Contacts of the helix formed by residues 861 - 888 (chain A) in PDB entry 3KSS


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 GLN 861 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677A  ILE*     4.3     6.4    -      -       -      +
    678A  LYS*     2.7    35.0    +      -       -      +
    679A  SER      3.9     1.7    +      -       -      +
    680A  PRO*     2.8    37.9    +      -       +      +
    829A  ARG*     4.7    12.1    +      -       -      +
    860A  GLY*     1.3    71.4    -      -       -      -
    862A  PHE*     1.3    57.0    +      -       -      +
    864A  LEU*     3.8     5.8    +      -       -      +
    865A  LEU*     3.2    25.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 862 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    680A  PRO      3.8     4.1    +      -       -      +
    681A  ILE*     3.6    35.2    -      -       +      -
    833A  MET*     5.1    12.8    -      -       +      +
    834A  VAL*     5.0    18.2    -      -       +      -
    837A  VAL*     3.4    41.7    -      -       +      -
    858A  PHE*     4.7    20.0    -      -       +      -
    859A  SER*     4.3    11.7    -      -       -      -
    860A  GLY*     2.9     2.8    +      -       -      -
    861A  GLN*     1.3    78.7    -      -       -      +
    863A  GLU*     1.3    82.3    +      -       +      +
    865A  LEU*     2.8    12.1    +      -       +      -
    866A  GLU*     2.5    49.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 863 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    858A  PHE      4.5     5.6    -      -       -      +
    859A  SER*     4.4    17.5    -      -       -      -
    860A  GLY      3.4    14.1    +      -       -      +
    862A  PHE*     1.3    97.4    -      -       +      +
    864A  LEU*     1.3    59.2    +      -       +      +
    866A  GLU*     4.0     6.1    -      -       -      +
    867A  ARG*     3.0    41.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 864 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467A  LEU*     6.2     0.2    -      -       +      -
    468A  GLU*     2.8    45.5    -      -       +      +
    469A  GLY*     3.7    16.2    -      -       -      -
    470A  GLN      5.0     0.7    -      -       -      +
    860A  GLY      4.5     1.5    +      -       -      +
    861A  GLN      3.8     6.3    +      -       -      +
    862A  PHE      3.2     0.2    -      -       -      -
    863A  GLU*     1.3    77.6    -      -       +      +
    865A  LEU*     1.3    61.2    +      -       -      +
    867A  ARG*     3.2    35.5    -      -       +      +
    868A  ALA*     2.9    26.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 865 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467A  LEU*     5.5     7.0    -      -       +      -
    471A  GLU*     6.0     1.6    -      -       -      +
    832A  ASP*     4.2    26.9    -      -       -      +
    834A  VAL*     5.3     6.5    -      -       +      -
    861A  GLN*     3.2    21.9    +      -       +      +
    862A  PHE*     2.8    13.5    +      -       +      +
    864A  LEU*     1.3    73.8    -      -       -      +
    866A  GLU*     1.3    61.0    +      -       +      +
    868A  ALA*     2.9    13.3    +      -       +      +
    869A  ASN*     2.7    43.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 866 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834A  VAL*     4.7    23.4    -      -       +      +
    862A  PHE*     2.5    38.4    +      -       +      +
    863A  GLU*     4.0     4.7    -      -       -      +
    865A  LEU*     1.3    79.1    -      -       +      +
    867A  ARG*     1.3    55.2    +      -       +      +
    869A  ASN*     3.4     7.2    +      -       -      +
    870A  HIS*     2.8    38.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 867 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468A  GLU*     4.5    15.4    +      -       -      -
    863A  GLU*     3.0    37.7    +      -       +      +
    864A  LEU*     3.2    37.2    -      -       +      +
    865A  LEU      3.2     0.4    -      -       -      -
    866A  GLU*     1.3    80.7    -      -       +      +
    868A  ALA*     1.3    54.4    +      -       -      +
    870A  HIS*     3.1     6.6    +      -       -      +
    871A  LYS*     2.7    66.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 868 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466A  THR*     4.1     9.8    -      -       -      +
    467A  LEU*     3.8    38.4    -      -       +      -
    468A  GLU*     4.2     4.3    -      -       -      +
    864A  LEU*     2.9    17.1    +      -       +      +
    865A  LEU*     2.9    14.8    +      -       +      +
    867A  ARG*     1.3    75.8    -      -       -      +
    869A  ASN*     1.3    57.3    +      -       -      +
    871A  LYS*     3.9     2.5    -      -       -      +
    872A  LEU*     2.8    34.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 869 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    832A  ASP*     5.1     8.1    +      -       -      -
    865A  LEU*     2.7    29.3    +      -       +      +
    866A  GLU*     3.6     8.7    +      -       -      +
    868A  ALA*     1.3    71.4    -      -       -      +
    870A  HIS*     1.3    65.1    +      -       -      +
    872A  LEU*     3.3     5.3    +      -       -      +
    873A  LYS*     3.0    48.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 870 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    866A  GLU*     2.8    25.1    +      -       +      +
    867A  ARG*     3.1     6.5    +      -       -      +
    869A  ASN*     1.3    77.1    -      -       -      +
    871A  LYS*     1.3    97.0    +      -       +      +
    873A  LYS*     3.3    12.5    +      -       -      +
    874A  LEU*     3.3    16.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 871 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466A  THR*     3.3    21.3    -      -       +      +
    867A  ARG*     2.7    64.1    +      -       +      +
    868A  ALA*     4.0     1.8    -      -       -      +
    870A  HIS*     1.3   100.3    +      -       +      +
    872A  LEU*     1.3    65.4    +      -       -      +
    874A  LEU*     3.0    18.6    +      -       +      +
    875A  MET*     3.0    22.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 872 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463A  PRO*     2.9    50.9    -      -       +      +
    464A  ILE*     5.1     2.7    -      -       +      -
    466A  THR*     3.3    10.6    -      -       +      +
    467A  LEU*     4.3    11.9    -      -       +      +
    868A  ALA      2.8    18.4    +      -       -      +
    869A  ASN*     3.5     7.2    -      -       -      +
    871A  LYS*     1.3    75.5    -      -       -      +
    873A  LYS*     1.3    73.3    +      -       -      +
    875A  MET*     2.8    21.3    +      -       -      +
    876A  VAL*     3.1    18.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 873 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    869A  ASN*     3.0    40.2    +      -       -      +
    870A  HIS*     3.7     6.7    -      -       -      +
    871A  LYS      3.2     0.4    -      -       -      -
    872A  LEU*     1.3    90.7    -      -       +      +
    874A  LEU*     1.3    58.8    +      -       -      +
    876A  VAL*     3.4    19.3    -      -       +      +
    877A  PRO*     2.9    22.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 874 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870A  HIS*     3.3    16.4    +      -       +      +
    871A  LYS*     3.0    13.8    +      -       +      +
    873A  LYS*     1.3    75.4    -      -       -      +
    875A  MET*     1.3    83.7    +      -       +      +
    877A  PRO*     3.0    20.4    -      -       +      +
    878A  MET*     3.3    33.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 875 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462A  ILE*     3.2    30.6    -      -       +      +
    463A  PRO*     4.3     9.6    -      -       +      -
    466A  THR*     2.9    38.1    -      -       +      +
    871A  LYS*     3.1    18.2    -      -       +      +
    872A  LEU*     2.8    12.0    +      -       -      +
    874A  LEU*     1.3    94.6    -      -       +      +
    876A  VAL*     1.3    53.7    +      -       -      +
    878A  MET*     3.8     6.0    -      -       -      +
    879A  THR*     2.5    42.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 876 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463A  PRO*     5.2     4.3    -      -       +      -
    872A  LEU*     3.1    20.0    +      -       +      +
    873A  LYS*     3.4    33.0    -      -       +      +
    875A  MET*     1.3    77.2    -      -       -      +
    877A  PRO*     1.3    72.1    -      -       +      +
    879A  THR*     3.1    13.1    -      -       +      +
    880A  LEU*     2.9    38.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 877 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    873A  LYS      2.9    29.4    -      -       -      +
    874A  LEU*     3.0    15.7    -      -       +      +
    876A  VAL*     1.3    90.5    -      -       +      +
    878A  MET*     1.3    60.3    +      -       +      +
    880A  LEU*     3.3     4.0    +      -       +      +
    881A  MET*     2.9    49.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 878 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462A  ILE*     6.3     0.4    -      -       +      -
    874A  LEU*     3.3    37.3    +      -       +      +
    875A  MET*     3.2     9.5    +      -       -      +
    877A  PRO*     1.3    81.2    -      -       +      +
    879A  THR*     1.3    59.5    +      -       -      +
    881A  MET*     3.5    13.6    +      -       +      +
    882A  ILE*     3.0    27.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 879 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  LEU      4.2     4.9    +      -       -      -
    460A  SER*     3.9    25.5    +      -       -      +
    462A  ILE*     4.3     9.1    -      -       -      +
    463A  PRO*     4.7    12.1    -      -       +      -
    875A  MET      2.5    28.3    +      -       -      +
    876A  VAL*     3.1    22.9    -      -       +      +
    878A  MET*     1.3    70.5    -      -       -      +
    880A  LEU*     1.3    71.1    +      -       +      +
    882A  ILE*     2.9    23.7    -      -       -      +
    883A  ILE*     2.9    19.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 880 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    876A  VAL*     2.9    23.9    +      -       +      +
    877A  PRO*     3.8     5.4    -      -       +      +
    879A  THR*     1.3    83.2    -      -       +      +
    881A  MET*     1.3    62.1    +      -       +      +
    883A  ILE*     3.1    20.9    +      -       +      +
    884A  PHE*     2.6    37.7    +      -       -      +
    901A  ILE*     5.2    24.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 881 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    877A  PRO*     2.9    39.4    +      -       +      +
    878A  MET*     3.8    17.0    -      -       +      +
    880A  LEU*     1.3    81.4    -      -       +      +
    882A  ILE*     1.3    59.9    +      -       -      +
    884A  PHE*     3.4    14.6    +      -       +      +
    885A  VAL*     3.1    31.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 882 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  LEU*     3.4    33.0    -      -       +      -
    878A  MET      3.0    14.8    +      -       -      +
    879A  THR*     2.9    28.3    -      -       -      +
    881A  MET*     1.3    73.8    -      -       -      +
    883A  ILE*     1.3    68.6    +      -       +      +
    885A  VAL*     3.2     9.8    +      -       +      +
    886A  LEU*     2.9    42.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 883 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456A  ILE*     3.6    38.3    -      -       +      +
    459A  LEU*     4.7    10.5    -      -       +      -
    460A  SER*     4.7    10.5    -      -       -      +
    879A  THR*     2.9    29.5    +      -       -      +
    880A  LEU*     3.4    24.0    -      -       +      +
    882A  ILE*     1.3    84.7    -      -       +      +
    884A  PHE*     1.3    58.5    +      -       -      +
    886A  LEU*     3.1     5.2    +      -       +      +
    887A  LEU*     2.8    50.1    +      -       +      +
    900A  ILE*     5.3     2.0    -      -       +      -
    901A  ILE*     4.7     5.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 884 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    880A  LEU      2.6    19.9    +      -       -      +
    881A  MET*     3.6    19.5    -      -       +      +
    883A  ILE*     1.3    76.8    -      -       -      +
    885A  VAL*     1.3    75.5    +      -       +      +
    887A  LEU*     3.7     7.7    -      -       -      +
    888A  TYR*     2.9    63.3    +      +       +      +
    894A  VAL*     5.2    14.4    -      -       +      -
    897A  ALA*     5.3     6.7    -      -       +      -
    898A  LEU*     5.7     4.3    -      -       +      -
    901A  ILE*     4.8    11.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 885 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    881A  MET      3.1    18.1    +      -       -      +
    882A  ILE*     3.6    12.3    -      -       +      +
    884A  PHE*     1.3    93.1    -      -       +      +
    886A  LEU*     1.3    65.4    +      -       +      +
    887A  LEU      3.4     0.2    -      -       -      -
    888A  TYR*     2.8    33.9    -      -       +      +
    889A  LEU*     3.6     9.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 886 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  ILE*     3.8    15.6    -      -       +      +
    455A  LEU*     4.9    14.6    -      -       +      -
    456A  ILE*     4.1    39.1    -      -       +      +
    459A  LEU*     4.2    15.7    -      -       +      -
    882A  ILE*     2.9    41.0    +      -       +      +
    883A  ILE*     3.1     5.1    +      -       +      +
    885A  VAL*     1.3    89.2    -      -       +      +
    887A  LEU*     1.3    59.9    +      -       -      +
    889A  LEU*     2.9    32.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 887 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456A  ILE*     4.0    17.0    -      -       +      -
    883A  ILE*     2.8    34.8    +      -       +      +
    884A  PHE*     3.1     5.4    +      -       -      +
    886A  LEU*     1.3    80.4    -      -       -      +
    888A  TYR*     1.3    59.0    +      -       -      +
    889A  LEU*     3.3     9.4    +      -       -      +
    890A  ALA*     4.1     6.8    +      -       -      +
    891A  PHE*     5.2     1.9    -      -       -      -
    896A  GLU*     4.7     9.0    -      -       -      +
    897A  ALA*     3.9    22.0    -      -       +      +
    900A  ILE*     3.3    48.5    -      -       +      -
    901A  ILE*     3.7    17.3    -      -       +      -
    938A  ALA*     5.6     1.6    -      -       +      -
    942A  VAL*     4.8    19.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 888 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    884A  PHE*     2.9    46.9    +      +       +      +
    885A  VAL*     2.8    24.9    -      -       +      +
    887A  LEU*     1.3    75.1    -      -       -      +
    889A  LEU*     1.3    70.0    +      -       -      +
    892A  ARG*     3.1    40.8    -      -       +      +
    893A  ARG      4.8     1.6    -      -       -      +
    894A  VAL*     5.9     1.3    -      -       +      -
    896A  GLU*     5.8     0.2    -      -       -      -
    897A  ALA*     4.4    10.7    -      -       +      +
----------------------------------------------------------
 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