      -       -      -
    236A  ASP      3.9     1.0    +      -       -      -
    237A  TYR*     1.3    75.0    -      -       -      +
    239A  LEU*     1.3    72.9    +      -       -      +
    248A  LEU      3.7     0.2    -      -       -      -
    249A  ARG*     2.8    72.7    +      -       +      +
    251A  LYS*     4.3     6.3    -      -       -      -
    252A  GLY      3.8    22.4    -      -       -      -
    273A  LEU*     3.6    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  GLY      4.2     2.0    -      -       -      +
    232A  VAL*     3.1    29.8    +      -       +      +
    233A  ASN*     4.8     4.0    -      -       -      +
    238A  HIS*     1.3    87.7    -      -       -      +
    240A  ASN*     1.3    61.2    +      -       -      +
    241A  HIS*     4.2    13.7    +      -       +      +
    246A  THR*     4.2    17.3    -      -       +      -
    247A  TRP      3.3     5.4    -      -       -      +
    248A  LEU*     3.6    31.4    -      -       +      -
    266A  GLN*     4.2    22.7    -      -       +      +
    269A  TYR*     3.9    24.5    -      -       +      -
    270A  THR*     4.3     9.0    -      -       +      -
    273A  LEU*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  LEU*     1.3    72.9    -      -       -      +
    241A  HIS*     1.3    66.5    +      -       -      +
    242A  GLN*     3.0    28.7    +      -       -      +
    245A  GLU      3.9     0.2    -      -       -      +
    246A  THR*     3.5     1.9    -      -       -      -
    247A  TRP*     2.9    36.4    +      -       +      +
    249A  ARG*     3.4    45.7    +      -       +      +
    254A  LYS*     3.2    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  VAL*     4.6    10.1    -      -       +      -
    233A  ASN*     4.7     8.8    +      -       -      -
    239A  LEU*     4.5    19.3    +      -       +      +
    240A  ASN*     1.3    79.2    +      -       -      +
    242A  GLN*     1.3    69.0    +      -       -      +
    243A  GLN      4.0     2.5    -      -       -      +
    244A  GLY      6.2     0.9    -      -       -      +
    245A  GLU      3.3     5.6    -      -       -      +
    246A  THR*     3.1    33.0    +      -       +      +
    266A  GLN*     4.5    17.9    +      -       -      +
    269A  TYR*     6.3     0.2    -      -       -      -
----------------------------------------------------------
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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