Contacts of the helix formed by residues 89 - 115 (chain A) in PDB entry 2F3M


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 89 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  GLU*     1.3    83.6    -      -       +      +
     90A  GLU*     1.3    65.8    +      -       -      +
     91A  GLU*     2.9    18.4    +      -       -      +
     92A  GLU*     3.1    32.8    +      -       +      +
     93A  LYS*     3.2    22.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  THR*     1.3    74.8    +      -       -      +
     91A  GLU*     1.3    66.7    +      -       -      +
     93A  LYS*     3.1     8.9    +      -       -      +
     94A  ILE*     3.1    29.9    +      -       +      +
     67B  HIS*     4.8    10.3    -      -       +      +
     78B  TYR*     3.6    22.5    -      -       +      +
     81B  ARG*     3.1    46.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  THR*     2.9     7.4    +      -       -      +
     90A  GLU*     1.3    80.8    -      -       -      +
     92A  GLU*     1.3    62.2    +      -       +      +
     94A  ILE*     3.4     9.5    +      -       -      +
     95A  ARG*     3.2    42.9    +      -       -      +
     67B  HIS*     3.4    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  GLY*     3.7     7.2    -      -       -      -
     88A  GLU*     2.9    39.5    +      -       -      +
     89A  THR*     3.1    39.6    +      -       +      +
     91A  GLU*     1.3    78.5    -      -       +      +
     93A  LYS*     1.3    57.1    +      -       -      +
     95A  ARG*     3.4     2.8    +      -       -      +
     96A  VAL*     3.0    33.6    +      -       -      +
    148A  ALA*     3.9    28.7    -      -       +      +
    149A  GLY*     5.5     2.6    -      -       -      -
    150A  ASN      5.4     1.9    +      -       -      -
    151A  LYS*     4.7    16.0    +      -       -      +
    153A  THR*     4.6     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  CYS      4.2     9.4    -      -       -      +
     87A  GLY      3.6    23.1    -      -       -      +
     88A  GLU      4.0     7.7    +      -       -      +
     89A  THR      3.2    15.7    +      -       -      +
     90A  GLU*     3.1    12.0    +      -       -      +
     92A  GLU*     1.3    77.5    -      -       -      +
     94A  ILE*     1.3    58.7    +      -       -      +
     96A  VAL*     3.3     7.0    +      -       +      +
     97A  ASP*     2.8    35.6    +      -       -      +
     81B  ARG*     3.8    40.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  GLU*     3.1    27.1    +      -       +      +
     91A  GLU*     3.7    13.0    -      -       -      +
     93A  LYS*     1.3    77.0    -      -       -      +
     95A  ARG*     1.3    67.9    +      -       +      +
     97A  ASP*     3.1     5.1    +      -       -      +
     98A  ILE*     2.9    43.0    +      -       +      +
     67B  HIS*     3.1    38.4    -      -       +      +
     68B  LYS      5.4     0.7    -      -       -      +
     69B  ILE*     3.9    18.2    -      -       +      -
     74B  ALA*     6.2     0.4    -      -       +      -
     78B  TYR*     3.7    22.4    -      -       +      -
     81B  ARG*     3.9     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  GLU*     3.2    30.8    +      -       -      +
     92A  GLU      3.7     6.3    -      -       -      +
     94A  ILE*     1.3    83.2    -      -       +      +
     96A  VAL*     1.3    61.8    +      -       -      +
     98A  ILE*     3.3     4.9    +      -       +      +
     99A  LEU*     2.9    30.9    +      -       +      +
    140A  PHE*     2.9    67.3    +      -       +      -
    141A  LEU*     4.6     1.2    -      -       -      +
    144A  ARG*     3.3    35.2    -      -       -      +
    147A  PHE      2.7    32.3    +      -       -      +
    148A  ALA*     3.4    21.2    +      -       -      -
    155A  VAL*     5.4     0.2    -      -       -      -
     55B  ASP*     5.4     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  CYS*     4.1    23.6    -      -       -      +
     87A  GLY*     4.7     1.3    -      -       -      -
     92A  GLU      3.0    19.4    +      -       -      +
     93A  LYS*     3.5     9.9    -      -       -      +
     94A  ILE      3.2     0.2    -      -       -      -
     95A  ARG*     1.3    76.6    -      -       -      +
     97A  ASP*     1.3    64.1    +      -       -      +
    100A  GLU*     2.8    34.7    +      -       -      +
    148A  ALA*     4.4     7.0    -      -       +      -
    153A  THR*     4.4    11.4    -      -       -      +
    154A  PHE*     3.6    31.9    -      -       +      -
    155A  VAL*     3.5    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  LYS*     2.8    22.1    +      -       -      +
     94A  ILE*     3.6     5.6    -      -       -      +
     96A  VAL*     1.3    78.9    -      -       -      +
     98A  ILE*     1.3    61.9    +      -       -      +
    100A  GLU*     3.4    16.1    -      -       -      +
    101A  ASN*     2.8    30.3    +      -       -      +
     74B  ALA*     3.7    22.7    -      -       +      +
     77B  CYS*     3.7    18.6    -      -       -      +
     81B  ARG*     3.1    32.8    +      -       -      -
    100B  GLU*     5.6     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ILE*     2.9    35.6    +      -       +      +
     95A  ARG*     3.6     9.4    -      -       +      +
     97A  ASP*     1.3    76.5    -      -       -      +
     99A  LEU*     1.3    53.1    +      -       -      +
    101A  ASN*     3.0     4.7    +      -       -      -
    102A  GLN*     2.7    35.2    +      -       +      +
    140A  PHE*     5.1    10.1    -      -       +      -
     55B  ASP*     5.2     8.7    -      -       +      +
     56B  PHE*     3.9    29.6    -      -       +      +
     68B  LYS      4.5     5.4    -      -       -      +
     69B  ILE*     4.5     7.0    -      -       +      -
     70B  THR*     3.8    37.0    -      -       -      +
     71B  GLN*     3.8     9.6    -      -       +      +
     74B  ALA*     4.1     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  ARG      2.9    17.1    +      -       -      +
     98A  ILE*     1.3    71.1    -      -       -      +
    100A  GLU*     1.3    67.7    +      -       -      +
    102A  GLN*     3.9     4.5    -      -       +      -
    103A  THR*     2.9    30.2    +      -       -      +
    137A  TYR*     4.0    19.3    -      -       +      -
    140A  PHE*     3.5    34.8    -      -       +      -
    147A  PHE*     3.3    37.9    -      -       +      -
    155A  VAL*     3.9    24.5    -      -       +      -
    158A  LEU*     5.4     0.2    -      -       -      -
    159A  VAL*     4.0    11.9    -      -       +      -
     56B  PHE*     4.0    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ASN*     3.1    60.4    +      -       -      +
     77A  CYS*     4.9     4.6    -      -       -      +
     96A  VAL*     2.8    18.1    +      -       -      +
     97A  ASP*     3.4    24.5    -      -       -      +
     99A  LEU*     1.3    77.8    -      -       -      +
    101A  ASN*     1.3    67.1    +      -       -      +
    103A  THR*     3.4    10.4    +      -       -      -
    104A  MET*     3.7     4.5    -      -       -      +
    154A  PHE*     3.9    21.6    -      -       +      -
    155A  VAL*     3.7    11.4    -      -       +      +
    158A  LEU*     4.2     5.6    -      -       -      -
     97B  ASP*     5.8     2.6    -      -       -      +
    100B  GLU*     4.9    15.4    -      -       -      +
    101B  ASN*     5.1     2.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ASN*     4.6     4.0    +      -       -      -
     97A  ASP*     2.8    24.5    +      -       -      +
     98A  ILE      3.0     2.4    +      -       -      +
    100A  GLU*     1.3    86.8    +      -       -      +
    102A  GLN*     1.3    67.4    +      -       -      +
    103A  THR      3.4     0.4    -      -       -      -
    104A  MET*     3.3     7.8    +      -       -      +
    105A  ASP*     3.1    26.4    +      -       -      +
     71B  GLN*     3.3    29.2    -      -       +      +
     73B  ASN*     3.9    36.1    +      -       -      +
     74B  ALA      4.1     7.5    -      -       -      +
    100B  GLU*     5.0     2.8    +      -       -      +
    101B  ASN*     4.5     9.0    -      -       -      +
   2218B  GTD      5.5     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ILE*     2.7    26.2    +      -       +      +
     99A  LEU*     3.9     9.2    -      -       +      +
    101A  ASN*     1.3    71.8    -      -       -      +
    103A  THR*     1.3    62.9    +      -       -      +
    105A  ASP*     3.1    15.5    +      -       -      +
    106A  ASN*     3.1    41.7    +      -       -      +
    136A  LEU*     5.5     3.2    -      -       -      +
    137A  TYR*     3.8     7.9    -      -       +      +
     56B  PHE*     3.5    54.1    -      -       +      +
     58B  ASN*     4.7     6.0    +      -       -      +
     71B  GLN*     3.1    24.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  LEU*     2.9    27.5    +      -       +      +
    100A  GLU      3.4     6.8    +      -       -      -
    102A  GLN*     1.3    72.0    -      -       -      +
    104A  MET*     1.3    65.2    +      -       -      +
    105A  ASP      3.1     0.2    +      -       -      -
    106A  ASN*     3.2     2.3    +      -       -      +
    107A  HIS*     2.8    32.9    +      -       -      +
    137A  TYR*     3.6    19.1    -      -       +      +
    158A  LEU*     3.6    27.9    -      -       +      +
    159A  VAL*     3.8    39.9    -      -       +      +
    162A  VAL*     3.9     9.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     4.6    20.6    -      -       +      -
     72A  SER*     5.1     3.6    -      -       -      +
     73A  ASN*     4.5    12.8    -      -       -      +
    100A  GLU      3.7    11.9    -      -       -      +
    101A  ASN*     3.3    14.1    +      -       -      +
    103A  THR*     1.3    81.2    +      -       -      +
    105A  ASP*     1.3    60.8    +      -       -      +
    107A  HIS*     3.6     8.4    +      -       +      +
    108A  MET*     3.0    39.6    +      -       +      +
    158A  LEU*     6.6     0.2    -      -       -      -
   1218A  GTD      3.6    39.5    -      -       +      +
    101B  ASN*     6.0     0.4    -      -       -      +
    105B  ASP*     5.4     2.9    -      -       -      +
    108B  MET*     6.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ASN      3.1    14.2    +      -       -      +
    102A  GLN*     3.4    11.4    -      -       -      +
    103A  THR      3.1     0.4    -      -       -      -
    104A  MET*     1.3    77.7    -      -       -      +
    106A  ASN*     1.3    62.8    +      -       -      +
    108A  MET*     3.2    25.1    +      -       +      +
    109A  GLN*     2.9    44.9    +      -       -      +
     58B  ASN*     4.8     2.6    +      -       -      -
     71B  GLN*     3.1    21.2    +      -       -      +
   2218B  GTD      3.2    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  GLN*     3.1    27.9    +      -       -      +
    103A  THR      3.9     4.7    -      -       -      +
    105A  ASP*     1.3    75.7    -      -       -      +
    107A  HIS*     1.3    61.8    +      -       -      +
    109A  GLN*     2.9    26.7    +      -       -      +
    110A  LEU*     3.1    22.0    +      -       -      +
    126A  TYR*     4.1     4.0    +      -       -      -
    133A  LYS*     4.0    23.4    -      -       +      +
    137A  TYR*     2.5    38.5    +      -       +      +
    162A  VAL*     4.6    11.4    -      -       +      -
    166A  HIS*     4.6     7.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLY*     4.2    15.0    -      -       -      -
     12A  LEU*     3.6    31.5    -      -       +      +
    103A  THR      2.8    18.8    +      -       -      +
    104A  MET*     3.7    11.0    -      -       +      +
    106A  ASN*     1.3    73.2    -      -       -      +
    108A  MET*     1.3    68.1    +      -       -      +
    110A  LEU*     3.1     9.1    +      -       -      +
    111A  GLY      2.8    19.1    +      -       -      -
    161A  ASP*     4.1     7.4    +      -       -      -
    162A  VAL*     4.1    13.5    -      -       +      +
    165A  LEU*     3.9    28.1    -      -       +      +
    166A  HIS*     6.0     0.2    -      -       -      -
    207A  VAL*     6.1     0.2    -      -       +      -
    208A  PHE*     4.1    15.4    -      +       -      -
   1218A  GTD      3.8    27.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  MET*     3.0    27.3    +      -       +      +
    105A  ASP*     3.3    33.9    -      -       +      +
    107A  HIS*     1.3    75.1    -      -       +      +
    109A  GLN*     1.3    54.4    +      -       +      +
    111A  GLY      3.0     1.9    +      -       -      -
    112A  MET*     2.7    56.3    +      -       +      +
   1218A  GTD      3.9    17.8    +      -       -      +
    108B  MET*     3.3    40.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  ASP*     2.9    29.0    +      -       -      +
    106A  ASN*     2.9    33.7    +      -       -      +
    108A  MET*     1.3    79.5    -      -       +      +
    110A  LEU*     1.3    63.7    +      -       -      +
    112A  MET*     3.3    33.8    +      -       +      +
    113A  ILE*     3.6     8.5    +      -       -      +
    126A  TYR*     3.8    11.1    -      -       +      -
    133A  LYS*     2.9    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ASN      3.1     7.8    +      -       -      +
    107A  HIS*     3.1    11.5    +      -       +      +
    109A  GLN*     1.3    77.4    -      -       -      +
    111A  GLY*     1.3    65.9    +      -       -      +
    112A  MET      3.0     1.2    +      -       -      -
    113A  ILE*     3.2     9.4    +      -       +      +
    114A  CYS*     3.1    33.7    +      -       -      +
    126A  TYR*     3.2    36.7    +      -       +      +
    162A  VAL*     6.6     0.2    -      -       +      -
    165A  LEU*     4.1    29.6    -      -       +      +
    166A  HIS*     3.9    24.0    -      -       +      +
    169A  PHE*     4.5    14.4    -      -       +      -
    208A  PHE*     4.1    19.5    -      -       +      -
    214A  TRP*     5.2     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  HIS      2.8    13.4    +      -       -      -
    108A  MET      3.4     3.6    -      -       -      -
    110A  LEU*     1.3    77.2    -      -       -      +
    112A  MET*     1.3    63.0    +      -       -      +
    113A  ILE      3.4     0.2    -      -       -      -
    114A  CYS*     4.0     0.9    -      -       -      -
    115A  TYR*     2.9    35.7    +      -       -      +
    208A  PHE*     3.9    24.8    -      -       -      -
   1218A  GTD      4.1    12.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  MET*     2.7    32.4    +      -       +      +
    109A  GLN*     3.5    35.9    -      -       +      +
    110A  LEU      3.0     1.0    +      -       -      -
    111A  GLY*     1.3    75.3    -      -       -      +
    113A  ILE*     1.3    65.3    +      -       +      +
    115A  TYR*     3.6     3.3    +      -       -      +
    116A  ASN*     3.3    21.8    +      -       -      +
   1218A  GTD      4.7     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  GLN      3.9    11.2    -      -       -      +
    110A  LEU*     3.2    10.7    +      -       +      +
    112A  MET*     1.3    75.5    -      -       +      +
    114A  CYS*     1.3    64.1    +      -       -      +
    115A  TYR      3.0     4.7    -      -       -      -
    116A  ASN*     2.9    32.8    +      -       -      +
    119A  PHE*     3.3    31.1    -      -       +      +
    122A  LEU*     4.4    24.9    -      -       +      -
    123A  LYS*     4.5    14.1    -      -       -      +
    126A  TYR*     3.8    43.5    -      -       +      -
    169A  PHE*     4.9     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  LEU*     3.1    28.9    +      -       -      +
    111A  GLY      4.0     2.2    -      -       -      +
    113A  ILE*     1.3    82.0    -      -       -      +
    115A  TYR*     1.3    58.4    +      -       -      +
    119A  PHE*     3.7    24.0    -      -       -      -
    169A  PHE*     4.0     2.2    -      -       -      -
    208A  PHE*     3.6    27.6    -      -       +      -
    212A  ALA*     3.5     5.4    -      -       -      +
    213A  VAL*     2.9    26.7    +      -       -      -
    214A  TRP*     3.4    37.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  GLY*     2.9    28.6    +      -       -      +
    112A  MET*     4.0     3.4    -      -       -      +
    113A  ILE      3.0     0.6    -      -       -      -
    114A  CYS*     1.3    78.6    -      -       -      +
    116A  ASN*     1.3    59.7    +      -       -      +
    117A  PRO*     3.4    11.4    -      -       -      +
    208A  PHE*     3.4    29.1    -      +       +      +
    209A  SER*     3.0    36.0    +      -       -      -
    211A  MET*     4.1    35.2    -      -       +      +
    212A  ALA*     4.2    13.0    -      -       -      +
    213A  VAL*     4.9     4.1    -      -       -      +
   1218A  GTD      2.8    54.7    +      -       -      +
----------------------------------------------------------
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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