Contacts of the helix formed by residues 180 - 207 (chain F) in PDB entry 6VVT
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 ASN 180 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F LEU* 1.3 74.4 - - - +
181F ALA* 1.3 65.3 + - - +
182F GLU* 2.9 26.9 + - + +
183F GLU* 2.5 57.9 + - - +
184F GLU* 3.3 23.6 + - - +
280F LYS* 4.3 5.8 - - - +
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Residues in contact with ALA 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F ASN* 1.3 76.3 - - - +
182F GLU* 1.3 76.9 + - - +
184F GLU* 3.5 18.6 + - - +
185F VAL* 3.5 20.3 + - - +
280F LYS* 3.7 26.3 - - + +
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Residues in contact with GLU 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F ASN* 2.9 19.4 - - - +
181F ALA* 1.3 89.1 + - - +
183F GLU* 1.3 63.4 + - + +
185F VAL* 3.4 13.7 + - - +
186F GLU* 3.4 10.9 + - - +
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Residues in contact with GLU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F LEU 4.3 4.0 - - - +
179F LEU* 3.5 31.2 - - + +
180F ASN* 2.5 56.0 + - - +
182F GLU* 1.3 71.7 - - + +
184F GLU* 1.3 65.4 + - - +
186F GLU* 3.1 8.3 + - - +
187F LEU* 3.0 31.6 + - + +
232F HIS* 5.1 4.2 - - + -
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Residues in contact with GLU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F LEU* 4.2 21.3 - - + +
180F ASN 3.3 15.4 + - - +
181F ALA* 3.8 16.5 - - - +
182F GLU 3.3 0.4 - - - -
183F GLU* 1.3 77.4 - - - +
185F VAL* 1.3 59.4 + - + +
187F LEU* 3.4 7.0 + - - +
188F ALA* 2.8 29.6 + - - +
233F LEU* 4.8 13.3 - - + +
237F ASN* 4.7 1.8 - - - +
273F PHE* 4.9 9.9 - - + -
279F TYR 4.9 1.4 - - - +
280F LYS* 3.9 13.4 - - - +
281F PHE* 3.2 48.1 + - + +
31O T 3.9 14.7 - - - +
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Residues in contact with VAL 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F ALA 3.5 15.5 - - - +
182F GLU* 3.4 7.4 + - - +
183F GLU 3.2 0.8 - - - -
184F GLU* 1.3 78.1 - - + +
186F GLU* 1.3 58.8 + - - +
188F ALA* 3.2 5.9 + - - +
189F LYS* 2.7 47.8 + - - +
273F PHE* 5.7 2.7 - - + -
275F TYR* 3.3 45.5 - - + +
278F GLY* 6.3 1.6 - - - -
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Residues in contact with GLU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F GLU 3.4 9.1 + - - +
183F GLU* 3.1 11.7 + - - +
185F VAL* 1.3 77.4 - - - +
187F LEU* 1.3 61.0 + - + +
189F LYS* 3.2 15.1 + - - +
190F ARG* 2.9 39.5 + - + +
101J ARG* 2.5 42.5 + - - +
104J LEU* 4.8 4.0 - - - +
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F LEU* 3.4 33.0 - - + -
183F GLU* 3.0 15.7 + - + +
184F GLU 3.9 4.5 - - - +
186F GLU* 1.3 78.2 - - + +
188F ALA* 1.3 62.7 + - - +
190F ARG* 3.2 31.9 + - - +
191F ILE* 2.9 31.2 + - - +
229F ALA* 3.7 14.3 - - + +
232F HIS* 3.7 28.7 - - + +
233F LEU* 4.2 21.3 - - + +
502F SO4 4.3 0.4 - - - +
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Residues in contact with ALA 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F GLU 2.8 22.1 + - - +
185F VAL 3.2 5.1 + - - +
187F LEU* 1.3 73.2 - - - +
189F LYS* 1.3 62.9 + - - +
191F ILE* 3.3 10.9 + - - +
192F GLU* 3.1 27.0 + - + +
233F LEU* 5.1 5.3 - - + +
273F PHE* 4.2 17.9 - - + +
275F TYR* 3.7 28.7 - - + -
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Residues in contact with LYS 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F VAL* 2.7 33.5 + - - +
186F GLU* 3.5 15.8 + - - +
188F ALA* 1.3 72.7 - - - +
190F ARG* 1.3 57.6 + - - +
191F ILE 3.2 0.2 + - - -
192F GLU* 3.2 3.3 + - - +
193F ALA* 2.8 31.1 + - - +
275F TYR* 3.8 35.4 - - + +
97J LEU* 3.9 23.4 - - + +
100J GLU* 4.6 12.0 + - - +
101J ARG* 3.7 26.7 - - - +
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Residues in contact with ARG 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F GLU* 2.9 27.2 + - + +
187F LEU* 3.4 27.8 - - - +
189F LYS* 1.3 75.1 - - - +
191F ILE* 1.3 56.8 + - - +
193F ALA* 3.5 7.2 + - - +
194F GLY 2.9 21.3 + - - -
222F ILE* 4.6 2.2 - - - +
225F ASP* 2.6 51.2 + - - +
226F GLY* 3.5 11.9 + - - -
229F ALA* 3.5 23.8 - - + +
502F SO4 2.7 43.0 + - - -
101J ARG* 3.7 26.5 - - - +
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Residues in contact with ILE 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F LEU 2.9 18.5 + - - +
188F ALA* 3.6 6.3 - - - +
189F LYS 3.1 0.2 - - - -
190F ARG* 1.3 74.0 - - - +
192F GLU* 1.3 64.9 + - + +
194F GLY* 2.9 16.1 + - - -
195F LEU* 3.0 15.0 + - + +
226F GLY* 3.9 7.9 - - - +
229F ALA* 3.5 18.2 - - + +
230F LYS* 3.5 34.3 - - + +
233F LEU* 4.1 11.9 - - + -
270F VAL* 3.9 22.7 - - + +
81J HIS* 3.8 29.2 - - + +
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Residues in contact with GLU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F ALA* 3.1 16.1 + - - +
189F LYS 3.8 2.9 - - - +
191F ILE* 1.3 77.2 - - + +
193F ALA* 1.3 61.9 + - - +
195F LEU* 3.3 3.4 + - + +
196F TYR* 3.1 24.8 + - - +
273F PHE 4.2 3.3 - - - +
275F TYR* 3.3 24.8 + - - -
85J LEU* 3.4 34.3 - - + +
88J ARG* 3.1 29.8 + - - +
89J ARG* 3.2 34.7 + - - +
94J LEU* 4.3 5.0 - - + +
97J LEU* 4.1 11.0 - - + +
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Residues in contact with ALA 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F LYS 2.8 17.6 + - - +
190F ARG* 3.8 6.3 - - - +
192F GLU* 1.3 76.7 - - - +
194F GLY* 1.3 57.8 + - - +
196F TYR* 4.3 3.7 - - - +
197F ALA* 2.9 31.7 + - - +
222F ILE* 3.6 13.1 - - + +
94J LEU 6.2 0.2 - - - -
97J LEU* 4.3 10.6 - - + +
98J LEU* 4.4 11.9 - - + +
101J ARG* 3.8 28.0 - - + -
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Residues in contact with GLY 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ARG 2.9 16.2 + - - -
191F ILE 2.9 4.9 + - - -
193F ALA* 1.3 75.4 - - - +
195F LEU* 1.3 59.9 + - - +
197F ALA* 4.0 1.3 - - - +
198F THR* 2.7 34.4 + - - -
222F ILE* 3.9 20.4 - - - -
223F CYS* 4.1 5.2 - - - -
226F GLY* 4.4 5.2 - - - -
227F ASP* 5.8 2.2 - - - -
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Residues in contact with LEU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F ILE* 3.0 16.1 + - + +
192F GLU* 3.3 1.5 + - + -
194F GLY* 1.3 75.2 - - - +
196F TYR* 1.3 59.5 + - - +
198F THR* 3.3 6.9 + - - -
199F GLN* 2.9 29.3 + - - +
81J HIS* 3.2 67.5 - - + +
82J TRP* 4.1 17.0 - - + +
85J LEU* 3.8 26.2 - - + -
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Residues in contact with TYR 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F GLU 3.1 17.2 + - - +
193F ALA* 4.3 3.1 - - - +
195F LEU* 1.3 73.8 - - - +
197F ALA* 1.3 56.7 + - - +
199F GLN* 3.1 1.5 + - + -
200F LYS* 2.7 50.1 + - + +
203F GLU* 5.3 7.0 - - - -
82J TRP* 3.7 31.1 - + + -
91J VAL* 4.1 17.7 + - + +
94J LEU* 3.6 35.2 - - + +
95J GLU* 3.5 48.6 + - - +
98J LEU* 3.8 20.0 - - + -
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Residues in contact with ALA 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F ALA 2.9 21.9 + - - +
194F GLY 4.0 2.9 - - - +
196F TYR* 1.3 78.8 - - - +
198F THR* 1.3 61.0 + - - +
200F LYS* 3.4 6.3 + - - +
201F LEU* 3.1 31.1 + - - +
219F MET* 3.9 28.9 - - + +
222F ILE* 4.0 11.4 - - + -
223F CYS* 4.4 2.9 - - - -
98J LEU* 4.4 15.9 - - + +
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Residues in contact with THR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F GLY 2.7 23.5 + - - -
195F LEU* 3.7 7.6 - - - -
197F ALA* 1.3 76.8 - - - +
199F GLN* 1.3 63.0 + - - +
201F LEU* 3.5 7.0 + - + +
202F ALA* 3.3 20.3 + - + +
223F CYS* 2.9 25.3 - - - +
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Residues in contact with GLN 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F LEU 2.9 17.4 + - - +
196F TYR* 3.7 3.8 - - + +
198F THR* 1.3 74.5 - - - +
200F LYS* 1.3 60.1 + - - +
202F ALA* 3.2 10.3 + - - +
203F GLU* 2.9 67.1 + - - +
206F GLU* 5.2 4.6 + - - -
82J TRP* 3.4 54.4 - - + +
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Residues in contact with LYS 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F TYR* 2.7 38.0 + - + +
197F ALA* 3.7 6.7 - - - +
199F GLN* 1.3 73.0 - - - +
201F LEU* 1.3 58.8 + - + +
203F GLU* 3.2 10.0 + - - +
204F LEU* 2.9 43.1 + - + +
219F MET* 4.7 16.2 - - + -
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Residues in contact with LEU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F ALA 3.1 18.0 + - - +
198F THR* 3.9 8.5 - - + +
200F LYS* 1.3 77.4 - - - +
202F ALA* 1.3 61.3 + - - +
204F LEU* 3.6 12.3 + - + +
205F ALA* 3.6 18.2 + - - +
216F ARG* 4.3 19.5 - - + -
219F MET* 3.8 32.5 - - + +
220F GLN* 3.8 40.4 - - + +
223F CYS* 5.0 3.6 - - - -
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Residues in contact with ALA 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F THR* 3.3 11.1 + - + +
199F GLN* 3.2 16.5 + - - +
200F LYS 3.2 0.4 - - - -
201F LEU* 1.3 77.6 - - - +
203F GLU* 1.3 61.2 + - - +
205F ALA* 3.5 6.6 + - - +
206F GLU* 3.0 34.6 + - - +
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Residues in contact with GLU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F TYR* 5.3 7.2 - - - -
199F GLN* 2.9 52.4 + - - +
200F LYS* 3.8 8.0 - - - +
202F ALA* 1.3 75.0 - - - +
204F LEU* 1.3 61.6 + - + +
206F GLU* 3.1 19.6 + - - +
207F LYS* 2.9 59.4 + - - +
82J TRP* 4.4 7.6 + - - -
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Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F LYS* 2.9 29.5 + - + +
201F LEU* 4.0 11.0 - - + +
202F ALA 3.3 0.2 - - - -
203F GLU* 1.3 77.7 - - + +
205F ALA* 1.3 60.0 + - - +
207F LYS* 3.5 3.9 + - + +
208F GLY 3.1 3.8 + - - -
209F GLU* 2.8 75.4 + - + +
210F LYS 5.0 1.1 - - - +
211F LEU* 3.2 46.0 - - + -
216F ARG* 6.2 0.4 - - + -
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Residues in contact with ALA 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F LEU 3.6 9.1 + - - +
202F ALA* 3.5 9.5 + - - +
203F GLU 3.2 0.6 - - - -
204F LEU* 1.3 76.4 - - - +
206F GLU* 1.3 68.2 + - + +
208F GLY* 3.4 9.7 + - - -
209F GLU 4.9 1.6 - - - -
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Residues in contact with GLU 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F GLN* 5.2 4.0 + - - -
202F ALA* 3.0 26.9 - - - +
203F GLU* 3.1 22.2 + - - +
205F ALA* 1.3 78.9 - - + +
207F LYS* 1.3 63.7 + - + +
208F GLY 3.2 3.5 + - - -
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Residues in contact with LYS 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F GLU* 2.9 46.4 + - + +
204F LEU* 4.3 2.0 - - + +
205F ALA 3.3 0.2 - - - -
206F GLU* 1.3 81.3 - - + +
208F GLY* 1.3 65.5 + - - +
209F GLU* 3.3 33.3 + - + +
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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