Contacts of the strand formed by residues 423 - 444 (chain C) in PDB entry 2C11


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 LYS 423 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173C  PHE*     6.3     0.4    -      -       -      -
    414C  HIS*     3.4     3.5    -      -       -      +
    415C  PHE*     3.0    66.9    +      -       +      -
    417C  LEU      3.7     8.5    +      -       -      -
    418C  GLU*     5.1     1.0    +      -       -      +
    419C  SER*     3.7    23.4    +      -       -      +
    421C  ALA*     3.7    18.4    -      -       +      +
    422C  PRO*     1.3    78.4    -      -       -      +
    424C  THR*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 424 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  ARG*     3.7    22.5    +      -       -      +
    412C  ASP*     3.7    26.2    -      -       +      +
    413C  TRP      3.2     6.7    -      -       -      +
    414C  HIS*     3.1    37.7    +      -       +      +
    415C  PHE*     4.1     1.8    -      -       -      -
    422C  PRO      5.3     0.5    +      -       -      -
    423C  LYS*     1.3    79.7    -      -       -      +
    425C  ILE*     1.3    68.3    +      -       -      +
    426C  ARG*     4.0     5.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 425 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393C  LYS      4.6     7.9    -      -       -      +
    395C  THR*     3.0    42.4    -      -       +      +
    396C  THR      4.3     0.2    -      -       -      -
    397C  PRO*     3.7    29.8    -      -       +      -
    412C  ASP*     3.3     4.7    -      -       -      -
    413C  TRP*     2.8    39.9    +      -       +      +
    415C  PHE*     3.5    28.5    -      -       +      -
    424C  THR*     1.3    72.2    -      -       -      +
    426C  ARG*     1.3    67.3    +      -       -      +
    428C  ALA*     3.7    17.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 426 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397C  PRO*     3.3    23.8    -      -       +      +
    412C  ASP*     3.3    21.1    -      -       -      +
    424C  THR*     4.0     4.4    +      -       +      +
    425C  ILE*     1.3    73.1    -      -       -      +
    427C  ASP*     1.3    85.3    +      -       -      +
    428C  ALA      3.1     0.7    +      -       -      -
    728D  ASP*     5.0    17.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 427 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397C  PRO*     5.3     0.8    -      -       +      +
    398C  LEU*     2.7    43.9    +      -       -      +
    400C  ARG*     3.0    40.7    +      -       -      -
    410C  TYR*     3.6    24.0    -      -       +      +
    411C  VAL      2.8    16.7    +      -       -      +
    412C  ASP*     3.2    10.5    +      -       -      +
    426C  ARG*     1.3    83.4    -      -       -      +
    428C  ALA*     1.3    63.4    -      -       -      +
    429C  PHE      3.3     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 428 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341C  LEU*     5.3     0.2    -      -       +      -
    395C  THR*     4.3    16.9    +      -       +      +
    396C  THR      4.5     3.6    -      -       -      +
    398C  LEU*     3.4    17.3    -      -       -      +
    411C  VAL      2.6     8.0    +      -       -      +
    413C  TRP*     3.8    22.7    -      -       +      -
    425C  ILE*     3.8    27.1    -      -       +      +
    426C  ARG      3.1     3.0    +      -       -      -
    427C  ASP*     1.3    74.8    -      -       -      +
    429C  PHE*     1.3    67.3    +      -       +      +
    464C  SER*     3.6    16.4    +      -       -      +
    465C  MET      4.3     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 429 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  ASP*     4.3     0.7    -      -       -      -
    339C  PHE*     3.8    33.0    -      +       +      -
    340C  GLY*     3.5    29.4    -      -       -      -
    341C  LEU*     3.5    35.9    -      -       +      -
    347C  PRO*     5.7     1.3    -      -       +      -
    398C  LEU*     3.7     0.4    -      -       -      -
    410C  TYR*     3.6     2.4    -      -       -      +
    411C  VAL*     2.8    37.5    +      -       +      +
    412C  ASP      3.8    15.9    -      -       -      -
    413C  TRP*     3.8    25.4    -      +       +      -
    427C  ASP*     3.9     3.8    -      -       -      -
    428C  ALA*     1.3    85.5    -      -       +      +
    430C  CYS*     1.3    64.0    +      -       -      +
    431C  VAL*     5.3     3.1    -      -       +      -
    462C  VAL*     5.0     8.5    -      -       +      -
    463C  ARG      3.3     8.1    -      -       -      +
    464C  SER*     4.4    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 430 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398C  LEU*     3.3    12.1    -      -       +      -
    404C  CYS*     2.0    53.6    -      -       +      -
    408C  ALA*     4.7     2.2    -      -       +      -
    409C  THR      3.3     7.0    -      -       -      +
    410C  TYR*     3.9    13.2    -      -       +      -
    429C  PHE*     1.3    73.8    -      -       -      +
    431C  VAL*     1.3    61.8    +      -       -      +
    432C  PHE*     4.0     8.7    -      -       -      -
    461C  VAL      3.8     0.7    -      -       -      +
    462C  VAL*     3.7     1.4    -      -       -      -
    463C  ARG*     3.0    39.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 431 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323C  PHE*     3.5    27.0    -      -       +      -
    325C  VAL*     4.5     8.3    -      -       +      -
    330C  VAL*     4.2    31.0    -      -       +      -
    339C  PHE*     4.4    11.4    -      -       +      -
    409C  THR*     2.7    42.4    +      -       -      +
    411C  VAL*     5.1     4.7    -      -       +      -
    429C  PHE*     5.3     0.4    -      -       +      -
    430C  CYS*     1.3    81.7    -      -       -      +
    432C  PHE*     1.3    65.3    +      -       -      +
    460C  LEU*     4.2     7.0    -      -       +      -
    461C  VAL      3.2    13.7    -      -       -      +
    462C  VAL*     4.3    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 432 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317C  TYR*     3.4    13.7    -      -       -      +
    323C  PHE*     3.5     6.3    -      -       -      -
    405C  PRO*     3.5    40.6    -      -       +      -
    407C  LEU      4.2     2.0    -      -       -      +
    408C  ALA*     3.6    14.4    -      -       +      -
    430C  CYS*     4.0    24.5    -      -       -      -
    431C  VAL*     1.3    81.5    -      -       -      +
    433C  GLU*     1.3    71.7    +      -       -      +
    434C  GLN*     3.9    15.7    -      -       +      -
    460C  LEU*     2.9    22.7    -      -       -      +
    461C  VAL*     2.9    54.7    +      -       +      -
    463C  ARG*     4.1    19.7    -      -       -      -
    436D  GLN      5.6     0.2    -      -       -      -
    437D  GLY*     4.6     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 433 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315C  GLN*     3.3    14.4    +      -       -      -
    317C  TYR*     2.7    37.0    +      -       +      -
    322C  ARG*     3.0    56.6    +      -       -      +
    323C  PHE*     3.9     9.4    -      -       +      -
    405C  PRO*     5.6     0.3    -      -       -      +
    432C  PHE*     1.3    82.7    -      -       -      +
    434C  GLN*     1.3    60.6    +      -       -      +
    458C  THR*     3.3    24.2    -      -       +      +
    459C  VAL      3.1     9.9    -      -       -      +
    460C  LEU*     4.5     5.2    -      -       +      -
    313D  PRO*     4.0     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 434 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315C  GLN*     2.7    33.6    +      -       -      +
    405C  PRO*     3.9    22.5    -      -       -      +
    432C  PHE*     3.9    15.3    -      -       +      -
    433C  GLU*     1.3    74.0    -      -       -      +
    435C  ASN*     1.3    73.1    +      -       -      +
    436C  GLN*     2.9    25.9    +      -       -      +
    458C  THR*     4.1     2.0    -      -       -      -
    459C  VAL*     2.5    44.6    +      -       +      -
    461C  VAL*     4.7     0.9    -      -       +      -
    315D  GLN*     3.5     4.6    -      -       -      +
    434D  GLN*     3.8     1.0    -      -       -      +
    435D  ASN      3.2    22.8    +      -       -      -
    436D  GLN*     3.9    18.8    +      -       -      +
    437D  GLY*     4.0     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 435 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315C  GLN*     2.6    29.6    +      -       -      +
    434C  GLN*     1.3    79.6    +      -       -      +
    436C  GLN*     1.3    60.5    +      -       -      +
    437C  GLY*     3.1    25.8    +      -       -      +
    456C  ALA*     4.6    10.7    -      -       -      +
    457C  GLU      3.7     8.8    -      -       -      +
    458C  THR*     3.7    11.0    +      -       -      +
    313D  PRO*     3.4    29.5    +      -       +      +
    314D  LEU*     5.2     0.4    -      -       -      +
    315D  GLN*     3.3    35.4    -      -       -      +
    405D  PRO*     4.7     6.7    -      -       -      +
    434D  GLN*     3.2     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 436 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434C  GLN*     2.9    30.7    +      -       -      +
    435C  ASN*     1.3    72.5    -      -       -      +
    437C  GLY*     1.3    60.4    +      -       -      +
    438C  LEU*     4.2    13.8    -      -       +      +
    457C  GLU*     2.7    51.2    +      -       +      +
    459C  VAL*     3.5    28.4    -      -       +      +
    478C  VAL*     5.2     1.2    -      -       -      +
    480C  HIS*     4.8     6.3    -      -       -      -
    434D  GLN*     3.7    17.1    +      -       -      +
    436D  GLN*     5.2     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 437 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435C  ASN*     3.1    17.5    +      -       -      -
    436C  GLN*     1.3    78.7    -      -       -      +
    438C  LEU*     1.3    56.5    +      -       -      +
    456C  ALA*     5.5     3.6    -      -       -      -
    457C  GLU      4.0     1.0    +      -       -      -
    402D  VAL      5.6     0.7    -      -       -      -
    403D  ASP      5.1     0.7    -      -       -      -
    404D  CYS*     5.5     0.4    -      -       -      -
    405D  PRO*     3.7    34.2    -      -       -      +
    432D  PHE*     3.9     3.3    -      -       -      -
    434D  GLN*     3.9     6.7    -      -       -      -
    463D  ARG*     2.9    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 438 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435C  ASN*     4.9     0.2    +      -       -      -
    436C  GLN*     3.2    11.8    -      -       +      +
    437C  GLY*     1.3    80.4    -      -       -      +
    439C  PRO*     1.3    76.4    -      -       +      +
    456C  ALA*     4.1     3.5    -      -       -      +
    457C  GLU*     2.8    35.9    +      -       -      +
    402D  VAL      4.4     0.4    -      -       -      -
    463D  ARG*     3.3    27.8    -      -       -      +
    474D  VAL*     4.7     3.6    -      -       +      -
    476D  ASP*     3.7    14.4    -      -       -      +
    490D  TYR*     3.7    46.0    -      -       +      +
    696D  THR*     3.9    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 439 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438C  LEU*     1.3    96.2    -      -       +      +
    440C  LEU*     1.3    54.1    +      -       -      +
    441C  ARG      4.0     2.5    -      -       -      +
    442C  ARG*     4.0    25.6    -      -       +      -
    455C  LEU      4.1     2.2    -      -       -      +
    456C  ALA*     3.5     9.4    -      -       -      -
    457C  GLU*     4.4     0.6    -      -       -      +
    402D  VAL*     3.6    16.8    -      -       +      +
    403D  ASP      3.6    19.1    -      -       -      +
    463D  ARG*     3.6     5.4    -      -       -      +
    465D  MET*     3.8    22.7    -      -       +      -
    474D  VAL*     5.0     8.5    -      -       +      -
    492D  THR*     5.9     0.4    -      -       +      -
    696D  THR*     2.8    33.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 440 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439C  PRO*     1.3    73.0    -      -       -      +
    441C  ARG*     1.3    56.7    -      -       -      +
    455C  LEU*     2.7    29.2    +      -       +      +
    457C  GLU*     3.6    27.4    -      -       +      +
    481C  PRO*     3.5    29.4    -      -       +      -
    482C  SER*     4.7     3.1    -      -       -      +
    716C  SER*     3.7    31.6    -      -       -      +
    695D  VAL*     3.0    21.4    -      -       +      -
    696D  THR*     2.8    34.2    +      -       -      +
    697D  VAL*     3.6    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 441 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439C  PRO*     4.0     2.0    -      -       -      +
    440C  LEU*     1.3    79.7    -      -       +      +
    442C  ARG*     1.3    68.3    +      -       -      +
    453C  GLY      4.9     2.0    -      -       -      -
    454C  GLY*     3.4    14.7    +      -       -      +
    455C  LEU*     3.2    37.5    +      -       +      +
    714C  ASP*     3.7    13.2    +      -       -      +
    716C  SER*     2.4    57.3    +      -       -      +
    717C  PHE*     3.4    20.2    +      -       -      +
    722C  SER*     2.9    30.3    +      -       -      -
    302D  LEU*     4.8    13.6    +      -       -      +
    492D  THR*     3.5     8.5    -      -       -      -
    692D  PRO*     4.9     4.4    -      -       -      +
    693D  ASN*     3.7    28.7    -      -       +      -
    694D  THR      4.1     3.4    -      -       -      +
    695D  VAL*     4.6     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 442 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439C  PRO*     4.0    15.7    -      -       +      -
    441C  ARG*     1.3    79.5    -      -       -      +
    443C  HIS*     1.3    58.9    +      -       -      +
    444C  HIS*     3.4    19.9    +      -       -      +
    452C  PHE*     3.7    13.8    -      -       +      -
    453C  GLY      3.4     8.1    -      -       -      -
    454C  GLY*     4.4     1.1    -      -       -      -
    396D  THR*     2.5    22.4    +      -       -      -
    397D  PRO      3.6    14.6    +      -       -      -
    402D  VAL*     4.9     0.4    -      -       +      -
    403D  ASP*     2.9    35.3    +      -       -      +
    465D  MET*     3.1    27.2    -      -       -      +
    467D  THR*     3.0    11.5    +      -       -      -
    472D  ASP*     2.8    56.0    +      -       -      +
    492D  THR*     3.1    19.7    +      -       +      +
    493D  GLY*     3.7     1.6    -      -       -      -
    693D  ASN*     3.3     8.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 443 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442C  ARG*     1.3    73.1    -      -       -      +
    444C  HIS*     1.3    60.8    +      -       -      +
    445C  SER*     3.9    12.3    +      -       -      -
    451C  TYR*     3.2    38.0    +      +       -      -
    452C  PHE*     3.2     8.7    -      -       -      -
    453C  GLY      2.9    33.6    +      -       -      +
    239D  PHE*     3.9     7.5    -      +       -      -
    302D  LEU*     4.5     3.5    -      -       +      +
    467D  THR*     3.8    19.3    -      -       +      -
    469D  LEU      3.8     8.7    +      -       -      -
    470D  ASN      3.1    23.0    +      -       -      -
    472D  ASP*     2.8    22.1    +      -       -      +
    493D  GLY*     4.2     0.2    -      -       -      -
    494D  TYR*     3.4    25.9    +      +       +      -
    693D  ASN*     3.3    15.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 444 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442C  ARG*     3.4    24.8    -      -       -      +
    443C  HIS*     1.3    75.1    -      -       -      +
    445C  SER*     1.3    61.6    +      -       -      +
    446C  ASP*     3.4    20.9    +      -       -      -
    451C  TYR      3.9     1.6    -      -       -      -
    452C  PHE*     3.3    27.7    -      +       +      -
    725C  PHE*     5.4     2.0    -      +       -      -
    727C  GLY      4.3    11.4    -      -       -      -
    728C  ASP*     6.1     0.4    -      -       -      -
   1745C   CU      2.5    27.1    -      -       -      -
    396D  THR*     3.8    17.7    -      -       -      +
    397D  PRO*     3.5    29.4    +      -       +      +
    399D  THR*     4.1     5.5    +      -       -      -
    467D  THR*     3.5    22.5    +      -       -      +
    472D  ASP*     3.4     5.9    +      -       -      -
----------------------------------------------------------
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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