Contacts of the helix formed by residues 457 - 478 (chain A) in PDB entry 4BBZ


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 THR 457 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426A  SER*     4.1    17.0    +      -       -      -
    455A  GLN      4.0     0.8    +      -       -      +
    456A  TYR*     1.3    78.0    -      -       -      +
    458A  LYS*     1.3    63.2    +      -       -      +
    459A  ALA*     3.4     9.8    +      -       -      +
    460A  GLU*     3.1    40.5    +      -       -      +
    461A  GLU*     3.2    11.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  ARG*     5.5     4.4    -      -       -      +
    456A  TYR      3.9     0.4    +      -       -      -
    457A  THR*     1.3    70.6    -      -       -      +
    459A  ALA*     1.3    59.9    +      -       -      +
    461A  GLU*     3.0    37.4    +      -       -      +
    462A  ILE*     2.9    45.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457A  THR*     3.2     9.7    +      -       -      +
    458A  LYS*     1.3    79.0    -      -       -      +
    460A  GLU*     1.3    57.7    +      -       -      +
    462A  ILE*     3.7     8.4    +      -       -      +
    463A  LEU*     3.1    20.1    +      -       -      +
    505A  THR*     3.5    36.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 460 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423A  HIS*     2.7    39.6    +      -       +      +
    425A  SER*     3.4     3.6    -      -       -      -
    426A  SER*     2.7    45.4    +      -       -      -
    444A  PHE*     3.8    16.6    -      -       +      -
    449A  PRO*     3.6     3.5    -      -       +      +
    456A  TYR*     3.2    21.8    -      -       +      -
    457A  THR*     3.1    30.8    +      -       -      +
    458A  LYS      3.1     0.6    -      -       -      -
    459A  ALA*     1.3    76.9    -      -       -      +
    461A  GLU*     1.3    65.4    +      -       -      +
    463A  LEU*     3.9     1.5    -      -       -      +
    464A  SER*     2.9    26.9    +      -       -      -
    505A  THR*     4.4     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 461 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449A  PRO*     3.6    26.8    -      -       -      +
    450A  LEU*     3.5    29.9    -      -       +      +
    452A  ARG*     4.5    21.3    +      -       +      +
    457A  THR      3.2     9.8    +      -       -      +
    458A  LYS*     3.0    46.4    +      -       -      +
    460A  GLU*     1.3    77.6    -      -       -      +
    462A  ILE*     1.3    66.8    +      -       +      +
    464A  SER      3.4     0.2    +      -       -      -
    465A  ARG*     3.0    22.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 462 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458A  LYS*     2.9    40.0    +      -       +      +
    459A  ALA*     3.9     8.7    -      -       -      +
    461A  GLU*     1.3    81.7    -      -       +      +
    463A  LEU*     1.3    63.5    +      -       -      +
    465A  ARG*     3.1     8.1    +      -       +      +
    466A  SER*     3.0    23.1    +      -       -      -
    580A  NAG      4.1    31.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 463 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421A  PHE*     4.4    13.7    -      -       +      -
    423A  HIS*     4.0    23.3    -      -       +      -
    444A  PHE*     4.4     9.4    -      -       +      -
    459A  ALA      3.1    18.5    +      -       -      +
    460A  GLU      3.9     3.8    -      -       -      +
    462A  ILE*     1.3    77.0    -      -       -      +
    464A  SER*     1.3    57.2    +      -       -      +
    466A  SER*     3.2    10.1    +      -       -      +
    467A  ILE*     3.0    43.2    +      -       +      +
    503A  LEU*     4.6     8.1    -      -       +      -
    504A  ASN*     3.7    29.4    -      -       -      +
    505A  THR*     3.9    24.0    -      -       +      -
    508A  THR*     5.7     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 464 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444A  PHE*     2.6    37.0    +      -       -      -
    447A  GLY*     3.4    17.0    -      -       -      -
    449A  PRO*     3.6    18.9    -      -       -      +
    450A  LEU*     4.4     5.4    -      -       -      -
    460A  GLU      2.9    18.1    +      -       -      -
    461A  GLU      3.7     3.8    -      -       -      -
    463A  LEU*     1.3    76.7    -      -       -      +
    465A  ARG*     1.3    55.0    +      -       -      +
    467A  ILE*     3.2     3.9    +      -       -      +
    468A  VAL*     2.8    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 465 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  VAL*     3.5    32.4    +      -       -      +
    137A  GLU*     2.8    30.7    +      -       -      -
    450A  LEU*     3.9    18.6    -      -       +      -
    461A  GLU*     3.0    14.7    +      -       +      +
    462A  ILE*     3.1    13.4    +      -       +      +
    464A  SER*     1.3    77.4    -      -       -      +
    466A  SER*     1.3    57.5    +      -       -      +
    468A  VAL*     4.0     6.0    -      -       -      +
    469A  LYS*     3.1    25.9    +      -       -      +
    580A  NAG      3.6    49.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 466 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462A  ILE*     3.0    14.2    +      -       -      -
    463A  LEU*     3.6    14.5    +      -       -      +
    465A  ARG*     1.3    76.3    -      -       -      +
    467A  ILE*     1.3    57.0    +      -       -      +
    469A  LYS*     3.1     6.4    +      -       -      +
    470A  ARG*     2.8    55.9    +      -       -      +
    482A  GLU*     4.9     8.9    -      -       -      +
    503A  LEU*     5.6     1.9    -      -       -      +
    580A  NAG      4.3    11.8    +      -       -      -
    704A  SO4      5.5     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 467 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421A  PHE*     3.9    23.1    -      -       +      -
    441A  GLU*     6.2     0.4    -      -       +      -
    444A  PHE*     4.1    12.1    -      -       +      +
    445A  VAL*     3.8    35.4    -      -       +      -
    463A  LEU*     3.0    42.1    +      -       +      +
    464A  SER*     3.6     4.3    -      -       -      +
    466A  SER*     1.3    73.4    +      -       -      +
    468A  VAL*     1.3    61.1    +      -       -      +
    470A  ARG*     3.1     3.9    +      -       -      +
    471A  TRP*     2.8    56.1    +      -       +      +
    503A  LEU*     4.2    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 468 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  PHE      6.2     0.2    -      -       -      -
    133A  LEU*     3.7    17.0    -      -       +      +
    136A  VAL*     4.6     8.7    -      -       +      -
    137A  GLU*     3.5    26.5    -      -       +      +
    444A  PHE      3.8     7.6    -      -       -      +
    445A  VAL      3.3    25.6    -      -       -      +
    447A  GLY*     3.9    16.2    -      -       -      -
    450A  LEU*     4.5     5.8    -      -       +      -
    464A  SER      2.8    24.0    +      -       -      +
    465A  ARG*     3.9    10.8    -      -       -      +
    467A  ILE*     1.3    73.4    -      -       -      +
    469A  LYS*     1.3    61.5    +      -       -      +
    471A  TRP*     3.9     4.9    -      -       -      +
    472A  ALA*     3.1    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  GLU*     2.8    37.0    +      -       -      +
    465A  ARG*     3.1    33.8    +      -       -      +
    466A  SER*     3.1     6.0    +      -       -      +
    468A  VAL*     1.3    76.0    -      -       -      +
    470A  ARG*     1.3    59.0    +      -       -      +
    472A  ALA*     3.3     0.5    +      -       -      +
    473A  ASN*     2.9    52.7    +      -       -      +
    476A  LYS*     5.1     2.4    -      -       -      +
    482A  GLU*     3.8    26.0    -      -       +      +
    484A  GLN*     4.9    10.2    +      -       -      -
    580A  NAG      4.0    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466A  SER*     2.8    38.8    +      -       -      +
    467A  ILE*     3.1     5.6    +      -       -      +
    469A  LYS*     1.3    72.6    -      -       -      +
    471A  TRP*     1.3    66.2    +      -       +      +
    473A  ASN*     3.2     1.2    +      -       -      -
    474A  PHE*     2.8    26.7    +      -       -      +
    480A  PRO*     3.0    48.1    +      -       +      +
    481A  GLN*     3.9    18.4    -      -       -      +
    482A  GLU*     4.2     8.4    -      -       +      +
    487A  SER*     3.8    19.2    +      -       -      -
    488A  THR*     3.0    25.0    +      -       -      -
    490A  TRP*     3.6    35.9    -      -       +      +
    501A  LEU*     4.0    14.0    -      -       -      +
    503A  LEU*     4.8    10.8    -      -       -      +
    508A  THR*     4.8     1.0    -      -       -      +
    704A  SO4      3.9    12.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  LEU*     5.1     8.4    -      -       +      +
    133A  LEU*     5.6     3.8    -      -       +      -
    195A  PHE*     4.3     7.4    -      +       -      -
    221A  ILE*     3.7    31.7    -      -       +      +
    223A  GLN*     2.9    24.6    +      -       +      -
    318A  LEU*     4.0    11.7    -      -       +      -
    419A  TYR*     3.8    40.8    -      +       -      -
    441A  GLU*     6.1     0.4    -      -       +      -
    445A  VAL*     3.5    36.6    -      -       +      +
    467A  ILE*     2.8    39.9    +      -       +      +
    468A  VAL*     3.9     6.3    -      -       -      +
    470A  ARG*     1.3    79.1    -      -       +      +
    472A  ALA*     1.3    57.2    +      -       -      +
    474A  PHE*     3.3     7.5    +      -       -      +
    475A  ALA*     3.0    28.1    +      -       -      +
    490A  TRP*     4.1    20.6    -      +       -      -
    503A  LEU*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  LEU*     5.2     3.8    -      -       -      -
    133A  LEU*     5.6     3.1    -      -       +      -
    137A  GLU*     3.8    33.7    -      -       +      +
    139A  VAL*     4.6    10.1    -      -       +      -
    468A  VAL      3.1    21.0    +      -       -      +
    469A  LYS*     3.8     3.1    -      -       +      +
    471A  TRP*     1.3    75.1    -      -       -      +
    473A  ASN*     1.3    61.9    +      -       -      +
    475A  ALA*     3.2     6.0    +      -       -      +
    476A  LYS*     2.8    42.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469A  LYS*     2.9    37.9    +      -       -      +
    470A  ARG      3.8     1.1    -      -       -      +
    472A  ALA*     1.3    75.7    -      -       -      +
    474A  PHE*     1.3    61.9    +      -       -      +
    476A  LYS*     4.6     5.0    +      -       -      +
    477A  TYR*     2.8    61.5    +      -       +      +
    478A  GLY      3.5     0.3    +      -       -      -
    479A  ASN      3.5    17.8    +      -       -      +
    481A  GLN*     3.0    23.4    +      -       -      +
    482A  GLU*     4.7     2.0    -      -       -      +
    483A  THR*     4.9    11.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  THR*     4.3     1.3    -      -       +      -
    219A  ARG*     3.0    28.7    +      -       +      -
    220A  ALA      3.3    29.8    -      -       -      -
    221A  ILE*     3.5    26.7    -      -       +      -
    316A  GLN*     3.5    36.1    -      -       +      -
    317A  ILE      3.9    10.8    -      -       -      -
    318A  LEU*     3.6    26.0    -      -       +      -
    417A  PHE*     4.4     3.8    -      +       -      -
    470A  ARG      2.8    17.1    +      -       -      +
    471A  TRP      3.5     4.0    -      -       -      +
    473A  ASN*     1.3    78.4    -      -       -      +
    475A  ALA*     1.3    60.0    +      -       -      +
    478A  GLY*     2.7    36.6    +      -       -      -
    479A  ASN      3.7     8.9    +      -       -      +
    480A  PRO*     3.9    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  THR*     3.8    18.2    -      -       +      +
    110A  LEU*     3.5    27.1    -      -       +      -
    139A  VAL*     5.6     0.9    -      -       +      -
    191A  SER*     3.9     3.1    +      -       -      -
    193A  THR*     3.2    28.7    +      -       +      +
    219A  ARG*     2.6    27.6    +      -       -      +
    471A  TRP      3.0    14.3    +      -       -      +
    472A  ALA*     3.7     5.8    -      -       -      +
    474A  PHE*     1.3    78.5    -      -       -      +
    476A  LYS*     1.3    53.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  THR*     3.5    28.3    +      -       +      +
    137A  GLU*     2.9    46.6    +      -       -      +
    138A  ARG      5.3     1.1    -      -       -      -
    139A  VAL*     3.7    15.9    -      -       +      +
    191A  SER*     4.5     3.5    +      -       -      -
    219A  ARG*     3.4     9.1    +      -       -      -
    469A  LYS*     5.1     2.4    -      -       -      +
    472A  ALA*     2.8    22.8    +      -       -      +
    473A  ASN*     4.6     2.7    +      -       -      +
    475A  ALA*     1.3    78.1    -      -       -      +
    477A  TYR*     1.3   102.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  ARG*     4.2     4.7    -      -       -      +
    473A  ASN*     2.8    46.5    +      -       +      +
    476A  LYS*     1.3   108.7    +      -       +      +
    478A  GLY*     1.3    66.4    +      -       -      +
    479A  ASN*     3.2    12.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  ARG*     3.4    28.4    -      -       -      -
    316A  GLN*     3.9    15.9    -      -       -      +
    415A  ASN*     5.3     2.6    +      -       -      -
    417A  PHE*     3.9    15.6    -      -       -      -
    474A  PHE*     2.7    30.3    +      -       -      -
    477A  TYR*     1.3    72.3    -      -       -      +
    479A  ASN*     1.3    57.3    +      -       -      +
----------------------------------------------------------
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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).

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