Contacts of the helix formed by residues 512 - 543 (chain A) in PDB entry 5JAJ


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 PRO 512 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    510A  ALA      3.5     4.2    -      -       -      +
    511A  MET*     1.3    89.0    -      -       +      +
    513A  GLU*     1.3    65.6    +      -       -      +
    514A  ARG*     3.2     4.9    -      -       +      +
    515A  LYS*     3.1    27.4    +      -       +      +
    516A  TYR*     2.9    19.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 513 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  MET      3.3     4.6    +      -       -      -
    512A  PRO*     1.3    71.0    -      -       -      +
    514A  ARG*     1.3    59.2    +      -       -      +
    516A  TYR*     3.3     7.9    +      -       +      +
    517A  ARG*     2.7    78.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 514 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    512A  PRO*     3.2     3.9    -      -       +      +
    513A  GLU*     1.3    78.9    +      -       -      +
    515A  LYS*     1.3    63.6    +      -       -      +
    517A  ARG*     4.0     5.3    -      -       -      +
    518A  LEU*     3.1    42.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 515 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  MET*     3.7    21.6    -      -       +      +
    512A  PRO*     3.1    31.2    +      -       +      +
    514A  ARG*     1.3    79.6    -      -       -      +
    516A  TYR*     1.3    62.4    +      -       -      +
    518A  LEU*     3.5     6.9    +      -       -      +
    519A  LYS*     3.1    23.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 516 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  LEU*     3.9    16.8    -      -       +      -
    189A  CYS*     3.3    23.0    -      -       -      +
    194A  THR*     2.7    33.4    +      -       -      +
    195A  GLU*     3.7    16.2    -      -       -      -
    508A  VAL*     3.9    15.0    -      -       +      -
    511A  MET*     3.7    23.3    -      -       +      +
    512A  PRO      2.9    16.7    +      -       -      +
    513A  GLU*     3.7     8.7    -      -       +      +
    515A  LYS*     1.3    77.1    -      -       -      +
    517A  ARG*     1.3    73.8    +      -       +      +
    519A  LYS*     3.2     4.0    +      -       -      +
    520A  ILE*     2.9    50.0    +      -       +      +
    707A  EDO      3.8    28.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 517 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  GLU*     5.4     5.5    +      -       -      -
    513A  GLU*     2.7    64.8    +      -       +      +
    514A  ARG*     4.0     6.1    -      -       -      +
    516A  TYR*     1.3    81.2    -      -       +      +
    518A  LEU*     1.3    58.3    +      -       +      +
    520A  ILE*     3.3     7.4    +      -       -      +
    521A  VAL*     3.0    36.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 518 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    514A  ARG*     3.1    34.7    +      -       +      +
    515A  LYS*     3.9     5.6    -      -       -      +
    517A  ARG*     1.3    77.3    -      -       +      +
    519A  LYS*     1.3    63.1    +      -       -      +
    521A  VAL*     3.4    13.7    +      -       +      +
    522A  GLU*     3.0    25.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 519 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  GLU*     2.9    40.8    +      -       -      -
    186A  LEU*     3.7    28.3    -      -       +      -
    511A  MET*     5.0     3.4    -      -       +      -
    515A  LYS*     3.1    18.8    +      -       +      +
    516A  TYR*     3.5     6.7    -      -       -      +
    518A  LEU*     1.3    76.6    -      -       -      +
    520A  ILE*     1.3    63.3    +      -       -      +
    522A  GLU*     3.2    30.3    +      -       -      +
    523A  LEU*     2.9    39.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 520 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LYS*     5.3     1.6    -      -       -      +
    186A  LEU*     3.7    15.7    -      -       +      +
    189A  CYS*     3.7    14.8    -      -       +      +
    190A  ALA*     3.7    27.1    -      -       +      +
    193A  ASP*     4.8     3.4    -      -       -      +
    194A  THR      4.7     5.2    -      -       -      +
    516A  TYR*     2.9    49.5    +      -       +      +
    517A  ARG*     3.7     6.3    -      -       -      +
    519A  LYS*     1.3    74.7    -      -       -      +
    521A  VAL*     1.3    59.1    +      -       +      +
    523A  LEU*     3.2     4.8    +      -       +      +
    524A  GLN*     2.8    57.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 521 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LYS*     6.2     1.8    -      -       -      +
    517A  ARG*     3.0    24.1    +      -       +      +
    518A  LEU*     3.6    16.4    -      -       +      +
    520A  ILE*     1.3    76.2    -      -       +      +
    522A  GLU*     1.3    63.0    +      -       -      +
    524A  GLN*     3.2     9.1    +      -       -      +
    525A  ARG*     2.9    67.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 522 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    518A  LEU      3.0    13.3    +      -       -      +
    519A  LYS*     3.5    37.7    +      -       -      +
    521A  VAL*     1.3    80.0    -      -       -      +
    523A  LEU*     1.3    59.5    +      -       +      +
    525A  ARG*     3.7     7.6    -      -       -      +
    526A  ASN*     3.0    49.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 523 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  GLU*     3.4    25.4    -      -       -      +
    186A  LEU*     3.6    40.2    -      -       +      +
    187A  GLN*     3.7    24.2    +      -       -      +
    190A  ALA*     3.6    16.2    -      -       +      -
    519A  LYS*     2.9    36.8    +      -       +      +
    520A  ILE*     3.7     1.3    -      -       -      +
    522A  GLU*     1.3    75.3    -      -       +      +
    524A  GLN*     1.3    61.8    +      -       -      +
    526A  ASN*     3.4    14.5    +      -       +      +
    527A  ALA*     2.9    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 524 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  LEU*     3.4    23.6    -      -       +      +
    153A  LYS*     3.1    20.1    +      -       -      -
    154A  LEU*     4.0    21.0    -      -       +      +
    190A  ALA*     3.0    33.3    +      -       +      +
    193A  ASP*     3.0    25.0    +      -       -      +
    520A  ILE*     2.8    39.0    +      -       -      +
    521A  VAL*     3.8     7.2    -      -       -      +
    523A  LEU*     1.3    69.8    -      -       -      +
    525A  ARG*     1.3    66.4    +      -       -      +
    527A  ALA*     3.2     7.0    +      -       -      +
    528A  VAL*     3.1    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 525 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  LEU*     3.9    19.4    -      -       +      +
    521A  VAL*     2.9    46.6    +      -       +      +
    522A  GLU*     3.7     6.7    -      -       -      +
    524A  GLN*     1.3    77.4    -      -       -      +
    526A  ASN*     1.3    64.5    +      -       -      +
    528A  VAL*     3.3     5.1    +      -       +      +
    529A  LEU*     3.0    35.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 526 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    522A  GLU*     3.0    39.0    +      -       -      +
    523A  LEU*     3.7    15.6    -      -       +      +
    525A  ARG*     1.3    78.1    -      -       -      +
    527A  ALA*     1.3    56.9    +      -       -      +
    529A  LEU*     3.9    11.1    -      -       -      +
    530A  SER*     2.8    39.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 527 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  LEU*     4.0    19.6    -      -       +      +
    150A  LEU*     4.6     7.0    -      -       +      -
    187A  GLN*     5.0    11.0    -      -       -      +
    191A  ASN*     5.1     3.8    -      -       -      +
    523A  LEU      2.9    16.8    +      -       -      +
    524A  GLN*     3.2     9.1    +      -       -      +
    526A  ASN*     1.3    77.9    -      -       -      +
    528A  VAL*     1.3    56.9    +      -       -      +
    530A  SER*     3.4     5.1    +      -       -      -
    531A  TRP*     3.0    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 528 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  LEU*     4.0    19.3    -      -       +      -
    150A  LEU*     4.0    20.6    -      -       +      -
    151A  GLN*     4.0    26.1    +      -       +      +
    154A  LEU*     3.9    19.5    -      -       +      -
    524A  GLN      3.1    15.9    +      -       -      +
    525A  ARG*     3.4    13.7    -      -       +      +
    527A  ALA*     1.3    76.2    -      -       +      +
    529A  LEU*     1.3    67.2    +      -       +      +
    531A  TRP*     3.6     6.2    +      -       -      +
    532A  GLN*     3.3    26.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 529 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525A  ARG*     3.0    29.0    +      -       +      +
    526A  ASN*     3.9    11.0    -      -       -      +
    528A  VAL*     1.3    80.6    -      -       +      +
    530A  SER*     1.3    64.7    +      -       -      +
    532A  GLN*     3.2    12.1    +      -       +      +
    533A  VAL*     3.1    27.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 530 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    526A  ASN*     2.8    29.9    +      -       -      +
    527A  ALA*     3.8     5.8    -      -       -      -
    529A  LEU*     1.3    73.0    -      -       -      +
    531A  TRP*     1.3    56.9    +      -       -      +
    533A  VAL*     3.3     8.6    +      -       -      +
    534A  LYS*     2.9    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 531 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  GLU*     6.0     0.4    -      -       -      -
    147A  LEU*     3.2    32.3    -      -       +      +
    151A  GLN*     3.2    31.6    -      -       -      +
    527A  ALA      3.0    17.6    +      -       -      +
    528A  VAL*     3.7     5.8    -      -       -      +
    530A  SER*     1.3    77.6    -      -       -      +
    532A  GLN*     1.3    89.4    +      -       +      +
    534A  LYS*     3.3     9.3    +      -       +      +
    535A  GLU*     2.9    63.3    +      -       +      +
    706A  EDO      3.6    19.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 532 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  GLN*     4.1     6.7    -      -       -      +
    528A  VAL      3.3    13.8    +      -       -      +
    529A  LEU*     3.2    14.2    +      -       +      +
    531A  TRP*     1.3   107.8    -      -       -      +
    533A  VAL*     1.3    58.2    +      -       +      +
    535A  GLU*     3.3     5.3    +      -       -      +
    536A  ALA*     3.0    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 533 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    529A  LEU*     3.1    15.3    +      -       +      +
    530A  SER*     3.7     9.9    -      -       -      +
    531A  TRP      3.3     0.2    -      -       -      -
    532A  GLN*     1.3    74.1    -      -       +      +
    534A  LYS*     1.3    67.8    +      -       -      +
    536A  ALA*     3.3     8.2    +      -       -      +
    537A  ARG*     3.0    25.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 534 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  GLU*     2.6    37.6    +      -       -      +
    530A  SER      2.9    17.8    +      -       -      +
    531A  TRP*     3.7    10.1    -      -       +      +
    533A  VAL*     1.3    78.2    -      -       -      +
    535A  GLU*     1.3    62.7    +      -       -      +
    537A  ARG*     3.2    10.4    +      -       +      +
    538A  SER*     3.0    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 535 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    531A  TRP*     2.9    67.4    +      -       +      +
    532A  GLN*     3.7     7.4    -      -       -      +
    534A  LYS*     1.3    83.8    -      -       -      +
    536A  ALA*     1.3    57.8    +      -       -      +
    538A  SER*     3.4     9.8    +      -       -      -
    539A  SER*     2.9    30.0    +      -       -      -
    542A  ARG*     5.0     4.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 536 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532A  GLN      3.0    17.4    +      -       -      +
    533A  VAL*     3.6     7.6    -      -       -      +
    535A  GLU*     1.3    77.0    -      -       -      +
    537A  ARG*     1.3    56.3    +      -       -      +
    539A  SER*     3.3     6.6    +      -       -      -
    540A  GLU*     3.0    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 537 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533A  VAL*     3.0    19.7    +      -       +      +
    534A  LYS*     3.7     9.2    -      -       -      +
    536A  ALA*     1.3    72.7    -      -       -      +
    538A  SER*     1.3    65.8    +      -       -      +
    540A  GLU*     3.3    11.3    +      -       -      +
    541A  ARG*     3.1    23.0    +      -       +      +
      1Y    G      3.9    21.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 538 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534A  LYS*     3.0    26.2    +      -       -      +
    535A  GLU*     3.7    12.8    +      -       -      -
    537A  ARG*     1.3    78.8    -      -       -      +
    539A  SER*     1.3    61.4    +      -       -      +
    541A  ARG*     3.4     7.5    +      -       -      +
    542A  ARG*     3.1    42.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 539 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535A  GLU      2.9    19.5    +      -       -      -
    536A  ALA*     3.6     7.0    -      -       -      -
    538A  SER*     1.3    73.9    -      -       -      +
    540A  GLU*     1.3    65.3    +      -       -      +
    542A  ARG*     3.2    21.8    +      -       -      +
    543A  GLN*     3.1    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 540 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536A  ALA      3.0    17.1    +      -       -      +
    537A  ARG*     3.3    10.1    +      -       -      +
    539A  SER*     1.3    76.9    -      -       -      +
    541A  ARG*     1.3    63.1    +      -       -      +
    543A  GLN*     3.3    12.0    +      -       -      +
    544A  LEU*     3.6    23.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 541 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537A  ARG*     3.1    13.2    +      -       +      +
    538A  SER*     3.7    10.8    -      -       -      +
    540A  GLU*     1.3    77.9    -      -       -      +
    542A  ARG*     1.3    61.9    +      -       -      +
    543A  GLN      3.3     0.9    +      -       -      -
    544A  LEU*     3.3    23.2    +      -       +      +
    643A  GLU*     5.6     2.8    +      -       -      -
    645A  LYS*     3.6    23.4    -      -       -      +
    647A  TYR*     3.4    19.2    +      -       -      -
    652A  THR*     3.0    36.8    +      -       -      +
    653A  VAL      4.5     1.8    -      -       -      +
    654A  THR*     3.2    34.9    -      -       +      +
      1Y    G      5.2    12.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 542 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535A  GLU*     5.0     4.6    +      -       -      -
    538A  SER*     3.1    36.5    +      -       -      +
    539A  SER*     3.2    32.7    +      -       -      +
    541A  ARG*     1.3    76.8    -      -       -      +
    543A  GLN*     1.3    69.1    -      -       -      +
    544A  LEU      3.4     0.4    -      -       -      -
    651A  SER      5.0    11.3    +      -       -      -
    653A  VAL*     3.9    15.0    -      -       +      +
    654A  THR      4.0     0.2    -      -       -      -
    655A  PHE*     2.9    44.1    -      -       -      +
    656A  PRO*     3.1    14.2    -      -       +      +
    657A  ILE      5.4     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 543 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    539A  SER*     3.1    26.8    +      -       -      +
    540A  GLU*     3.3     6.5    +      -       -      +
    541A  ARG      3.2     0.6    -      -       -      -
    542A  ARG*     1.3    91.2    -      -       -      +
    544A  LEU*     1.3    62.2    +      -       -      +
    545A  HIS*     3.3     6.6    +      -       -      +
    656A  PRO*     3.8    32.5    -      -       -      +
----------------------------------------------------------
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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