Contacts of the helix formed by residues 359 - 392 (chain D) in PDB entry 1AM9


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

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

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LYS 359 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335C  TYR*     4.2     3.4    +      -       -      -
    339C  ILE*     3.9    20.1    -      -       +      +
    340D  ASN*     3.2    27.3    +      -       -      +
    343D  ILE*     4.1    34.5    -      -       +      -
    357D  LEU      3.7     0.6    +      -       -      -
    358D  ASN*     1.3    70.8    -      -       -      +
    360D  SER*     1.3    65.3    +      -       -      +
    362D  VAL*     3.0     5.3    +      -       -      +
    363D  LEU*     3.0    26.5    +      -       -      +
     64H    C      3.2    40.3    +      -       -      +
     65H    A      2.4    33.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 360 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335C  TYR*     5.9     1.8    -      -       -      -
    338C  SER*     3.7    40.0    +      -       -      -
    339C  ILE*     4.1     8.6    -      -       -      +
    342C  LYS*     3.1    21.0    +      -       -      +
    358D  ASN*     3.1    20.6    +      -       -      +
    359D  LYS*     1.3    79.7    -      -       -      +
    361D  ALA*     1.3    57.0    +      -       -      +
    363D  LEU*     4.4     2.0    -      -       -      -
    364D  ARG*     2.9    24.8    +      -       -      +
     63H    T      4.7     5.1    +      -       -      -
     64H    C      4.6     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 361 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357D  LEU*     3.3    22.9    -      -       +      -
    358D  ASN*     2.9    28.6    +      -       -      +
    360D  SER*     1.3    79.1    +      -       -      +
    362D  VAL*     1.3    64.8    -      -       -      +
    364D  ARG*     3.7     7.4    -      -       -      +
    365D  LYS*     3.0    31.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 362 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343D  ILE*     3.3    35.9    -      -       +      +
    346D  LEU*     3.6    14.8    -      -       +      +
    347D  LYS*     3.4    41.7    -      -       +      +
    350D  VAL*     4.3     4.4    -      -       +      +
    357D  LEU*     3.8    22.0    -      -       +      +
    358D  ASN      3.0    18.1    +      -       -      +
    359D  LYS*     3.4     6.7    -      -       -      +
    361D  ALA*     1.3    77.7    -      -       -      +
    363D  LEU*     1.3    59.1    +      -       -      +
    365D  LYS*     3.2     2.4    +      -       -      +
    366D  ALA*     2.8    27.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 363 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  ILE*     3.7    45.8    -      -       +      +
    342C  LYS*     3.5    18.6    -      -       +      -
    343C  ILE*     4.1     7.0    -      -       +      -
    346C  LEU*     4.0    10.5    -      -       +      +
    363C  LEU*     3.9    27.8    -      -       +      -
    343D  ILE*     4.2    17.5    -      -       +      -
    346D  LEU*     4.0    10.1    -      -       +      -
    359D  LYS      3.0    15.1    +      -       -      +
    360D  SER*     3.7     5.2    -      -       -      +
    362D  VAL*     1.3    74.7    -      -       -      +
    364D  ARG*     1.3    57.1    +      -       -      +
    366D  ALA*     3.3     5.5    +      -       -      +
    367D  ILE*     2.8    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 364 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342C  LYS*     3.5    23.9    -      -       -      +
    345C  GLU*     2.9    32.1    +      -       -      -
    360D  SER      2.9    22.3    +      -       -      +
    361D  ALA*     3.7     8.3    -      -       -      +
    363D  LEU*     1.3    70.8    -      -       -      +
    365D  LYS*     1.3    61.5    +      -       +      +
    367D  ILE*     3.3    24.3    +      -       -      +
    368D  ASP*     2.9    68.2    +      -       -      +
    371D  ARG*     3.7     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 365 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350D  VAL*     3.9    21.5    +      -       +      +
    351D  VAL*     3.5    27.1    -      -       +      +
    357D  LEU*     3.4    32.1    -      -       +      -
    361D  ALA*     3.0    14.5    +      -       +      +
    362D  VAL      3.5     3.6    -      -       -      +
    364D  ARG*     1.3    76.1    -      -       +      +
    366D  ALA*     1.3    56.0    +      -       -      +
    368D  ASP*     3.1     5.8    +      -       -      +
    369D  TYR*     2.7    36.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 366 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346C  LEU*     4.7     6.7    -      -       +      -
    370C  ILE*     4.1     6.3    -      -       +      -
    346D  LEU*     3.9    37.7    -      -       +      -
    350D  VAL*     3.9    13.6    -      -       +      +
    362D  VAL      2.8    20.5    +      -       -      +
    363D  LEU*     3.6     4.7    -      -       -      +
    365D  LYS*     1.3    72.0    -      -       -      +
    367D  ILE*     1.3    63.7    +      -       -      +
    369D  TYR*     3.7     2.3    -      -       -      +
    370D  ILE*     3.0    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 367 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342C  LYS*     3.5    21.8    -      -       +      +
    345C  GLU*     3.3    36.8    -      -       +      +
    346C  LEU*     3.6    25.4    -      -       +      -
    349C  LEU*     4.0     6.2    -      -       +      +
    363D  LEU      2.8    25.2    +      -       -      +
    364D  ARG*     3.4    16.4    -      -       -      +
    366D  ALA*     1.3    77.9    -      -       -      +
    368D  ASP*     1.3    57.1    +      -       -      +
    370D  ILE*     3.4     2.4    +      -       -      +
    371D  ARG*     3.0    69.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 368 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364D  ARG*     2.9    53.9    +      -       -      +
    365D  LYS*     3.9     5.6    -      -       -      +
    367D  ILE*     1.3    73.2    -      -       -      +
    369D  TYR*     1.3    60.4    +      -       -      +
    371D  ARG*     3.6    17.3    +      -       -      +
    372D  PHE*     2.8    30.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 369 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370C  ILE*     3.8    23.3    -      -       +      -
    374C  GLN*     2.8    37.5    +      -       -      +
    349D  LEU      4.5     9.0    -      -       -      -
    350D  VAL*     4.3    17.5    -      -       +      -
    365D  LYS      2.7    21.7    +      -       -      +
    366D  ALA*     3.7     5.6    -      -       -      +
    368D  ASP*     1.3    71.2    -      -       -      +
    370D  ILE*     1.3    59.5    +      -       -      +
    372D  PHE*     3.2    20.3    +      +       -      -
    373D  LEU*     2.8    57.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 370 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346C  LEU*     3.5    27.1    -      -       +      -
    349C  LEU*     3.8    18.2    -      -       +      -
    350C  VAL*     5.1     0.9    -      -       +      -
    366C  ALA*     4.3    13.2    -      -       +      +
    369C  TYR*     3.7    33.0    -      -       +      -
    370C  ILE*     3.3    29.8    -      -       +      -
    373C  LEU*     3.7    13.1    -      -       +      +
    366D  ALA*     3.0    20.5    +      -       +      +
    367D  ILE      3.6     3.4    -      -       -      +
    369D  TYR*     1.3    76.6    -      -       -      +
    371D  ARG*     1.3    58.3    +      -       -      +
    373D  LEU*     3.3     1.7    +      -       -      -
    374D  GLN*     2.8    37.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 371 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345C  GLU*     2.9    40.2    +      -       -      +
    349C  LEU*     4.1    25.8    -      -       +      +
    364D  ARG*     3.7     3.0    -      -       -      +
    367D  ILE*     3.0    35.6    +      -       -      +
    368D  ASP*     3.6    19.3    +      -       -      +
    370D  ILE*     1.3    75.1    -      -       -      +
    372D  PHE*     1.3    62.3    +      -       -      +
    374D  GLN*     3.3    11.1    +      -       -      +
    375D  HIS*     3.0    40.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 372 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377C  ASN*     6.0     0.4    -      -       -      -
    368D  ASP      2.8    20.1    +      -       -      +
    369D  TYR*     3.4    28.0    -      +       -      +
    371D  ARG*     1.3    76.2    -      -       -      +
    373D  LEU*     1.3    69.0    +      -       +      +
    375D  HIS*     3.5     4.5    +      -       -      +
    376D  SER*     2.8    44.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 373 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370C  ILE*     3.9     5.6    -      -       +      +
    373C  LEU*     3.7    43.1    -      -       +      +
    374C  GLN*     3.8    15.7    -      -       +      -
    377C  ASN*     4.3    19.3    -      -       +      +
    369D  TYR*     2.8    64.2    +      -       +      +
    370D  ILE*     3.7     3.6    -      -       -      +
    372D  PHE*     1.3    79.6    -      -       +      +
    374D  GLN*     1.3    60.8    +      -       -      +
    376D  SER*     4.1     2.7    -      -       -      -
    377D  ASN*     2.8    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 374 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349C  LEU*     3.4    31.0    +      -       -      +
    369C  TYR*     2.7    43.0    +      -       -      +
    373C  LEU*     4.1    13.2    -      -       +      -
    370D  ILE*     2.8    22.8    +      -       -      +
    371D  ARG*     3.5    12.7    -      -       -      +
    373D  LEU*     1.3    76.5    -      -       -      +
    375D  HIS*     1.3    66.3    +      -       +      +
    377D  ASN*     3.8     2.5    -      -       -      +
    378D  GLN*     3.0    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 375 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371D  ARG*     3.0    29.8    +      -       +      +
    372D  PHE*     4.1     3.8    -      -       -      +
    374D  GLN*     1.3    82.0    +      -       +      +
    376D  SER*     1.3    66.2    +      -       -      +
    378D  GLN*     3.7    21.5    -      -       -      +
    379D  LYS*     2.9    27.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 376 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377C  ASN*     3.1    21.8    +      -       -      -
    381C  LYS*     5.0     3.6    -      -       -      -
    372D  PHE*     2.8    37.1    +      -       -      -
    373D  LEU*     3.7     6.1    -      -       -      -
    375D  HIS*     1.3    76.0    -      -       -      +
    377D  ASN*     1.3    58.5    +      -       -      +
    379D  LYS*     3.3     6.0    +      -       -      +
    380D  LEU*     3.0    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 377 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372C  PHE*     5.5     0.2    -      -       -      -
    373C  LEU*     3.1    42.4    +      -       +      +
    376C  SER*     3.8     9.8    +      -       -      +
    377C  ASN*     2.9    37.5    +      -       -      +
    380C  LEU*     3.3    21.1    -      -       +      +
    373D  LEU      2.8    20.6    +      -       -      +
    374D  GLN*     3.8     3.8    -      -       -      +
    376D  SER*     1.3    77.3    -      -       -      +
    378D  GLN*     1.3    55.7    +      -       -      +
    380D  LEU*     3.4     1.9    +      -       -      -
    381D  LYS*     2.9    39.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 378 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374D  GLN      3.0    17.5    +      -       -      +
    375D  HIS*     3.7    25.7    -      -       -      +
    377D  ASN*     1.3    72.5    -      -       -      +
    379D  LYS*     1.3    61.2    +      -       -      +
    381D  LYS*     3.2    11.7    +      -       +      +
    382D  GLN*     2.8    53.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 379 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375D  HIS*     2.9    17.6    +      -       +      +
    376D  SER*     3.5     6.5    -      -       -      +
    378D  GLN*     1.3    74.8    -      -       -      +
    380D  LEU*     1.3    59.6    +      -       -      +
    382D  GLN*     3.2    33.9    +      -       -      +
    383D  GLU*     2.9    44.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 380 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377C  ASN*     3.7    24.2    -      -       -      +
    380C  LEU*     3.9    23.6    -      -       +      +
    381C  LYS*     3.9    29.2    -      -       +      -
    384C  ASN*     3.8    32.5    -      -       +      +
    376D  SER*     3.0    25.4    +      -       -      +
    377D  ASN*     3.7     6.7    -      -       -      +
    378D  GLN      3.3     0.2    -      -       -      -
    379D  LYS*     1.3    77.2    -      -       +      +
    381D  LYS*     1.3    58.3    +      -       -      +
    383D  GLU*     3.6     9.1    -      -       -      +
    384D  ASN*     2.8    37.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 381 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372C  PHE*     6.3     1.4    -      -       -      -
    376C  SER*     4.9     5.5    +      -       -      -
    380C  LEU*     3.5    32.1    -      -       +      -
    377D  ASN*     2.9    25.2    +      -       -      +
    378D  GLN*     3.3    14.8    -      -       +      +
    380D  LEU*     1.3    77.0    -      -       -      +
    382D  GLN*     1.3    71.7    +      -       -      +
    384D  ASN*     3.3     6.4    +      -       -      +
    385D  LEU*     3.0    24.1    +      -       -      +
    388D  ARG*     5.2     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 382 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378D  GLN*     2.8    43.0    +      -       -      +
    379D  LYS*     3.2    27.6    +      -       -      +
    381D  LYS*     1.3    80.2    +      -       -      +
    383D  GLU*     1.3    63.9    +      -       -      +
    385D  LEU*     3.0    35.5    -      -       +      +
    386D  SER*     3.2    11.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 383 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384C  ASN*     2.7    29.5    +      -       -      +
    388C  ARG*     2.8    29.4    +      -       -      +
    379D  LYS*     2.9    32.1    +      -       -      +
    380D  LEU*     3.6    11.5    -      -       -      +
    382D  GLN*     1.3    76.6    -      -       -      +
    384D  ASN*     1.3    58.2    +      -       -      +
    385D  LEU      3.2     0.3    +      -       -      -
    386D  SER*     3.2     8.4    +      -       -      -
    387D  LEU*     2.8    36.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 384 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380C  LEU*     3.1    34.6    +      -       -      +
    383C  GLU*     2.9    20.6    +      -       -      +
    384C  ASN*     2.7    44.8    +      -       -      +
    387C  LEU*     3.1    13.3    -      -       +      +
    380D  LEU      2.8    25.0    +      -       -      +
    381D  LYS*     3.3     5.8    +      -       -      +
    383D  GLU*     1.3    69.4    -      -       -      +
    385D  LEU*     1.3    59.8    +      -       -      +
    387D  LEU*     4.2     1.6    -      -       -      -
    388D  ARG*     3.0    46.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 385 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381D  LYS      3.0    12.1    +      -       -      +
    382D  GLN*     3.0    28.7    -      -       +      +
    383D  GLU      3.1     0.2    -      -       -      -
    384D  ASN*     1.3    75.3    -      -       -      +
    386D  SER*     1.3    58.1    +      -       -      +
    388D  ARG*     2.9    21.0    +      -       +      +
    389D  THR*     2.8    44.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 386 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382D  GLN      3.3    12.0    +      -       -      -
    383D  GLU*     3.5     8.0    -      -       -      -
    385D  LEU*     1.3    76.0    -      -       -      +
    387D  LEU*     1.3    55.7    +      -       -      +
    389D  THR*     2.8     8.6    +      -       -      -
    390D  ALA*     2.6    38.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 387 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384C  ASN*     3.5    36.1    -      -       -      +
    387C  LEU*     3.6    19.3    -      -       +      -
    388C  ARG*     3.5    39.9    -      -       +      +
    391C  VAL*     3.8    25.7    -      -       +      +
    383D  GLU*     2.8    24.6    +      -       +      +
    384D  ASN*     4.3     1.1    -      -       -      +
    386D  SER*     1.3    73.3    -      -       -      +
    388D  ARG*     1.3    57.0    +      -       -      +
    390D  ALA*     3.5     7.7    -      -       +      +
    391D  VAL*     3.0    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 388 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383C  GLU*     2.7    43.6    +      -       -      -
    387C  LEU*     3.8    17.6    -      -       +      +
    381D  LYS      5.2     0.4    +      -       -      -
    384D  ASN*     3.0    44.6    +      -       -      +
    385D  LEU*     2.9    28.1    +      -       +      +
    387D  LEU*     1.3    76.7    -      -       -      +
    389D  THR*     1.3    59.7    +      -       -      +
    391D  VAL*     3.1    23.9    -      -       +      +
    392D  HIS*     3.1     8.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 389 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385D  LEU*     2.8    25.3    +      -       -      +
    386D  SER*     3.5     7.0    -      -       -      -
    388D  ARG*     1.3    74.8    -      -       -      +
    390D  ALA*     1.3    55.5    +      -       -      +
    392D  HIS*     3.0    13.3    +      -       +      +
    393D  LYS*     2.7    36.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 390 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391C  VAL*     4.5    12.6    -      -       +      -
    386D  SER      2.6    20.6    +      -       -      +
    387D  LEU*     3.5    12.8    -      -       +      +
    389D  THR*     1.3    70.7    -      -       -      +
    391D  VAL*     1.3    66.0    +      -       -      +
    393D  LYS*     2.9    30.2    +      -       -      +
    394D  SER*     3.3     5.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 391 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387C  LEU*     4.3    17.3    -      -       +      +
    390C  ALA*     4.3    13.9    -      -       +      -
    391C  VAL*     3.5    22.2    -      -       +      +
    394C  SER*     6.4     0.7    -      -       -      -
    387D  LEU      3.0    21.2    +      -       -      +
    388D  ARG*     3.1    15.0    -      -       +      +
    390D  ALA*     1.3    79.7    -      -       -      +
    392D  HIS*     1.3    64.1    +      -       -      +
    394D  SER*     3.2    22.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 392 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388D  ARG      3.1     6.2    +      -       -      +
    389D  THR*     3.0    19.4    +      -       +      +
    391D  VAL*     1.3    81.6    -      -       -      +
    393D  LYS*     1.3    52.6    +      -       +      +
    394D  SER      2.6    23.7    +      -       -      +
----------------------------------------------------------
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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