Contacts of the strand formed by residues 159 - 164 (chain A) in PDB entry 2DOU


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 ALA 159 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  LEU*     3.8    10.1    -      -       -      -
    115A  LEU*     3.3    39.9    -      -       +      -
    155A  VAL      3.1    14.4    +      -       -      +
    156A  TRP      3.3    10.5    +      -       -      +
    157A  ARG      4.4     2.8    -      -       -      +
    158A  GLU*     1.3    81.0    -      -       -      +
    160A  LYS*     1.3    58.6    +      -       -      +
    161A  VAL      4.7     0.7    -      -       -      +
    190A  HIS      4.8     0.5    -      -       -      +
    191A  GLY      5.0     0.7    -      -       -      +
    192A  LEU*     3.0    25.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  LEU      5.6     1.8    -      -       -      +
    108A  THR*     5.3     2.0    -      -       +      -
    112A  ASP*     4.4    24.0    -      -       +      +
    113A  LEU      3.0    13.6    +      -       -      +
    158A  GLU      4.8     1.3    -      -       -      +
    159A  ALA*     1.3    74.6    -      -       -      +
    161A  VAL*     1.3    72.6    +      -       +      +
    191A  GLY      5.2     1.8    -      -       -      -
    192A  LEU*     3.6     8.5    -      -       -      +
    193A  TRP*     3.0    29.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  LEU*     4.4     2.5    -      -       +      -
    107A  LEU*     4.7     4.5    -      -       +      +
    108A  THR*     3.9    28.9    -      -       +      -
    113A  LEU      3.5     4.1    +      -       -      +
    114A  LEU*     3.4    25.5    -      -       +      +
    115A  LEU*     2.9    30.7    +      -       -      +
    133A  LEU*     6.1     0.2    -      -       +      -
    160A  LYS*     1.3    89.8    -      -       +      +
    162A  LEU*     1.3    68.7    +      -       -      +
    192A  LEU*     4.5     4.2    -      -       -      +
    193A  TRP*     3.6    24.2    -      -       +      +
    195A  ILE*     3.8    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  LEU*     3.6    26.0    -      -       +      +
    138A  ILE*     3.9    17.0    -      -       +      -
    148A  LEU*     5.1     4.7    -      -       +      -
    156A  TRP*     4.5    19.3    -      -       +      -
    161A  VAL*     1.3    76.9    -      -       -      +
    163A  LEU*     1.3    71.1    +      -       -      +
    164A  LEU*     4.0    27.4    -      -       +      -
    183A  ALA*     4.4    21.5    -      -       +      +
    187A  ALA*     5.0     4.0    -      -       +      -
    192A  LEU*     4.4    11.9    -      -       +      +
    193A  TRP      3.0    12.4    +      -       -      +
    194A  LEU*     3.7    12.7    -      -       +      +
    195A  ILE*     2.9    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  LEU*     3.7    23.6    -      -       +      -
    104A  LEU*     5.3     4.5    -      -       +      -
    114A  LEU*     4.3    18.4    -      -       +      -
    115A  LEU      2.8    16.3    +      -       -      +
    116A  LEU*     3.8    15.1    -      -       +      -
    117A  PRO*     3.6    15.6    -      -       -      +
    124A  TYR*     3.6    44.0    -      -       +      -
    162A  LEU*     1.3    74.5    -      -       -      +
    164A  LEU*     1.3    79.2    +      -       -      +
    195A  ILE*     3.5    38.4    -      -       +      +
    197A  ASP*     5.0     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PRO*     4.3     8.5    -      -       +      -
    124A  TYR*     5.3     0.7    -      -       -      -
    138A  ILE*     5.2     1.3    -      -       +      -
    146A  ALA*     4.2    20.0    -      -       +      -
    148A  LEU*     4.7     4.0    -      -       +      -
    162A  LEU*     4.0    32.1    -      -       +      -
    163A  LEU*     1.3    88.2    -      -       -      +
    165A  ASN*     1.3    61.7    -      -       -      +
    166A  TYR*     3.9    19.7    -      -       +      -
    179A  TYR*     4.2    15.0    -      -       +      +
    180A  PHE*     5.1     5.2    -      -       +      -
    183A  ALA*     4.0    20.2    -      -       +      -
    194A  LEU*     4.7     7.9    -      -       +      -
    195A  ILE      3.0     8.5    +      -       -      +
    196A  HIS*     3.4    17.2    -      -       +      -
    197A  ASP*     3.0    26.2    +      -       -      +
----------------------------------------------------------
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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