Contacts of the helix formed by residues 1856 - 1868 (chain F) in PDB entry 6X34


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 GLY1856 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1809F  ARG*     4.6     4.6    -      -       -      +
   1854F  ILE      3.3     6.5    +      -       -      -
   1855F  PHE*     1.3    75.6    -      -       -      +
   1857F  ASP*     1.3    66.5    +      -       -      -
   1858F  GLU      3.4     2.7    -      -       -      -
   1859F  ASP*     3.6     9.0    -      -       -      +
   1860F  VAL*     3.1    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP1857 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1765F  GLY      5.6     0.7    -      -       -      -
   1766F  VAL*     5.6     9.2    -      -       +      +
   1856F  GLY*     1.3    69.0    -      -       -      -
   1858F  GLU*     1.3    61.4    +      -       -      +
   1860F  VAL*     3.2    11.8    -      -       -      +
   1861F  LYS*     2.9    45.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1858 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1856F  GLY*     4.5     0.2    -      -       -      -
   1857F  ASP*     1.3    78.4    -      -       -      +
   1859F  ASP*     1.3    57.7    +      -       -      +
   1861F  LYS*     3.4    10.9    +      -       -      +
   1862F  GLN*     2.9    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP1859 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1809F  ARG*     4.1    13.8    -      -       -      +
   1813F  LEU*     4.7    16.3    -      -       +      +
   1855F  PHE*     3.6    24.0    -      -       +      -
   1856F  GLY*     3.4    24.0    +      -       -      +
   1857F  ASP      3.2     0.6    -      -       -      -
   1858F  GLU*     1.3    79.8    -      -       -      +
   1860F  VAL*     1.3    59.3    +      -       -      +
   1862F  GLN*     3.3     5.8    +      -       -      +
   1863F  ILE*     2.9    35.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1860 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1764F  PRO      4.8     8.2    -      -       -      +
   1765F  GLY*     3.5    27.4    -      -       -      +
   1766F  VAL*     4.0    16.2    -      -       +      -
   1850F  LEU*     3.9    26.9    -      -       +      -
   1855F  PHE*     3.9    11.4    -      -       +      +
   1856F  GLY      3.1    16.3    +      -       -      +
   1857F  ASP*     3.2    15.0    -      -       -      +
   1859F  ASP*     1.3    74.9    -      -       -      +
   1861F  LYS*     1.3    60.6    +      -       -      +
   1863F  ILE*     3.6     9.0    -      -       -      +
   1864F  LEU*     2.9    30.3    +      -       -      +
   1947F  PHE*     6.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1861 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1763F  LEU*     3.9    26.8    -      -       +      +
   1766F  VAL*     4.1    21.7    -      -       +      +
   1857F  ASP*     2.9    31.8    +      -       -      +
   1858F  GLU*     3.6     9.0    -      -       -      +
   1859F  ASP      3.2     0.2    -      -       -      -
   1860F  VAL*     1.3    77.5    -      -       -      +
   1862F  GLN*     1.3    56.8    +      -       -      +
   1864F  LEU*     3.3     5.5    +      -       -      +
   1865F  LYS*     2.9    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1862 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1813F  LEU*     5.1    13.2    -      -       +      -
   1858F  GLU      2.9    17.8    +      -       -      +
   1859F  ASP*     3.7     5.8    -      -       -      +
   1861F  LYS*     1.3    75.0    -      -       -      +
   1863F  ILE*     1.3    58.4    +      -       -      +
   1865F  LYS*     3.3     6.8    +      -       -      +
   1866F  MET*     2.9    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1863 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1813F  LEU*     4.6    13.2    -      -       +      -
   1846F  VAL*     4.1    17.5    -      -       +      -
   1850F  LEU*     4.2    13.0    -      -       +      -
   1855F  PHE*     3.6    38.1    -      -       +      -
   1859F  ASP      2.9    21.2    +      -       -      +
   1860F  VAL*     3.6     7.0    -      -       +      +
   1861F  LYS      3.2     0.2    -      -       -      -
   1862F  GLN*     1.3    76.4    -      -       -      +
   1864F  LEU*     1.3    57.7    +      -       -      +
   1866F  MET*     3.2     7.6    +      -       -      +
   1867F  ILE*     2.9    43.2    +      -       +      +
   1943F  LEU*     5.8     4.0    -      -       +      -
   1947F  PHE*     4.0    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1864 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1763F  LEU*     5.6     7.2    -      -       +      -
   1764F  PRO*     5.3    17.3    -      -       +      +
   1860F  VAL      2.9    17.4    +      -       -      +
   1861F  LYS*     3.8     5.8    -      -       -      +
   1863F  ILE*     1.3    78.8    -      -       -      +
   1865F  LYS*     1.3    60.0    +      -       -      +
   1867F  ILE*     3.6     5.8    +      -       -      +
   1868F  GLU      2.9    26.3    +      -       -      +
   1871F  VAL*     3.8    25.9    -      -       +      +
   1947F  PHE*     5.9     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1865 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1861F  LYS      2.9    17.6    +      -       -      +
   1862F  GLN*     3.7     7.4    -      -       -      +
   1863F  ILE      3.2     0.2    -      -       -      -
   1864F  LEU*     1.3    76.2    -      -       -      +
   1866F  MET*     1.3    61.4    +      -       -      +
   1868F  GLU      3.4    17.6    -      -       -      +
   1869F  PRO*     4.1     6.3    -      -       -      +
   1871F  VAL      5.3     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET1866 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1816F  LEU*     3.7    45.3    -      -       +      +
   1817F  GLY*     4.8     1.6    -      -       -      -
   1819F  ALA*     5.9     1.1    -      -       +      -
   1820F  VAL*     4.1    29.5    -      -       +      +
   1843F  LEU*     5.4     8.3    -      -       +      -
   1862F  GLN      2.9    18.5    +      -       -      +
   1863F  ILE*     3.7     7.9    -      -       -      +
   1865F  LYS*     1.3    75.2    -      -       -      +
   1867F  ILE*     1.3    72.0    +      -       +      +
   1868F  GLU*     4.6     0.2    -      -       -      -
   1925F  GLU      4.8     7.1    -      -       -      +
   1926F  GLY*     5.7     0.2    -      -       -      -
   1927F  LEU*     4.4    31.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1867 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1843F  LEU*     6.1     1.1    -      -       +      -
   1863F  ILE*     2.9    33.1    +      -       +      +
   1864F  LEU*     4.0     7.0    -      -       -      +
   1865F  LYS      3.4     0.2    -      -       -      -
   1866F  MET*     1.3    85.6    -      -       +      +
   1868F  GLU*     1.3    65.8    +      -       +      +
   1869F  PRO*     4.9     0.3    -      -       -      +
   1871F  VAL*     6.0     2.5    -      -       +      -
   1926F  GLY*     5.5     1.4    -      -       -      -
   1927F  LEU*     4.5    14.6    +      -       +      -
   1928F  LEU*     3.4    35.5    +      -       +      +
   1929F  GLN*     5.2     1.6    -      -       -      +
   1940F  MET*     3.6    29.2    -      -       +      -
   1943F  LEU*     4.8     8.5    -      -       +      -
   1944F  LEU*     5.4    12.6    -      -       +      -
   1947F  PHE*     4.8    12.3    -      -       +      -
   2098F  LEU*     6.0     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1868 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1864F  LEU      2.9    17.4    +      -       -      +
   1865F  LYS*     3.4     8.4    -      -       -      +
   1866F  MET      3.4     0.4    -      -       -      -
   1867F  ILE*     1.3    86.6    -      -       +      +
   1869F  PRO*     1.3    75.0    -      -       +      +
   1870F  GLU*     3.5     3.3    +      -       +      +
   1871F  VAL*     3.5    28.3    +      -       +      +
   1928F  LEU*     5.8     2.0    -      -       +      -
   1929F  GLN*     6.1     0.7    -      -       -      +
   2098F  LEU*     5.3    11.2    -      -       +      -
----------------------------------------------------------
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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