Contacts of the helix formed by residues 178 - 205 (chain N) in PDB entry 1VF5
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 ALA 178 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE 5.1 4.3 - - - +
57A TYR* 6.3 3.4 - - + -
59A LYS* 6.3 0.7 - - - +
170N ARG 4.1 3.8 - - - +
171N GLY* 4.1 22.7 - - - +
176N GLY 2.7 4.4 + - - -
177N GLN* 1.3 84.3 - - + +
179N THR* 1.3 64.9 + - - +
180N LEU 3.2 1.3 - - - -
181N THR* 3.5 9.4 - - - -
182N ARG* 2.9 36.7 + - + +
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Residues in contact with THR 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N TRP* 5.2 2.5 - - + +
148N VAL* 3.9 28.3 - - + -
169N LEU 4.7 0.2 - - - -
170N ARG* 3.2 33.9 + - + +
174N SER 3.6 1.9 + - - -
175N VAL* 3.4 14.8 - - + -
176N GLY 2.7 33.8 + - - -
178N ALA* 1.3 73.9 - - - +
180N LEU* 1.3 52.5 + - - +
182N ARG* 3.8 0.7 - - - +
183N TYR* 2.8 54.8 + - + +
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Residues in contact with LEU 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58N TYR* 3.5 20.9 - - - +
60N PRO* 3.7 21.5 - - + +
61N THR 3.5 29.4 - - - +
62N VAL* 4.0 13.2 - - + +
65N ALA* 4.0 9.2 - - + -
137N SER 5.4 0.2 - - - -
138N LEU* 3.8 18.4 - - + +
140N TRP* 4.2 31.8 - - + +
176N GLY 3.3 8.4 + - - +
177N GLN 4.5 4.5 - - - +
179N THR* 1.3 78.7 - - - +
181N THR* 1.3 59.4 + - - +
183N TYR* 4.1 4.9 - - + -
184N TYR* 2.9 28.8 + - - +
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Residues in contact with THR 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR 3.5 19.0 - - - +
56A PHE 3.4 24.5 - - - +
57A TYR* 4.2 3.8 - - - +
58A TYR 3.9 16.2 - - - +
59A LYS* 4.7 15.3 - - + +
60N PRO* 4.7 9.8 + - - -
177N GLN 3.1 14.9 + - - -
178N ALA* 3.2 14.7 + - - -
180N LEU* 1.3 75.8 - - - +
182N ARG* 1.3 60.9 + - - +
184N TYR* 3.4 5.4 + - - +
185N SER 3.1 21.3 + - - -
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Residues in contact with ARG 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.7 44.2 + - + +
57A TYR* 2.8 40.2 + - - -
42D PHE* 3.2 23.0 + - - +
44D PRO* 3.7 13.1 - - - +
168N LEU* 2.9 30.9 + - - +
169N LEU 4.1 4.3 - - - +
171N GLY* 3.2 29.3 + - - +
178N ALA* 2.9 23.8 + - - +
179N THR 3.8 2.5 - - - +
181N THR* 1.3 73.3 - - - +
183N TYR* 1.3 61.4 + - - +
185N SER* 3.3 7.2 + - - -
186N ALA 2.9 24.9 + - - -
1304N TDS 3.0 24.3 - - - +
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Residues in contact with TYR 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133N VAL* 3.9 10.4 - - + +
134N THR* 3.5 43.6 - - + -
137N SER* 4.2 15.3 - - - -
138N LEU* 4.3 9.4 - - + +
148N VAL* 3.9 19.1 - - + +
151N VAL* 4.0 14.1 - - + +
152N SER* 4.8 4.0 + - - -
169N LEU* 3.6 15.0 - - + -
170N ARG* 5.3 0.9 - - + -
179N THR* 2.8 37.7 + - + +
180N LEU* 3.9 8.3 - - + +
182N ARG* 1.3 78.7 - - - +
184N TYR* 1.3 56.6 + - - +
186N ALA* 3.7 3.1 + - - +
187N HIS* 3.1 27.9 + - - +
1304N TDS 3.1 47.6 - - + +
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Residues in contact with TYR 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 5.4 0.9 - - + -
184A TYR* 4.4 27.1 - + - -
55N THR* 3.4 33.4 + - - +
58N TYR* 3.7 37.9 + + - -
60N PRO* 4.1 26.0 - - + -
138N LEU* 4.0 16.6 - - + -
180N LEU 2.9 19.0 + - - +
181N THR* 3.8 5.2 - - - +
182N ARG 3.2 0.4 - - - -
183N TYR* 1.3 74.7 - - - +
185N SER* 1.3 68.0 + - - +
187N HIS* 3.1 1.2 + - - -
188N THR* 2.8 59.7 + - + +
301N HEM 4.2 7.6 - - + -
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Residues in contact with SER 185 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.6 7.6 - - - -
55A THR* 2.7 37.5 + - - -
56A PHE* 3.0 25.2 - - - -
181N THR 3.1 14.3 + - - -
182N ARG 3.3 4.2 + - - -
184N TYR* 1.3 80.0 - - - +
186N ALA* 1.3 55.4 + - - +
188N THR* 4.4 3.4 - - - -
189N PHE* 2.7 34.7 + - - +
190N VAL* 3.0 8.4 + - - -
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Residues in contact with ALA 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.9 0.4 - - - -
134N THR* 4.3 2.5 - - + -
182N ARG 2.9 16.9 + - - +
183N TYR* 3.8 5.2 - - - +
185N SER* 1.3 78.8 - - - +
187N HIS* 1.3 58.4 + - - +
190N VAL* 3.8 11.4 - - - -
191N LEU* 2.8 36.6 + - - +
1304N TDS 3.2 47.1 - - + -
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Residues in contact with HIS 187 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131N PHE* 2.9 41.4 + + - -
134N THR* 2.8 25.0 + - - +
135N GLY* 3.0 19.3 + - - -
138N LEU* 4.3 8.5 - - + -
183N TYR 3.1 18.9 + - - +
184N TYR 3.1 3.3 + - - +
186N ALA* 1.3 77.9 - - - +
188N THR* 1.3 61.5 + - + +
191N LEU* 4.4 3.4 - - - -
192N PRO* 3.4 3.3 - - - +
301N HEM 2.1 75.7 + + + -
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Residues in contact with THR 188 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A THR 5.1 0.9 - - - +
189A PHE* 3.5 22.1 - - - +
193A TRP* 3.9 1.7 - - - -
55N THR* 4.6 1.1 - - + -
184N TYR* 2.8 60.1 + - + +
185N SER* 4.2 1.4 + - - -
187N HIS* 1.3 83.8 - - + +
189N PHE* 1.3 61.4 + - - +
192N PRO* 3.2 16.6 - - - +
193N TRP* 4.6 0.2 - - - -
301N HEM 3.3 41.5 - - + -
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Residues in contact with PHE 189 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.6 36.8 - + - -
52A PHE* 3.4 38.1 - + + -
55A THR* 5.0 2.9 - - + +
188A THR* 3.5 11.9 - - - +
301A HEM 3.2 48.5 - - + -
185N SER* 2.7 26.3 + - - +
188N THR* 1.3 75.6 + - - +
190N VAL* 1.3 72.1 + - + +
192N PRO* 3.1 6.2 - - - +
193N TRP* 2.6 53.9 - + + -
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Residues in contact with VAL 190 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.2 42.2 - - + -
56A PHE* 4.6 3.6 - - + -
185N SER* 3.0 12.1 + - - +
186N ALA* 3.8 10.5 - - + +
189N PHE* 1.3 74.0 - - + +
191N LEU* 1.3 67.1 + - - +
193N TRP* 2.7 20.2 + - - +
194N LEU* 3.2 21.3 + - + +
1304N TDS 2.9 37.7 - - + +
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Residues in contact with LEU 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N ILE* 3.8 25.9 - - + +
130N SER* 3.8 14.4 - - - -
131N PHE* 3.3 49.6 - - + +
134N THR* 3.9 10.1 - - - +
186N ALA 2.8 25.5 + - - +
190N VAL* 1.3 74.1 - - - +
192N PRO* 1.3 66.5 - - + +
194N LEU* 3.2 12.0 + - + +
195N ILE* 3.1 21.1 + - - +
1304N TDS 2.8 37.9 - - + +
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Residues in contact with PRO 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TRP* 3.7 22.1 - - + -
44N PHE* 5.0 4.5 - - + -
48N PHE* 5.6 1.3 - - + -
131N PHE* 3.5 13.7 - - + -
186N ALA 3.8 1.1 - - - +
187N HIS 3.4 15.9 - - - +
188N THR* 3.2 24.2 - - - +
189N PHE 3.1 20.0 - - - +
190N VAL 3.3 1.3 - - - -
191N LEU* 1.3 95.0 - - + +
193N TRP* 1.3 56.9 + - - +
195N ILE* 3.0 20.2 - - + +
196N ALA* 3.2 11.8 + - - +
301N HEM 4.3 14.4 - - + -
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Residues in contact with TRP 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.8 28.7 - + + -
188A THR 4.0 0.7 - - - -
192A PRO* 3.7 32.5 - - + -
193A TRP* 3.4 58.4 - + - +
196A ALA* 5.4 8.1 - - - +
306D OPC 4.7 27.4 - - + +
189N PHE* 2.6 69.7 + + + +
190N VAL* 2.7 12.7 + - - +
192N PRO* 1.3 73.1 - - - +
194N LEU* 1.3 65.0 + - + +
196N ALA* 3.6 7.8 + - + +
197N VAL* 3.0 32.5 + - + +
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Residues in contact with LEU 194 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D OPC 4.9 27.1 - - + -
127N ILE* 3.8 19.7 - - + -
190N VAL* 3.8 31.6 - - + +
191N LEU* 3.2 14.9 + - + +
193N TRP* 1.3 78.7 - - + +
195N ILE* 1.3 66.4 + - - +
197N VAL* 3.0 4.5 + - + +
198N PHE* 2.9 39.7 + - + -
1304N TDS 4.1 13.0 - - - -
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Residues in contact with ILE 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N PHE* 3.8 26.0 - - + -
93N MET* 4.0 11.2 - - + -
124N LEU* 4.1 5.8 - - + +
127N ILE* 3.8 23.5 - - + +
128N THR* 3.5 25.4 - - - +
131N PHE* 3.9 10.3 - - + -
191N LEU 3.1 13.8 + - - +
192N PRO* 3.0 17.5 - - + +
194N LEU* 1.3 76.8 - - - +
196N ALA* 1.3 55.2 + - - +
199N MET* 2.7 61.5 + - + +
302N HEM 3.7 15.0 - - + -
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Residues in contact with ALA 196 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TRP* 5.4 7.9 - - - +
44N PHE* 6.1 1.1 - - + -
192N PRO 3.3 14.4 - - - +
193N TRP* 3.7 12.1 - - + +
194N LEU 3.1 0.2 - - - -
195N ILE* 1.3 85.2 - - + +
197N VAL* 1.3 57.6 + - + +
199N MET* 4.2 1.4 - - - +
200N LEU* 2.9 32.9 + - - +
1306N OPC 4.3 27.8 - - + +
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Residues in contact with VAL 197 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D OPC 3.8 56.3 - - + -
193N TRP* 3.0 23.1 - - + +
194N LEU* 3.0 10.1 + - + +
196N ALA* 1.3 78.6 - - + +
198N PHE* 1.3 70.7 + - + +
200N LEU* 3.1 20.4 - - + +
201N LEU* 3.1 22.6 + - + +
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Residues in contact with PHE 198 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D OPC 4.4 22.9 - - + -
120N SER* 4.3 10.8 + - - +
123N ILE* 3.6 45.5 - - + -
124N LEU* 3.3 25.5 - - + +
127N ILE* 4.0 11.0 - - + -
194N LEU* 2.9 32.5 + - + +
197N VAL* 1.3 86.2 - - + +
199N MET* 1.3 61.9 + - - +
200N LEU 3.1 1.1 - - - -
201N LEU* 3.7 20.6 - - + +
202N HIS* 3.0 28.9 + - - +
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Residues in contact with MET 199 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N LEU* 3.7 26.5 - - + -
44N PHE* 4.3 24.0 - - + -
124N LEU* 3.9 10.8 - - + -
195N ILE* 2.7 52.8 + - + +
196N ALA 4.3 2.2 - - - +
198N PHE* 1.3 71.9 - - - +
200N LEU* 1.3 59.9 + - - +
202N HIS* 4.0 6.7 - - - -
203N PHE* 2.9 50.9 + - + -
302N HEM 3.3 36.1 - - + -
1306N OPC 4.4 14.4 - - + -
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Residues in contact with LEU 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196N ALA 2.9 18.8 + - - +
197N VAL* 3.1 14.6 - - + +
199N MET* 1.3 82.1 - - - +
201N LEU* 1.3 60.8 + - + +
203N PHE* 4.1 1.5 - - - +
204N LEU* 2.8 59.7 + - + +
1306N OPC 3.2 61.2 - - + -
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Residues in contact with LEU 201 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D OPC 3.7 57.9 - - + -
120N SER* 5.0 5.4 - - - -
197N VAL* 3.1 23.7 + - + +
198N PHE* 3.6 28.0 + - + +
200N LEU* 1.3 76.2 - - + +
202N HIS* 1.3 60.6 + - - +
204N LEU* 3.0 11.3 + - + -
205N MET* 2.8 52.4 + - + +
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Residues in contact with HIS 202 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N THR* 2.8 38.6 + - + +
120N SER* 3.0 10.1 + - - +
121N GLY* 3.7 7.5 + - - -
124N LEU* 3.7 11.8 - - + +
198N PHE 3.0 18.6 + - - +
199N MET* 3.7 4.3 - - - +
201N LEU* 1.3 79.5 - - - +
203N PHE* 1.3 61.3 + + - +
205N MET* 3.6 10.5 + - - +
206N ILE* 3.0 26.3 - - - +
302N HEM 2.2 84.9 + + + -
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Residues in contact with PHE 203 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N LEU* 4.1 28.3 - - + -
199N MET* 2.9 48.2 + - + +
200N LEU 4.1 2.7 - - - +
202N HIS* 1.3 81.7 - + - +
204N LEU* 1.3 68.9 + - + +
206N ILE* 3.1 15.2 + - + +
302N HEM 3.5 48.5 - + + -
303N HEM 2.9 49.2 - - + +
1306N OPC 4.0 36.1 - - + -
1305Q PL9 5.3 1.8 - - + -
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Residues in contact with LEU 204 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B OPC 5.1 15.3 - - + -
306D OPC 6.0 7.2 - - + -
200N LEU* 2.8 45.1 - - + +
201N LEU* 3.0 11.5 + - + +
203N PHE* 1.3 73.4 - - - +
205N MET* 1.3 55.4 + - + +
206N ILE 2.6 23.8 + - - +
207N ARG* 3.6 15.2 + - - +
1306N OPC 4.6 32.1 - - + -
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Residues in contact with MET 205 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 5.9 6.1 - - + -
306D OPC 3.9 35.9 - - + -
114N ARG* 6.0 0.3 - - - -
116N LEU* 3.7 35.2 - - + +
117N THR* 3.4 29.2 + - - +
120N SER* 3.4 29.8 - - - +
201N LEU* 2.8 37.7 + - + +
202N HIS* 3.6 4.5 - - - +
203N PHE 3.3 0.2 - - - -
204N LEU* 1.3 69.5 - - + +
206N ILE* 1.3 60.2 + - - +
207N ARG* 3.4 5.7 + - - -
208N LYS* 3.8 22.3 - - - +
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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