Contacts of the helix formed by residues 254 - 265 (chain A) in PDB entry 1V0O


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 254 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  LYS*     5.3     4.5    +      -       -      -
    252A  GLY      4.3     0.4    -      -       -      -
    253A  LEU*     1.3    76.7    -      -       -      +
    255A  GLU*     1.3    71.3    +      -       -      +
    256A  SER*     3.7     7.8    +      -       -      -
    257A  GLY*     3.1    31.0    +      -       -      -
    258A  ILE*     3.1    12.0    +      -       -      +
    283A  TYR*     4.0    14.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254A  ASP*     1.3    76.5    -      -       -      +
    256A  SER*     1.3    57.4    +      -       -      +
    258A  ILE*     3.4     9.8    +      -       -      +
    259A  ASP*     3.1    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254A  ASP*     3.2     9.4    +      -       -      -
    255A  GLU*     1.3    76.5    -      -       -      +
    257A  GLY*     1.3    60.5    +      -       -      +
    259A  ASP*     3.5     3.5    +      -       -      -
    260A  LEU*     3.1    24.1    +      -       -      +
    281A  HIS*     3.2    16.3    -      -       -      -
    282A  ALA*     4.4    10.8    +      -       -      +
    283A  TYR*     4.0    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  PHE*     3.5     7.7    -      -       -      -
    253A  LEU*     3.4    18.0    -      -       -      +
    254A  ASP*     3.1    14.9    +      -       -      -
    256A  SER*     1.3    74.9    -      -       -      +
    258A  ILE*     1.3    58.5    +      -       -      +
    260A  LEU*     3.7     0.6    +      -       -      +
    261A  LEU*     3.1    28.2    +      -       -      +
    283A  TYR*     3.5    26.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  TRP*     3.5    45.4    -      -       +      +
    247A  GLU*     4.4    25.1    -      -       +      +
    250A  LEU*     4.7     7.0    -      -       +      +
    253A  LEU*     3.8    34.1    -      -       +      +
    254A  ASP      3.1    14.4    +      -       -      +
    255A  GLU*     3.7    11.0    -      -       -      +
    256A  SER      3.3     0.2    -      -       -      -
    257A  GLY*     1.3    75.2    -      -       -      +
    259A  ASP*     1.3    60.6    +      -       -      +
    261A  LEU*     3.4     4.0    +      -       -      +
    262A  SER*     2.9    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  GLU      3.1    16.8    +      -       -      +
    256A  SER*     3.7     7.0    -      -       -      +
    258A  ILE*     1.3    77.9    -      -       -      +
    260A  LEU*     1.3    59.7    +      -       -      +
    262A  SER*     2.8    23.1    +      -       -      -
    263A  LYS*     3.1    41.2    +      -       -      +
    281A  HIS*     2.8    25.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     3.8    28.3    -      -       +      -
    110A  LEU*     4.8     0.2    -      -       +      -
    191A  PHE*     4.1     2.9    -      -       +      -
    256A  SER      3.1    16.1    +      -       -      +
    257A  GLY      4.0     4.0    -      -       -      +
    259A  ASP*     1.3    75.8    -      -       -      +
    261A  LEU*     1.3    63.1    +      -       -      +
    263A  LYS*     3.1    13.1    +      -       -      +
    264A  MET*     3.3    24.8    +      -       +      +
    273A  ILE*     4.0    15.9    -      -       +      -
    278A  ALA*     3.9    25.1    -      -       +      -
    281A  HIS*     3.7    23.9    +      -       +      +
    283A  TYR*     3.9    19.7    -      -       +      -
    284A  PHE*     3.9    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  GLY*     3.4    33.4    -      -       -      +
    191A  PHE*     3.7    24.2    -      -       +      -
    192A  ALA*     4.3     7.4    -      -       +      +
    246A  TRP*     4.6     8.0    -      -       +      -
    249A  PHE*     5.6     0.4    -      -       +      -
    250A  LEU*     3.4    45.1    -      -       +      -
    253A  LEU*     4.1    10.1    -      -       +      -
    257A  GLY      3.1    16.3    +      -       -      +
    258A  ILE      3.7     3.6    -      -       -      +
    260A  LEU*     1.3    81.4    -      -       -      +
    262A  SER*     1.3    62.0    +      -       -      +
    264A  MET*     3.2     4.9    +      -       -      +
    265A  LEU*     3.1    33.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  TRP*     3.4    43.8    -      -       -      -
    258A  ILE*     2.9    15.1    +      -       -      -
    259A  ASP*     2.8    25.5    +      -       -      -
    261A  LEU*     1.3    76.0    -      -       -      +
    263A  LYS*     1.3    63.8    +      -       -      +
    265A  LEU      3.8     2.4    -      -       -      +
    266A  LYS*     3.5    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  ASP*     3.1    41.6    +      -       -      +
    260A  LEU      3.1    10.1    +      -       -      +
    262A  SER*     1.3    81.7    +      -       -      +
    264A  MET*     1.3    59.1    +      -       -      +
    266A  LYS*     3.7    23.0    -      -       -      +
    271A  GLN      5.7     0.2    -      -       -      +
    272A  ARG*     3.4     8.3    -      -       -      -
    273A  ILE*     2.9    54.6    +      -       +      +
    281A  HIS*     4.8     7.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with MET 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     4.3     3.8    -      -       +      -
    110A  LEU*     3.8    28.7    -      -       +      -
    184A  ILE*     3.9    18.9    -      -       +      +
    185A  TRP*     4.1     9.0    -      -       -      -
    187A  VAL*     3.6    26.2    -      -       +      -
    188A  GLY*     3.9    27.6    -      -       -      -
    191A  PHE*     4.2    17.3    -      -       -      -
    260A  LEU*     3.5    30.7    -      -       +      +
    261A  LEU*     3.2     6.8    +      -       -      +
    263A  LYS*     1.3    78.1    -      -       -      +
    265A  LEU*     1.3    58.9    +      -       -      +
    266A  LYS      3.3     2.2    -      -       -      -
    272A  ARG*     3.3    25.6    +      -       -      +
    273A  ILE*     3.8    11.7    -      -       +      -
    278A  ALA*     4.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  TRP*     3.5    50.9    -      -       +      +
    188A  GLY*     3.8    11.0    -      -       -      +
    189A  CYS*     3.8    11.7    -      -       -      +
    200A  LEU*     3.8    29.2    -      -       +      -
    201A  PHE*     4.5     3.8    -      -       +      -
    217A  LEU*     3.9    23.6    -      -       +      +
    246A  TRP*     4.4    22.6    -      -       +      -
    261A  LEU*     3.1    31.8    +      -       +      +
    262A  SER      3.8     6.3    -      -       -      +
    264A  MET*     1.3    75.8    -      -       -      +
    266A  LYS*     1.3    60.7    +      -       -      +
    267A  LEU*     3.7     3.8    +      -       -      +
----------------------------------------------------------
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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