Contacts of the helix formed by residues 2083 - 2109 (chain D) in PDB entry 3SUA
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 GLY2083 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1585D LEU* 3.5 21.6 - - - +
1586D HIS* 5.0 2.5 - - - -
1643D VAL* 4.1 5.2 - - - -
2081D ASP* 3.1 8.3 + - - -
2082D LEU* 1.3 80.4 - - - +
2084D ALA* 1.4 63.1 + - - +
2085D ARG* 3.0 6.4 + - - -
2086D VAL* 3.0 10.4 + - - +
2087D ALA* 3.0 17.8 + - - +
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Residues in contact with ALA2084 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1643D VAL* 3.7 19.8 - - + +
1644D ALA* 5.1 5.6 - - - +
2078D TYR* 5.7 3.1 - - - +
2081D ASP* 4.9 14.7 - - + +
2082D LEU 4.5 2.6 - - - +
2083D GLY* 1.4 74.4 - - - +
2085D ARG* 1.4 64.7 + - + +
2087D ALA* 3.3 11.3 - - - +
2088D LEU* 3.0 31.9 + - + +
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Residues in contact with ARG2085 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587D ARG 5.4 1.8 + - - -
1588D ASP* 3.6 20.8 + - - +
1589D LEU* 3.4 48.0 - - + +
1596D ARG* 6.0 0.4 - - - +
1600D GLU* 3.1 28.5 + - - +
1603D LEU* 4.6 5.1 - - + +
2081D ASP* 5.8 6.5 - - + +
2083D GLY 3.0 1.9 + - - +
2084D ALA* 1.4 79.6 - - - +
2086D VAL* 1.3 69.6 + - + +
2088D LEU* 3.0 17.5 + - - +
2089D HIS* 3.1 11.8 + - - +
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Residues in contact with VAL2086 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584D PRO 3.8 0.9 - - - +
1585D LEU* 3.2 39.5 - - + +
1587D ARG* 3.5 46.4 - - + +
1589D LEU* 4.6 8.1 - - + +
2083D GLY* 3.0 6.2 + - - +
2085D ARG* 1.3 80.5 - - + +
2087D ALA* 1.3 55.0 + - - +
2089D HIS* 3.2 8.6 + - - +
2090D GLU* 2.7 55.8 + - + +
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Residues in contact with ALA2087 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1585D LEU* 3.8 16.3 - - + +
1640D LEU* 3.7 36.6 - - + +
1643D VAL* 4.1 3.8 - - + -
1644D ALA* 4.5 7.6 - - + +
2083D GLY 3.0 7.4 + - - +
2084D ALA* 3.3 22.2 - - - +
2086D VAL* 1.3 76.0 - - - +
2088D LEU* 1.3 56.6 - - - +
2090D GLU 3.7 0.2 + - - -
2091D LEU* 3.0 29.9 + - - +
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Residues in contact with LEU2088 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1603D LEU* 3.7 32.8 - - + +
1604D GLY* 5.3 1.1 - - - +
1606D LEU* 3.3 21.8 - - + +
1607D SER* 4.2 21.3 - - - +
1610D LEU* 3.8 29.4 - - + -
1644D ALA* 4.6 13.9 - - + -
2084D ALA* 3.0 24.4 + - + +
2085D ARG* 3.0 10.9 + - - +
2087D ALA* 1.3 75.3 - - + +
2089D HIS* 1.4 53.3 + - - +
2091D LEU* 3.2 4.0 + - + +
2092D TYR* 2.8 29.5 + - - +
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Residues in contact with HIS2089 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587D ARG* 3.6 16.7 + - - -
1589D LEU* 3.2 58.3 + - + +
1590D GLY 5.7 0.2 + - - -
1591D VAL* 4.7 10.0 - - + +
1599D VAL* 5.3 8.5 - - + -
1603D LEU* 3.4 16.9 - - + +
2085D ARG 3.1 5.0 + - - +
2086D VAL* 3.2 7.6 + - - +
2088D LEU* 1.4 75.4 - - - +
2090D GLU* 1.4 55.2 + - - +
2092D TYR* 3.1 11.3 + + - +
2093D LYS* 3.0 57.9 + - + +
2128D VAL* 5.3 8.9 - - + +
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Residues in contact with GLU2090 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584D PRO* 4.1 6.1 - - - +
1585D LEU* 5.2 0.2 - - + -
1587D ARG* 3.6 28.4 + - - +
1636D TYR* 2.8 33.6 + - - +
1640D LEU* 3.8 22.4 - - + -
2086D VAL* 2.7 37.2 + - + +
2089D HIS* 1.4 68.0 - - - +
2091D LEU* 1.3 62.8 + - - +
2093D LYS* 3.2 34.9 + - - +
2094D TYR* 3.3 16.6 - - - -
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Residues in contact with LEU2091 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1606D LEU* 4.9 2.5 - - + -
1610D LEU* 3.9 37.0 - - + -
1619D PHE* 4.2 22.2 - - + -
1637D VAL* 4.2 21.3 - - + +
1640D LEU* 3.8 30.0 - - + +
1641D LEU* 4.2 15.5 - - + +
1644D ALA* 5.5 4.5 - - + -
2087D ALA 3.0 18.6 + - - +
2088D LEU* 3.5 7.0 - - - +
2090D GLU* 1.3 73.9 - - - +
2092D TYR* 1.4 61.3 + - - +
2094D TYR* 3.4 9.2 - - + +
2095D ILE* 3.3 29.7 + - + +
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Residues in contact with TYR2092 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1603D LEU* 5.1 4.5 - - + -
1606D LEU* 4.4 9.2 - - + -
2088D LEU 2.8 14.1 + - - +
2089D HIS* 3.1 17.0 + + - +
2091D LEU* 1.4 73.6 - - - +
2093D LYS* 1.4 57.9 + - + +
2094D TYR 3.1 0.2 - - - -
2095D ILE* 3.1 23.9 + - + +
2096D ASN* 2.7 68.0 + - + +
2099D TYR* 6.1 1.8 - + - -
2124D ILE* 5.6 7.0 - - + -
2125D ALA* 3.8 24.7 + - + +
2128D VAL* 3.6 39.7 - - + -
2129D GLU* 3.2 26.9 + - - +
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Residues in contact with LYS2093 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587D ARG* 3.2 28.1 - - - +
2089D HIS* 3.0 33.4 + - + +
2090D GLU* 3.2 35.2 + - - +
2092D TYR* 1.4 78.1 - - + +
2094D TYR* 1.4 62.9 + - + +
2096D ASN* 3.7 9.1 + - - +
2097D LYS* 3.6 15.1 + - - +
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Residues in contact with TYR2094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619D PHE* 5.1 5.6 - - + -
1623D LEU* 4.6 9.9 - - + -
1629D PHE* 4.0 8.7 - + - -
1633D ASP* 3.7 40.6 + - + +
1636D TYR* 3.4 34.9 - + - +
1637D VAL* 3.7 32.1 - - + -
1640D LEU* 4.2 2.7 - - + -
2090D GLU* 3.3 25.4 - - - -
2091D LEU* 3.4 12.7 + - + +
2092D TYR 3.1 0.2 - - - -
2093D LYS* 1.4 75.4 - - + +
2095D ILE* 1.4 57.7 + - + +
2097D LYS* 2.8 29.2 + - - +
2098D TYR* 3.1 30.9 + + - -
2102D ILE* 5.5 0.2 - - - -
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Residues in contact with ILE2095 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1606D LEU* 3.7 29.4 - - + -
1610D LEU* 6.2 0.2 - - + -
1615D PHE* 5.5 2.7 - - + -
1619D PHE* 3.6 28.0 - - + -
2091D LEU* 3.3 20.9 - - + +
2092D TYR* 3.1 27.6 + - + +
2094D TYR* 1.4 72.8 - - - +
2096D ASN* 1.3 54.5 + - - +
2099D TYR* 2.7 44.3 + - + -
2102D ILE* 4.0 16.4 - - + -
2121D LEU* 4.2 32.5 - - + -
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Residues in contact with ASN2096 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2092D TYR* 2.7 53.8 + - + +
2093D LYS* 3.7 10.1 + - - +
2094D TYR 3.1 0.2 + - - -
2095D ILE* 1.3 73.1 - - - +
2097D LYS* 1.3 62.4 + - - +
2099D TYR* 3.7 15.1 - - - +
2129D GLU* 3.0 18.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS2097 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1628D THR* 3.4 26.7 + - - +
2093D LYS 3.6 8.8 + - - +
2094D TYR* 2.8 15.5 + - - +
2096D ASN* 1.3 77.8 - - - +
2098D TYR* 1.3 98.6 + - + +
2099D TYR* 3.4 1.8 + - - +
2100D ASP* 5.5 1.2 - - - +
2101D GLN* 4.4 6.1 + - - +
----------------------------------------------------------
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Residues in contact with TYR2098 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622D THR* 6.3 0.4 - - + -
1623D LEU* 3.8 25.4 - - + -
1626D GLN* 3.5 35.9 - - + -
1628D THR* 3.2 43.5 + - - -
1629D PHE* 3.7 10.2 + + + -
1633D ASP* 4.4 4.3 + - - -
2094D TYR* 3.1 31.9 + + - +
2095D ILE 3.5 2.0 - - - -
2097D LYS* 1.3 105.2 + - + +
2099D TYR* 1.3 63.7 + - - +
2101D GLN* 3.0 30.0 + - + +
2102D ILE* 3.3 24.9 + - + +
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Residues in contact with TYR2099 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2092D TYR* 6.1 1.8 - + - -
2095D ILE* 2.7 27.6 + - + +
2096D ASN* 3.7 15.0 - - - +
2097D LYS 3.4 3.0 + - - +
2098D TYR* 1.3 72.2 - - - +
2100D ASP* 1.3 80.5 + - - +
2102D ILE* 3.3 10.9 - - - +
2103D ILE* 3.2 39.9 + - + +
2121D LEU* 3.6 27.1 - - + -
2122D GLN* 3.4 29.6 - - - +
2125D ALA* 4.0 21.4 - - + +
----------------------------------------------------------
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Residues in contact with ASP2100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2097D LYS 5.5 1.2 - - - +
2098D TYR 3.4 0.6 - - - -
2099D TYR* 1.3 91.0 + - - +
2101D GLN* 1.3 68.8 + - - +
2102D ILE 3.0 2.2 - - - -
2103D ILE* 2.9 27.6 + - + +
2104D THR* 3.0 13.4 + - - -
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Residues in contact with GLN2101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622D THR* 3.3 23.8 - - + +
1626D GLN* 3.2 43.5 - - + +
2097D LYS 4.4 4.4 + - - +
2098D TYR* 3.0 33.9 - - + +
2100D ASP* 1.3 81.5 + - - +
2102D ILE* 1.3 55.9 + - - +
2104D THR* 3.1 26.2 - - - -
2105D ALA* 3.9 1.7 + - - +
----------------------------------------------------------
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Residues in contact with ILE2102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615D PHE* 5.1 3.8 - - + -
1619D PHE* 4.1 33.4 - - + +
1622D THR* 4.1 17.9 - - + +
1623D LEU* 5.5 4.5 - - + -
2095D ILE* 4.0 27.8 - - + +
2098D TYR* 3.4 31.2 - - + +
2099D TYR* 3.3 8.1 - - - +
2100D ASP 3.0 0.2 - - - -
2101D GLN* 1.3 74.0 - - - +
2103D ILE* 1.4 57.9 + - - +
2104D THR 3.1 2.3 + - - -
2105D ALA* 3.1 6.3 + - + +
2106D LEU* 2.9 50.0 + - + +
2121D LEU* 4.6 14.1 - - + -
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Residues in contact with ILE2103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2099D TYR* 3.2 48.2 + - + +
2100D ASP* 2.9 16.2 + - - +
2102D ILE* 1.4 74.3 - - - +
2104D THR* 1.3 60.8 - - - +
2106D LEU* 3.3 13.2 - - + +
2107D GLU* 3.0 31.0 + - + +
2118D GLY* 5.1 2.9 - - - +
2121D LEU* 3.7 21.5 - - + -
2122D GLN* 5.1 12.3 - - + +
----------------------------------------------------------
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Residues in contact with THR2104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2100D ASP 3.0 15.1 + - - -
2101D GLN* 3.1 17.9 + - - -
2103D ILE* 1.3 75.1 - - - +
2105D ALA* 1.4 53.3 + - + +
2107D GLU* 3.8 0.5 - - - +
2108D GLU* 2.9 41.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA2105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618D LYS* 3.8 37.3 - - + +
1622D THR* 3.6 24.0 - - + +
2101D GLN 3.9 2.4 + - - +
2102D ILE 3.1 6.5 + - - +
2104D THR* 1.4 77.7 - - + +
2106D LEU* 1.4 63.5 + - - +
2107D GLU 3.2 0.6 + - - -
2108D GLU* 4.1 6.5 - - - -
2109D ASP* 3.9 21.7 + - - +
2112D ALA* 4.3 1.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU2106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615D PHE* 4.4 21.5 - - + -
1618D LYS* 6.1 4.5 - - + -
2102D ILE* 2.9 34.9 + - + +
2103D ILE* 3.2 36.7 + - + +
2105D ALA* 1.4 77.0 - - - +
2107D GLU* 1.3 71.9 + - + +
2112D ALA* 3.2 21.7 - - - +
2117D LEU* 3.8 31.4 - - + +
2118D GLY* 4.1 19.7 + - - +
2121D LEU* 3.8 14.8 - - + -
----------------------------------------------------------
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Residues in contact with GLU2107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2103D ILE* 3.0 19.8 + - + +
2104D THR 4.6 0.4 - - - +
2106D LEU* 1.3 95.0 - - + +
2108D GLU* 1.4 62.2 + - - +
2109D ASP 3.1 5.1 + - - +
2112D ALA 3.6 3.3 - - - +
2113D GLN* 3.4 57.2 + - - +
2116D GLN* 5.5 1.0 - - - -
2117D LEU 5.1 0.3 + - - -
2118D GLY* 4.4 14.7 + - - -
----------------------------------------------------------
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Residues in contact with GLU2108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618D LYS* 5.9 2.7 - - - +
2104D THR* 2.9 25.9 + - + +
2105D ALA* 3.9 5.1 + - - -
2107D GLU* 1.4 75.5 - - - +
2109D ASP* 1.3 58.4 + - - +
2110D GLY 4.0 0.7 + - - -
2113D GLN* 4.8 1.5 - - - +
----------------------------------------------------------
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Residues in contact with ASP2109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618D LYS* 3.7 27.8 + - + +
2105D ALA 3.9 10.3 + - - +
2107D GLU 3.1 1.1 - - - +
2108D GLU* 1.3 78.4 - - - +
2110D GLY* 1.3 60.2 + - - +
2111D THR* 2.8 36.9 + - - -
2112D ALA* 3.2 22.8 + - + +
2113D GLN* 3.2 28.2 + - - +
----------------------------------------------------------
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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