Contacts of the helix formed by residues 1868 - 1894 (chain B) in PDB entry 5WBY
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.
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 LYS1868 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867B LYS* 1.3 77.1 - - + +
1869B VAL* 1.3 66.5 + - + +
1871B GLU* 3.6 16.7 + - - +
1872B ASP* 3.0 52.4 + - - +
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Residues in contact with VAL1869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1808B ASN* 3.6 26.7 - - - +
1811B ARG* 6.0 2.2 - - + -
1812B ASP* 5.2 4.3 - - - +
1867B LYS 3.4 7.8 - - - +
1868B LYS* 1.3 80.4 - - + +
1870B THR* 1.3 62.5 + - - +
1872B ASP* 3.6 4.6 + - - +
1873B LEU* 3.0 25.6 + - - +
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Residues in contact with THR1870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867B LYS* 4.3 11.9 + - - -
1868B LYS 3.5 0.2 - - - -
1869B VAL* 1.3 77.3 - - - +
1871B GLU* 1.3 60.7 + - - +
1873B LEU* 3.9 17.5 - - + -
1874B SER* 2.9 43.2 + - - +
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Residues in contact with GLU1871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867B LYS 3.4 19.8 + - - +
1868B LYS* 3.6 24.2 + - - +
1869B VAL 3.4 0.6 - - - -
1870B THR* 1.3 77.6 - - - +
1872B ASP* 1.3 64.2 + - - +
1874B SER* 3.6 4.9 + - - -
1875B LYS* 3.3 31.2 + - - +
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Residues in contact with ASP1872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1868B LYS* 3.0 47.8 + - - +
1869B VAL* 3.9 4.0 - - - +
1871B GLU* 1.3 73.3 - - - +
1873B LEU* 1.3 54.2 + - - +
1875B LYS* 3.4 7.4 + - - +
1876B THR* 2.6 44.9 + - - +
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Residues in contact with LEU1873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804B TYR* 4.2 15.5 - - + +
1805B LYS* 5.1 1.6 - - - -
1808B ASN* 3.5 43.7 - - + +
1869B VAL* 3.0 20.3 + - + +
1870B THR* 3.5 18.6 - - + +
1871B GLU 3.3 0.2 - - - -
1872B ASP* 1.3 76.1 - - - +
1874B SER* 1.3 52.9 + - - +
1876B THR* 3.1 6.1 + - - -
1877B LEU* 2.7 66.0 + - + +
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Residues in contact with SER1874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1870B THR* 2.9 30.6 + - - +
1871B GLU* 3.8 6.5 - - - -
1872B ASP 3.4 0.2 - - - -
1873B LEU* 1.3 72.7 - - - +
1875B LYS* 1.3 59.0 + - - +
1877B LEU* 4.2 1.2 - - - +
1878B LEU* 2.9 34.9 + - - +
1916B TRP* 4.4 20.2 - - - -
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Residues in contact with LYS1875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1871B GLU* 3.3 20.4 + - - +
1872B ASP* 3.8 6.5 - - - +
1874B SER* 1.3 78.4 - - - +
1876B THR* 1.3 56.6 + - - +
1878B LEU* 4.2 5.5 - - - +
1879B MET* 3.2 30.8 + - - +
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Residues in contact with THR1876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804B TYR* 3.5 49.8 - - + -
1872B ASP* 2.6 31.9 + - - +
1873B LEU* 3.5 8.9 - - - -
1875B LYS* 1.3 73.2 - - - +
1877B LEU* 1.3 62.5 + - - +
1879B MET* 3.5 20.2 - - + +
1880B TYR* 3.2 29.2 - - + -
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Residues in contact with LEU1877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1801B VAL* 3.5 42.2 - - + +
1804B TYR* 4.4 9.6 - - + -
1805B LYS* 4.2 19.5 - - + +
1873B LEU* 2.7 48.8 + - + +
1874B SER* 5.2 0.4 - - - -
1876B THR* 1.3 70.7 - - - +
1878B LEU* 1.3 58.6 + - - +
1880B TYR* 3.3 2.2 + - + -
1881B THR* 2.6 39.6 + - - +
1913B TYR* 4.5 13.0 - - + +
1916B TRP* 3.7 26.0 - - + -
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Residues in contact with LEU1878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1874B SER 2.9 20.0 + - - +
1875B LYS* 4.4 4.7 - - - +
1877B LEU* 1.3 74.2 - - - +
1879B MET* 1.3 66.9 + - - +
1880B TYR 3.4 0.3 + - - -
1881B THR* 4.3 3.1 - - - -
1882B VAL* 3.5 29.0 + - + +
1916B TRP* 3.7 33.9 - - + -
1917B PRO* 5.9 1.8 - - + -
1918B ASP* 4.0 39.3 - - + +
1919B VAL* 4.9 0.7 - - + -
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Residues in contact with MET1879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1875B LYS 3.2 23.5 + - - +
1876B THR* 3.5 21.8 - - + +
1877B LEU 3.3 0.2 - - - -
1878B LEU* 1.3 80.2 - - - +
1880B TYR* 1.3 85.8 + - + +
1883B PRO* 3.1 22.3 - - - +
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Residues in contact with TYR1880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1769B ILE* 3.9 16.6 - - + +
1770B PRO* 5.3 5.7 - - - +
1773B LEU* 3.7 22.2 - - + +
1797B ASN* 3.6 25.3 - - - +
1800B ALA* 3.7 16.4 - - + -
1801B VAL* 3.5 19.5 - - + -
1804B TYR* 3.6 35.2 + + - -
1876B THR* 3.2 26.8 + - + -
1877B LEU* 3.3 3.1 + - + +
1878B LEU 3.3 0.2 - - - -
1879B MET* 1.3 101.6 - - + +
1881B THR* 1.3 64.1 + - - +
1882B VAL 3.5 0.7 - - - -
1883B PRO* 3.4 5.9 - - - +
1884B ALA* 3.2 22.9 + - - +
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Residues in contact with THR1881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1801B VAL* 3.6 15.8 - - - +
1877B LEU* 2.6 32.8 + - - +
1878B LEU* 3.6 2.6 + - - -
1880B TYR* 1.3 73.5 - - - +
1882B VAL* 1.3 57.1 + - - +
1884B ALA* 3.2 6.2 + - - +
1885B VAL* 3.0 29.7 + - + +
1909B LEU* 4.1 15.7 - - + -
1913B TYR* 3.9 20.4 - - + -
1916B TRP* 4.2 5.4 - - - -
1919B VAL* 3.5 37.9 - - + -
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Residues in contact with VAL1882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1878B LEU* 3.5 17.4 + - + +
1881B THR* 1.3 76.6 - - - +
1883B PRO* 1.4 69.5 - - + +
1885B VAL* 3.4 7.7 + - - +
1886B GLN* 3.1 43.3 + - - +
1918B ASP* 3.7 37.5 - - + +
1919B VAL* 3.9 13.5 - - + -
1922B ALA* 4.2 11.6 - - + +
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Residues in contact with PRO1883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1793B TRP* 3.3 39.7 - - + -
1797B ASN* 3.6 16.4 - - - +
1879B MET 3.1 26.7 - - - +
1880B TYR 3.4 11.4 - - - +
1882B VAL* 1.4 94.3 - - + +
1884B ALA* 1.3 57.7 + - - +
1886B GLN* 3.3 7.9 + - + +
1887B GLY* 2.8 26.2 + - - -
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Residues in contact with ALA1884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1794B ALA* 3.8 9.0 - - - +
1797B ASN* 3.7 17.8 - - + +
1798B PHE* 3.8 16.8 - - + +
1880B TYR 3.2 13.1 + - - +
1881B THR* 3.2 11.4 + - - +
1883B PRO* 1.3 77.1 - - - +
1885B VAL* 1.3 64.9 + - - +
1887B GLY* 3.2 1.2 + - - -
1888B PHE* 3.0 31.8 + - + -
1909B LEU* 3.9 16.4 - - + -
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Residues in contact with VAL1885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1881B THR* 3.0 18.3 + - + +
1882B VAL* 3.6 7.6 - - - +
1883B PRO 3.3 0.2 - - - -
1884B ALA* 1.3 76.7 - - - +
1886B GLN* 1.3 63.4 + - - +
1888B PHE* 3.4 3.9 + - - +
1889B PHE* 3.2 51.7 + - + -
1906B VAL* 4.6 4.2 - - + +
1909B LEU* 3.8 31.4 - - + -
1919B VAL* 4.2 18.8 - - + -
1922B ALA* 3.9 19.7 - - + -
1923B LEU* 4.0 16.4 - - + +
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Residues in contact with GLN1886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1790B TRP* 5.6 2.0 - - + -
1793B TRP* 4.2 15.8 - - + -
1882B VAL* 3.1 36.1 + - - +
1883B PRO* 3.5 10.0 - - - +
1885B VAL* 1.3 79.7 - - - +
1887B GLY* 1.3 63.0 + - - +
1889B PHE* 3.2 9.3 + - - +
1890B ARG* 3.1 25.7 + - - +
1922B ALA* 4.5 13.2 - - + +
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Residues in contact with GLY1887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1790B TRP* 3.7 12.8 - - - +
1793B TRP* 3.7 22.4 - - - -
1794B ALA* 3.6 10.3 - - - -
1883B PRO 2.8 19.9 + - - -
1884B ALA 3.7 1.3 - - - -
1886B GLN* 1.3 73.0 - - - +
1888B PHE* 1.3 57.7 + - - +
1890B ARG* 3.3 2.3 + - - -
1891B SER* 2.9 29.1 + - - -
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Residues in contact with PHE1888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1791B HIS* 4.6 1.3 - + - -
1794B ALA* 3.4 28.6 - - + +
1795B VAL* 3.9 19.3 - - + -
1798B PHE* 3.9 25.6 - + + -
1884B ALA 3.0 28.8 + - - +
1885B VAL* 3.8 0.9 - - - +
1887B GLY* 1.3 74.6 - - - +
1889B PHE* 1.3 59.1 + - - +
1891B SER* 3.0 6.2 + - - -
1892B ILE* 2.8 36.0 + - + +
1901B GLN* 5.4 0.2 - - - -
1902B ASP* 3.4 32.3 - - - +
1905B ARG* 3.7 31.9 - - + -
1906B VAL* 3.5 21.8 - - + -
1909B LEU* 4.0 16.8 - - + -
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Residues in contact with PHE1889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1885B VAL* 3.2 47.4 + - + -
1886B GLN* 3.2 9.8 + - - +
1888B PHE* 1.3 76.5 - - - +
1890B ARG* 1.3 61.2 + - - +
1892B ILE* 3.5 7.5 + - + +
1893B SER* 3.3 21.7 + - - -
1906B VAL* 3.5 25.1 - - + -
1922B ALA 4.0 6.7 - - - -
1923B LEU* 3.9 16.8 - - + -
1926B GLY* 3.6 44.2 - - - -
1927B VAL* 3.9 3.1 - - + -
1929B ALA* 6.5 0.7 - - + -
1930B ILE* 4.4 17.1 - - + +
1935B TRP* 4.0 25.1 - + - -
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Residues in contact with ARG1890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1784B ARG* 3.1 34.0 - - - +
1790B TRP* 3.6 51.2 - - + +
1886B GLN* 3.1 16.2 + - - +
1887B GLY 4.1 2.2 - - - +
1889B PHE* 1.3 74.0 - - - +
1891B SER* 1.3 64.0 + - - +
1893B SER* 2.9 23.5 + - - +
1894B LEU* 3.2 22.3 + - + +
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Residues in contact with SER1891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1787B TYR* 3.4 15.8 - - - -
1790B TRP* 3.9 6.7 - - - +
1791B HIS* 3.6 29.1 - - - -
1887B GLY 2.9 15.1 + - - -
1888B PHE* 3.0 16.2 + - - -
1890B ARG* 1.3 76.5 - - - +
1892B ILE* 1.3 54.4 + - - +
1894B LEU* 3.3 4.0 + - - +
1895B SER* 2.6 31.7 + - - -
1902B ASP* 3.1 24.1 + - - -
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Residues in contact with ILE1892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1888B PHE 2.8 28.5 + - - +
1889B PHE* 3.7 10.1 - - + +
1890B ARG 3.3 0.2 - - - -
1891B SER* 1.3 70.9 + - - +
1893B SER* 1.3 65.6 + - - +
1895B SER* 3.0 15.6 + - - -
1896B ARG* 3.3 13.2 + - - +
1899B ASN* 3.3 17.5 - - + +
1902B ASP* 3.4 19.5 - - + -
1903B THR* 3.7 21.8 - - + +
1906B VAL* 3.7 27.6 - - + -
1930B ILE* 3.4 33.2 - - + -
1934B THR* 3.8 11.2 - - + +
1935B TRP* 6.0 0.9 - - + -
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Residues in contact with SER1893 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1889B PHE 3.3 11.6 + - - -
1890B ARG* 2.9 25.8 + - - +
1892B ILE* 1.3 78.9 - - - +
1894B LEU* 1.3 62.7 + - - +
1895B SER 3.3 0.7 + - - -
1896B ARG* 4.3 14.9 - - - +
1929B ALA 6.0 1.1 - - - -
1930B ILE* 5.3 14.1 - - - +
1931B GLN* 6.0 1.1 - - - +
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Residues in contact with LEU1894 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1784B ARG 3.9 4.5 - - - +
1785B SER* 4.1 21.8 - - - +
1786B TRP 3.7 19.5 - - - +
1787B TYR* 3.7 25.1 + - - +
1790B TRP* 3.5 32.8 - - + +
1890B ARG* 3.2 20.9 + - + +
1891B SER 3.6 6.3 - - - +
1892B ILE 3.1 1.0 - - - -
1893B SER* 1.3 82.2 - - - +
1895B SER* 1.3 56.2 + - - +
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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