Contacts of the helix formed by residues 171 - 201 (chain J) in PDB entry 5XTE
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 ASP 171 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J ALA* 3.7 13.2 - - - +
135J TRP* 4.2 17.9 - - - -
169J SER* 3.4 9.9 + - - +
170J VAL* 1.3 78.9 - - - +
172J SER* 1.3 87.1 + - - +
173J PRO* 3.4 17.8 - - + +
174J THR* 3.2 6.5 + - - -
175J LEU* 3.1 19.2 + - - +
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Residues in contact with SER 172 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J PRO 4.5 0.5 - - - +
58J ASP* 4.5 8.3 - - - -
59J ALA* 3.5 37.2 - - - +
171J ASP* 1.3 83.6 + - - +
173J PRO* 1.4 77.8 - - - +
175J LEU* 3.0 5.8 + - - +
176J THR* 2.9 26.3 + - - -
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Residues in contact with PRO 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J TRP 4.3 11.2 - - - +
166J GLY* 4.4 15.3 - - - +
167J GLY* 5.9 0.7 - - - -
169J SER 5.9 0.4 - - - +
171J ASP* 3.4 17.0 - - + +
172J SER* 1.4 97.8 - - - +
174J THR* 1.3 56.5 - - - +
176J THR* 3.2 9.3 + - - +
177J ARG* 2.9 39.6 + - - +
143P SER* 6.0 1.3 - - - +
146P VAL* 5.2 11.7 - - + -
53V MET 4.3 4.3 - - - +
54V HIS* 5.3 11.4 - - + +
68V HIS* 6.2 1.3 - - - +
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Residues in contact with THR 174 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J VAL* 5.7 0.4 - - + -
164J ILE 4.4 7.4 - - - +
165J TRP* 2.1 46.0 + - + +
170J VAL* 4.2 14.8 - - + -
171J ASP 3.2 21.2 + - - -
172J SER 3.1 0.4 - - - -
173J PRO* 1.3 76.2 - - - +
175J LEU* 1.3 61.2 + - - +
177J ARG* 3.1 10.3 + - + +
178J PHE* 2.9 58.6 + - + -
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Residues in contact with LEU 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J TYR* 3.4 26.9 - - - +
57J PRO* 4.5 5.2 - - + +
58J ASP 3.3 35.2 - - - +
59J ALA* 4.2 4.7 - - - +
62J ALA* 3.8 7.4 - - + -
132J VAL* 3.6 32.8 - - + +
133J LEU* 3.7 9.6 - - + +
135J TRP* 4.4 18.8 - - + -
170J VAL* 5.8 0.6 - - - +
171J ASP 3.1 11.6 + - - +
172J SER* 3.0 10.0 + - - +
174J THR* 1.3 77.3 - - - +
176J THR* 1.3 58.8 + - - +
178J PHE* 3.5 4.3 + - + +
179J PHE* 2.9 26.2 + - - +
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Residues in contact with THR 176 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J PRO* 2.9 29.2 + - + +
58J ASP* 4.2 3.6 + - - -
172J SER 2.9 11.6 + - - -
173J PRO* 3.5 6.8 - - - +
175J LEU* 1.3 75.7 - - - +
177J ARG* 1.3 65.0 + - - +
179J PHE* 3.1 6.8 + - + +
180J THR* 3.0 22.6 + - + +
52V ALA 3.4 19.5 - - - +
53V MET 3.1 26.7 - - - +
54V HIS* 4.0 4.6 + - - +
55V TYR 4.3 10.8 - - - +
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Residues in contact with ARG 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J TRP 3.3 15.2 + - - -
164J ILE* 3.3 26.4 + - - +
166J GLY* 3.3 20.4 + - - -
173J PRO* 2.9 29.8 + - - +
174J THR* 3.1 14.8 + - - +
176J THR* 1.3 75.4 - - - +
178J PHE* 1.3 65.3 + - + +
180J THR* 2.5 27.0 + - - -
181J PHE* 2.9 24.9 + - + -
139P SER 4.9 1.0 + - - -
140P MET* 2.5 48.9 + - - +
141P SER 3.8 1.4 + - - -
142P ALA* 5.3 1.0 - - - +
53V MET* 4.0 32.7 + - - +
54V HIS* 4.9 15.0 + - - -
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Residues in contact with PHE 178 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J PHE* 4.9 11.0 - + - -
129J MET* 3.7 40.6 - - + +
132J VAL* 3.6 40.2 - - + -
133J LEU* 4.2 4.5 - - + -
143J ALA* 4.5 9.6 - - + -
147J THR* 4.8 7.9 - - - -
164J ILE* 4.2 23.6 - - + -
165J TRP* 6.0 0.2 - + - -
170J VAL* 6.2 0.2 - - + -
174J THR* 2.9 41.7 + - + +
175J LEU* 4.0 5.2 - - - +
177J ARG* 1.3 81.1 - - + +
179J PHE* 1.3 61.5 + - - +
181J PHE* 4.5 5.6 - + - +
182J HIS* 2.9 34.7 + - - +
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Residues in contact with PHE 179 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J ALA* 4.5 14.8 - - + -
55J TYR* 3.5 37.2 - + + -
57J PRO* 3.8 28.3 - - + -
133J LEU* 3.6 17.4 - - + +
175J LEU 2.9 16.4 + - - +
176J THR* 3.1 9.8 + - + +
178J PHE* 1.3 77.9 - - - +
180J THR* 1.3 63.9 + - + +
182J HIS* 3.9 1.0 - - - +
183J PHE* 3.0 50.4 + + - +
401J HEM 3.9 17.5 - - + -
52V ALA 5.5 0.9 - - - -
179V PHE* 3.8 30.7 - + - -
180V THR* 6.0 0.7 - - + -
183V PHE* 4.9 2.9 - + - -
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Residues in contact with THR 180 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J THR 3.0 10.2 + - - +
177J ARG 2.5 20.6 + - - -
179J PHE* 1.3 81.3 - - + +
181J PHE* 1.3 66.5 + - - +
183J PHE* 3.0 8.8 + - - +
184J ILE* 2.9 29.6 + - - +
49V LEU* 4.7 13.2 - - - -
52V ALA* 3.2 46.7 - - + +
53V MET* 3.6 18.5 - - + +
183V PHE* 4.4 7.4 - - + -
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Residues in contact with PHE 181 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J MET* 3.4 29.6 - - + -
177J ARG* 2.9 39.0 + - + +
178J PHE* 4.4 4.7 - + - +
180J THR* 1.3 82.1 + - - +
182J HIS* 1.3 60.2 + - - +
184J ILE* 3.0 10.5 + - + -
185J LEU* 2.9 46.5 + - + +
140P MET* 3.8 22.2 - - + -
49V LEU* 5.5 7.0 - - + -
50V PHE* 5.6 1.1 - + - -
53V MET* 3.4 32.3 - - + -
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Residues in contact with HIS 182 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J THR* 2.5 42.2 + - + +
129J MET* 4.1 9.3 - - + +
130J GLY* 3.3 26.8 + - - +
133J LEU* 3.6 10.1 - - + -
178J PHE 2.9 20.9 + - - +
179J PHE 4.2 1.3 - - - +
181J PHE* 1.3 76.6 - - - +
183J PHE* 1.3 60.8 + - - +
185J LEU 4.9 0.2 - - - +
186J PRO* 3.4 18.9 - - - +
401J HEM 2.4 77.7 + + + -
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Residues in contact with PHE 183 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J LEU* 3.9 13.9 - - + -
52J ALA* 3.7 20.9 - - + -
179J PHE* 3.0 38.5 + + + +
180J THR 3.0 6.2 + - - +
182J HIS* 1.3 80.4 - - - +
184J ILE* 1.3 57.2 + - + +
186J PRO* 4.0 1.6 - - - +
187J PHE* 3.1 30.1 - + - -
401J HEM 3.3 45.2 - + + +
179V PHE* 6.4 0.2 - + - -
180V THR* 4.6 6.3 - - + -
183V PHE* 3.6 54.3 - + + -
184V ILE* 4.8 4.5 - - + -
187V PHE* 6.3 1.3 - + - -
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Residues in contact with ILE 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180J THR 2.9 16.3 + - - +
181J PHE* 3.0 27.1 + - + +
183J PHE* 1.3 79.5 - - + +
185J LEU* 1.3 73.7 + - + +
186J PRO 3.4 0.9 - - - -
187J PHE* 3.2 19.9 + - + +
188J ILE* 3.6 20.9 + - + +
45V ILE* 5.8 1.1 - - + -
49V LEU* 4.6 24.0 - - + -
183V PHE* 5.2 6.5 - - + -
187V PHE* 3.4 41.7 - - + -
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Residues in contact with LEU 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA* 3.6 18.8 - - + +
125J ALA* 3.8 8.3 - - + -
126J THR* 3.2 28.0 - - + +
129J MET* 3.5 28.0 - - + -
181J PHE* 2.9 37.3 + - + +
184J ILE* 1.3 85.6 - - + +
186J PRO* 1.3 67.8 - - + +
188J ILE* 2.8 29.1 + - + +
189J ILE* 2.9 15.2 + - + +
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Residues in contact with PRO 186 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU* 4.2 12.6 - - + +
45J ILE* 4.7 3.6 - - + -
126J THR* 3.8 7.6 - - + -
182J HIS 3.4 15.3 - - - +
183J PHE 4.0 3.6 - - - +
184J ILE 3.5 2.9 - - - -
185J LEU* 1.3 92.3 - - + +
187J PHE* 1.3 56.8 + - + +
189J ILE* 2.9 28.7 + - + +
190J ALA* 2.9 14.4 + - - +
401J HEM 3.4 62.1 - - + -
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Residues in contact with PHE 187 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J ILE* 3.8 40.4 - - + -
183J PHE* 3.1 33.4 - + - -
184J ILE* 3.2 18.5 + - + +
185J LEU 3.1 0.6 - - - -
186J PRO* 1.3 75.8 - - + +
188J ILE* 1.3 62.2 + - - +
190J ALA* 3.8 9.3 + - + +
191J ALA* 3.7 15.9 + - - +
401J HEM 3.9 22.4 - - + -
184V ILE* 3.4 34.8 - - + -
187V PHE* 5.4 18.8 - + + -
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Residues in contact with ILE 188 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA* 6.1 3.8 - - + -
184J ILE* 4.0 25.6 - - + +
185J LEU* 2.8 23.4 + - + +
187J PHE* 1.3 76.1 - - - +
189J ILE* 1.3 61.7 + - + +
190J ALA 3.1 0.2 - - - -
191J ALA* 3.1 6.9 + - + +
192J LEU* 2.9 50.4 + - + +
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Residues in contact with ILE 189 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU* 4.5 12.1 - - + -
90J PHE* 5.6 1.1 - - + -
119J LEU* 4.5 9.7 - - + +
122J ALA* 4.0 25.6 - - + +
123J THR* 4.2 16.8 - - - +
126J THR* 3.5 26.9 - - + +
185J LEU 2.9 12.4 + - - +
186J PRO* 2.9 22.4 + - + +
188J ILE* 1.3 77.8 - - + +
190J ALA* 1.3 54.9 + - - +
192J LEU* 3.8 7.9 - - - +
193J ALA* 2.9 26.5 + - - +
401J HEM 4.7 9.2 - - + -
402J HEM 4.0 25.6 - - + -
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Residues in contact with ALA 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU* 4.1 18.1 - - + +
45J ILE* 5.7 5.2 - - + -
186J PRO 2.9 11.3 + - - +
187J PHE* 3.9 13.0 - - + +
188J ILE 3.1 0.2 - - - -
189J ILE* 1.3 77.4 - - - +
191J ALA* 1.3 57.4 + - - +
193J ALA* 3.2 7.1 + - - +
194J THR* 2.9 31.9 + - + +
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Residues in contact with ALA 191 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J PHE 3.7 9.1 + - - +
188J ILE* 3.1 10.4 + - + +
190J ALA* 1.3 75.3 - - - +
192J LEU* 1.3 67.9 + - + +
194J THR* 2.2 30.8 + - - -
195J LEU* 3.0 15.4 + - + +
404J CDL 3.8 24.6 - - + +
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Residues in contact with LEU 192 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J ILE* 3.7 8.2 - - + +
118J ILE* 3.6 33.2 - - + +
119J LEU* 3.5 22.4 - - + -
122J ALA* 5.5 5.8 - - + -
188J ILE* 2.9 41.6 + - + +
189J ILE* 4.0 4.9 - - - +
191J ALA* 1.3 81.6 - - + +
193J ALA* 1.3 56.8 + - - +
195J LEU* 3.2 22.5 + - + +
196J HIS* 2.9 26.2 + - - +
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Residues in contact with ALA 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU* 5.6 2.9 - - + -
119J LEU* 4.0 13.2 - - + +
189J ILE* 2.9 20.0 + - + +
190J ALA* 3.3 9.9 - - - +
191J ALA 3.1 0.2 - - - -
192J LEU* 1.3 74.5 - - - +
194J THR* 1.3 59.5 + - - +
196J HIS* 3.0 10.6 + - + +
197J LEU* 3.0 36.6 + - + +
402J HEM 4.2 20.0 - - + -
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Residues in contact with THR 194 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190J ALA* 2.9 19.7 + - + +
191J ALA* 2.2 29.3 + - - -
193J ALA* 1.3 75.1 - - + +
195J LEU* 1.3 59.2 + - - +
198J LEU* 2.9 27.6 + - - +
404J CDL 3.2 76.1 - - + +
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Residues in contact with LEU 195 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J ILE* 4.7 10.3 - - + -
191J ALA* 3.0 18.1 + - + +
192J LEU* 3.4 25.8 - - + +
194J THR* 1.3 78.0 + - - +
196J HIS* 1.3 55.6 - - - +
198J LEU* 3.1 13.9 + - + +
199J PHE* 2.9 45.7 + - + -
404J CDL 3.3 29.8 - - + -
10V LEU* 4.0 30.1 - - + -
13V LEU* 6.3 0.2 - - + -
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Residues in contact with HIS 196 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J THR* 2.9 44.9 + - + +
115J ILE* 3.8 11.9 - - + +
116J GLY* 3.5 17.0 + - - -
119J LEU* 4.5 4.9 - - + -
192J LEU 2.9 13.6 + - - +
193J ALA* 3.1 14.8 - - - +
195J LEU* 1.3 78.6 - - - +
197J LEU* 1.3 58.0 + - - +
199J PHE* 3.3 2.6 + - - +
200J LEU* 3.0 26.2 + - - +
402J HEM 2.5 78.7 + + + -
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Residues in contact with LEU 197 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J PHE* 5.7 5.8 - - + -
193J ALA* 3.0 24.1 + - + +
194J THR* 5.2 0.2 - - - -
196J HIS* 1.3 79.8 - - + +
198J LEU* 1.3 57.2 + - - +
200J LEU* 3.9 8.3 - - + -
201J HIS* 2.9 58.3 + - + +
402J HEM 4.1 44.6 - - + -
404J CDL 3.7 38.8 - - + -
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Residues in contact with LEU 198 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194J THR 2.9 17.9 + - - +
195J LEU* 3.1 14.6 + - + +
197J LEU* 1.3 78.6 - - - +
199J PHE* 1.3 69.1 + - + +
200J LEU 3.6 0.2 + - - -
201J HIS 4.2 1.6 + - - -
202J GLU* 4.0 22.2 + - - +
404J CDL 3.4 68.2 - - + +
9V PRO* 3.8 28.0 - - + -
10V LEU* 4.3 10.8 - - - +
13V LEU* 3.5 16.4 - - + -
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Residues in contact with PHE 199 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J TYR* 5.9 1.2 - - - +
111J GLU* 3.5 38.4 - - + -
112J THR* 3.2 25.4 + - - +
115J ILE* 4.2 16.2 - - + -
195J LEU* 2.9 36.8 + - + +
196J HIS* 4.0 2.0 - - - +
198J LEU* 1.3 80.3 - - + +
200J LEU* 1.3 61.9 + - - +
202J GLU* 4.6 5.1 + - - +
203J THR* 4.5 9.7 + - - -
8V ASN* 5.6 3.6 - - + -
9V PRO* 3.7 32.1 - - + -
10V LEU* 4.0 35.7 - - + -
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Residues in contact with LEU 200 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J TYR* 4.3 12.1 - - + -
112J THR* 3.8 9.4 - - + +
196J HIS 3.0 17.0 + - - +
197J LEU* 3.1 8.5 + - + +
199J PHE* 1.3 80.0 - - - +
201J HIS* 1.3 80.2 + - + +
202J GLU 3.3 1.4 + - - -
203J THR* 3.3 5.4 + - - -
204J GLY* 3.3 26.2 + - - +
205J SER* 4.8 4.0 - - - -
402J HEM 3.4 82.3 - - + +
----------------------------------------------------------
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Residues in contact with HIS 201 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 4.0 14.9 + - - +
17J SER* 4.0 12.5 - - - -
21J LEU* 3.6 36.8 - - + +
197J LEU* 2.9 47.4 + - + +
198J LEU 4.2 0.2 + - - -
199J PHE 3.7 0.2 - - - -
200J LEU* 1.3 84.9 - - + +
202J GLU* 1.3 61.2 + - - +
203J THR 3.1 6.5 + - - -
204J GLY* 3.9 8.4 + - - +
205J SER 6.3 0.9 - - - -
402J HEM 5.6 2.4 - - - +
404J CDL 3.2 42.0 + - + +
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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