Contacts of the helix formed by residues 1786 - 1814 (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 TRP1786 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1748B ALA* 3.6 39.9 - - + -
1749B ARG* 3.6 29.2 - - + -
1752B LEU* 3.8 22.9 - - + -
1783B ASP* 3.2 33.1 + - + +
1784B ARG 3.4 2.2 + - - -
1785B SER* 1.3 77.0 - - - +
1787B TYR* 1.3 77.6 + - + +
1788B LYS* 3.5 33.5 + - + +
1789B ALA* 3.5 27.4 + - + +
1790B TRP* 3.4 18.4 + - - -
1894B LEU* 3.7 4.2 - - - +
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Residues in contact with TYR1787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1785B SER 4.3 0.4 - - - -
1786B TRP* 1.3 78.5 - - + +
1788B LYS* 1.3 70.9 + - + +
1790B TRP* 3.4 2.8 + - - +
1791B HIS* 2.9 48.3 + + + +
1891B SER* 3.4 25.4 - - - +
1894B LEU* 3.7 28.9 - - - +
1895B SER* 3.3 23.8 - - - -
1898B ASN 4.6 6.6 + - - -
1899B ASN* 5.6 0.2 - - - -
1901B GLN* 5.6 1.7 + - - +
1902B ASP* 3.1 24.3 + - - -
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Residues in contact with LYS1788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1752B LEU* 4.0 17.0 - - + +
1786B TRP* 3.4 34.2 - - + +
1787B TYR* 1.3 92.4 - - + +
1789B ALA* 1.3 57.8 + - - +
1791B HIS* 3.5 9.6 - - + +
1792B ALA* 2.8 34.1 + - - +
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Residues in contact with ALA1789 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1752B LEU* 3.7 11.8 - - - +
1776B TYR 4.2 4.2 - - - +
1779B ALA* 3.9 8.5 - - + +
1780B THR* 3.8 30.5 + - - +
1783B ASP 4.6 1.3 - - - +
1786B TRP* 3.5 32.8 + - + +
1787B TYR 3.3 0.6 - - - -
1788B LYS* 1.3 79.1 - - - +
1790B TRP* 1.3 58.6 + - + +
1792B ALA* 3.5 2.1 + - - +
1793B TRP* 3.1 29.3 + - - +
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Residues in contact with TRP1790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1780B THR* 3.2 45.4 + - + +
1783B ASP 4.8 0.2 + - - -
1784B ARG* 2.7 46.2 + - - +
1786B TRP 3.4 18.1 + - - -
1787B TYR 3.4 5.7 + - - +
1789B ALA* 1.3 77.4 - - + +
1791B HIS* 1.3 61.3 + - - +
1793B TRP* 3.6 33.0 + + - +
1794B ALA* 3.0 30.0 + - - +
1886B GLN* 5.6 1.8 - - + -
1887B GLY* 3.7 9.7 - - - +
1890B ARG* 3.6 56.0 - - + +
1891B SER* 3.9 21.1 - - - +
1894B LEU* 3.5 12.3 - - + -
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Residues in contact with HIS1791 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1787B TYR* 2.9 39.8 + + + +
1788B LYS* 3.5 11.0 - - + +
1789B ALA 3.3 0.2 - - - -
1790B TRP* 1.3 75.8 - - - +
1792B ALA* 1.3 56.4 + - - +
1794B ALA* 3.0 6.2 + - - +
1795B VAL* 2.8 60.3 + - + +
1888B PHE* 4.6 0.6 - + - -
1891B SER* 3.6 6.6 - - - -
1901B GLN* 3.7 26.1 + - - -
1902B ASP* 2.6 35.6 + - - -
2412B ASP* 5.4 3.6 + - - -
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Residues in contact with ALA1792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1752B LEU* 3.9 10.8 - - + -
1776B TYR* 3.3 45.8 - - + -
1788B LYS 2.8 20.4 + - - +
1789B ALA 3.9 0.4 - - - +
1791B HIS* 1.3 77.8 - - + +
1793B TRP* 1.3 57.7 + - - +
1795B VAL* 4.0 6.5 - - - +
1796B MET* 3.0 23.2 + - - +
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Residues in contact with TRP1793 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773B LEU* 4.0 17.9 + - + +
1776B TYR* 3.9 15.6 - - + +
1777B SER* 3.8 36.3 - - - -
1780B THR* 4.5 6.1 - - + +
1789B ALA 3.1 18.2 + - - +
1790B TRP* 3.8 26.7 - + - +
1792B ALA* 1.3 73.1 - - - +
1794B ALA* 1.3 64.5 + - - +
1796B MET* 4.0 1.3 - - - +
1797B ASN* 2.9 53.8 + - - +
1883B PRO* 3.3 41.7 - - + -
1886B GLN* 4.2 12.8 - - + -
1887B GLY* 3.7 25.8 - - - -
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Residues in contact with ALA1794 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1790B TRP 3.0 19.4 + - - +
1791B HIS* 3.0 4.7 + - - +
1793B TRP* 1.3 77.9 - - - +
1795B VAL* 1.3 51.4 + - - +
1797B ASN* 3.3 4.2 + - - +
1798B PHE* 2.8 35.0 + - - +
1884B ALA* 3.8 13.7 - - - +
1887B GLY* 3.6 4.5 - - - -
1888B PHE* 3.4 47.1 - - + +
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Residues in contact with VAL1795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1791B HIS* 2.8 54.5 + - + +
1792B ALA* 4.0 6.3 - - - +
1794B ALA* 1.3 71.2 - - - +
1796B MET* 1.3 58.4 + - + +
1798B PHE* 3.3 11.7 + - + +
1799B GLU* 2.8 49.0 + - + +
1888B PHE* 3.9 12.6 - - + -
1901B GLN* 4.6 6.7 - - - +
2412B ASP* 5.2 9.4 - - - +
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Residues in contact with MET1796 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1759B LEU* 3.4 43.3 - - + -
1764B ILE* 4.5 15.3 - - + -
1769B ILE* 4.7 19.3 - - - +
1772B VAL* 3.5 26.7 - - + -
1773B LEU* 3.7 18.2 - - + -
1776B TYR* 3.7 13.0 - - + -
1792B ALA 3.0 18.4 + - - +
1793B TRP 4.0 2.7 - - - +
1795B VAL* 1.3 76.3 - - + +
1797B ASN* 1.3 55.2 + - - +
1799B GLU* 3.3 7.8 + - - +
1800B ALA* 2.7 34.6 + - - +
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Residues in contact with ASN1797 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773B LEU* 3.4 14.7 - - - +
1793B TRP* 2.9 63.9 + - - +
1794B ALA 3.6 4.5 - - - +
1796B MET* 1.3 76.0 - - - +
1798B PHE* 1.3 57.3 + - - +
1800B ALA* 3.3 7.4 + - - +
1801B VAL* 3.1 31.2 + - - +
1880B TYR* 3.6 26.8 - - - +
1883B PRO* 3.6 23.1 - - - +
1884B ALA* 3.7 10.5 - - + +
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Residues in contact with PHE1798 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1794B ALA 2.8 20.0 + - - +
1795B VAL* 3.4 9.9 - - + +
1796B MET 3.2 0.2 - - - -
1797B ASN* 1.3 74.3 - - - +
1799B GLU* 1.3 65.4 + - + +
1801B VAL* 3.4 9.1 - - + +
1802B LEU* 3.2 55.0 + - + +
1884B ALA* 3.8 6.2 - - + +
1888B PHE* 3.9 17.5 - + + -
1905B ARG* 3.7 45.5 - - - -
1908B THR* 4.6 19.1 - - + -
1909B LEU* 3.9 35.9 - - + -
1913B TYR* 6.3 0.7 - + - -
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Residues in contact with GLU1799 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1764B ILE* 3.5 34.9 - - + +
1795B VAL* 2.8 36.6 + - - +
1796B MET* 4.0 11.8 - - + +
1798B PHE* 1.3 82.0 - - + +
1800B ALA* 1.3 60.4 + - - +
1801B VAL 3.3 0.4 - - - -
1802B LEU* 3.9 15.4 - - + +
1803B HIS* 3.0 27.7 + - - +
2412B ASP* 5.6 1.9 - - - +
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Residues in contact with ALA1800 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1769B ILE* 3.8 28.5 - - + -
1773B LEU* 5.0 0.2 - - + -
1796B MET* 2.7 21.6 + - - +
1797B ASN* 3.4 7.9 - - - +
1799B GLU* 1.3 72.0 - - - +
1801B VAL* 1.3 66.0 + - - +
1803B HIS* 3.5 5.5 + - - +
1804B TYR* 3.3 30.1 + - - -
1880B TYR* 3.7 28.0 - - + -
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Residues in contact with VAL1801 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797B ASN 3.1 15.1 + - - +
1798B PHE* 3.4 12.8 - - + +
1799B GLU 3.3 0.2 - - - -
1800B ALA* 1.3 76.8 - - - +
1802B LEU* 1.3 68.9 + - + +
1804B TYR 3.4 0.2 + - - -
1805B LYS* 3.1 20.1 + - + +
1877B LEU* 3.5 21.9 - - + +
1880B TYR* 3.5 20.6 - - + -
1881B THR* 3.6 25.1 - - - +
1909B LEU* 5.0 6.1 - - + -
1913B TYR* 3.7 37.2 - - + +
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Residues in contact with LEU1802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1798B PHE* 3.2 46.9 + - + +
1799B GLU* 4.0 14.8 - - + +
1800B ALA 3.4 0.2 - - - -
1801B VAL* 1.3 84.1 - - + +
1803B HIS* 1.3 54.7 - - - +
1805B LYS* 4.0 28.5 - - - +
1806B HIS* 2.8 61.3 + - + +
1913B TYR* 6.3 0.4 - - + -
----------------------------------------------------------
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Residues in contact with HIS1803 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1764B ILE* 3.8 28.5 + - + -
1765B ASN* 3.8 18.1 - - - +
1766B GLU* 4.2 7.9 - - + -
1769B ILE* 3.6 22.9 - - + +
1799B GLU 3.0 19.9 + - - +
1800B ALA* 3.6 7.2 - - - +
1801B VAL 3.2 0.4 - - - -
1802B LEU* 1.3 76.2 - - - +
1804B TYR* 1.3 70.4 + + - +
1806B HIS* 3.9 4.6 - - - +
1807B GLN* 3.0 48.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR1804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1766B GLU* 2.7 47.2 + - - +
1769B ILE* 4.3 10.4 - - + +
1800B ALA 3.3 23.4 + - - +
1801B VAL* 4.1 2.5 - - - +
1803B HIS* 1.3 89.9 - + - +
1805B LYS* 1.3 61.3 + - - +
1807B GLN* 3.4 24.1 + - - +
1808B ASN* 3.0 28.2 + - - +
1873B LEU* 4.2 8.7 - - + +
1876B THR* 3.5 28.7 - - + -
1877B LEU* 4.4 7.9 - - + -
1880B TYR* 3.6 31.8 + + - -
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Residues in contact with LYS1805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1801B VAL 3.1 17.8 + - - +
1802B LEU* 3.7 27.1 - - - +
1804B TYR* 1.3 76.0 - - - +
1806B HIS* 1.3 71.0 + - - +
1808B ASN* 3.1 7.7 + - - +
1809B GLN* 3.0 49.2 + - + +
1873B LEU* 5.1 2.5 - - - -
1877B LEU* 4.2 13.6 - - + +
1912B ASP* 4.2 14.8 + - - -
1913B TYR* 3.3 27.1 + - + +
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Residues in contact with HIS1806 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1802B LEU* 2.8 51.0 + - + +
1803B HIS* 4.2 4.0 - - - +
1805B LYS* 1.3 85.7 - - - +
1807B GLN* 1.3 62.0 + - - +
1809B GLN* 3.3 24.9 + - - +
1810B ALA* 3.5 18.9 + - - +
2498B ILE* 6.1 5.8 - - + -
----------------------------------------------------------
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Residues in contact with GLN1807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1766B GLU* 4.7 11.1 + - - +
1803B HIS* 3.0 41.0 + - + +
1804B TYR* 3.5 23.3 - - - +
1806B HIS* 1.3 77.6 - - - +
1808B ASN* 1.3 57.5 + - - +
1810B ALA* 3.1 9.8 + - + +
1811B ARG* 2.8 66.6 + - + +
----------------------------------------------------------
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Residues in contact with ASN1808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804B TYR 3.0 18.4 + - - +
1805B LYS* 3.1 4.7 + - - +
1807B GLN* 1.3 72.3 - - - +
1809B GLN* 1.3 59.5 + - + +
1811B ARG* 3.9 13.4 - - - +
1812B ASP* 2.9 52.3 + - - +
1869B VAL* 3.6 25.6 - - - +
1873B LEU* 3.5 37.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN1809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805B LYS* 3.0 43.6 + - + +
1806B HIS* 3.3 28.2 + - - +
1808B ASN* 1.3 75.6 - - + +
1810B ALA* 1.3 61.6 + - - +
1812B ASP* 3.8 6.5 + - - +
1813B GLU* 3.3 25.3 + - - +
2494B ASN* 5.5 7.1 - - - +
2498B ILE* 5.5 5.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA1810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1806B HIS 3.5 11.3 + - - +
1807B GLN* 3.1 11.7 + - + +
1809B GLN* 1.3 77.4 - - - +
1811B ARG* 1.3 62.7 + - - +
1813B GLU* 3.3 20.5 - - - +
1814B LYS* 3.6 13.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG1811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1807B GLN* 2.8 54.9 + - + +
1808B ASN* 3.4 22.9 + - - +
1810B ALA* 1.3 73.4 - - + +
1812B ASP* 1.3 63.1 + - - +
1813B GLU 3.4 0.9 + - - -
1814B LYS* 3.4 20.5 + - - +
1869B VAL* 6.0 2.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP1812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1808B ASN* 2.9 37.6 + - - +
1809B GLN* 4.0 7.6 - - - +
1811B ARG* 1.3 73.7 - - - +
1813B GLU* 1.3 65.2 + - - +
1814B LYS 3.4 5.4 + - - +
1869B VAL* 5.2 3.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU1813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809B GLN 3.3 17.3 + - - +
1810B ALA* 3.3 15.5 - - - +
1811B ARG 3.2 0.4 - - - -
1812B ASP* 1.3 78.8 - - - +
1814B LYS* 1.3 77.1 + - + +
----------------------------------------------------------
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Residues in contact with LYS1814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1810B ALA* 3.6 11.7 + - - +
1811B ARG* 3.4 16.6 + - - +
1812B ASP 3.4 4.9 - - - +
1813B GLU* 1.3 97.5 - - + +
----------------------------------------------------------
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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