Contacts of the strand formed by residues 226 - 229 (chain H) in PDB entry 2WWA


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 GLU 226 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203H  ARG*     5.3     3.8    -      -       -      +
    205H  PRO      3.4     5.1    +      -       -      -
    206H  LEU*     3.7    16.6    -      -       +      -
    207H  VAL*     3.0    22.2    +      -       -      +
    224H  GLY      4.8     1.1    -      -       -      +
    225H  VAL*     1.3    84.0    -      -       -      +
    227H  THR*     1.4    67.2    +      -       -      +
    236H  LEU      4.4     4.2    -      -       -      +
    237H  GLN*     3.6    28.2    +      -       -      +
    240H  PRO*     5.0     3.6    -      -       -      +
    246H  ARG*     3.1    33.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 227 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156H  LEU*     5.5     3.1    -      -       +      -
    207H  VAL*     3.4    21.0    -      -       +      +
    208H  VAL*     5.7     0.7    -      -       -      -
    209H  TYR*     6.0     0.9    -      -       +      +
    214H  GLY      3.8     8.5    -      -       -      +
    215H  ILE*     3.6    50.5    -      -       +      +
    219H  LEU*     4.0    25.9    +      -       +      +
    225H  VAL*     5.0     4.9    -      -       -      +
    226H  GLU*     1.4    77.1    +      -       -      +
    228H  ALA*     1.4    65.8    +      -       -      +
    237H  GLN*     3.3    14.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 228 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206H  LEU*     4.1     9.9    -      -       +      -
    207H  VAL      3.1    11.3    +      -       -      +
    208H  VAL*     3.7    10.9    -      -       +      -
    209H  TYR      3.5    17.3    +      -       -      +
    212H  ASP*     4.7     0.3    -      -       -      +
    213H  ASN*     3.4    15.3    +      -       -      +
    214H  GLY      4.9     0.2    -      -       -      +
    215H  ILE*     5.3     1.1    -      -       -      -
    227H  THR*     1.4    78.0    -      -       -      +
    229H  ASN*     1.4    66.3    +      -       -      +
    232H  SER      4.4     1.6    -      -       -      +
    233H  LEU*     4.3     7.2    -      -       +      -
    237H  GLN*     3.5    28.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 229 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208H  VAL*     3.8     4.3    -      -       -      -
    209H  TYR      3.0    17.8    +      -       -      -
    210H  ALA      3.2    15.3    +      -       -      +
    211H  GLU      3.1    17.7    +      -       -      +
    212H  ASP*     3.0    27.5    +      -       -      -
    213H  ASN*     3.6    20.0    -      -       -      +
    228H  ALA*     1.4    73.7    -      -       -      +
    230H  VAL*     1.4    59.9    +      -       -      +
    231H  ALA*     3.3    25.2    +      -       -      +
    232H  SER*     2.9    29.5    +      -       -      +
    233H  LEU*     3.4    16.3    -      -       -      +
    257H  LYS*     4.3     0.7    +      -       -      -
----------------------------------------------------------
 Back to top of page


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