Contacts of the strand formed by residues 1868 - 1877 (chain A) in PDB entry 2V5P


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 ARG1868 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1792A  PRO*     5.1    10.8    +      -       -      +
   1793A  VAL*     6.1     8.9    -      -       -      +
   1795A  CYS      5.5     4.2    +      -       -      -
   1796A  PRO      6.0     0.2    -      -       -      -
   1797A  ASP*     3.0    27.5    +      -       -      -
   1851A  LYS      5.4     0.2    -      -       -      +
   1852A  ASP*     3.3    33.7    +      -       +      +
   1865A  SER*     5.3     1.8    -      -       -      +
   1867A  GLY*     1.3    69.9    -      -       -      -
   1869A  LEU*     1.3    56.9    -      -       -      +
   1870A  GLN*     3.0    16.3    -      -       -      +
   1871A  SER*     2.6    49.1    +      -       -      +
   1887A  TYR*     3.9     3.7    -      -       -      +
   1888A  VAL      2.9    10.4    +      -       -      +
   1889A  ASN*     3.4    33.6    +      -       -      +
   1890A  GLY*     5.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1869 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1839A  CYS*     3.8    11.2    -      -       -      +
   1840A  THR*     3.6    31.6    -      -       -      +
   1841A  PHE*     3.5    48.9    -      -       +      +
   1852A  ASP      2.6    18.9    +      -       -      +
   1854A  GLY*     4.3     7.6    -      -       -      +
   1867A  GLY      3.3     2.4    +      -       -      -
   1868A  ARG*     1.3    70.3    -      -       -      +
   1870A  GLN*     1.3    65.5    +      -       -      +
   1872A  MET*     3.4    22.1    -      -       -      +
   1887A  TYR*     3.7    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN1870 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1797A  ASP*     3.4    42.8    +      -       +      +
   1798A  GLU*     4.3    16.5    +      -       -      +
   1841A  PHE*     4.5    12.3    -      -       -      -
   1852A  ASP*     3.3    35.0    +      -       -      +
   1868A  ARG*     2.9    14.0    +      -       -      +
   1869A  LEU*     1.3    84.1    +      -       +      +
   1871A  SER*     1.3    57.2    +      -       -      +
   1872A  MET*     3.1    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER1871 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1868A  ARG*     2.6    34.0    +      -       -      +
   1870A  GLN*     1.3    77.2    -      -       -      +
   1872A  MET*     1.3    62.7    +      -       -      +
   1873A  LYS*     3.4    13.5    +      -       -      +
   1886A  SER      3.7     5.7    -      -       -      +
   1887A  TYR*     4.5     0.3    -      -       -      -
   1888A  VAL*     2.8    52.1    +      -       -      +
   1889A  ASN*     4.8     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET1872 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1800A  ARG*     4.4    25.3    +      -       +      +
   1804A  CYS*     4.4     3.1    -      -       -      -
   1817A  LEU*     5.2     0.9    -      -       +      -
   1838A  VAL*     5.1     1.1    -      -       +      -
   1839A  CYS*     3.6    37.0    -      -       -      -
   1868A  ARG      4.1     0.8    +      -       -      -
   1869A  LEU*     3.4    17.1    +      -       -      +
   1870A  GLN      3.1     5.3    -      -       -      +
   1871A  SER*     1.3    77.4    +      -       -      +
   1873A  LYS*     1.3    66.5    +      -       -      +
   1874A  LEU*     3.8    31.6    -      -       +      -
   1885A  LEU*     3.5    33.9    -      -       +      -
   1886A  SER      3.4     7.6    -      -       -      -
   1887A  TYR*     3.7    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1873 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1800A  ARG*     5.4     2.0    -      -       -      +
   1871A  SER      3.7    10.1    -      -       -      +
   1872A  MET*     1.3    80.0    -      -       -      +
   1874A  LEU*     1.3    62.3    +      -       -      +
   1875A  ASP*     4.4    19.8    +      -       -      +
   1884A  VAL      3.4     5.5    -      -       -      +
   1885A  LEU*     3.4     3.6    -      -       -      +
   1886A  SER*     3.1    42.1    +      -       -      +
   1888A  VAL*     6.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1874 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1800A  ARG*     3.3    41.4    +      -       -      +
   1804A  CYS      4.6     0.2    -      -       -      -
   1805A  THR      3.4    27.1    -      -       -      +
   1806A  LEU*     3.9    17.8    -      -       +      +
   1817A  LEU*     3.8    21.5    -      -       +      -
   1872A  MET*     3.8    16.6    -      -       +      -
   1873A  LYS*     1.3    71.1    -      -       -      +
   1875A  ASP*     1.3    70.2    +      -       -      +
   1883A  VAL*     3.8    20.2    -      -       +      -
   1884A  VAL      3.4    13.5    -      -       -      +
   1885A  LEU*     3.7    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP1875 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1806A  LEU*     4.1     6.7    -      -       -      -
   1873A  LYS*     4.4    23.2    +      -       -      +
   1874A  LEU*     1.3    83.4    -      -       -      +
   1876A  TYR*     1.3    63.8    +      -       -      +
   1883A  VAL*     3.6     6.6    -      -       -      +
   1884A  VAL*     2.8    43.0    +      -       +      +
   1886A  SER*     5.6     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR1876 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1806A  LEU*     4.0    17.2    -      -       +      +
   1808A  ASP*     3.9    25.8    +      -       +      +
   1811A  LEU*     3.7    32.8    -      -       +      +
   1813A  TYR*     5.5     1.9    +      -       -      -
   1815A  PHE*     4.0    19.9    -      +       -      -
   1875A  ASP*     1.3    76.5    -      -       -      +
   1877A  ARG*     1.3    75.4    +      -       -      +
   1878A  HIS*     3.2    48.7    +      +       +      -
   1881A  GLU*     3.8    28.8    +      -       +      +
   1882A  ALA      3.6    11.0    -      -       -      -
   1883A  VAL*     4.3     6.5    -      -       +      -
   1884A  VAL*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1877 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1875A  ASP      4.1     1.0    +      -       -      -
   1876A  TYR*     1.3    77.3    -      -       -      +
   1878A  HIS*     1.3    60.8    +      -       -      +
   1879A  GLN*     3.4    15.3    -      -       +      +
   1880A  ASP*     3.4    44.5    +      -       -      +
   1881A  GLU*     3.2     8.0    -      -       -      -
   1882A  ALA*     2.8    44.0    +      -       +      +
   1884A  VAL*     4.3    12.9    -      -       +      +
   1954A  ILE*     3.5    45.9    -      -       -      +
----------------------------------------------------------
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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