Contacts of the helix formed by residues 229 - 236 (chain J) in PDB entry 6O81


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 ILE 229 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128J  LEU*     5.2     5.2    -      -       -      -
    130J  MET*     5.3     8.3    -      -       +      -
    167J  LEU*     5.8     0.3    -      -       -      +
    170J  MET*     3.7    33.2    -      -       +      +
    224J  ILE      3.9     3.0    +      -       -      -
    225J  ARG*     3.5    21.5    -      -       -      +
    226J  SER      5.1     0.2    -      -       -      -
    227J  GLU      3.2     0.4    -      -       -      -
    228J  LEU*     1.3    79.2    -      -       -      +
    230J  PRO*     1.3    59.7    -      -       +      +
    232J  LEU*     4.2     0.5    -      -       -      +
    233J  VAL*     2.9    32.4    +      -       -      +
    263J  ILE*     5.0     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 230 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170J  MET*     5.4     9.4    -      -       +      +
    226J  SER*     3.5    20.8    -      -       -      +
    227J  GLU      3.5     2.2    -      -       -      -
    229J  ILE*     1.3    76.9    -      -       +      +
    231J  TYR*     1.3    61.9    +      -       -      +
    233J  VAL*     3.3     5.5    +      -       +      +
    234J  ARG*     2.9    29.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 231 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214J  PHE*     3.6    41.9    -      +       -      -
    227J  GLU*     3.0    18.5    +      -       +      +
    228J  LEU*     5.3     0.7    -      -       -      -
    230J  PRO*     1.3    75.8    -      -       -      +
    232J  LEU*     1.3    60.3    +      -       -      +
    234J  ARG*     3.4     7.0    +      -       +      +
    235J  LYS*     2.9    39.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 232 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127J  SER*     5.8     1.8    -      -       -      +
    128J  LEU*     5.0     6.7    -      -       +      -
    211J  ILE*     5.7    10.8    -      -       +      -
    228J  LEU*     3.3    23.0    +      -       -      +
    229J  ILE      3.6     1.0    +      -       -      +
    230J  PRO      3.3     0.2    -      -       -      -
    231J  TYR*     1.3    77.9    -      -       -      +
    233J  VAL*     1.3    59.8    +      -       -      +
    235J  LYS*     4.3     5.4    -      -       -      +
    236J  GLN*     2.9    24.6    +      -       -      +
    261J  LEU*     3.7    13.3    -      -       +      +
    263J  ILE*     3.4    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 233 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167J  LEU*     4.6    15.5    -      -       +      -
    168J  LEU      4.6    15.4    -      -       -      +
    169J  PHE*     5.3     1.1    -      -       +      -
    170J  MET*     4.7    13.9    -      -       +      +
    229J  ILE      2.9    20.7    +      -       -      +
    230J  PRO*     3.8     6.3    -      -       +      +
    231J  TYR      3.3     0.4    -      -       -      -
    232J  LEU*     1.3    76.1    -      -       -      +
    234J  ARG*     1.3    60.5    +      -       -      +
    236J  GLN*     3.8    10.8    +      -       -      +
    237J  PHE*     4.0     7.4    +      -       -      +
    263J  ILE*     3.7    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 234 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183J  LYS*     5.5     8.3    -      -       -      +
    230J  PRO      2.9    17.0    +      -       -      +
    231J  TYR*     3.7     8.3    -      -       +      +
    233J  VAL*     1.3    78.8    -      -       -      +
    235J  LYS*     1.3    61.9    +      -       -      +
    237J  PHE*     3.3    22.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 235 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231J  TYR*     2.9    30.2    +      -       +      +
    232J  LEU*     3.3     7.4    +      -       -      +
    234J  ARG*     1.3    73.4    -      -       -      +
    236J  GLN*     1.3    61.7    -      -       -      +
    237J  PHE      3.2     2.4    +      -       -      -
    238J  SER*     4.1    12.1    +      -       -      -
    260J  SER*     5.4     2.8    -      -       -      -
    261J  LEU*     4.6    17.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 236 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166J  ARG*     4.8    14.5    +      -       -      +
    167J  LEU      6.1     0.4    -      -       -      +
    232J  LEU      2.9    17.4    +      -       -      +
    233J  VAL*     4.0     7.4    -      -       -      +
    234J  ARG      3.3     0.4    -      -       -      -
    235J  LYS*     1.3    76.9    -      -       -      +
    237J  PHE*     1.3    57.7    +      -       -      +
    238J  SER*     3.1     7.8    +      -       -      -
    260J  SER*     4.8     8.4    -      -       -      -
    261J  LEU*     3.9    28.3    -      -       +      +
    263J  ILE*     4.3     9.6    -      -       +      +
----------------------------------------------------------
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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