Contacts of the helix formed by residues 163 - 173 (chain F) in PDB entry 3FZ7


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 GLN 163 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  PHE*     3.7    26.7    -      -       -      +
    162F  VAL*     1.3    81.0    -      -       -      +
    164F  ILE*     1.3    81.2    +      -       -      +
    165F  CYS*     3.0    35.6    +      -       -      +
    166F  TRP*     3.1    17.3    +      -       -      +
    167F  HIS*     4.0     1.0    -      -       -      -
    208F  THR*     5.0     5.2    +      -       +      +
    212F  THR*     3.3    28.1    +      -       +      +
    213F  TYR*     3.8     5.8    -      -       -      +
    243F  ASP*     4.4    15.3    +      -       -      +
    276F  LYS*     5.9     3.0    -      -       -      +
    465F  HIS*     3.0    27.3    +      -       +      +
    466F  THR*     4.9     0.6    -      -       -      -
    467F  PO4      4.2    12.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 164 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  PHE*     4.0    35.0    -      -       +      -
    302A  ASN      5.4     0.4    -      -       -      +
    303A  VAL*     3.7    28.3    -      -       +      -
    312A  THR*     6.0     0.7    -      -       -      +
    317A  PHE*     4.0    27.1    -      -       +      -
    162F  VAL      3.9     0.2    +      -       -      -
    163F  GLN*     1.3    93.0    +      -       -      +
    165F  CYS*     1.3    59.1    +      -       +      +
    167F  HIS*     2.8    32.5    +      -       +      -
    168F  LYS*     2.9    19.2    +      -       +      +
    213F  TYR*     4.1     4.0    +      -       -      -
    465F  HIS*     4.0    18.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 165 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  PHE*     6.2     0.4    -      -       +      -
    126F  SER*     4.5     4.7    -      -       -      -
    127F  SER*     3.5    30.1    -      -       -      +
    130F  CYS*     3.3    40.6    -      -       +      +
    131F  MET*     4.4     4.4    -      -       -      +
    163F  GLN*     3.0    21.0    +      -       -      +
    164F  ILE*     1.3    77.7    -      -       -      +
    166F  TRP*     1.3    70.8    +      -       -      +
    168F  LYS*     3.5    13.3    +      -       -      +
    169F  PHE*     2.9    27.4    +      -       -      +
    243F  ASP*     4.4     2.9    -      -       -      -
    467F  PO4      5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 166 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130F  CYS*     3.4    48.5    -      -       +      -
    134F  GLY*     4.1     7.4    -      -       -      -
    137F  MET*     4.1    15.3    -      -       +      -
    157F  LEU*     4.8     8.5    -      -       +      -
    162F  VAL*     3.8    36.8    -      -       +      -
    163F  GLN      3.1    10.2    +      -       -      +
    164F  ILE      3.0     0.8    -      -       -      -
    165F  CYS*     1.3    82.7    -      -       -      +
    167F  HIS*     1.3    59.5    +      -       -      +
    169F  PHE*     3.8    23.8    -      +       +      +
    170F  ALA*     3.1    28.8    +      -       -      +
    177F  LEU*     4.2    11.0    -      -       +      +
    206F  VAL*     3.8    27.1    -      -       +      +
    241F  HIS*     3.5    30.5    -      +       -      -
    243F  ASP*     2.7    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 167 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  PHE*     3.4    28.9    -      +       +      -
    162F  VAL*     3.9    17.2    +      -       +      +
    163F  GLN      4.0    15.0    -      -       -      -
    164F  ILE*     2.8    19.6    +      -       +      +
    166F  TRP*     1.3    76.8    -      -       -      +
    168F  LYS*     1.3    62.8    +      -       -      +
    170F  ALA*     3.6     3.8    +      -       -      +
    171F  ARG*     3.1    20.7    +      -       -      +
    177F  LEU*     3.8    15.7    -      -       +      +
    179F  GLU*     3.1    29.3    +      -       -      -
    213F  TYR*     5.3     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 168 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  PHE*     3.8    33.4    -      -       +      -
    312A  THR*     4.9    11.3    +      -       -      -
    314A  ALA*     2.8    33.4    +      -       -      +
    315A  ILE      4.1     3.8    +      -       -      +
    316A  ASN      3.3    20.4    +      -       -      -
    317A  PHE*     4.0    19.9    -      -       +      -
    127F  SER*     4.4     6.7    +      -       -      +
    131F  MET*     5.0     5.4    -      -       +      -
    164F  ILE*     2.9    25.6    +      -       +      +
    165F  CYS*     3.7    15.3    -      -       -      +
    167F  HIS*     1.3    74.9    -      -       -      +
    169F  PHE*     1.3    56.8    +      -       -      +
    171F  ARG      3.4     0.3    +      -       -      -
    172F  TYR*     2.7    57.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 169 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130F  CYS      5.6     0.2    -      -       -      -
    131F  MET*     4.1    16.3    -      -       -      +
    134F  GLY*     3.4    43.7    -      -       -      -
    135F  MET*     3.5     5.6    -      -       -      -
    138F  LYS*     4.8     2.7    -      -       +      -
    157F  LEU*     4.9     6.3    -      -       +      -
    165F  CYS      2.9    18.3    +      -       -      +
    166F  TRP*     4.0    29.6    -      +       +      +
    167F  HIS      3.4     0.2    -      -       -      -
    168F  LYS*     1.3    75.8    -      -       -      +
    170F  ALA*     1.3    59.8    +      -       +      +
    173F  TRP*     2.8    75.2    +      +       +      +
    175F  VAL*     4.0    32.3    -      -       +      -
    203F  ILE*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 170 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157F  LEU*     6.0     0.2    -      -       +      -
    166F  TRP      3.1    19.3    +      -       -      +
    167F  HIS*     4.0     4.0    -      -       -      +
    169F  PHE*     1.3    82.2    -      -       +      +
    171F  ARG*     1.3    61.6    +      -       -      +
    174F  ASP*     3.1     4.5    +      -       -      -
    175F  VAL*     3.0    49.1    +      -       +      +
    177F  LEU*     3.8    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 171 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  TRP*     3.3    29.3    -      -       +      +
    298A  GLU*     3.5    40.7    +      -       -      +
    299A  LEU*     4.9     0.7    -      -       +      -
    300A  VAL      5.4     2.8    +      -       -      -
    301A  PHE*     3.2    38.1    -      -       +      -
    167F  HIS*     3.1    16.5    +      -       -      +
    168F  LYS      3.9     2.2    -      -       -      +
    170F  ALA*     1.3    80.6    -      -       -      +
    172F  TYR*     1.3    73.2    +      -       +      +
    173F  TRP      3.4     0.2    +      -       -      -
    174F  ASP*     3.4     7.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 172 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  MET*     3.5    35.9    -      -       +      -
    139A  TRP*     3.5    13.4    -      -       -      -
    173A  TRP*     3.1    24.1    +      -       -      +
    299A  LEU*     2.7    48.7    +      -       +      -
    301A  PHE*     3.6    25.0    -      +       -      -
    312A  THR      4.6     0.2    +      -       -      -
    313A  PHE*     3.2    17.9    -      +       -      -
    314A  ALA      3.8    20.8    +      -       -      -
    315A  ILE*     4.9     2.5    -      -       +      -
    131F  MET*     4.8     5.6    -      -       +      -
    168F  LYS*     2.7    40.7    +      -       +      +
    171F  ARG*     1.3    77.3    -      -       +      +
    173F  TRP*     1.3    78.5    +      +       +      +
    174F  ASP*     4.6     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 173 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  TYR      2.9    29.9    +      -       -      -
    173A  TRP*     3.3    38.0    -      +       -      -
    315A  ILE*     5.3     0.9    -      -       +      -
    131F  MET*     3.7    42.4    -      -       +      -
    135F  MET*     3.4    38.8    -      -       +      -
    138F  LYS*     2.7    40.4    +      -       +      +
    139F  TRP*     5.0     3.8    -      +       -      -
    169F  PHE*     2.8    59.5    +      +       +      +
    170F  ALA      3.9     0.2    -      -       -      -
    172F  TYR*     1.3    87.0    -      +       +      +
    174F  ASP*     1.3    65.0    +      -       -      +
    175F  VAL*     3.3     6.5    +      -       +      +
    315F  ILE*     3.9     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