Contacts of the helix formed by residues 2202 - 2222 (chain B) in PDB entry 5G1N
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 ALA2202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2062B THR* 4.5 3.1 - - + -
2066B GLU* 3.9 31.2 - - + +
2180B VAL* 4.1 10.8 - - + -
2181B VAL 3.1 13.9 + - - +
2182B MET* 4.5 7.9 - - + -
2200B ARG 3.1 1.4 + - - -
2201B ALA* 1.3 71.2 - - - +
2203B TYR* 1.3 59.7 + - - +
2204B PHE 3.3 2.7 - - - -
2205B ARG* 3.2 19.0 + - - +
2206B GLN* 2.8 30.7 + - - +
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Residues in contact with TYR2203 (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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2181B VAL* 3.7 31.4 + - + -
2183B HIS* 3.9 18.6 - - + +
2185B MET* 3.8 35.6 - - + +
2187B ARG* 3.6 15.8 + - - -
2191B ILE* 4.0 18.1 - - + +
2195B VAL* 3.7 5.1 - - + +
2196B ASP* 2.3 45.9 + - + -
2201B ALA* 3.4 23.4 - - + -
2202B ALA* 1.3 78.9 - - - +
2204B PHE* 1.3 93.7 + + - +
2206B GLN* 3.6 11.9 - - - +
2207B ALA* 3.5 18.4 + - - +
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Residues in contact with PHE2204 (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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2185B MET* 4.6 11.0 - - + -
2187B ARG* 4.7 1.1 - - - -
2196B ASP* 4.1 13.5 - - + -
2201B ALA 5.0 2.0 + - - -
2203B TYR* 1.3 105.5 - + - +
2205B ARG* 1.3 64.4 + - - +
2207B ALA* 3.6 4.8 + - + +
2208B GLU* 3.4 16.8 + - - +
2009C ASP* 3.8 26.0 - - + -
2012C GLN* 3.3 57.4 - - + +
2013C THR* 3.5 25.1 - - - -
2016C CYS* 3.6 24.7 - - - -
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Residues in contact with ARG2205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2066B GLU* 3.1 38.2 + - - +
2180B VAL* 5.0 0.4 - - - +
2198B ASP 5.6 0.2 + - - -
2199B PRO* 2.6 28.0 + - - +
2200B ARG* 3.9 3.4 - - - +
2201B ALA 3.2 29.4 + - - +
2202B ALA* 3.2 11.5 + - + +
2204B PHE* 1.3 77.2 - - + +
2206B GLN* 1.3 59.7 + - - +
2208B GLU* 3.2 9.6 + - - +
2209B ASN* 2.8 39.2 + - - +
1949D MET* 4.7 10.1 - - - -
1953D LYS* 4.3 33.1 - - + +
1955D ARG* 3.4 25.8 - - - +
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Residues in contact with GLN2206 (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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2055B GLN* 3.5 14.7 - - - +
2058B LEU* 2.9 31.9 - - + +
2059B ASP* 2.6 32.5 + - - +
2062B THR* 3.7 24.2 - - + +
2143B TYR* 4.4 2.0 - - - -
2182B MET* 3.5 18.0 - - - +
2183B HIS 3.2 41.2 + - - +
2184B PRO* 3.6 6.6 - - - +
2185B MET* 6.0 0.2 - - - -
2202B ALA 2.8 17.0 + - - +
2203B TYR* 3.6 7.9 - - - +
2205B ARG* 1.3 73.7 - - - +
2207B ALA* 1.3 56.3 + - - +
2209B ASN* 3.4 1.7 + - - +
2210B GLY 3.1 11.4 + - - -
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Residues in contact with ALA2207 (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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1975B ARG* 4.4 17.9 - - + -
2058B LEU* 5.3 1.3 - - - -
2185B MET* 5.5 2.0 - - + -
2203B TYR 3.5 9.9 + - - +
2204B PHE* 3.9 9.4 - - + +
2205B ARG 3.3 0.2 - - - -
2206B GLN* 1.3 78.4 - - - +
2208B GLU* 1.3 62.7 + - - +
2210B GLY* 3.3 10.6 + - - +
2211B MET 3.5 2.1 + - - -
2013C THR* 5.4 4.5 - - - +
2016C CYS* 4.8 9.0 - - - -
2017C TYR* 3.2 40.6 + - + +
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Residues in contact with GLU2208 (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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1948B ARG* 4.0 25.3 + - - +
2204B PHE 3.4 10.1 + - - +
2205B ARG* 3.2 11.5 + - - +
2207B ALA* 1.3 75.6 - - - +
2209B ASN* 1.3 64.0 + - - +
2210B GLY 3.5 0.2 + - - -
2211B MET* 3.5 10.2 + - + +
2212B TYR* 3.1 34.2 + - + -
2016C CYS* 3.4 33.1 - - + +
2017C TYR* 4.7 1.3 - - - -
2039C ARG* 2.9 36.9 + - - -
2040C ARG* 5.3 1.4 + - - -
1953D LYS* 5.5 6.5 + - - -
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Residues in contact with ASN2209 (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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1948B ARG* 3.6 18.2 + - - +
2058B LEU* 4.6 2.2 - - + -
2061B PHE* 3.7 27.6 - - + -
2062B THR* 3.0 41.1 + - - +
2065B GLU* 4.6 10.5 - - - +
2066B GLU* 5.0 1.6 + - - -
2205B ARG* 2.8 23.8 + - - +
2206B GLN 3.5 7.6 - - - +
2208B GLU* 1.3 78.3 - - - +
2210B GLY* 1.3 56.5 + - - +
2212B TYR* 3.2 6.0 + - - +
2213B ILE* 2.9 32.8 + - - +
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Residues in contact with GLY2210 (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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1979B SER* 4.4 0.2 - - - -
2058B LEU* 3.8 32.5 - - - +
2206B GLN 3.1 10.3 + - - -
2207B ALA* 3.3 6.4 + - - -
2208B GLU 3.2 0.8 - - - -
2209B ASN* 1.3 73.2 - - - +
2211B MET* 1.3 64.9 + - - +
2213B ILE* 3.8 0.8 - - - +
2214B ARG* 3.0 39.0 + - - +
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Residues in contact with MET2211 (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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1979B SER* 4.0 15.3 - - - +
1982B ALA* 3.6 25.1 - - + -
1983B ALA* 3.9 3.5 - - - +
1986B ARG* 3.2 38.6 - - - +
2207B ALA 3.5 5.1 + - - -
2208B GLU* 3.5 12.9 + - + +
2209B ASN 3.3 0.4 - - - -
2210B GLY* 1.3 74.8 - - - +
2212B TYR* 1.3 89.1 + - + +
2214B ARG* 3.0 6.6 + - - +
2215B MET* 3.0 39.9 + - - +
2016C CYS 4.1 10.1 - - - +
2017C TYR* 3.9 30.3 - - + +
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Residues in contact with TYR2212 (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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1944B ALA* 3.6 24.3 - - + +
1947B LEU* 4.9 1.3 - - + +
1948B ARG* 3.1 79.7 + - + +
1951B VAL* 3.7 30.6 - - + +
1952B GLN* 5.5 3.1 - - - +
1986B ARG* 5.5 0.2 - - - -
2061B PHE* 6.0 2.0 - - + -
2208B GLU* 3.1 28.6 + - + -
2209B ASN* 3.2 7.8 + - - +
2211B MET* 1.3 101.1 - - + +
2213B ILE* 1.3 60.1 + - - +
2215B MET* 3.7 21.5 + - - +
2216B ALA* 3.3 21.8 + - - +
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Residues in contact with ILE2213 (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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1940B LEU* 4.1 13.9 - - + +
1941B PHE* 3.4 40.2 - - + -
1944B ALA* 4.3 7.9 - - + -
2054B THR* 4.5 7.6 - - - +
2057B LEU* 4.4 9.6 - - + +
2058B LEU* 4.0 32.5 - - + +
2061B PHE* 3.8 20.6 - - + -
2209B ASN 2.9 18.4 + - - +
2210B GLY 3.8 4.7 - - - +
2211B MET 3.2 0.2 - - - -
2212B TYR* 1.3 76.7 - - - +
2214B ARG* 1.3 64.4 + - + +
2216B ALA* 3.3 6.6 - - - +
2217B LEU* 3.0 25.4 + - + +
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Residues in contact with ARG2214 (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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1975B ARG* 4.3 2.2 + - - +
1976B THR* 3.8 25.6 + - - +
1979B SER* 2.7 43.1 + - - +
1980B PHE* 3.3 42.5 - - + +
1983B ALA* 3.9 3.4 - - + -
2052B HIS* 4.0 4.2 - - - -
2054B THR* 2.9 44.3 + - + -
2055B GLN* 3.7 5.5 + - - +
2058B LEU* 3.7 25.0 - - - +
2207B ALA 5.7 0.2 + - - -
2210B GLY* 3.0 16.3 + - - +
2211B MET 3.0 5.1 + - - +
2213B ILE* 1.3 80.3 - - + +
2215B MET* 1.3 58.5 + - - +
2216B ALA 3.1 1.1 - - - -
2217B LEU* 4.0 6.6 - - + +
2218B LEU* 2.9 36.0 + - - +
2017C TYR* 5.3 1.2 + - - -
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Residues in contact with MET2215 (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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1947B LEU* 3.5 18.6 - - + -
1951B VAL* 3.8 17.7 - - + -
1957B LEU* 4.4 0.9 - - + -
1983B ALA* 3.2 30.2 - - + +
1986B ARG* 3.6 27.6 - - + +
1987B LEU* 3.1 43.5 - - + +
2211B MET* 3.0 18.2 + - - +
2212B TYR* 3.7 37.0 - - - +
2213B ILE 3.5 0.2 - - - -
2214B ARG* 1.3 76.1 - - - +
2216B ALA* 1.3 56.1 + - - +
2218B LEU* 4.4 0.7 - - - -
2219B ALA* 3.0 25.5 + - - +
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Residues in contact with ALA2216 (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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1940B LEU* 3.4 19.3 - - + +
1943B VAL* 3.8 15.5 - - + -
1944B ALA* 3.6 23.3 - - - +
1947B LEU* 3.7 1.5 - - - +
2212B TYR 3.3 12.2 + - - +
2213B ILE* 3.3 10.8 - - - +
2214B ARG 3.1 0.2 - - - -
2215B MET* 1.3 78.1 - - - +
2217B LEU* 1.3 60.0 + - - +
2219B ALA* 3.2 2.1 + - - +
2220B THR* 2.9 34.5 + - - +
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Residues in contact with LEU2217 (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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1921B LEU* 4.5 12.1 - - + -
1926B ILE* 4.1 28.3 - - + -
1932B PHE* 4.9 2.2 - - + -
1940B LEU* 3.5 14.3 - - + +
1980B PHE* 5.1 5.4 - - + -
2043B ILE* 4.5 11.9 - - + -
2054B THR* 3.7 31.0 - - + -
2057B LEU* 4.8 12.8 - - + -
2213B ILE* 3.0 17.9 + - + +
2214B ARG* 3.4 6.7 + - + +
2216B ALA* 1.3 75.5 - - - +
2218B LEU* 1.3 54.6 + - + +
2220B THR* 3.0 8.4 + - - +
2221B VAL* 2.7 57.7 + - + +
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Residues in contact with LEU2218 (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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1960B LEU* 4.2 12.5 - - + +
1965B MET* 4.2 13.2 - - - -
1980B PHE* 4.1 20.9 - - + +
1983B ALA* 3.8 24.0 - - + -
1984B MET* 3.8 23.3 - - + +
2020B VAL* 4.0 27.8 - - + -
2022B VAL* 5.2 0.4 - - + -
2043B ILE* 4.6 15.9 - - + -
2214B ARG 2.9 25.3 + - - +
2215B MET* 3.9 3.8 - - - +
2217B LEU* 1.3 76.2 - - + +
2219B ALA* 1.3 62.8 + - - +
2221B VAL* 4.7 3.4 - - - +
2222B LEU* 3.1 33.7 + - + +
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Residues in contact with ALA2219 (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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1943B VAL* 4.8 1.1 - - + -
1947B LEU* 4.3 9.6 - - + -
1959B ILE* 5.0 4.9 - - + -
1960B LEU* 4.6 9.4 - - - -
1987B LEU* 4.2 10.9 - - + +
2215B MET 3.0 21.0 + - - +
2216B ALA 3.7 4.0 - - - +
2218B LEU* 1.3 79.0 - - - +
2220B THR* 1.3 57.8 + - - +
2222B LEU 4.1 0.2 - - - -
2223B GLY 3.7 0.3 + - - -
2224B ARG 3.1 30.3 + - - +
2225B PHE* 3.3 28.3 + - + -
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Residues in contact with THR2220 (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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1921B LEU* 3.6 35.9 - - + +
1922B VAL* 3.7 14.9 + - - +
1939B HIS* 4.5 6.1 - - + +
1940B LEU* 4.5 4.3 - - + +
1943B VAL* 4.0 27.6 - - + -
2216B ALA 2.9 19.7 + - - +
2217B LEU* 3.0 15.4 + - - +
2219B ALA* 1.3 75.3 - - - +
2221B VAL* 1.3 69.7 + - - +
2222B LEU 3.2 1.3 - - - -
2223B GLY* 3.2 11.6 + - - -
2225B PHE 4.1 15.3 - - - +
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Residues in contact with VAL2221 (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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1921B LEU* 3.3 17.7 - - + +
1922B VAL* 3.4 1.2 - - - +
1923B GLY* 2.6 29.4 + - - +
1924B GLN 4.1 3.4 - - - +
1926B ILE* 3.9 30.1 - - + -
2020B VAL* 4.8 8.5 - - + -
2041B PRO* 3.6 35.2 - - + -
2043B ILE* 5.0 4.7 - - + -
2217B LEU* 2.7 36.1 + - + +
2218B LEU* 4.4 3.6 - - - +
2220B THR* 1.3 74.0 + - - +
2222B LEU* 1.3 62.9 + - + +
2223B GLY 3.3 4.0 + - - -
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Residues in contact with LEU2222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1922B VAL* 5.3 1.1 - - - -
1960B LEU* 3.9 32.1 - - + -
1963B LYS* 3.9 28.3 + - + +
1984B MET* 4.4 10.1 - - + -
2019B ASP* 3.9 32.1 - - + +
2020B VAL* 4.1 26.2 - - + -
2041B PRO* 4.7 3.4 - - + -
2218B LEU* 3.1 23.6 + - + +
2219B ALA 4.1 0.4 - - - +
2220B THR 3.2 0.2 - - - -
2221B VAL* 1.3 84.6 - - + +
2223B GLY* 1.3 55.4 + - - +
2224B ARG* 2.9 18.9 + - + +
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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