Contacts of the helix formed by residues 178 - 207 (chain B) in PDB entry 3N3B
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 LEU 178 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 3.4 44.6 - - + +
44B ALA* 3.6 10.7 - - + +
45B TRP* 3.7 33.7 - - + +
48B LEU* 3.9 19.7 - - + -
56B THR* 4.8 6.5 - - + -
112B LEU* 4.3 8.5 - - + -
169B PRO* 5.0 2.3 - - + +
172B PHE* 3.8 28.9 - - + -
177B LYS* 1.3 76.7 - - + +
179B THR* 1.3 58.5 + - - +
180B ASN 3.4 2.5 - - - -
181B THR* 3.5 14.1 + - + +
182B ALA* 3.1 25.6 + - - +
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 3.5 3.6 + - - -
173B SER* 5.1 8.7 - - - +
176B GLY* 4.1 29.8 - - - +
177B LYS 4.1 2.7 - - - +
178B LEU* 1.3 76.1 - - - +
180B ASN* 1.3 70.0 + - - +
182B ALA* 3.4 8.7 + - - +
183B ASP* 3.0 35.6 + - - +
186B ARG* 4.0 3.2 + - - +
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 3.3 17.1 - - + +
37B PRO* 3.3 43.4 + - - +
38B LEU* 4.2 2.7 - - - -
40B ASN* 3.4 24.1 + - - +
41B ASP* 2.8 25.9 + - - +
179B THR* 1.3 82.9 + - - +
181B THR* 1.3 63.5 + - - +
183B ASP* 3.2 12.3 + - - +
184B LEU* 3.0 18.2 + - - +
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.9 16.7 - - - +
41B ASP* 2.7 28.5 + - - +
60B PHE* 4.2 20.0 - - + -
108B ILE* 3.9 30.9 - - + +
112B LEU* 4.0 16.2 - - + +
169B PRO* 5.2 3.4 - - + -
178B LEU* 3.7 18.3 - - + +
180B ASN* 1.3 71.8 - - - +
182B ALA* 1.3 56.7 + - - +
184B LEU* 3.2 3.9 + - - +
185B ILE* 3.0 30.1 + - + +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PRO* 3.6 24.2 - - - +
170B MET* 3.7 9.7 - - + +
173B SER* 3.8 17.9 - - - -
178B LEU 3.1 15.2 + - - +
179B THR* 3.4 11.4 - - - +
181B THR* 1.3 77.4 - - - +
183B ASP* 1.3 56.5 + - - +
185B ILE* 3.4 2.7 + - - -
186B ARG* 3.0 42.9 + - - +
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Residues in contact with ASP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.8 6.7 - - + -
179B THR* 3.0 23.8 + - - +
180B ASN* 3.2 16.6 + - - +
182B ALA* 1.3 76.0 - - - +
184B LEU* 1.3 62.0 + - - +
186B ARG* 2.7 33.3 + - - +
187B LEU* 3.3 26.8 + - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 4.2 8.9 - - + -
33B PRO* 4.0 26.9 - - + -
36B VAL* 4.2 11.8 - - + +
38B LEU* 3.8 34.1 - - + -
104B SER* 3.7 25.8 - - - +
108B ILE* 4.1 20.0 - - + -
180B ASN 3.0 12.3 + - - +
181B THR 3.2 8.7 + - - +
183B ASP* 1.3 73.7 - - - +
185B ILE* 1.3 68.0 - - + +
187B LEU* 3.1 22.6 + - - +
188B ILE* 3.2 23.3 + - + +
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.7 28.5 - - + -
105B TYR* 4.3 5.8 - - + -
108B ILE* 4.8 1.1 - - + -
166B PHE* 3.6 31.0 - - + -
169B PRO* 3.8 25.6 - - + -
170B MET* 4.0 10.3 - - + -
181B THR* 3.0 20.7 + - + +
182B ALA 3.4 4.9 + - - +
184B LEU* 1.3 83.6 - - + +
186B ARG* 1.3 57.9 + - - +
188B ILE* 3.2 23.9 + - + +
189B ILE* 2.8 37.6 + - + +
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Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET* 4.0 20.0 - - + +
173B SER* 3.4 24.9 + - - -
179B THR* 4.0 3.4 + - - +
182B ALA* 3.0 22.6 + - - +
183B ASP* 2.7 43.4 + - - +
184B LEU 3.3 0.2 - - - -
185B ILE* 1.3 76.0 - - - +
187B LEU* 1.3 58.6 + - + +
189B ILE* 3.8 10.5 - - + +
190B ARG* 2.9 28.8 + - - +
285B ALA* 2.8 35.8 + - - +
286B LEU* 4.3 13.5 - - + +
288B PRO* 5.3 11.0 - - - +
85C ASN 4.7 2.6 - - - +
87C GLY* 5.9 2.2 - - - -
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 3.6 45.2 + - + +
35B LYS* 6.4 0.2 - - + -
36B VAL* 4.0 23.8 - - + -
183B ASP 3.3 14.0 + - - +
184B LEU* 3.1 9.0 + - - +
186B ARG* 1.3 75.7 - - - +
188B ILE* 1.3 62.3 + - - +
190B ARG* 3.5 39.6 + - - +
191B ASP* 3.2 27.9 + - - +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 3.6 20.0 - - + -
67B ASP* 4.9 1.1 - - - +
101B HIS* 3.7 31.4 - - + +
104B SER* 3.6 22.7 - - - +
105B TYR* 3.9 18.6 - - + +
162B PHE* 5.7 0.4 - - + -
166B PHE* 3.7 23.3 - - + -
184B LEU* 3.2 20.3 + - + +
185B ILE* 3.2 23.0 + - + +
187B LEU* 1.3 73.7 - - - +
189B ILE* 1.3 59.8 + - - +
191B ASP* 3.2 5.0 + - - +
192B GLU* 3.0 31.2 + - + +
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR* 3.8 8.7 - - + +
166B PHE* 3.9 35.7 - - + -
170B MET* 4.6 6.7 - - + -
185B ILE* 2.8 35.5 + - + +
186B ARG* 3.8 9.4 - - + +
188B ILE* 1.3 77.2 - - - +
190B ARG* 1.3 56.0 + - - +
192B GLU* 3.2 7.1 + - - +
193B ALA* 3.0 29.5 + - - +
286B LEU* 3.9 24.5 - - + -
85C ASN* 3.5 40.7 + - + +
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Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.6 26.6 - - - +
29B ASN* 3.3 51.8 + - - +
30B PHE 5.3 0.2 + - - -
31B TRP* 4.4 5.1 - - - +
186B ARG 2.9 18.4 + - - +
187B LEU* 3.5 36.3 + - - +
188B ILE 3.3 0.2 - - - -
189B ILE* 1.3 77.3 - - - +
191B ASP* 1.3 62.6 + - - +
193B ALA* 3.8 5.2 + - - +
194B VAL* 3.4 21.8 + - - +
85C ASN 4.0 12.1 - - - +
86C PHE* 4.3 14.6 - - + +
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.6 13.6 - - - +
29B ASN* 4.4 18.4 - - - +
31B TRP* 2.8 26.8 + - - -
97B MET* 3.4 15.3 - - - +
101B HIS* 2.9 26.6 + - + +
187B LEU 3.2 8.5 + - - +
188B ILE 3.2 9.1 + - - +
190B ARG* 1.3 80.1 + - - +
192B GLU* 1.3 59.3 + - - +
194B VAL* 3.2 6.1 + - - +
195B HIS* 2.9 40.6 + - - +
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 3.1 0.7 - - - +
101B HIS* 3.2 7.3 - - - -
158B GLU* 3.0 36.4 - - + +
159B SER* 4.0 6.5 + - - -
162B PHE* 5.7 0.7 - - + -
163B TYR* 5.0 4.0 - - - +
166B PHE* 5.0 7.6 - - + -
188B ILE* 3.0 27.7 + - + +
189B ILE* 3.2 6.9 + - - +
191B ASP* 1.3 73.6 - - - +
193B ALA* 1.3 59.6 + - - +
195B HIS* 3.2 7.5 + - - +
196B GLY* 2.9 26.7 + - - -
320B MN 2.1 37.3 + - - +
321B MN 2.2 28.7 + - - -
322B PEO 4.7 1.8 - - - -
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE 3.0 15.8 + - - +
190B ARG* 4.0 6.1 - - - +
191B ASP 3.3 0.2 - - - -
192B GLU* 1.3 77.2 - - - +
194B VAL* 1.3 58.0 + - - +
196B GLY* 4.1 0.3 - - - -
197B TYR* 3.1 27.0 + - - +
264B ASN* 4.9 1.7 + - - +
322B PEO 3.8 18.5 + - - +
83C ASN* 4.2 10.2 + - - +
85C ASN* 3.7 28.1 - - + +
86C PHE* 4.4 14.6 - - + -
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.9 27.1 - - + -
25B ARG* 4.2 22.0 - - + +
26B LEU* 3.8 22.9 - - + -
29B ASN* 5.6 1.8 - - - +
190B ARG 3.4 16.8 - - - +
191B ASP* 3.2 6.6 + - - +
193B ALA* 1.3 75.2 - - - +
195B HIS* 1.3 59.5 + - - +
197B TYR* 3.3 8.6 + - + +
198B TYR* 2.8 30.5 + - - +
86C PHE* 3.8 25.1 - - + -
134C FMN 5.3 6.1 - - + -
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.8 21.4 - - + +
93B ASN* 5.0 0.2 + - - -
94B ILE* 3.6 42.1 - - + +
97B MET* 4.6 6.5 - - + +
98B GLU* 3.1 12.5 + - - -
101B HIS* 4.3 11.0 - + - -
191B ASP* 2.9 28.4 + - + +
192B GLU* 3.2 23.8 + - - +
194B VAL* 1.3 75.8 - - - +
196B GLY* 1.3 57.6 + - - +
198B TYR* 3.4 3.5 + - - +
199B ILE* 3.0 46.0 + - + +
321B MN 2.3 33.7 + - - +
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Residues in contact with GLY 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.9 15.6 - - - +
159B SER* 3.7 21.8 - - - -
192B GLU 2.9 11.8 + - - -
193B ALA 4.2 0.2 - - - -
195B HIS* 1.3 71.4 - - - +
197B TYR* 1.3 60.0 + - - +
199B ILE* 4.9 1.1 - - - -
200B GLY* 2.9 27.4 + - - -
264B ASN* 3.6 15.8 - - - +
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 2.9 35.4 + - + -
22B VAL* 4.5 9.4 - - + -
193B ALA 3.1 20.6 + - - +
194B VAL* 3.3 9.4 + - + +
196B GLY* 1.3 76.7 - - - +
198B TYR* 1.3 63.0 + + - +
200B GLY* 3.8 0.3 - - - -
201B TYR* 2.9 35.9 + + + +
264B ASN* 3.8 19.0 - - - +
11C SER* 2.8 34.5 + - - -
13C ASN* 4.0 12.8 - - - -
49C TYR* 3.4 3.7 + - - -
111C LEU* 5.3 1.1 - - + -
134C FMN 3.5 59.5 - + + -
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Residues in contact with TYR 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 4.1 16.6 - - + -
19B ASP* 2.6 32.5 + - - -
22B VAL* 3.5 33.7 - - + -
87B GLU* 3.3 35.8 - - + +
90B VAL* 3.7 28.0 - - + +
91B LEU* 5.1 4.7 - - + -
94B ILE* 4.3 13.5 - - + -
194B VAL 2.8 20.0 + - - +
195B HIS* 3.9 4.3 - - - +
197B TYR* 1.3 75.5 - + - +
199B ILE* 1.3 64.6 + - + +
201B TYR* 3.2 10.7 + + - +
202B LYS* 2.9 48.9 + - + +
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Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.9 22.2 - - + -
91B LEU* 5.1 2.7 - - + -
94B ILE* 4.9 16.6 - - + -
151B LYS* 3.7 43.8 - - + +
154B SER* 3.5 23.6 - - - +
155B VAL* 3.9 7.9 - - + -
195B HIS* 3.0 31.6 + - + +
196B GLY* 5.3 0.4 - - - -
198B TYR* 1.3 83.0 - - + +
200B GLY* 1.3 57.5 + - - +
202B LYS* 3.4 6.1 + - - +
203B TYR* 3.0 27.0 + - - +
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Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.9 9.5 - - - +
196B GLY 2.9 17.9 + - - -
199B ILE* 1.3 75.3 - - - +
201B TYR* 1.3 62.2 + - - +
203B TYR* 3.4 5.1 - - - +
204B GLN* 3.2 27.0 + - - +
264B ASN 3.3 24.6 - - - +
265B LEU* 4.2 7.2 - - - -
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 2.7 38.7 + - - -
18B LYS* 3.8 23.6 - - + -
197B TYR* 2.9 26.3 + + + +
198B TYR* 3.5 12.8 - + - +
200B GLY* 1.3 75.6 - - - +
202B LYS* 1.3 73.0 + - + +
204B GLN* 3.3 14.2 + - + +
205B LYS* 3.1 53.1 + - + +
264B ASN 3.9 1.0 + - - -
10C SER* 3.6 36.7 + - - -
11C SER* 3.8 25.8 - - - -
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 4.1 11.9 + - - +
19B ASP* 3.0 35.8 + - - -
83B LEU* 4.5 18.8 - - + +
84B THR* 4.0 4.8 + - - +
87B GLU* 3.2 33.9 + - - +
151B LYS* 3.8 15.7 - - - -
198B TYR* 2.9 43.7 + - + +
199B ILE* 3.8 6.5 - - - +
201B TYR* 1.3 85.7 - - + +
203B TYR* 1.3 58.8 + - - +
205B LYS* 3.3 5.0 + - + +
206B ASN* 2.8 39.9 + - - +
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Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.6 44.9 - - + +
151B LYS* 3.7 18.1 - - + +
152B ILE* 3.6 33.4 - - + +
199B ILE 3.0 13.9 + - - +
200B GLY 3.4 10.1 - - - +
201B TYR 3.3 0.2 - - - -
202B LYS* 1.3 76.7 - - - +
204B GLN* 1.3 59.4 + - + +
206B ASN 3.5 0.9 + - - -
207B MET* 3.1 57.1 + - + +
218B LEU* 3.8 8.2 + - + +
265B LEU* 3.7 38.8 - - + -
267B TYR* 2.8 29.2 + + - -
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLY 3.2 9.3 + - - +
201B TYR* 3.3 13.7 + - + +
203B TYR* 1.3 77.7 - - + +
205B LYS* 1.3 65.7 + - + +
207B MET* 3.5 15.4 + - + +
208B GLU* 3.4 22.8 + - - +
263B MET 4.5 0.4 + - - -
264B ASN 2.9 28.3 + - - -
265B LEU 3.2 26.6 - - - +
266B GLY* 3.2 7.4 - - - +
11C SER* 4.2 4.5 + - - +
13C ASN* 5.6 0.2 + - - -
16C ARG* 3.0 36.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 3.9 11.8 + - - +
83B LEU* 4.1 21.7 - - + +
201B TYR* 3.1 55.9 + - + +
202B LYS* 3.7 7.6 - - + +
203B TYR 3.3 0.2 - - - -
204B GLN* 1.3 75.7 - - - +
206B ASN* 1.3 62.3 + - - +
208B GLU* 3.5 39.6 + - - +
209B LYS* 4.4 9.9 + - - +
10C SER* 5.8 1.8 - - - +
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASP 4.5 7.0 + - - +
83B LEU* 3.4 34.4 - - - +
87B GLU* 5.4 1.0 + - - -
148B LEU* 3.6 24.4 - - + +
151B LYS* 3.7 25.9 - - - +
202B LYS* 2.8 28.9 + - - +
203B TYR 3.8 0.2 - - - +
205B LYS* 1.3 76.7 - - - +
207B MET* 1.3 60.7 + - - +
208B GLU 3.2 0.7 - - - -
209B LYS* 3.4 22.0 + - - +
210B ILE* 4.2 9.0 + - - +
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.8 13.9 - - + -
203B TYR* 3.1 46.7 + - + +
204B GLN* 3.9 10.5 - - + +
205B LYS 3.3 0.6 - - - -
206B ASN* 1.3 73.5 - - - +
208B GLU* 1.3 59.4 + - - +
209B LYS 3.1 5.8 - - - -
210B ILE* 3.3 25.1 + - + +
215B ARG* 3.5 42.6 + - + +
218B LEU* 3.8 19.3 - - - -
265B LEU 5.5 1.1 - - - +
267B TYR* 3.5 26.7 - - + +
----------------------------------------------------------
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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