Contacts of the strand formed by residues 231 - 236 (chain A) in PDB entry 3OEH


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 SER 231 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     4.7     0.2    -      -       -      -
    107A  GLY*     2.8    33.4    +      -       -      -
    108A  ARG      3.9     0.9    +      -       -      +
    185A  ILE*     3.9    10.8    -      -       -      +
    203A  CYS*     3.0    21.6    -      -       -      +
    205A  TYR*     6.1     1.1    -      -       -      -
    222A  LEU*     4.6     7.6    -      -       -      +
    227A  ALA      2.8    23.8    +      -       -      -
    228A  MET*     2.7    27.7    +      -       -      +
    229A  LYS      3.6     0.6    +      -       -      -
    230A  TYR*     1.3    75.7    -      -       -      +
    232A  ILE*     1.3    65.1    +      -       -      +
    233A  ILE*     5.4     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  LEU*     3.4    35.4    -      -       +      +
    106A  LEU*     4.1    10.5    -      -       +      -
    108A  ARG      3.7     9.2    -      -       -      +
    110A  VAL*     4.6     7.2    -      -       +      -
    203A  CYS      2.6    12.1    +      -       -      +
    204A  VAL*     3.4    13.9    -      -       +      +
    205A  TYR*     2.8    27.7    +      -       -      +
    231A  SER*     1.3    77.1    -      -       -      +
    233A  ILE*     1.3    72.2    +      -       -      +
    234A  VAL*     4.0    11.8    +      -       +      -
    255A  ILE*     3.5    34.1    -      -       +      -
    259A  PHE*     3.8    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  ARG      3.1     6.5    +      -       -      -
    109A  VAL*     3.3    27.7    -      -       +      -
    110A  VAL*     2.9    30.7    +      -       -      +
    205A  TYR*     3.4    39.7    -      -       +      +
    207A  ALA*     4.8     0.4    -      -       +      -
    215A  VAL*     3.9    22.0    -      -       +      -
    218A  LEU*     4.5     4.5    -      -       +      -
    219A  VAL*     3.8    21.1    -      -       +      -
    222A  LEU*     4.1    21.5    -      -       +      -
    228A  MET*     4.3    10.5    -      -       -      -
    231A  SER*     5.4     2.2    -      -       -      -
    232A  ILE*     1.3    74.4    -      -       -      +
    234A  VAL*     1.3    63.9    +      -       -      +
    235A  ALA*     4.2     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  VAL*     3.6    19.5    -      -       +      -
    111A  ASP      4.2     9.9    -      -       -      +
    112A  ALA*     4.2     2.5    -      -       -      -
    204A  VAL*     4.6     2.5    -      -       +      -
    205A  TYR      3.0     9.0    +      -       -      +
    206A  VAL*     3.4     4.3    -      -       +      +
    207A  ALA      2.7    32.9    +      -       -      +
    232A  ILE*     4.0     7.7    +      -       +      -
    233A  ILE*     1.3    71.1    -      -       -      +
    235A  ALA*     1.3    53.9    +      -       -      +
    248A  ALA*     4.0    23.8    -      -       +      +
    251A  THR*     3.9    21.8    -      -       +      -
    252A  ALA*     3.5    26.0    -      -       +      -
    255A  ILE*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  VAL*     4.6     0.4    -      -       +      -
    110A  VAL      3.0    14.8    +      -       -      +
    111A  ASP*     4.0    16.1    -      -       -      +
    112A  ALA      4.9     0.9    -      -       -      -
    117A  ILE*     4.5    17.5    -      -       +      +
    207A  ALA*     3.4    10.8    -      -       +      -
    215A  VAL*     4.0    26.7    -      -       +      -
    233A  ILE*     3.9     5.6    -      -       +      -
    234A  VAL*     1.3    73.9    -      -       -      +
    236A  ALA*     1.3    60.8    +      -       -      +
    237A  THR*     3.8    11.8    +      -       +      +
    240A  GLU*     3.3    11.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ALA*     4.2     7.6    -      -       +      +
    207A  ALA      2.8    11.4    +      -       -      +
    208A  VAL*     3.3     1.8    -      -       -      -
    209A  GLY      2.9    22.3    +      -       -      -
    234A  VAL      4.1     1.0    +      -       -      -
    235A  ALA*     1.3    69.9    -      -       -      +
    237A  THR*     1.3    62.6    +      -       -      +
    240A  GLU*     3.3     7.4    -      -       -      +
    244A  LEU*     3.4    37.2    -      -       +      +
    245A  GLN*     3.7    10.0    -      -       +      +
    248A  ALA*     3.6    16.9    -      -       +      +
----------------------------------------------------------
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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