Contacts of the strand formed by residues 232 - 234 (chain A) in PDB entry 1DTQ


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 232 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ILE*     4.0    15.5    -      -       +      +
     96A  HIS*     4.5     9.1    -      -       -      -
     97A  PRO*     3.5    34.7    -      -       +      +
    227A  PHE      3.6     1.0    -      -       -      +
    228A  LEU*     3.6     2.9    -      -       -      +
    229A  TRP*     2.6    78.3    +      +       -      +
    230A  MET*     2.8    22.2    +      -       +      -
    231A  GLY*     1.3    73.4    -      -       -      -
    233A  GLU*     1.3    56.1    +      -       -      +
    234A  LEU*     3.7    12.3    +      -       +      -
    239A  TRP*     3.6    21.3    -      +       +      -
    240A  THR      3.0    18.2    -      -       -      +
    241A  VAL*     4.0     2.2    -      -       +      +
    242A  GLN*     4.4     3.6    -      -       -      -
    266A  TRP*     3.7    23.8    -      +       -      -
    269A  GLN*     3.6    20.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  PRO*     4.4    19.7    -      -       +      +
    227A  PHE      3.9     2.2    -      -       -      -
    228A  LEU*     3.6    29.4    -      -       +      +
    232A  TYR*     1.3    70.1    -      -       -      +
    234A  LEU*     1.3    61.8    +      -       -      +
    235A  HIS*     3.8    24.8    +      -       +      -
    238A  LYS      4.2     0.2    -      -       -      +
    239A  TRP*     3.7     4.3    -      -       -      -
    240A  THR*     2.8    43.4    +      -       +      +
    242A  GLN*     4.2     6.4    -      -       -      +
    243A  PRO*     3.7    20.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  PRO*     3.9    20.0    -      -       +      -
    100A  LEU*     4.6     8.7    -      -       +      -
    225A  PRO*     4.2     0.9    -      -       -      +
    226A  PRO*     3.8     2.8    -      -       -      +
    227A  PHE*     2.8    47.8    +      -       +      +
    229A  TRP*     3.5    37.0    -      -       +      -
    232A  TYR*     4.0     9.0    -      -       +      +
    233A  GLU*     1.3    73.5    -      -       -      +
    235A  HIS*     1.3    60.6    +      -       -      +
    238A  LYS      4.2     0.2    -      -       -      -
    239A  TRP*     3.4    27.6    -      -       +      -
    318A  TYR*     4.0     4.5    -      -       +      +
    999A  FPT      3.0    46.1    +      -       +      +
----------------------------------------------------------
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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