Contacts of the helix formed by residues 145 - 162 (chain A) in PDB entry 3DVA


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 GLY 145 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ILE*     1.3    77.2    -      -       -      +
    146A  ALA*     1.3    64.2    +      -       -      +
    147A  GLN*     3.1    17.0    +      -       -      +
    148A  TYR*     3.0    25.4    +      -       -      +
    149A  ILE      3.7     0.9    +      -       -      -
    171A  THR*     4.6     2.6    +      -       -      -
    175A  GLY      5.1     2.5    -      -       -      -
    178A  GLN*     4.7     4.3    -      -       -      -
    180A  ASP*     3.3    24.8    -      -       -      +
    181A  PHE*     4.5     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  GLN*     3.7     7.4    -      -       -      +
    143A  ILE*     3.0    17.8    +      -       +      +
    144A  ILE      3.4     1.4    +      -       -      -
    145A  GLY*     1.3    77.2    -      -       -      +
    147A  GLN*     1.3    63.0    +      -       -      +
    148A  TYR      3.1     0.9    +      -       -      -
    149A  ILE*     3.4     9.7    +      -       +      +
    150A  GLN*     3.2    29.3    +      -       -      +
    180A  ASP*     4.2    10.9    +      -       -      +
     91B  ASP*     3.8    10.8    -      -       -      +
     96B  GLN*     3.5    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  LEU*     3.6    23.1    -      -       +      +
    100A  PRO      4.3     3.1    -      -       -      +
    101A  GLY*     4.4     8.7    -      -       -      -
    138A  LEU*     6.3     0.4    -      -       +      -
    141A  GLN*     3.6    24.2    +      -       +      +
    143A  ILE      3.3     5.7    -      -       -      +
    144A  ILE*     4.6     3.8    -      -       -      +
    145A  GLY*     3.1    13.4    +      -       -      +
    146A  ALA*     1.3    81.6    +      -       -      +
    148A  TYR*     1.3    60.0    +      -       +      +
    150A  GLN*     4.5     9.2    -      -       -      -
    151A  ALA*     2.9    29.7    +      -       -      +
    169A  THR*     3.0    26.8    +      -       -      +
    170A  TYR      3.1    22.7    +      -       -      +
    171A  THR*     3.7    18.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  GLY*     3.0    13.8    +      -       -      +
    147A  GLN*     1.3    84.0    -      -       +      +
    149A  ILE*     1.3    65.8    +      -       -      +
    151A  ALA*     3.2    15.0    +      -       -      +
    152A  ALA      3.2     9.7    +      -       -      -
    169A  THR*     3.7    21.3    -      -       +      -
    170A  TYR      4.1     0.4    -      -       -      -
    171A  THR*     3.4    38.6    -      -       +      +
    180A  ASP      3.6    10.1    -      -       -      +
    181A  PHE*     3.3    41.3    -      +       -      -
    184A  GLY*     3.7     9.9    -      -       -      -
    185A  ILE*     3.7     2.5    -      -       +      -
    197A  PHE*     3.3    38.7    -      +       +      +
    198A  VAL      3.0    32.1    +      -       -      -
    199A  VAL*     3.5     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  ALA*     3.4    15.9    -      -       +      +
    148A  TYR*     1.3    75.5    -      -       -      +
    150A  GLN*     1.3    66.1    +      -       +      +
    152A  ALA*     3.5     5.8    +      -       -      +
    153A  GLY      3.4    10.6    +      -       -      -
    180A  ASP*     3.3    37.7    -      -       -      +
    183A  GLU*     3.8    13.9    -      -       +      -
    184A  GLY*     3.5    18.4    -      -       -      +
    187A  PHE*     6.3     0.2    -      -       +      -
     60B  SER*     3.3    36.6    -      -       -      +
     61B  GLY*     4.1    11.6    -      -       -      +
     64B  GLY*     3.1    24.4    -      -       -      +
     65B  LEU      3.8     1.0    +      -       -      -
     91B  ASP*     6.0     0.9    -      -       -      +
     92B  SER*     3.7    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  LEU*     3.7    12.8    -      -       +      +
    138A  LEU*     3.5    23.8    -      -       +      +
    141A  GLN*     3.7    10.9    +      -       -      +
    146A  ALA*     3.2    21.1    +      -       -      +
    147A  GLN*     4.0     2.5    -      -       -      +
    149A  ILE*     1.3    77.1    -      -       +      +
    151A  ALA*     1.3    58.8    +      -       -      +
    153A  GLY*     3.1     3.3    +      -       -      -
    154A  VAL*     2.9    30.0    +      -       +      +
     64B  GLY*     3.3    12.3    -      -       -      +
     67B  ILE*     3.8    36.7    -      -       +      +
     68B  GLY*     3.5     3.4    -      -       -      +
     71B  LEU*     5.5     0.2    -      -       +      -
     92B  SER*     5.8     0.4    +      -       -      -
     96B  GLN*     3.1    41.6    +      -       -      +
    100B  ILE*     5.3     2.0    -      -       -      +
    103B  ARG*     5.1     0.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  LEU*     3.7    17.0    -      -       +      -
    147A  GLN      2.9    20.2    +      -       -      +
    148A  TYR      3.2     7.2    +      -       -      +
    150A  GLN*     1.3    73.3    -      -       -      +
    152A  ALA*     1.3    65.9    +      -       -      +
    153A  GLY      3.0     2.2    -      -       -      -
    154A  VAL*     3.1     1.6    +      -       -      +
    155A  ALA*     2.9    27.1    +      -       -      +
    167A  ALA*     3.9     6.7    -      -       +      +
    169A  THR*     3.7    26.9    -      -       +      +
    195A  ALA*     4.9     3.6    -      -       +      -
    197A  PHE*     4.1     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  TYR      3.2     5.8    +      -       -      +
    149A  ILE      3.7     9.9    -      -       -      +
    151A  ALA*     1.3    78.6    -      -       -      +
    153A  GLY*     1.3    60.2    +      -       -      +
    155A  ALA*     3.9     3.6    +      -       -      +
    156A  LEU*     3.3    22.2    +      -       -      +
    184A  GLY*     3.5    26.0    -      -       -      +
    187A  PHE*     4.0    12.1    -      -       +      -
    188A  ALA*     3.9    24.0    -      -       +      +
    191A  PHE*     6.0     0.9    -      -       -      +
    193A  ALA*     4.4     4.2    -      -       -      +
    197A  PHE*     4.6     1.9    -      -       +      -
     65B  LEU*     3.8     8.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  ILE      3.4     4.0    +      -       -      -
    150A  GLN      3.1     7.3    +      -       -      -
    151A  ALA      3.0     0.8    -      -       -      -
    152A  ALA*     1.3    78.4    -      -       -      +
    154A  VAL*     1.3    63.9    +      -       -      +
    156A  LEU*     3.4     3.6    +      -       -      +
    157A  GLY      3.1    17.0    +      -       -      -
     65B  LEU*     3.6    33.8    -      -       -      +
     68B  GLY*     3.5     8.2    -      -       -      -
     69B  LEU*     3.5    10.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  PHE*     3.8    31.6    -      -       +      -
     99A  LEU*     4.0    14.6    -      -       +      -
    150A  GLN      2.9    18.7    +      -       -      +
    151A  ALA      3.1     5.1    +      -       -      +
    153A  GLY*     1.3    75.4    -      -       -      +
    155A  ALA*     1.3    64.4    +      -       -      +
    157A  GLY*     3.0    12.0    +      -       -      -
    158A  LEU*     3.0    14.9    +      -       +      +
    167A  ALA*     3.8    15.0    -      -       +      -
     68B  GLY*     3.6    22.4    -      -       -      +
     71B  LEU*     3.8    20.0    -      -       +      -
     72B  GLN*     3.5    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ALA      2.9    15.1    +      -       -      +
    152A  ALA      4.1     1.6    -      -       -      +
    154A  VAL*     1.3    77.1    -      -       -      +
    156A  LEU*     1.3    62.7    +      -       -      +
    158A  LEU*     3.2     6.2    +      -       -      +
    159A  LYS      3.0    18.0    +      -       -      -
    167A  ALA*     3.7     8.2    -      -       +      +
    193A  ALA*     3.8     9.4    -      -       +      -
    194A  PRO*     3.3    48.1    -      -       -      +
    195A  ALA*     3.7    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ALA      3.3    16.0    +      -       -      +
    153A  GLY      3.6     5.6    -      -       -      +
    154A  VAL      3.2     0.4    -      -       -      -
    155A  ALA*     1.3    78.7    -      -       -      +
    157A  GLY*     1.3    57.7    +      -       -      +
    159A  LYS*     3.1    20.4    +      -       +      +
    160A  MET*     2.9    49.4    +      -       +      +
    191A  PHE*     4.2    35.0    -      -       +      +
    193A  ALA*     4.0     6.4    -      -       +      +
     53B  PHE*     4.5    10.3    -      -       +      -
     65B  LEU*     3.8    31.6    -      -       +      -
     69B  LEU*     4.0    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  GLY      3.1     8.0    +      -       -      -
    154A  VAL      3.0     8.2    +      -       -      -
    156A  LEU*     1.3    78.0    -      -       -      +
    158A  LEU*     1.3    60.4    +      -       -      +
    160A  MET      3.4     0.3    +      -       -      -
    161A  ARG*     3.0    28.4    +      -       -      +
     69B  LEU*     3.7     9.3    -      -       -      +
     72B  GLN*     3.8    16.4    -      -       -      -
     74B  PHE*     3.6    21.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  GLU      4.8     6.5    -      -       -      +
     97A  PHE*     4.8     3.8    -      -       +      +
    154A  VAL*     3.0    25.7    +      -       +      +
    155A  ALA*     3.2    10.1    +      -       -      +
    157A  GLY*     1.3    76.0    -      -       -      +
    159A  LYS*     1.3    61.2    +      -       -      +
    161A  ARG      3.3     1.2    +      -       -      -
    162A  GLY      3.1     3.6    +      -       -      -
    163A  LYS*     2.9    59.8    +      -       +      +
    165A  ALA*     3.8    25.8    -      -       +      +
    166A  VAL*     3.6    33.7    -      -       -      +
    167A  ALA      3.9     3.1    -      -       -      +
    194A  PRO*     4.6     1.1    -      -       +      -
     72B  GLN*     3.4    29.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ALA      3.0    14.1    +      -       -      +
    156A  LEU*     3.3    19.9    -      -       +      +
    158A  LEU*     1.3    76.0    -      -       -      +
    160A  MET*     1.3    60.3    +      -       +      +
    162A  GLY*     2.9    20.6    +      -       -      -
    163A  LYS      5.1     3.1    -      -       -      +
    191A  PHE      2.9    26.7    +      -       -      +
    192A  LYS*     2.9    31.5    +      -       -      +
    193A  ALA*     4.5     0.4    -      -       -      -
    194A  PRO*     3.9    15.7    -      -       +      +
    255A  GLY*     5.4     9.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  LEU*     2.9    36.3    +      -       +      +
    157A  GLY      3.9     0.2    -      -       -      +
    159A  LYS*     1.3    77.1    -      -       +      +
    161A  ARG*     1.3    61.7    +      -       -      +
    162A  GLY*     3.4     0.7    +      -       -      -
     24B  LEU*     3.8    25.1    -      -       +      -
     50B  ASP*     3.2    37.2    -      -       +      +
     51B  ARG*     5.8     0.4    -      -       +      -
     53B  PHE*     5.0     5.2    -      -       +      -
     69B  LEU*     4.0    24.0    -      -       -      -
     74B  PHE*     3.7    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  GLY      3.0    22.4    +      -       -      +
    158A  LEU      3.7     0.2    -      -       -      +
    159A  LYS      3.2     0.4    -      -       -      -
    160A  MET*     1.3    75.0    -      -       -      +
    162A  GLY*     1.3    61.0    +      -       -      +
    163A  LYS*     3.3    36.5    +      -       +      +
     22B  ASN*     2.9    28.9    +      -       -      +
     72B  GLN*     3.1    27.6    +      -       -      +
     73B  GLY*     3.3    18.4    +      -       -      -
     74B  PHE*     3.3    24.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  LYS*     2.9    16.4    +      -       -      -
    160A  MET      3.1     1.9    -      -       -      -
    161A  ARG*     1.3    80.2    -      -       -      +
    163A  LYS*     1.3    63.5    +      -       -      +
    164A  LYS*     3.7    19.6    +      -       -      +
----------------------------------------------------------
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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