Contacts of the helix formed by residues 207 - 220 (chain P) in PDB entry 1JVP


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 207 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166P  LEU*     3.3    12.2    -      -       -      +
    205P  GLY      3.5     0.8    -      -       -      -
    206P  ASP*     1.3    80.6    -      -       -      +
    208P  GLU*     1.3    58.8    +      -       -      +
    209P  ILE*     3.7    10.4    +      -       -      +
    210P  ASP*     3.1    24.6    +      -       -      +
    211P  GLN*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 208 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166P  LEU*     3.6    23.2    -      -       +      +
    173P  ILE      5.3     0.7    -      -       -      +
    174P  LEU*     4.0    34.3    -      -       +      +
    207P  SER*     1.3    74.0    -      -       -      +
    209P  ILE*     1.3    57.0    +      -       -      +
    211P  GLN*     3.5     4.6    -      -       -      +
    212P  LEU*     3.0    26.7    +      -       -      +
    235P  ASP*     5.7     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 209 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207P  SER*     3.7     9.4    +      -       -      +
    208P  GLU*     1.3    78.7    -      -       -      +
    210P  ASP*     1.3    66.9    +      -       +      +
    212P  LEU*     3.7    10.7    -      -       +      +
    213P  PHE*     2.9    69.9    +      -       +      +
    240P  PHE*     4.2    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 210 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204P  PRO      4.0     0.5    -      -       -      +
    205P  GLY*     3.0    14.9    -      -       -      -
    206P  ASP*     3.1    20.4    +      -       -      +
    207P  SER*     3.1    19.8    +      -       -      +
    209P  ILE*     1.3    83.0    -      -       +      +
    211P  GLN*     1.3    57.6    +      -       -      +
    213P  PHE*     3.9     4.1    -      -       -      +
    214P  ARG*     2.9    65.5    +      -       -      +
    217P  ARG*     4.1    11.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 211 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166P  LEU*     3.0    43.9    +      -       +      +
    167P  TRP      3.3     7.5    +      -       -      -
    169P  ARG      4.9     1.4    +      -       -      +
    174P  LEU*     3.7    20.0    -      -       +      -
    187P  TRP*     6.1     0.2    -      -       -      +
    203P  PHE*     2.9    37.4    +      -       -      +
    205P  GLY*     2.9    29.8    +      -       -      +
    207P  SER      2.9    18.4    +      -       -      +
    208P  GLU*     3.5     6.3    -      -       -      +
    210P  ASP*     1.3    73.8    -      -       -      +
    212P  LEU*     1.3    65.4    +      -       -      +
    214P  ARG*     3.3     5.1    +      -       -      +
    215P  ILE*     3.1    32.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 212 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171P  PRO*     4.6    10.5    -      -       +      +
    174P  LEU*     4.0    36.3    -      -       +      +
    175P  LEU*     3.7    28.3    -      -       +      -
    208P  GLU      3.0    11.7    +      -       -      +
    209P  ILE*     3.7    14.4    -      -       +      +
    211P  GLN*     1.3    79.6    -      -       -      +
    213P  PHE*     1.3    61.8    +      -       +      +
    215P  ILE*     3.1     8.3    +      -       +      +
    216P  PHE*     2.9    70.2    +      -       +      -
    235P  ASP      5.6     0.2    -      -       -      +
    240P  PHE*     3.8    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 213 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209P  ILE*     2.9    45.8    +      -       +      +
    210P  ASP*     4.2     1.3    -      -       -      +
    212P  LEU*     1.3    76.8    -      -       +      +
    214P  ARG*     1.3    59.6    +      -       -      +
    216P  PHE*     3.6    26.3    -      +       -      +
    217P  ARG*     2.8    57.2    +      -       -      +
    240P  PHE*     3.6    29.6    -      +       -      -
    241P  PRO*     3.4    28.0    -      -       +      -
    243P  TRP*     3.6    14.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with ARG 214 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202P  LEU      5.5     0.2    +      -       -      -
    203P  PHE*     3.8    15.8    -      -       +      -
    204P  PRO*     3.2    40.4    +      -       -      +
    205P  GLY*     3.6    17.0    -      -       -      +
    210P  ASP*     2.9    48.5    +      -       -      +
    211P  GLN*     3.6     4.9    -      -       -      +
    213P  PHE*     1.3    72.3    -      -       -      +
    215P  ILE*     1.3    66.1    +      -       -      +
    217P  ARG*     3.5    19.6    +      -       -      +
    218P  THR*     3.4    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 215 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169P  ARG      4.1     7.4    -      -       -      +
    171P  PRO*     4.8     8.5    -      -       +      -
    174P  LEU*     3.9    24.7    -      -       +      -
    187P  TRP*     3.8    36.1    -      -       +      -
    203P  PHE*     3.8    29.4    -      -       +      -
    211P  GLN*     3.1    21.6    +      -       -      +
    212P  LEU*     3.1     9.1    +      -       +      +
    214P  ARG*     1.3    77.2    -      -       -      +
    216P  PHE*     1.3    57.2    +      -       +      +
    218P  THR*     3.2     2.4    +      -       -      -
    219P  LEU*     2.8    33.7    +      -       +      +
    269P  TYR*     3.5    22.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 216 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171P  PRO*     5.6     0.2    -      -       +      -
    175P  LEU*     4.8     5.6    -      -       +      -
    212P  LEU*     2.9    47.9    +      -       +      -
    213P  PHE*     3.6    31.4    -      +       -      +
    215P  ILE*     1.3    78.2    -      -       +      +
    217P  ARG*     1.3    57.1    +      -       -      +
    220P  GLY*     2.7    33.2    +      -       -      -
    221P  THR*     3.5    20.5    +      -       +      +
    222P  PRO*     3.3    28.0    -      -       +      -
    236P  TYR*     6.0     0.2    -      +       -      -
    240P  PHE*     3.6    31.6    -      +       -      -
    241P  PRO      4.6     1.3    -      -       -      -
    243P  TRP*     3.5    22.7    -      +       +      +
    269P  TYR*     3.4    21.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 217 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210P  ASP*     4.1    17.6    +      -       -      +
    213P  PHE*     2.8    46.5    +      -       -      +
    214P  ARG*     3.8    17.9    -      -       -      +
    215P  ILE      3.3     0.2    -      -       -      -
    216P  PHE*     1.3    74.1    -      -       -      +
    218P  THR*     1.3    59.8    +      -       -      +
    243P  TRP*     3.3    64.0    -      -       +      +
    244P  ALA      3.9    11.7    -      -       -      +
    246P  GLN*     4.0    11.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 218 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202P  LEU*     5.0     6.8    +      -       +      +
    203P  PHE*     3.7    29.9    -      -       +      -
    214P  ARG      3.4     8.4    +      -       -      -
    215P  ILE      3.2     1.6    +      -       -      -
    216P  PHE      3.2     0.2    -      -       -      -
    217P  ARG*     1.3    81.4    -      -       -      +
    219P  LEU*     1.3    70.9    +      -       +      +
    220P  GLY      3.4     0.9    -      -       -      -
    246P  GLN*     3.1    42.8    +      -       -      +
    251P  VAL*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 219 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187P  TRP*     3.5    32.1    -      -       +      -
    203P  PHE*     4.1    13.2    -      -       +      -
    215P  ILE*     2.8    24.1    +      -       +      +
    218P  THR*     1.3    84.9    -      -       +      +
    220P  GLY*     1.3    62.8    +      -       -      +
    245P  ARG*     3.1    45.8    +      -       +      +
    246P  GLN      5.7     0.4    -      -       -      +
    248P  PHE*     3.9    27.4    -      -       +      -
    251P  VAL*     6.5     0.2    -      -       +      -
    267P  LEU*     3.9    22.7    -      -       +      +
    269P  TYR*     3.6    18.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 220 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216P  PHE      2.7    21.2    +      -       -      -
    218P  THR      3.4     2.6    -      -       -      -
    219P  LEU*     1.3    71.2    -      -       -      +
    221P  THR*     1.3    67.5    +      -       -      -
    243P  TRP      3.3    12.8    -      -       -      -
    244P  ALA      3.7     1.1    +      -       -      -
    245P  ARG*     3.6    16.6    -      -       -      +
    269P  TYR*     2.7    30.9    +      -       -      -
----------------------------------------------------------
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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