Contacts of the helix formed by residues 136 - 151 (chain F) in PDB entry 4F2N


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 SER 136 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130F  ILE*     4.4     0.3    -      -       -      +
    131F  ALA*     3.7    16.1    +      -       -      -
    134F  PHE*     3.2     7.6    +      -       -      +
    135F  GLY*     1.3    77.8    -      -       -      +
    137F  VAL*     1.3    65.1    +      -       -      +
    138F  ASP*     3.6    10.3    +      -       -      +
    139F  ASP*     3.0    29.1    +      -       -      +
    140F  PHE*     3.1    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 137 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  MET*     3.9    30.1    -      -       +      -
    127F  GLU*     3.7    41.1    -      -       +      +
    130F  ILE*     4.2    14.4    -      -       +      -
    131F  ALA*     4.4     2.8    -      -       +      +
    136F  SER*     1.3    71.0    -      -       -      +
    138F  ASP*     1.3    60.0    +      -       -      +
    140F  PHE*     3.2     5.0    +      -       +      +
    141F  MET*     2.9    48.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 138 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136F  SER*     3.6     8.9    -      -       -      +
    137F  VAL*     1.3    78.4    -      -       -      +
    139F  ASP*     1.3    61.8    +      -       -      +
    141F  MET*     3.2    13.4    +      -       -      +
    142F  VAL*     3.0    34.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134F  PHE*     3.3    24.7    -      -       -      +
    135F  GLY*     4.7     2.6    -      -       -      -
    136F  SER*     3.0    19.3    +      -       -      +
    138F  ASP*     1.3    79.5    -      -       -      +
    140F  PHE*     1.3    66.7    +      -       -      +
    142F  VAL*     3.4     8.6    +      -       -      +
    143F  SER*     3.0    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 140 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130F  ILE*     3.4    35.0    -      -       +      -
    134F  PHE*     3.7    33.9    -      +       +      +
    136F  SER      3.1     8.8    +      -       -      +
    137F  VAL*     3.4     9.6    -      -       +      +
    139F  ASP*     1.3    76.7    -      -       -      +
    141F  MET*     1.3    64.6    +      -       +      +
    143F  SER*     3.2     3.7    +      -       -      -
    144F  PHE*     2.8    48.2    +      +       +      +
    159F  LEU*     3.7    37.5    -      -       +      -
    170F  ILE*     3.8    19.3    -      -       +      -
    188F  PHE*     5.0     2.5    -      +       -      -
    213F  TRP*     3.6    27.1    -      +       -      -
    218F  TRP*     4.3    11.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with MET 141 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  MET*     4.9     1.1    -      -       +      -
    137F  VAL*     2.9    38.5    +      -       +      +
    138F  ASP*     3.2    12.1    +      -       -      +
    140F  PHE*     1.3    81.1    -      -       +      +
    142F  VAL*     1.3    57.4    +      -       +      +
    144F  PHE*     3.4     1.0    +      -       -      +
    145F  GLN*     2.9    39.7    +      -       -      +
    213F  TRP*     3.6    58.7    -      -       +      +
    218F  TRP*     3.9    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138F  ASP*     3.0    23.4    +      -       +      +
    139F  ASP*     3.9     9.6    -      -       -      +
    140F  PHE      3.3     0.2    -      -       -      -
    141F  MET*     1.3    77.9    -      -       +      +
    143F  SER*     1.3    57.8    +      -       -      +
    145F  GLN*     3.4    14.4    +      -       -      +
    146F  GLN*     2.9    37.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 143 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134F  PHE*     5.1     7.1    -      -       -      -
    139F  ASP*     3.0    17.1    +      -       -      +
    140F  PHE*     3.7     4.9    -      -       -      -
    142F  VAL*     1.3    77.8    -      -       -      +
    144F  PHE*     1.3    58.6    +      -       -      +
    146F  GLN*     3.8    11.4    +      -       -      +
    147F  ALA*     3.0    28.9    +      -       -      +
    170F  ILE*     3.7    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 144 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140F  PHE*     2.8    39.3    +      +       +      +
    141F  MET      3.8     4.0    -      -       -      +
    143F  SER*     1.3    74.3    -      -       -      +
    145F  GLN*     1.3    68.3    +      -       +      +
    147F  ALA*     3.3     5.2    +      -       -      +
    148F  GLY*     3.0    19.2    +      -       -      -
    157F  THR*     3.4    43.8    -      -       +      +
    158F  TRP      3.9    12.6    -      -       -      -
    159F  LEU      4.0     0.7    -      -       -      -
    170F  ILE*     3.7    12.7    -      -       +      +
    188F  PHE*     3.5    33.0    -      +       -      -
    190F  ALA*     3.6    22.0    -      -       +      -
    209F  LEU*     4.5     9.0    -      -       +      -
    212F  LEU*     5.4     1.6    -      -       +      -
    213F  TRP*     3.5    24.7    -      +       +      -
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Residues in contact with GLN 145 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141F  MET*     2.9    24.0    +      -       -      +
    142F  VAL*     3.8    12.3    -      -       -      +
    144F  PHE*     1.3    76.0    -      -       -      +
    146F  GLN*     1.3    58.8    +      -       -      +
    148F  GLY*     3.3     2.1    +      -       -      -
    149F  VAL*     2.9    38.3    +      -       +      +
    206F  ALA      5.3     2.7    +      -       -      +
    209F  LEU*     3.8    26.5    -      -       +      +
    210F  LYS*     3.7    32.7    -      -       -      +
    213F  TRP*     2.7    36.3    +      -       +      +
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Residues in contact with GLN 146 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142F  VAL*     2.9    26.1    +      -       +      +
    143F  SER*     3.8    10.9    +      -       -      +
    144F  PHE      3.3     0.2    -      -       -      -
    145F  GLN*     1.3    77.8    -      -       -      +
    147F  ALA*     1.3    56.8    +      -       -      +
    149F  VAL*     3.4     5.0    +      -       -      +
    150F  ASN*     3.0    54.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 147 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143F  SER      3.0    17.8    +      -       -      +
    144F  PHE      3.6     4.7    -      -       -      +
    145F  GLN      3.3     0.2    -      -       -      -
    146F  GLN*     1.3    78.1    -      -       -      +
    148F  GLY*     1.3    61.8    +      -       -      +
    150F  ASN*     3.4     4.1    +      -       -      +
    151F  ASN*     3.1    23.4    +      -       -      +
    157F  THR*     3.8     9.4    -      -       +      -
    170F  ILE*     3.8    13.7    -      -       +      -
    172F  SER*     3.7    20.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 148 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144F  PHE      3.0    12.9    +      -       -      -
    145F  GLN      3.7     2.9    -      -       -      -
    147F  ALA*     1.3    76.4    -      -       -      +
    149F  VAL*     1.3    61.7    +      -       -      +
    151F  ASN*     3.3     7.6    +      -       -      +
    157F  THR*     3.2    21.0    +      -       -      -
    192F  VAL*     4.1     6.3    -      -       -      +
    205F  ARG*     3.0    23.2    +      -       -      -
    209F  LEU*     3.7    18.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 149 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145F  GLN*     2.9    27.3    +      -       +      +
    146F  GLN*     3.9     5.6    -      -       -      +
    148F  GLY*     1.3    73.2    -      -       -      +
    150F  ASN*     1.3    70.6    +      -       -      +
    151F  ASN      3.3     1.4    +      -       -      +
    205F  ARG*     3.9    16.6    +      -       +      +
    206F  ALA*     3.7    39.3    -      -       +      +
    209F  LEU*     4.0     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 150 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146F  GLN*     3.0    45.0    +      -       -      +
    147F  ALA*     3.8     4.5    -      -       -      +
    148F  GLY      3.3     0.2    -      -       -      -
    149F  VAL*     1.3    87.1    -      -       -      +
    151F  ASN*     1.3    59.0    +      -       -      +
    152F  PHE*     3.0    12.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 151 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147F  ALA      3.1    11.3    +      -       -      +
    148F  GLY*     3.4    13.2    -      -       -      +
    149F  VAL      3.3     2.6    -      -       -      +
    150F  ASN*     1.3    74.4    -      -       -      +
    152F  PHE*     1.3    68.3    +      -       -      +
    153F  GLY      3.4     4.5    +      -       -      +
    154F  SER      4.9     0.6    -      -       -      +
    155F  GLY*     3.9     4.0    -      -       -      -
    156F  TRP      3.2    25.9    +      -       -      +
    157F  THR*     3.9     1.0    +      -       -      -
    172F  SER*     3.9    16.3    -      -       -      +
    173F  THR      3.1    29.2    +      -       -      +
    174F  SER*     4.8     3.6    +      -       -      -
    192F  VAL*     3.5    10.6    -      -       +      +
    205F  ARG*     2.7    27.4    +      -       -      +
----------------------------------------------------------
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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