Contacts of the strand formed by residues 201 - 226 (chain D) in PDB entry 4OIP


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 GLY 201 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184D  GLU*     3.4    10.4    -      -       -      -
    185D  VAL*     2.6    47.9    +      -       -      +
    200D  ASP*     1.3    74.8    -      -       -      +
    202D  VAL*     1.3    60.4    +      -       -      -
    395D  VAL*     4.6     3.1    -      -       -      +
    396D  VAL      3.3     9.9    -      -       -      -
    397D  LYS*     4.3     4.9    -      -       -      -
    398D  ALA      4.9     2.2    -      -       -      -
    399D  ARG*     6.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182D  GLY*     3.7    20.0    -      -       -      +
    183D  GLU      4.3     2.2    -      -       -      -
    184D  GLU*     3.3    28.9    -      -       -      +
    201D  GLY*     1.3    71.1    -      -       -      -
    203D  ALA*     1.3    70.1    +      -       -      +
    204D  LEU*     3.7    20.7    +      -       +      +
    394D  LEU      3.7     2.1    -      -       -      +
    395D  VAL*     4.7     0.9    -      -       -      -
    396D  VAL*     2.8    31.6    +      -       +      +
    398D  ALA*     3.7    27.1    -      -       +      +
    400D  VAL*     4.2    24.0    -      -       +      +
    445D  ARG*     5.5     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 203 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179D  VAL*     4.7     8.1    -      -       +      -
    180D  LYS      4.9     4.7    -      -       -      +
    181D  ASP*     4.0     1.7    -      -       -      -
    182D  GLY*     3.0    27.0    +      -       -      -
    183D  GLU      3.6    11.0    +      -       -      +
    185D  VAL*     3.6    22.4    -      -       +      +
    191D  LEU*     4.3     9.0    -      -       +      -
    201D  GLY      3.7     2.6    +      -       -      -
    202D  VAL*     1.3    74.1    -      -       -      +
    204D  LEU*     1.3    65.2    +      -       -      +
    205D  TYR*     6.4     0.4    -      -       +      -
    393D  ILE*     4.1    17.0    -      -       +      -
    394D  LEU      3.7     4.5    -      -       -      -
    395D  VAL*     4.4     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181D  ASP*     3.4     5.8    -      -       -      +
    182D  GLY*     4.6     3.4    -      -       -      +
    202D  VAL*     4.0    19.7    -      -       +      +
    203D  ALA*     1.3    84.5    -      -       -      +
    205D  TYR*     1.3    67.5    +      -       -      +
    206D  ARG*     3.6     6.2    +      -       -      +
    393D  ILE*     3.5     4.1    -      -       -      +
    394D  LEU*     2.9    48.6    +      -       +      +
    396D  VAL*     4.6    14.8    -      -       +      -
    436D  GLU*     5.6     0.2    -      -       -      +
    441D  ARG*     3.8    31.2    -      -       -      +
    445D  ARG*     3.5    43.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 205 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176D  ASP*     4.9     2.3    +      -       -      -
    177D  ALA*     3.5    17.9    +      -       +      +
    179D  VAL*     2.7    27.7    +      -       +      -
    180D  LYS*     3.8     8.9    -      -       +      +
    181D  ASP*     2.6    46.3    +      -       +      +
    203D  ALA*     6.0     0.4    -      -       +      -
    204D  LEU*     1.3    74.4    -      -       -      +
    206D  ARG*     1.3    71.0    +      -       -      +
    207D  PHE      4.0     1.7    +      -       -      -
    208D  PRO*     4.6    13.3    -      -       +      +
    357D  GLU*     5.2     2.5    -      -       -      -
    387D  LEU*     3.3    43.1    +      -       +      -
    390D  PRO*     3.7    34.1    -      -       +      -
    392D  SER      4.2     0.7    -      -       -      -
    393D  ILE*     4.5    12.1    -      -       +      -
    441D  ARG*     3.6    12.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 206 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168D  THR*     5.1     3.6    -      -       +      -
    204D  LEU*     4.9     5.9    +      -       -      +
    205D  TYR*     1.3    86.9    +      -       -      +
    207D  PHE*     1.3    80.9    +      -       +      +
    208D  PRO      3.7     0.4    -      -       -      -
    390D  PRO*     4.4     0.8    -      -       -      +
    391D  ALA*     2.9    24.3    +      -       -      +
    392D  SER*     2.9    43.0    +      -       -      +
    394D  LEU*     3.8    44.0    -      -       +      +
    441D  ARG*     4.4    18.4    -      -       -      +
    445D  ARG*     5.7     2.2    -      -       -      +
     98F  GLU*     6.1     1.1    -      -       -      -
    101F  GLU*     3.2    31.6    +      -       -      -
    105F  LYS*     5.7     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 207 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205D  TYR      4.0     1.0    +      -       -      -
    206D  ARG*     1.3    98.1    -      -       +      +
    208D  PRO*     1.3    76.1    -      -       -      +
    209D  ARG*     3.5     5.2    +      -       -      -
    347D  VAL*     6.3     0.2    -      -       -      -
    349D  PRO      5.9     1.3    -      -       -      -
    351D  MET      5.8     3.8    -      -       -      -
    391D  ALA*     2.9    26.4    +      -       +      +
    392D  SER*     4.7     3.1    -      -       -      -
     97F  GLU*     3.7    34.1    -      -       +      +
     98F  GLU*     3.7    34.3    -      -       +      -
    101F  GLU*     3.1    50.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 208 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205D  TYR*     4.6    14.6    -      -       +      +
    206D  ARG      3.7     2.4    -      -       -      -
    207D  PHE*     1.3    88.7    -      -       -      +
    209D  ARG*     1.3    63.3    +      -       -      +
    210D  ARG      3.4     1.9    -      -       -      +
    211D  VAL*     5.0     0.2    -      -       -      +
    347D  VAL*     3.6    19.9    -      -       -      +
    353D  VAL*     4.3    15.4    -      -       +      +
    387D  LEU*     3.9    38.1    -      -       +      -
    388D  HIS      3.4    17.9    -      -       -      +
    389D  GLU      3.2     7.0    -      -       -      +
    390D  PRO*     3.5    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 209 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171D  LEU      4.8     5.7    +      -       -      -
    172D  PRO      6.0     0.6    -      -       -      -
    173D  PRO*     5.2    12.7    -      -       -      +
    207D  PHE      4.3     1.8    -      -       -      +
    208D  PRO*     1.3    73.4    -      -       -      +
    210D  ARG*     1.3    56.1    +      -       -      +
    346D  ARG*     3.3    27.9    -      -       -      +
    347D  VAL*     2.4    47.6    +      -       -      +
    349D  PRO*     6.0     3.6    -      -       -      -
    389D  GLU*     2.6    37.9    +      -       +      +
    391D  ALA*     3.5    32.9    +      -       -      +
     97F  GLU*     3.3    24.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 210 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176D  ASP*     3.4    10.3    +      -       -      +
    208D  PRO*     4.6     1.1    -      -       -      +
    209D  ARG*     1.3    79.6    -      -       -      +
    211D  VAL*     1.3    66.1    +      -       -      +
    212D  ARG*     3.4    38.7    -      -       -      +
    344D  ASP*     3.5    35.6    +      -       +      +
    345D  TYR      3.4     8.1    -      -       -      +
    346D  ARG*     3.7    30.4    -      -       -      +
    387D  LEU*     4.1     0.3    -      -       -      -
    388D  HIS*     2.9    73.6    +      -       -      +
    389D  GLU*     4.1     7.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 211 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208D  PRO      5.0     1.3    -      -       -      +
    210D  ARG*     1.3    73.2    -      -       -      +
    212D  ARG*     1.3    59.8    +      -       -      +
    213D  VAL*     4.2     8.5    -      -       +      -
    343D  LYS      3.5     4.5    -      -       -      +
    345D  TYR*     2.9    47.0    +      -       +      +
    347D  VAL*     3.7    24.5    -      -       +      -
    353D  VAL*     4.2    11.2    -      -       +      -
    367D  ILE*     4.0    15.7    -      -       +      -
    368D  VAL*     4.2     7.4    -      -       +      -
    385D  VAL*     3.8    29.6    -      -       +      -
    386D  HIS      3.8     4.0    -      -       -      +
    387D  LEU*     3.7    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 212 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210D  ARG*     3.4    31.0    +      -       -      +
    211D  VAL*     1.3    71.0    -      -       -      +
    213D  VAL*     1.3    62.3    +      -       -      +
    214D  GLU*     3.6    21.4    +      -       -      +
    342D  PRO*     3.3    31.9    -      -       +      +
    343D  LYS      3.6     4.0    -      -       -      +
    344D  ASP*     3.4    23.9    +      -       -      +
    385D  VAL      3.9     0.2    -      -       -      -
    386D  HIS*     2.9    52.6    +      -       +      +
    388D  HIS*     4.3    19.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 213 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211D  VAL*     4.2    10.8    -      -       +      -
    212D  ARG*     1.3    77.6    -      -       -      +
    214D  GLU*     1.3    63.2    +      -       -      +
    215D  TYR*     3.6    38.0    +      -       +      -
    341D  GLU      3.2     4.2    -      -       -      +
    342D  PRO*     3.5     0.8    -      -       -      +
    343D  LYS      2.9    34.7    +      -       -      +
    345D  TYR*     3.9    22.4    -      -       +      -
    361D  VAL*     4.6     5.6    -      -       +      -
    367D  ILE*     3.7    30.3    -      -       +      -
    384D  VAL      3.3    21.1    -      -       -      +
    385D  VAL*     4.8     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 214 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212D  ARG*     3.6    18.6    +      -       +      -
    213D  VAL*     1.3    71.7    -      -       -      +
    215D  TYR*     1.3    61.6    +      -       -      +
    216D  VAL*     3.7     2.3    +      -       -      +
    316D  GLN*     3.7    15.7    +      -       -      -
    340D  THR*     3.6    24.6    +      -       +      +
    341D  GLU      3.4    15.6    -      -       -      -
    342D  PRO*     3.4    22.0    -      -       -      +
    383D  GLY*     3.2     3.2    -      -       -      -
    384D  VAL*     2.9    48.7    +      -       +      +
    386D  HIS*     3.9    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 215 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213D  VAL*     3.7    32.4    -      -       +      +
    214D  GLU*     1.3    71.7    -      -       -      +
    216D  VAL*     1.3    64.4    +      -       -      +
    217D  LYS*     3.6    17.7    +      -       +      +
    340D  THR*     3.1     6.3    -      -       -      -
    341D  GLU*     2.9    36.2    +      -       +      +
    343D  LYS*     3.7    31.6    -      -       +      -
    345D  TYR*     3.2    24.6    +      -       -      -
    367D  ILE*     4.7     0.7    -      -       -      +
    379D  ALA*     3.9     9.2    -      -       +      -
    380D  GLU*     3.7    17.2    +      -       +      -
    381D  ALA*     3.1    54.3    -      -       +      -
    382D  GLU      3.6     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 216 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214D  GLU      4.5     0.9    -      -       -      +
    215D  TYR*     1.3    71.4    -      -       -      +
    217D  LYS*     1.3    66.3    +      -       -      +
    218D  LYS*     4.1    30.2    +      -       +      -
    338D  GLU*     6.1     1.3    -      -       +      -
    339D  TRP      3.8     7.6    -      -       -      +
    340D  THR*     4.1    13.5    -      -       +      -
    360D  ARG*     4.3    18.4    -      -       -      +
    381D  ALA*     5.6     3.1    -      -       -      +
    382D  GLU*     2.9    24.7    +      -       +      +
    383D  GLY*     3.9    19.5    -      -       -      +
    384D  VAL*     5.1     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 217 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215D  TYR*     4.0    16.4    -      -       +      +
    216D  VAL*     1.3    79.2    -      -       -      +
    218D  LYS*     1.3    62.2    +      -       -      +
    219D  GLU*     5.2     3.4    -      -       +      -
    262D  LYS*     3.8    13.7    -      -       -      +
    338D  GLU*     3.4     1.4    -      -       -      -
    339D  TRP*     2.9    70.4    +      -       +      +
    341D  GLU*     3.4    47.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 218 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216D  VAL*     4.1    21.1    -      -       +      -
    217D  LYS*     1.3    75.6    -      -       -      +
    219D  GLU*     1.3    71.7    +      -       -      +
    337D  LEU      3.3     7.6    -      -       -      +
    338D  GLU*     3.4    37.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 219 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217D  LYS*     5.1     2.5    -      -       +      -
    218D  LYS*     1.3    82.3    -      -       -      +
    220D  ARG*     1.3    67.0    +      -       -      +
    221D  ALA*     4.3     0.4    -      -       -      -
    269D  PHE*     4.9     6.3    -      -       +      -
    281D  THR*     6.0     2.2    -      -       +      -
    336D  PHE*     3.6     6.9    -      -       -      +
    337D  LEU*     2.9    33.6    +      -       -      +
    339D  TRP*     3.6    29.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 220 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  GLU*     1.3    83.2    +      -       -      +
    221D  ALA*     1.3    64.1    +      -       -      +
    281D  THR*     3.8    17.4    -      -       -      +
    332D  TYR*     6.0     2.2    -      -       -      -
    334D  THR*     3.3    39.0    +      -       +      +
    335D  LEU      3.4     6.1    -      -       -      +
    336D  PHE*     4.2    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 221 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  GLU      4.3     0.6    -      -       -      -
    220D  ARG*     1.3    76.8    -      -       -      +
    222D  GLY*     1.3    61.1    +      -       -      +
    269D  PHE*     3.9    14.4    -      -       +      -
    281D  THR*     3.4    24.5    -      -       +      +
    283D  PHE*     3.6    27.4    -      -       +      +
    334D  THR*     4.8     1.3    -      -       -      -
    335D  LEU*     2.9    38.4    +      -       -      +
    337D  LEU*     4.3     4.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 222 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221D  ALA*     1.3    73.9    -      -       -      +
    223D  LEU*     1.3    60.2    +      -       -      -
    281D  THR      3.0    10.5    +      -       -      -
    282D  TYR*     3.3    11.2    -      -       -      +
    283D  PHE*     3.0    23.1    +      -       -      -
    332D  TYR*     3.6    24.0    +      -       -      -
    333D  LEU      3.1    11.0    -      -       -      -
    334D  THR*     4.4     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 223 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222D  GLY*     1.3    74.8    -      -       -      +
    224D  ARG*     1.3    69.4    +      -       -      +
    225D  LEU*     4.1    22.8    +      -       +      -
    242D  LEU*     3.8    29.2    -      -       +      -
    251D  PHE*     3.6    27.6    -      -       +      -
    283D  PHE*     3.7    14.1    -      -       +      +
    285D  PRO*     3.8    19.7    -      -       +      -
    288D  MET*     3.6    22.7    -      -       +      -
    331D  VAL      3.8     0.5    -      -       -      +
    332D  TYR*     3.3     9.0    -      -       -      -
    333D  LEU*     2.8    43.0    +      -       +      +
    335D  LEU*     5.6     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 224 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223D  LEU*     1.3    73.8    -      -       -      +
    225D  LEU*     1.3    71.6    +      -       -      +
    249D  TYR*     3.4    31.4    +      -       -      +
    251D  PHE*     3.2    27.4    -      -       +      +
    252D  ARG      5.9     0.4    -      -       -      +
    254D  GLU*     2.3    38.2    +      -       -      +
    327D  GLU*     3.0    37.5    +      -       -      +
    330D  THR*     2.8    42.7    +      -       -      +
    331D  VAL      3.4     7.2    -      -       -      +
    332D  TYR*     3.5    35.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 225 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223D  LEU*     4.1    26.7    -      -       +      -
    224D  ARG*     1.3    82.0    -      -       -      +
    226D  PRO*     1.3    80.4    -      -       +      +
    230D  TRP*     4.3     8.7    -      -       +      -
    242D  LEU*     4.4     8.5    -      -       +      -
    243D  ALA*     4.1    22.7    -      -       +      -
    245D  LEU*     5.1     2.9    -      -       +      -
    249D  TYR*     4.6     7.9    -      -       +      -
    251D  PHE*     6.5     0.2    -      -       +      -
    288D  MET*     5.4     3.8    -      -       -      -
    311D  LEU*     4.3    20.9    -      -       +      -
    330D  THR*     3.3     8.6    -      -       -      -
    331D  VAL*     2.9    39.6    +      -       +      +
    333D  LEU*     4.0    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 226 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225D  LEU*     1.3    91.9    -      -       +      +
    227D  LEU*     1.3    65.3    +      -       -      +
    228D  ALA*     4.3     4.5    -      -       +      +
    229D  ALA*     4.0    21.5    -      -       +      +
    230D  TRP*     3.2    21.5    +      -       -      +
    245D  LEU*     4.9     6.1    -      -       +      -
    246D  PRO*     6.4     0.7    -      -       +      -
    249D  TYR*     3.9    41.3    -      -       +      -
    329D  GLU      4.0     6.3    -      -       -      +
    330D  THR*     4.5     5.6    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il