Contacts of the helix formed by residues 167 - 192 (chain B) in PDB entry 3GV5
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ASN* 2.8 27.2 + - + +
166B LEU* 1.3 78.3 - - - +
168B VAL* 1.3 68.2 + - - +
169B LEU* 3.2 22.2 + - - +
170B HIS* 3.1 33.7 + - + +
171B ILE* 3.0 25.3 + - - +
223B PRO* 6.1 0.2 - - - +
224B GLU* 4.6 3.6 - - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 5.6 3.8 - - + -
166B LEU 3.7 4.4 + - - -
167B ASP* 1.3 76.0 + - - +
169B LEU* 1.3 75.3 + - + +
171B ILE* 3.4 8.8 + - + +
172B ARG* 2.9 69.3 + - + +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 3.2 12.0 + - - +
168B VAL* 1.3 80.2 - - + +
170B HIS* 1.3 66.1 + - - +
172B ARG* 3.3 32.5 + - - +
173B LEU* 3.1 31.9 + - + +
223B PRO* 4.5 24.0 - - + -
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Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLN* 4.1 5.7 + - - -
162B SER 4.3 1.8 + - - -
163B ILE* 3.9 15.0 - - + -
164B ASN* 2.9 52.6 + - + +
167B ASP* 3.1 23.5 + - + +
169B LEU* 1.3 73.6 - - - +
171B ILE* 1.3 66.5 + - - +
173B LEU* 3.3 3.9 + - - +
174B LEU* 3.0 29.4 + - - +
222B LEU* 4.0 24.5 - - + +
223B PRO* 3.8 16.4 - - + +
224B GLU* 2.6 32.7 + - - -
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.4 34.3 - - + -
148B LEU* 4.5 15.5 - - + -
151B VAL* 4.1 17.7 - - + -
165B LEU* 3.5 53.8 - - + +
166B LEU 5.4 0.2 - - - -
167B ASP 3.0 14.5 + - - +
168B VAL* 3.6 11.7 - - + +
170B HIS* 1.3 74.6 - - + +
172B ARG* 1.3 64.5 + - - +
174B LEU* 3.2 8.0 + - + +
175B VAL* 3.1 27.0 + - + +
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.8 19.5 - - + +
133B THR* 6.1 1.8 - - - -
136B VAL* 3.6 25.0 - - + +
137B GLU* 6.4 1.3 - - - +
140B LEU* 3.8 21.6 - - + +
168B VAL* 2.9 48.7 + - - +
169B LEU* 3.5 32.7 - - + +
171B ILE* 1.3 78.1 - - - +
173B LEU* 1.3 57.0 + - + +
175B VAL 3.5 0.5 + - - -
176B GLY 3.1 20.8 + - - -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG 4.7 2.9 - - - +
29B VAL* 4.2 14.4 - - + -
169B LEU* 3.1 19.6 + - + +
170B HIS 3.8 3.6 - - - +
172B ARG* 1.3 74.5 - - + +
174B LEU* 1.3 57.5 + - - +
176B GLY* 3.3 3.8 + - - +
177B SER* 2.9 25.8 + - - -
199B VAL* 3.9 15.8 - - + +
200B ALA* 3.9 35.7 - - - +
201B SER* 4.3 5.4 - - - +
220B VAL* 3.8 16.1 - - + +
221B LEU 3.5 19.7 - - - +
222B LEU* 4.2 7.9 - - + -
223B PRO* 4.0 26.2 - - + -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.1 29.6 - - + +
152B THR 4.4 3.9 - - - +
153B VAL* 3.2 41.5 - - + +
157B VAL* 5.4 0.2 - - + -
163B ILE* 3.5 36.1 - - + -
165B LEU* 5.0 3.1 - - + -
170B HIS 3.0 20.7 + - - +
171B ILE* 3.6 12.8 - - + +
173B LEU* 1.3 73.4 - - - +
175B VAL* 1.3 66.2 + - - +
177B SER* 2.5 24.5 + - - +
178B GLN* 3.0 12.5 + - - +
220B VAL* 4.8 5.4 - - + -
222B LEU* 4.8 9.9 - - + -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.7 24.7 - - + -
139B ARG* 3.9 32.5 - - + +
140B LEU* 4.0 22.9 - - + -
143B LEU* 5.4 6.1 - - + -
151B VAL* 4.4 14.8 - - + -
171B ILE* 3.1 17.5 + - + +
172B ARG 3.7 4.5 - - - +
174B LEU* 1.3 74.5 - - - +
176B GLY* 1.3 63.5 + - - +
178B GLN* 3.2 18.2 + - - +
179B ILE* 3.0 21.8 + - + +
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.9 14.1 - - - -
132B LEU* 3.7 23.0 - - - +
136B VAL* 3.7 4.6 - - - +
172B ARG 3.1 11.3 + - - -
173B LEU 3.5 5.4 - - - -
174B LEU 3.2 0.2 - - - -
175B VAL* 1.3 75.8 - - - +
177B SER* 1.3 55.5 + - - +
179B ILE* 3.1 4.7 + - - +
180B ALA* 2.8 29.3 + - - +
199B VAL* 4.2 5.6 - - - -
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.1 2.6 - - - +
154B SER* 3.2 34.4 + - - -
173B LEU 2.9 16.1 + - - -
174B LEU* 2.5 24.3 + - - -
176B GLY* 1.3 70.7 - - - +
178B GLN* 1.3 57.2 + - - +
180B ALA* 3.3 0.7 + - - +
181B ALA* 3.0 17.0 + - - +
199B VAL* 4.1 11.1 - - - +
218B GLN* 2.9 22.6 - - - +
219B THR 6.3 0.2 - - - -
220B VAL* 4.4 19.7 - - - -
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Residues in contact with GLN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 4.9 6.5 + - - +
151B VAL* 4.4 7.5 - - - +
152B THR* 3.1 52.8 + - + +
154B SER* 4.0 12.1 - - - +
174B LEU 3.0 7.9 + - - +
175B VAL* 3.4 22.6 - - - +
177B SER* 1.3 79.0 + - - +
179B ILE* 1.3 63.7 + - - +
181B ALA* 3.3 4.4 + - - +
182B GLU* 3.0 34.7 + - - +
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Residues in contact with ILE 179 (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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116B PHE* 4.2 11.9 - - + -
132B LEU* 3.9 26.2 - - + -
135B MSE 3.6 40.8 - - + -
136B VAL* 3.9 22.2 - - + -
139B ARG* 3.5 34.5 - - - +
175B VAL 3.0 18.6 + - - +
176B GLY* 3.1 6.3 + - - +
178B GLN* 1.3 73.8 - - - +
180B ALA* 1.3 60.7 + - - +
182B GLU* 3.0 9.8 + - - +
183B MSE 2.8 31.4 + - + +
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Residues in contact with ALA 180 (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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31B VAL* 3.9 14.8 - - + -
132B LEU* 4.7 0.4 - - - +
176B GLY 2.8 16.1 + - - +
177B SER 3.5 8.7 - - - +
179B ILE* 1.3 73.0 - - - +
181B ALA* 1.3 57.0 + - - +
183B MSE 3.3 15.6 + - - +
184B ARG* 3.0 33.1 + - - +
197B ALA* 4.0 12.2 - - + +
199B VAL* 3.9 20.4 - - + -
218B GLN* 3.7 7.4 - - - +
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Residues in contact with ALA 181 (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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154B SER* 3.2 28.5 - - - +
177B SER 3.0 9.4 + - - +
178B GLN 3.4 9.0 - - - +
179B ILE 3.1 0.2 - - - -
180B ALA* 1.3 73.4 - - - +
182B GLU* 1.3 58.9 + - + +
184B ARG* 3.5 6.4 + - - +
185B GLU* 2.9 29.4 + - - +
218B GLN* 3.5 14.7 - - - +
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Residues in contact with GLU 182 (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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116B PHE* 3.9 19.1 - - + -
139B ARG* 2.7 47.0 + - - -
178B GLN* 3.0 20.0 + - - +
179B ILE* 3.4 6.9 - - - +
181B ALA* 1.3 70.9 - - + +
183B MSE 1.3 66.1 + - - +
185B GLU* 3.3 14.9 + - - +
186B ALA* 3.0 24.6 + - - +
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Residues in contact with MSE 183 (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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31B VAL* 3.8 20.4 - - - -
33B VAL* 4.6 9.0 - - + -
112B LEU* 4.2 0.9 - - - +
113B LEU* 3.8 28.0 - - + +
116B PHE* 3.6 46.2 - - + -
130B VAL* 3.8 22.2 - - + -
132B LEU* 3.6 23.8 - - + -
179B ILE* 2.8 21.6 + - + +
180B ALA* 3.3 19.5 - - - +
182B GLU* 1.3 72.3 - - - +
184B ARG* 1.3 57.4 + - + +
186B ALA* 3.2 4.2 + - - +
187B MSE 3.0 34.7 + - - +
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Residues in contact with ARG 184 (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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33B VAL* 5.5 3.8 - - + -
155B GLY* 5.9 0.8 - - - -
180B ALA 3.0 14.1 + - - +
181B ALA* 3.8 6.4 - - - +
183B MSE 1.3 76.9 - - + +
185B GLU* 1.3 57.4 + - - +
187B MSE 3.4 16.2 + - + +
188B TYR* 3.0 29.8 + - - +
193B LEU 4.5 1.2 - - - +
195B GLY 3.3 27.4 + - - +
196B CYS 4.2 0.7 - - - -
197B ALA* 4.2 17.5 - - + +
216B ASN* 3.0 39.2 + - - +
217B GLN* 4.1 8.9 - - - +
218B GLN* 2.7 43.1 - - - +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ALA 2.9 18.3 + - - +
182B GLU* 3.6 14.9 - - - +
183B MSE 3.3 0.2 - - - -
184B ARG* 1.3 75.5 - - - +
186B ALA* 1.3 57.0 - - - +
188B TYR* 3.4 4.3 + - - +
189B ASN* 3.0 53.3 + - - +
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Residues in contact with ALA 186 (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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112B LEU* 3.8 20.2 - - + -
116B PHE* 4.4 11.0 - - + -
182B GLU 3.0 13.4 + - - +
183B MSE 3.5 8.3 - - - +
185B GLU* 1.3 75.9 - - - +
187B MSE 1.3 57.1 + - - +
189B ASN* 4.6 4.7 - - - +
190B GLN* 2.9 52.0 + - - +
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Residues in contact with MSE 187 (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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33B VAL* 3.9 23.6 - - + -
35B LEU* 3.1 34.5 - - + -
109B VAL* 4.5 20.2 - - + -
112B LEU* 3.7 20.8 - - + +
113B LEU* 4.6 7.6 - - - -
183B MSE 3.0 20.4 + - - +
184B ARG* 3.5 16.8 - - + +
186B ALA* 1.3 75.9 - - - +
188B TYR* 1.3 58.8 + - - +
191B LEU* 2.9 34.9 + - + +
192B GLY 3.2 5.0 + - - -
193B LEU* 3.5 25.3 + - + +
195B GLY* 4.5 7.0 - - - +
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Residues in contact with TYR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG 3.0 17.8 + - - +
185B GLU* 3.9 4.3 - - - +
187B MSE 1.3 75.0 - - - +
189B ASN* 1.3 70.9 + - - +
192B GLY* 2.9 36.6 + - - -
193B LEU 3.4 23.1 + - - +
194B THR* 4.7 13.2 - - - -
216B ASN* 5.8 2.9 - - - -
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU* 3.0 44.6 + - - +
186B ALA* 4.0 5.4 - - - +
188B TYR* 1.3 86.4 - - - +
190B GLN* 1.3 65.5 + - + +
192B GLY 4.9 0.2 + - - -
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.2 34.1 - - + +
115B GLU* 4.6 9.5 + - - +
186B ALA* 2.9 25.7 + - - +
189B ASN* 1.3 83.2 - - + +
191B LEU* 1.3 77.4 + - + +
192B GLY 3.8 0.4 - - - -
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.8 17.0 - - - +
105B MSE 4.2 13.2 - - - +
108B LYS* 3.9 47.6 - - + +
109B VAL* 3.8 29.6 - - + -
112B LEU* 4.8 9.4 - - + -
187B MSE 2.9 17.8 + - + +
190B GLN* 1.3 98.0 - - + +
192B GLY* 1.3 60.5 + - - +
193B LEU* 3.4 13.7 + - + +
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 3.9 5.2 + - - -
45B ILE* 3.4 19.6 - - - +
187B MSE 3.2 0.2 + - - -
188B TYR* 2.9 35.7 + - - -
189B ASN 4.9 0.4 + - - -
190B GLN 3.8 0.4 - - - -
191B LEU* 1.3 78.1 - - - +
193B LEU* 1.3 58.4 + - - +
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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