Contacts of the helix formed by residues 286 - 300 (chain A) in PDB entry 5FS9


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 286 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  ASP*     3.9    24.2    +      -       -      +
    170A  TYR*     3.3    15.0    -      -       -      +
    172A  ARG*     4.0     6.5    -      -       -      +
    175A  LEU*     3.7    10.3    -      -       -      +
    283A  LEU      5.8     0.2    -      -       -      -
    284A  PHE*     5.1     0.7    -      -       -      -
    285A  ARG*     1.3    86.2    -      -       +      +
    287A  ILE*     1.3    67.2    +      -       +      +
    288A  GLY*     4.0     8.7    -      -       -      +
    289A  ASP*     2.9    37.2    +      -       -      +
    290A  PHE*     3.0     9.7    +      -       -      +
   1000A  FAD      6.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  GLU*     4.0    17.5    -      -       +      +
    170A  TYR*     3.1    54.2    +      -       +      +
    175A  LEU*     3.9    17.8    -      -       +      +
    191A  LEU*     3.8    27.1    -      -       +      -
    203A  ILE*     4.1     7.2    -      -       +      -
    204A  TYR*     3.9    14.8    -      -       +      +
    286A  LYS*     1.3    73.5    -      -       -      +
    288A  GLY*     1.3    58.4    +      -       -      +
    290A  PHE*     3.2     4.6    +      -       -      +
    291A  ARG*     3.0    56.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  LYS*     3.2     7.4    -      -       -      +
    287A  ILE*     1.3    81.9    -      -       -      +
    289A  ASP*     1.3    58.9    +      -       -      +
    291A  ARG*     3.9     7.3    -      -       -      +
    292A  SER*     3.0    29.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  THR*     3.9    12.0    -      -       +      +
    283A  LEU      3.3    14.4    +      -       -      +
    284A  PHE*     3.6    20.8    -      -       +      -
    285A  ARG*     2.9    24.0    +      -       -      +
    286A  LYS*     2.9    34.9    +      -       -      +
    288A  GLY*     1.3    75.2    -      -       -      +
    290A  PHE*     1.3    64.9    +      -       -      +
    292A  SER*     3.2     7.3    +      -       -      -
    293A  LEU*     2.9    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  LEU*     3.8    26.2    -      -       +      -
    179A  LEU*     3.6    47.8    -      -       +      -
    180A  TRP*     3.6    42.0    -      +       -      -
    187A  VAL*     4.7     3.8    -      -       +      -
    188A  THR*     4.0    26.9    -      -       -      -
    191A  LEU*     4.2    17.0    -      -       +      -
    284A  PHE*     3.7    13.9    -      -       +      -
    286A  LYS      3.0     6.2    +      -       -      +
    287A  ILE      3.5     6.5    -      -       -      +
    289A  ASP*     1.3    76.3    -      -       -      +
    291A  ARG*     1.3    68.1    +      -       +      +
    293A  LEU*     3.8     0.7    -      -       -      +
    294A  GLU*     2.9    43.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  GLU*     4.1    10.9    +      -       -      -
    188A  THR*     2.7    46.7    +      -       +      +
    189A  LYS*     3.4    16.7    +      -       -      +
    191A  LEU*     3.4    26.5    -      -       -      +
    287A  ILE*     3.0    36.4    +      -       +      +
    288A  GLY*     3.9     6.7    -      -       -      +
    290A  PHE*     1.3    86.6    -      -       +      +
    292A  SER*     1.3    62.2    +      -       -      +
    294A  GLU*     3.9     6.0    -      -       -      +
    295A  LYS*     3.2    23.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  THR*     4.4    11.4    +      -       -      +
    288A  GLY      3.0    16.3    +      -       -      -
    289A  ASP*     3.2    13.2    +      -       -      -
    290A  PHE      3.4     0.2    -      -       -      -
    291A  ARG*     1.3    75.3    -      -       -      +
    293A  LEU*     1.3    61.8    +      -       -      +
    295A  LYS*     3.2     8.9    +      -       -      +
    296A  ILE*     2.9    40.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TRP*     3.9    17.5    -      -       +      -
    282A  THR*     4.7     3.8    -      -       +      +
    284A  PHE*     3.9    25.4    -      -       +      -
    289A  ASP      2.9    15.3    +      -       -      +
    290A  PHE      4.1     1.3    -      -       -      +
    292A  SER*     1.3    81.5    +      -       -      +
    294A  GLU*     1.3    58.9    +      -       -      +
    296A  ILE*     3.2     6.2    +      -       +      +
    297A  SER*     2.8    29.3    +      -       -      -
    303A  ILE*     4.2    17.0    -      -       +      -
    315A  LEU*     4.7     5.8    -      -       +      -
    319A  LEU*     4.3    13.7    -      -       +      -
    393A  HIS*     4.1    17.7    -      -       +      +
    395A  VAL*     3.4    38.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TRP*     3.6    22.8    -      -       +      -
    187A  VAL*     6.1     1.8    -      -       +      -
    188A  THR*     3.5    29.4    +      -       -      +
    290A  PHE*     2.9    31.0    +      -       +      +
    291A  ARG      3.9     4.3    -      -       -      +
    293A  LEU*     1.3    76.0    -      -       -      +
    295A  LYS*     1.3    63.6    +      -       -      +
    297A  SER*     3.3    14.9    +      -       -      -
    298A  ARG*     2.9    37.5    +      -       -      +
    322A  LYS*     2.8    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 295 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  ARG      3.2    11.4    +      -       -      +
    292A  SER*     3.2    11.2    +      -       -      +
    293A  LEU      3.2     0.4    -      -       -      -
    294A  GLU*     1.3    78.8    +      -       -      +
    296A  ILE*     1.3    65.0    +      -       +      +
    298A  ARG*     3.1    39.7    +      -       -      +
    299A  GLU*     3.3    42.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  THR*     4.8     1.3    -      -       -      +
    292A  SER*     2.9    32.1    +      -       -      +
    293A  LEU*     3.2     7.8    +      -       +      +
    295A  LYS*     1.3    76.8    -      -       +      +
    297A  SER*     1.3    62.3    +      -       -      +
    299A  GLU*     3.0    13.2    +      -       -      +
    300A  VAL*     3.0    48.9    +      -       +      +
    303A  ILE*     3.9    11.4    -      -       +      -
    393A  HIS*     3.3    49.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TRP*     4.4     0.9    -      -       -      -
    293A  LEU      2.8    16.1    +      -       -      -
    294A  GLU*     3.4    14.6    -      -       -      -
    295A  LYS      3.3     0.2    -      -       -      -
    296A  ILE*     1.3    73.6    -      -       -      +
    298A  ARG*     1.3    59.9    +      -       -      +
    300A  VAL      4.1     9.7    -      -       -      +
    303A  ILE*     3.8    12.6    -      -       -      +
    319A  LEU*     3.9    22.6    +      -       -      +
    322A  LYS*     3.8    31.9    -      -       -      +
    323A  ALA      5.3     0.3    +      -       -      -
    326A  LEU*     3.7    11.1    -      -       -      +
    328A  THR*     4.6     9.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  THR*     6.2     0.4    -      -       -      +
    294A  GLU*     2.9    43.4    +      -       -      +
    295A  LYS*     3.1    37.7    +      -       -      +
    296A  ILE      3.1     0.8    -      -       -      -
    297A  SER*     1.3    76.6    -      -       -      +
    299A  GLU*     1.3    64.4    +      -       +      +
    300A  VAL      5.1     0.7    -      -       -      -
    322A  LYS*     4.0    11.2    -      -       -      +
    326A  LEU*     3.9    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  LYS*     3.3    49.3    +      -       -      +
    296A  ILE*     3.0    11.8    +      -       -      +
    298A  ARG*     1.3    84.8    +      -       +      +
    300A  VAL*     1.3    68.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  ILE*     3.0    33.2    +      -       +      +
    297A  SER*     4.1     5.6    -      -       -      +
    298A  ARG      5.1     0.2    -      -       -      -
    299A  GLU*     1.3    88.7    -      -       +      +
    301A  LYS*     1.3    60.3    +      -       -      +
    302A  SER      3.8     9.4    -      -       -      +
    303A  ILE*     3.7    29.4    -      -       +      -
    328A  THR*     3.3    20.8    -      -       -      +
    392A  ASP*     3.7    22.4    -      -       +      +
    393A  HIS*     4.9     1.6    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


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

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

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