Contacts of the helix formed by residues 313 - 333 (chain A) in PDB entry 2NPG


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 ASP 313 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  VAL*     3.5    44.3    -      -       +      +
    302A  LEU*     4.0    16.6    -      -       -      +
    303A  LYS      3.6    16.6    -      -       -      +
    310A  ASP*     2.9    41.2    +      -       -      +
    312A  CYS*     1.3    75.9    -      -       -      +
    314A  VAL*     1.3    55.9    +      -       +      +
    315A  PHE      3.2     0.2    -      -       -      -
    316A  GLY*     2.8    26.1    +      -       -      -
    317A  VAL      3.5     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ILE*     5.9     0.2    -      -       +      -
     31A  PHE*     3.7    29.2    -      -       +      -
     32A  TYR*     3.4    26.2    -      -       +      +
     35A  LEU*     4.1    12.8    -      -       +      -
    114A  LEU*     6.0     0.2    -      -       +      -
    311A  PRO*     3.2    19.7    -      -       +      +
    313A  ASP*     1.3    75.3    -      -       +      +
    315A  PHE*     1.3    59.2    +      -       +      +
    316A  GLY      3.0     4.7    -      -       -      -
    317A  VAL*     3.0    23.8    +      -       +      +
    318A  PHE*     3.1    38.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  TYR*     3.9     5.2    -      -       -      -
    114A  LEU*     3.3    28.0    -      -       +      -
    115A  ILE*     3.9     8.7    -      -       +      -
    118A  ALA*     3.3    33.7    -      -       +      -
    119A  LEU*     4.7     2.0    -      -       +      -
    171A  ALA*     3.8    18.4    -      -       +      -
    172A  ALA*     3.5    16.1    -      -       -      +
    175A  GLY*     3.5    34.1    -      -       -      -
    176A  LEU*     3.6    26.0    -      -       +      +
    312A  CYS*     2.9    37.7    +      -       +      +
    314A  VAL*     1.3    78.9    -      -       +      +
    316A  GLY*     1.3    56.8    +      -       -      +
    318A  PHE*     4.4     5.6    -      +       +      +
    319A  GLY*     2.9    27.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  LEU*     5.2     2.2    -      -       -      -
    298A  GLY*     4.9     1.6    -      -       -      -
    299A  VAL*     4.8    10.5    -      -       -      -
    302A  LEU*     3.7    21.0    -      -       -      +
    313A  ASP      2.8    13.9    +      -       -      -
    315A  PHE*     1.3    78.6    -      -       -      +
    317A  VAL*     1.3    57.1    +      -       -      +
    320A  VAL*     3.0    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  TRP*     3.8    20.6    -      -       +      -
    263A  SER*     4.5     7.2    -      -       -      +
    266A  ILE*     4.0    20.0    -      -       +      +
    267A  ALA*     3.9    29.6    -      -       +      +
    270A  VAL*     4.9     0.9    -      -       +      -
    295A  GLY*     4.4     3.8    -      -       -      +
    299A  VAL*     3.5    25.1    -      -       +      -
    313A  ASP      3.5     1.7    +      -       -      +
    314A  VAL*     3.0    12.1    +      -       +      +
    316A  GLY*     1.3    74.1    -      -       -      +
    318A  PHE*     1.3    62.4    +      -       +      +
    321A  CYS*     2.9    43.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ILE*     5.0     5.4    -      -       +      -
     31A  PHE*     5.6     3.4    -      +       -      -
    114A  LEU*     3.7    41.1    -      -       +      -
    168A  HIS*     3.5    38.3    -      +       +      +
    172A  ALA*     4.0     8.5    -      -       +      +
    208A  LEU*     5.9     2.2    -      -       +      -
    212A  TRP*     4.1    11.7    -      +       -      -
    266A  ILE*     3.6    28.9    -      -       +      -
    270A  VAL*     3.5    29.4    -      -       +      +
    314A  VAL*     3.1    40.2    +      -       +      +
    315A  PHE*     4.3     5.6    -      +       +      +
    317A  VAL*     1.3    80.5    -      -       +      +
    319A  GLY*     1.3    57.9    +      -       -      +
    322A  GLY*     3.1    24.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  HIS      4.8     0.7    -      -       -      -
    169A  ILE*     4.3     5.7    -      -       -      +
    172A  ALA*     3.4    19.5    -      -       -      +
    173A  ILE*     6.2     1.8    -      -       -      -
    176A  LEU*     5.8     2.0    -      -       -      -
    315A  PHE      2.9    15.3    +      -       -      -
    318A  PHE*     1.3    77.2    -      -       -      +
    320A  VAL*     1.3    64.7    +      -       -      +
    322A  GLY*     3.9     0.2    -      -       -      -
    323A  ILE*     3.0    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ALA*     3.4    40.8    -      -       +      +
    295A  GLY*     4.4     0.4    -      -       -      +
    297A  TRP*     4.3    17.7    -      -       +      -
    298A  GLY*     4.2    14.6    -      -       -      -
    316A  GLY*     3.0    25.1    +      -       -      +
    317A  VAL      4.4     0.2    -      -       -      +
    319A  GLY*     1.3    75.3    -      -       -      +
    321A  CYS*     1.3    60.8    +      -       -      +
    323A  ILE*     3.3    10.6    +      -       +      +
    324A  VAL*     3.0    31.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  ALA*     3.7    26.5    -      -       -      +
    270A  VAL*     3.6    15.5    -      -       +      -
    271A  GLY*     3.6     8.1    -      -       -      +
    291A  ALA*     3.4    29.6    -      -       +      -
    294A  ALA*     5.1     0.2    -      -       -      -
    295A  GLY*     3.7    20.4    -      -       -      -
    317A  VAL*     2.9    24.8    +      -       -      +
    320A  VAL*     1.3    73.6    -      -       -      +
    322A  GLY*     1.3    59.8    +      -       -      +
    324A  VAL*     3.8     7.8    -      -       -      +
    325A  GLY*     2.8    27.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  GLY*     4.5     8.5    -      -       -      -
    168A  HIS*     4.6     0.7    -      -       -      -
    169A  ILE*     3.6    15.3    -      -       -      -
    270A  VAL*     3.5    12.7    -      -       -      +
    274A  PRO*     4.8     0.7    -      -       -      +
    318A  PHE      3.1    21.1    +      -       -      -
    319A  GLY      3.9     0.4    -      -       -      -
    321A  CYS*     1.3    73.8    -      -       -      +
    323A  ILE*     1.3    65.7    +      -       -      +
    325A  GLY*     5.2     0.4    -      -       -      -
    326A  CYS*     3.0    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  ILE*     3.9    20.0    -      -       +      -
    173A  ILE*     6.2     2.0    -      -       +      -
    319A  GLY*     3.0    27.8    +      -       -      +
    320A  VAL*     3.7     8.3    -      -       +      +
    322A  GLY*     1.3    75.7    -      -       -      +
    324A  VAL*     1.3    65.8    +      -       +      +
    326A  CYS*     3.2     2.9    +      -       -      +
    327A  ILE*     2.9    43.1    +      -       +      +
    359A  ILE*     4.0    20.6    -      -       +      -
    363A  ILE*     4.3    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  ILE*     5.3     0.7    -      -       +      +
    290A  VAL*     3.9    16.2    -      -       +      -
    291A  ALA*     4.5    14.8    -      -       +      -
    294A  ALA*     3.9    21.1    -      -       +      -
    320A  VAL*     3.0    23.8    +      -       +      +
    321A  CYS*     3.8     6.7    -      -       -      +
    323A  ILE*     1.3    79.4    -      -       +      +
    325A  GLY*     1.3    57.7    +      -       -      +
    327A  ILE*     3.3     7.5    +      -       +      +
    328A  MET*     2.9    57.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  GLY*     3.2    26.9    -      -       -      +
    274A  PRO*     3.4     8.0    -      -       -      +
    275A  ALA*     4.5     1.6    -      -       -      +
    287A  ILE*     4.7     3.4    -      -       -      -
    321A  CYS      2.8    19.4    +      -       -      -
    322A  GLY      4.0     1.1    -      -       -      -
    324A  VAL*     1.3    75.4    -      -       -      +
    326A  CYS*     1.3    52.1    +      -       -      +
    328A  MET*     3.4     5.0    +      -       -      +
    329A  THR*     2.7    36.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  LEU      5.4     0.9    -      -       -      -
    160A  ASP*     4.7     1.8    -      -       -      -
    164A  GLY*     3.9    11.4    -      -       -      -
    165A  THR*     3.9    27.6    -      -       -      -
    169A  ILE*     4.0     3.8    -      -       -      -
    274A  PRO*     3.8    23.6    -      -       -      -
    322A  GLY      3.0    24.2    +      -       -      +
    323A  ILE      3.6     3.6    -      -       -      +
    325A  GLY*     1.3    72.4    -      -       -      +
    327A  ILE*     1.3    66.0    +      -       -      +
    329A  THR*     3.6     5.3    +      -       -      -
    355A  GLN*     2.9    36.1    +      -       +      +
    359A  ILE*     3.7    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  ILE*     2.9    38.7    +      -       +      +
    324A  VAL*     3.8     7.0    -      -       +      +
    326A  CYS*     1.3    77.2    -      -       -      +
    328A  MET*     1.3    61.3    -      -       +      +
    330A  GLY*     3.0    17.3    +      -       -      -
    331A  ILE*     3.7     7.2    +      -       +      -
    352A  LEU*     3.3    29.2    -      -       +      +
    355A  GLN*     4.4     6.3    -      -       +      -
    356A  LEU*     3.8    26.7    -      -       +      -
    359A  ILE*     3.6    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  ILE*     3.8    11.0    -      -       +      -
    287A  ILE*     3.8    29.8    -      -       +      -
    290A  VAL*     3.8    33.9    -      -       +      -
    324A  VAL*     2.9    40.5    +      -       +      +
    325A  GLY*     3.8     2.0    -      -       -      +
    327A  ILE*     1.3    75.3    -      -       +      +
    329A  THR*     1.3    59.6    +      -       -      +
    330A  GLY      3.1     0.2    -      -       -      -
    331A  ILE*     3.1    16.4    +      -       +      +
    332A  PHE*     2.9    57.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  LEU*     3.6    33.3    -      -       +      +
    274A  PRO*     3.5    17.3    -      -       -      +
    275A  ALA*     3.0    30.6    +      -       +      +
    278A  TYR*     3.9    13.2    -      -       +      -
    279A  ILE*     5.0     2.2    -      -       -      -
    325A  GLY      2.7    23.6    +      -       -      -
    326A  CYS*     3.6     8.5    -      -       -      -
    327A  ILE      3.2     0.4    -      -       -      -
    328A  MET*     1.3    76.7    -      -       -      +
    330A  GLY*     1.3    60.6    +      -       -      +
    331A  ILE      3.1     1.3    +      -       -      -
    333A  ALA*     3.3    24.3    +      -       -      +
    355A  GLN*     4.0     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  CYS      3.8     2.4    +      -       -      -
    327A  ILE      3.0    11.3    +      -       -      -
    329A  THR*     1.3    78.7    -      -       -      +
    331A  ILE*     1.3    59.6    +      -       -      +
    342A  PHE*     3.1    23.1    -      -       -      -
    348A  MET*     3.4    11.3    -      -       -      +
    351A  GLN*     4.0    14.8    -      -       -      +
    352A  LEU*     3.9     9.5    -      -       -      +
    355A  GLN*     3.9    17.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327A  ILE*     4.0     7.0    -      -       +      +
    328A  MET*     3.1    24.4    +      -       +      +
    329A  THR      3.1     0.4    -      -       -      -
    330A  GLY*     1.3    80.3    -      -       -      +
    332A  PHE*     1.3    76.0    +      -       +      +
    333A  ALA      3.4     0.7    -      -       -      -
    334A  ALA*     3.3    15.9    +      -       -      +
    337A  LEU*     3.6    18.9    -      -       +      +
    348A  MET*     3.2    33.1    -      -       +      +
    352A  LEU*     3.7    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  ILE*     3.7    24.9    -      -       +      +
    280A  GLY      4.4     0.2    +      -       -      -
    283A  GLY*     3.7    22.2    -      -       -      -
    286A  ILE*     3.9    36.3    -      -       +      -
    287A  ILE*     4.3     7.9    -      -       +      -
    328A  MET*     2.9    49.8    +      -       +      +
    331A  ILE*     1.3    90.5    -      -       +      +
    333A  ALA*     1.3    56.9    +      -       -      +
    334A  ALA      3.0     7.7    +      -       -      +
    337A  LEU*     4.0    37.1    -      -       +      +
    339A  GLY*     3.4    18.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  LEU*     3.8    22.7    -      -       +      -
    278A  TYR*     3.4    27.6    -      -       +      +
    279A  ILE*     4.1     0.4    -      -       -      +
    329A  THR      3.3    19.9    +      -       -      +
    331A  ILE      3.3     0.8    +      -       -      -
    332A  PHE*     1.3    75.3    -      -       -      +
    334A  ALA*     1.3    58.2    +      -       -      +
    339A  GLY*     3.5     2.3    -      -       -      -
    341A  GLY*     2.7    41.1    +      -       -      +
    342A  PHE*     4.1     9.4    -      -       +      -
----------------------------------------------------------
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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