Contacts of the helix formed by residues 413 - 439 (chain B) in PDB entry 5YWB


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 413 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407B  LEU      4.9     2.9    -      -       -      -
    409B  MET      3.8     3.5    +      -       -      -
    410B  GLY*     2.7    33.3    +      -       -      -
    411B  GLU      3.3     2.0    +      -       -      -
    412B  MET*     1.3    77.7    -      -       -      +
    414B  ALA*     1.3    60.5    -      -       -      +
    415B  GLY*     3.7    12.1    -      -       -      +
    416B  GLN*     3.0    15.5    +      -       +      +
    417B  ILE*     2.8    26.7    +      -       -      +
    497B  LYS*     4.7    17.7    -      -       +      +
    500B  ASN*     5.9     0.9    -      -       -      +
    501B  GLU*     5.9     0.4    -      -       -      +
   1477B  GLU*     3.2    29.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 414 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407B  LEU*     5.0     3.4    -      -       +      +
    412B  MET      3.4     2.4    +      -       -      -
    413B  THR*     1.3    73.1    -      -       -      +
    415B  GLY*     1.3    64.1    +      -       -      +
    417B  ILE*     3.0     3.5    +      -       -      +
    418B  CYS*     3.0    28.3    +      -       -      +
    504B  ARG*     5.5     3.8    -      -       -      +
   1205B  ALA*     5.3     3.6    -      -       +      +
   1208B  VAL*     3.6    29.9    -      -       +      +
   1209B  GLU*     3.8    29.6    -      -       +      +
   1477B  GLU*     5.0     1.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 415 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  THR*     3.3     8.3    -      -       -      +
    414B  ALA*     1.3    77.8    -      -       -      +
    416B  GLN*     1.3    56.5    +      -       -      +
    418B  CYS*     4.0     5.2    -      -       -      +
    419B  ASN*     2.9    39.6    +      -       -      +
    497B  LYS*     5.7     2.9    -      -       -      -
    500B  ASN*     3.6    26.9    -      -       -      -
    504B  ARG*     5.7     4.2    -      -       -      +
   1477B  GLU*     5.1     0.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 416 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410B  GLY      4.4     3.4    -      -       -      +
    411B  GLU*     3.9    16.8    -      -       -      +
    413B  THR*     3.0    30.6    +      -       -      +
    415B  GLY*     1.3    77.2    -      -       -      +
    417B  ILE*     1.3    57.1    +      -       +      +
    419B  ASN*     3.5     7.6    +      -       -      +
    420B  LEU*     2.9    27.4    +      -       +      +
    493B  ASN*     3.3    40.2    +      -       -      +
    497B  LYS*     3.8    24.3    +      -       +      +
    609B  LYS*     4.2    23.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 417 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399B  ILE*     3.7    20.2    -      -       +      -
    402B  LEU*     4.9     5.4    -      -       +      -
    407B  LEU*     5.0     2.0    -      -       +      -
    411B  GLU      5.0     1.6    -      -       -      +
    412B  MET*     4.0    25.4    -      -       +      +
    413B  THR      2.8    13.6    +      -       -      +
    414B  ALA      3.0     7.5    +      -       -      +
    416B  GLN*     1.3    77.3    -      -       +      +
    418B  CYS*     1.3    59.0    +      -       -      +
    420B  LEU*     3.1    12.0    -      -       +      +
    421B  VAL*     2.9    32.5    +      -       +      +
    613B  PHE*     3.7    37.9    -      -       +      -
   1204B  PHE*     5.1     0.7    -      -       +      -
   1208B  VAL*     3.7    37.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 418 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    414B  ALA      3.0    18.0    +      -       -      +
    415B  GLY*     4.0     5.2    -      -       -      +
    417B  ILE*     1.3    75.4    -      -       -      +
    419B  ASN*     1.3    67.0    +      -       -      +
    421B  VAL*     3.3     6.4    +      -       -      +
    422B  ALA*     3.0    26.5    +      -       -      +
   1201B  LEU*     4.2    12.8    -      -       +      +
   1204B  PHE*     4.2     8.7    -      -       -      -
   1205B  ALA*     3.5    45.3    -      -       -      -
   1208B  VAL*     5.3     3.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 419 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    415B  GLY*     2.9    24.8    +      -       -      +
    416B  GLN*     3.6    13.6    +      -       -      +
    418B  CYS*     1.3    77.9    -      -       -      +
    420B  LEU*     1.3    62.6    +      -       -      +
    422B  ALA*     4.9     1.3    -      -       -      -
    423B  ILE*     2.9    43.5    +      -       +      +
    493B  ASN*     4.2    11.6    +      -       -      +
    496B  LEU*     3.3    42.8    -      -       -      +
    497B  LYS*     5.4     2.8    -      -       -      +
    500B  ASN*     5.6     2.5    +      -       -      +
    609B  LYS*     5.6     2.0    -      -       -      +
   1122B  LEU*     5.1    10.9    -      -       -      +
   1126B  SER*     5.6     0.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 420 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395B  ILE*     3.7    28.9    -      -       +      -
    416B  GLN*     2.9    15.9    +      -       +      +
    417B  ILE*     3.1    15.9    -      -       +      +
    419B  ASN*     1.3    73.7    -      -       -      +
    421B  VAL*     1.3    65.8    +      -       +      +
    423B  ILE*     4.7     1.3    -      -       -      -
    424B  ASP*     2.8    52.7    +      -       +      +
    609B  LYS*     3.8    29.8    -      -       +      -
    610B  LEU*     4.2    23.8    -      -       +      -
    613B  PHE*     3.8    36.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 421 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391B  ILE*     5.7     1.9    -      -       -      +
    392B  GLN*     4.5    19.9    -      -       +      +
    395B  ILE*     3.6    26.7    -      -       +      -
    417B  ILE*     2.9    18.6    +      -       +      +
    418B  CYS*     3.7     7.4    -      -       -      +
    420B  LEU*     1.3    74.3    -      -       +      +
    422B  ALA*     1.3    64.3    +      -       -      +
    424B  ASP*     4.2     0.6    -      -       -      +
    425B  THR*     3.0    28.6    +      -       -      +
   1200B  LEU*     5.8     1.1    -      -       +      -
   1201B  LEU*     4.0    15.7    -      -       +      -
   1204B  PHE*     3.5    48.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 422 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418B  CYS      3.0    17.4    +      -       -      +
    419B  ASN*     4.2     1.8    -      -       -      +
    421B  VAL*     1.3    80.7    -      -       -      +
    423B  ILE*     1.3    68.7    +      -       +      +
    425B  THR*     3.3     4.6    -      -       -      -
    426B  ASN*     3.0    30.4    +      -       -      +
   1123B  ASN*     5.4     7.9    -      -       -      +
   1197B  GLN*     6.1     2.9    -      -       -      +
   1201B  LEU*     4.5    23.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 423 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419B  ASN*     2.9    39.3    +      -       +      +
    422B  ALA*     1.3    76.2    -      -       +      +
    424B  ASP*     1.3    75.2    +      -       -      +
    426B  ASN*     3.4    10.0    +      -       -      +
    427B  GLN*     2.9    46.4    +      -       +      +
    489B  LEU*     5.9     8.1    -      -       +      -
    496B  LEU*     5.8     3.1    -      -       +      -
    602B  LYS*     6.3     1.1    -      -       -      -
    606B  SER*     4.2     6.5    -      -       -      +
    609B  LYS*     3.7    20.6    -      -       -      +
   1126B  SER*     5.3     8.3    -      -       -      +
   1130B  ASN*     5.4     9.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 424 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391B  ILE*     5.1    11.2    -      -       +      -
    420B  LEU*     2.8    57.7    +      -       +      +
    421B  VAL*     4.2     0.7    -      -       -      +
    423B  ILE*     1.3    85.4    -      -       -      +
    425B  THR*     1.3    65.8    -      -       -      +
    426B  ASN      3.2     1.1    -      -       -      -
    427B  GLN      4.3     0.2    -      -       -      +
    428B  LEU*     2.9    35.6    +      -       +      +
    606B  SER*     2.7    44.5    +      -       -      +
    609B  LYS*     4.0     5.3    -      -       -      +
    610B  LEU*     5.1     5.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 425 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387B  LEU*     5.7     0.2    -      -       -      +
    388B  ARG*     3.4    38.3    -      -       -      +
    391B  ILE*     4.9     8.2    -      -       -      +
    392B  GLN*     2.7    32.4    +      -       -      +
    421B  VAL*     3.0    20.8    +      -       -      +
    422B  ALA*     3.3     4.9    -      -       -      +
    424B  ASP*     1.3    73.7    -      -       -      +
    426B  ASN*     1.3    77.4    +      -       -      +
    428B  LEU*     4.3     1.0    -      -       -      +
    429B  MET*     3.0    32.3    +      -       +      +
   1197B  GLN*     5.4     6.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 426 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  ALA*     3.0    16.9    +      -       -      +
    423B  ILE*     3.5    13.6    -      -       -      +
    424B  ASP      3.2     0.2    -      -       -      -
    425B  THR*     1.3    87.7    -      -       -      +
    427B  GLN*     1.3    65.3    +      -       -      +
    429B  MET*     3.7     6.2    -      -       -      +
    430B  TRP*     2.8    53.0    +      -       +      +
   1127B  SER*     5.6     4.2    +      -       -      -
   1197B  GLN*     4.8    10.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 427 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423B  ILE*     2.9    42.2    +      -       +      +
    424B  ASP      4.3     0.2    -      -       -      +
    426B  ASN*     1.3    80.5    -      -       -      +
    428B  LEU*     1.3    59.3    +      -       -      +
    430B  TRP*     3.3     9.3    +      -       -      +
    431B  PHE*     2.9    31.0    +      -       -      +
    489B  LEU*     6.4     0.4    -      -       +      -
    598B  ARG*     5.9     0.2    +      -       -      -
    599B  SER*     4.9    10.0    +      -       -      +
    602B  LYS*     3.2    61.4    -      -       +      +
    603B  ALA*     4.6     2.0    -      -       -      +
    606B  SER*     3.6    23.3    -      -       -      +
   1130B  ASN*     5.8     2.4    -      -       -      +
   1135B  HIS*     5.5     6.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 428 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  TRP*     5.8     1.8    -      -       +      -
    291B  LEU*     5.2     6.1    -      -       +      -
    387B  LEU*     3.5    32.5    -      -       +      +
    391B  ILE*     4.5    21.3    -      -       +      -
    424B  ASP*     2.9    22.4    +      -       +      +
    425B  THR*     4.3     1.1    -      -       -      +
    427B  GLN*     1.3    76.8    -      -       -      +
    429B  MET*     1.3    57.6    +      -       -      +
    431B  PHE*     3.5     7.9    +      -       +      +
    432B  PHE*     2.9    37.0    +      -       +      +
    603B  ALA*     4.5    17.9    -      -       +      +
    606B  SER*     4.8     9.4    -      -       -      -
    607B  VAL*     3.9    30.7    -      -       +      -
    610B  LEU*     4.7    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 429 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384B  GLY      3.7    19.7    -      -       -      +
    385B  ILE*     4.7     7.6    -      -       -      -
    387B  LEU*     4.2     4.4    -      -       +      +
    388B  ARG*     3.5    50.9    -      -       +      +
    425B  THR*     3.0    20.6    +      -       +      +
    426B  ASN*     3.7     5.8    -      -       -      +
    428B  LEU*     1.3    76.5    -      -       -      +
    430B  TRP*     1.3    71.4    +      -       +      +
    432B  PHE*     3.2     2.7    +      -       -      -
    433B  PHE*     2.9    65.7    +      -       +      -
   1238B  SER*     5.1     4.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 430 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381B  ILE*     5.8     0.4    -      -       +      -
    426B  ASN*     2.8    45.6    +      -       +      +
    427B  GLN*     3.9    12.1    -      -       -      +
    429B  MET*     1.3    86.4    -      -       +      +
    431B  PHE*     1.3    63.0    +      -       -      +
    433B  PHE*     3.2    43.4    +      +       +      +
    434B  LEU*     3.0    31.3    +      -       +      +
    599B  SER*     4.2    15.9    -      -       -      +
   1135B  HIS*     4.9    19.7    +      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 431 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  TRP*     4.3    26.7    -      +       -      -
    427B  GLN      2.9    12.6    +      -       -      +
    428B  LEU*     4.0     8.3    -      -       +      +
    430B  TRP*     1.3    75.4    -      -       -      +
    432B  PHE*     1.3    84.8    +      +       -      +
    434B  LEU*     4.4     4.3    -      -       +      +
    435B  CYS*     2.9    54.1    +      -       +      +
    438B  LEU*     5.0     7.6    -      -       +      -
    596B  VAL*     6.3     0.4    -      -       +      -
    599B  SER*     4.2    12.9    -      -       -      +
    600B  THR*     4.2    31.4    -      -       +      -
    603B  ALA*     3.5    31.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 432 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  TRP*     6.1     2.0    -      -       -      -
    291B  LEU*     5.1     6.1    -      -       +      -
    292B  CYS*     5.3    11.0    -      -       -      -
    295B  PHE*     3.2    41.5    -      +       -      -
    299B  LEU*     3.6    26.7    -      -       +      -
    380B  ALA*     4.0     7.4    -      -       -      +
    383B  THR*     3.5    24.5    -      -       +      -
    384B  GLY*     4.3    14.4    -      -       -      -
    387B  LEU*     4.6    14.4    -      -       +      -
    428B  LEU*     2.9    22.3    +      -       +      +
    429B  MET      3.6     3.6    -      -       -      +
    430B  TRP      3.2     0.2    -      -       -      -
    431B  PHE*     1.3    99.5    -      +       -      +
    433B  PHE*     1.3    64.3    +      -       -      +
    435B  CYS*     4.5     6.7    -      -       +      -
    436B  PRO*     3.4    16.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 433 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377B  TYR*     5.3    11.5    -      -       +      -
    380B  ALA*     3.8    16.4    -      -       +      +
    381B  ILE*     3.5    52.5    -      -       +      -
    384B  GLY*     3.7    18.4    -      -       -      -
    385B  ILE*     4.9     2.2    -      -       +      -
    429B  MET*     2.9    47.4    +      -       +      -
    430B  TRP*     3.2    42.8    +      +       +      +
    432B  PHE*     1.3    84.4    -      -       -      +
    434B  LEU*     1.3    65.5    +      -       +      +
    435B  CYS      3.4     0.4    -      -       -      -
    436B  PRO*     3.6    10.0    -      -       -      +
    437B  ASN*     4.4     5.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 434 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377B  TYR*     6.3     3.1    -      -       +      -
    430B  TRP*     3.0    18.7    +      -       +      +
    431B  PHE*     3.3     6.7    +      -       +      +
    433B  PHE*     1.3    81.5    -      -       +      +
    435B  CYS*     1.3    63.0    +      -       -      +
    436B  PRO      3.5     0.2    -      -       -      -
    437B  ASN*     3.4    24.5    +      -       +      +
    438B  LEU*     3.3    24.6    +      -       -      +
    595B  SER*     5.0     3.6    -      -       -      +
    596B  VAL*     4.2    33.2    -      -       +      +
    599B  SER*     4.0    26.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 435 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  LEU*     5.3    11.9    -      -       +      -
    431B  PHE*     2.9    43.2    +      -       +      +
    432B  PHE*     4.5     7.6    -      -       +      -
    434B  LEU*     1.3    73.1    -      -       -      +
    436B  PRO*     1.3    67.4    -      -       +      +
    437B  ASN      3.1     1.3    -      -       -      -
    438B  LEU*     3.2    19.6    +      -       -      +
    439B  TRP*     2.9    48.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 436 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  LEU*     3.6    26.9    -      -       +      -
    302B  SER*     3.6    16.8    -      -       -      +
    303B  SER*     5.0     7.0    -      -       -      +
    306B  ARG*     4.2    14.1    -      -       -      +
    376B  SER*     5.0     8.1    -      -       -      +
    380B  ALA*     3.7    24.5    -      -       +      -
    432B  PHE      3.4    15.5    -      -       -      +
    433B  PHE      3.6     7.2    -      -       -      +
    435B  CYS*     1.3    95.6    -      -       +      +
    437B  ASN*     1.3    60.2    +      -       -      +
    439B  TRP*     3.5    16.5    +      -       +      +
    440B  ALA*     3.8     6.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 437 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306B  ARG*     4.1    24.9    +      -       -      +
    377B  TYR*     4.7    21.1    +      -       +      +
    433B  PHE      4.4     4.1    +      -       -      +
    434B  LEU*     3.4    32.0    +      -       +      +
    435B  CYS      3.1     0.8    -      -       -      -
    436B  PRO*     1.3    80.2    -      -       -      +
    438B  LEU*     1.3    60.6    +      -       -      +
    440B  ALA*     3.6    11.4    +      -       -      +
    441B  MET*     3.8     7.6    +      -       -      +
    592B  LEU*     3.8    29.4    -      -       -      +
    596B  VAL*     5.2     5.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 438 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    431B  PHE*     5.0     8.7    -      -       +      -
    434B  LEU*     3.3    11.3    +      -       +      +
    435B  CYS*     3.3    22.9    -      -       +      +
    437B  ASN*     1.3    74.5    -      -       -      +
    439B  TRP*     1.3    74.8    +      -       +      +
    440B  ALA      2.9    10.3    +      -       -      -
    441B  MET*     3.3    27.9    +      -       +      +
    442B  PRO*     3.4    11.6    -      -       -      +
    596B  VAL*     3.7    32.5    -      -       +      +
    600B  THR*     4.8     6.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 439 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  LEU*     6.2     4.0    -      -       +      -
    303B  SER*     4.5    18.6    -      -       -      -
    307B  ILE*     4.4     9.2    -      -       -      +
    435B  CYS*     2.9    43.7    +      -       -      +
    436B  PRO*     3.5    11.4    +      -       +      +
    437B  ASN      3.4     0.6    -      -       -      -
    438B  LEU*     1.3    84.2    -      -       +      +
    440B  ALA*     1.3    56.3    +      -       -      +
    442B  PRO*     4.3     8.3    -      -       +      +
    443B  VAL*     4.3     6.9    -      -       -      +
----------------------------------------------------------
 Back to top of page


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