Contacts of the helix formed by residues 180 - 211 (chain B) in PDB entry 4DAJ
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 THR 180 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.7 9.6 - - - +
177B ALA 5.2 1.8 - - - +
178B LYS 3.4 12.2 + - - +
179B ARG* 1.3 82.7 - - - +
181B THR* 1.3 60.0 + - - +
182B LYS* 3.4 14.6 + - - +
183B ARG* 3.0 26.9 + - - +
184B ALA* 2.9 28.5 + - - +
1131C VAL* 5.6 4.9 - - + -
1132C ASN* 5.8 6.1 - - - +
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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
----------------------------------------------------------
99B LYS* 5.3 4.9 - - + +
100B THR* 4.3 30.3 - - - +
101B VAL* 4.6 3.5 - - + +
104B TYR* 4.1 24.9 + - + -
180B THR* 1.3 70.2 - - - +
182B LYS* 1.3 61.1 + - - +
184B ALA* 3.8 7.9 - - - +
185B GLY* 2.9 25.5 + - - -
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B THR* 3.4 12.5 + - - +
181B THR* 1.3 77.4 + - - +
183B ARG* 1.3 86.9 + - - +
185B GLY* 3.1 3.0 + - - -
186B VAL* 2.9 37.8 + - + +
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL* 3.9 31.6 + - - +
178B LYS* 3.4 47.9 + - - +
179B ARG* 4.2 4.9 - - + +
180B THR* 3.0 33.3 + - - +
182B LYS* 1.3 97.0 - - - +
184B ALA* 1.3 64.4 + - - +
186B VAL* 3.1 7.5 + - - +
187B MET* 2.9 36.9 + - - +
1131C VAL* 6.0 0.4 - - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.1 12.3 - - + +
104B TYR* 3.9 15.3 - - + -
105B PHE* 3.4 33.2 - - + -
180B THR 2.9 14.5 + - - +
181B THR* 3.8 6.5 - - - +
183B ARG* 1.3 75.2 - - - +
185B GLY* 1.3 65.3 + - - +
187B MET* 3.1 6.3 + - - +
188B ILE* 2.9 28.1 + - - +
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR* 3.4 26.6 - - - -
181B THR 2.9 14.5 + - - -
182B LYS 3.6 2.7 - - - -
184B ALA* 1.3 75.0 - - - +
186B VAL* 1.3 63.4 + - - +
188B ILE* 3.0 7.0 + - - +
189B GLY* 2.9 20.6 + - - -
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 4.0 29.4 - - + -
182B LYS* 2.9 33.2 + - + +
183B ARG* 3.4 9.2 - - - +
185B GLY* 1.3 75.0 - - - +
187B MET* 1.3 58.9 + - + +
189B GLY* 3.4 1.9 + - - +
190B LEU* 2.9 27.3 + - + +
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Residues in contact with MET 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 5.4 9.9 - - + -
105B PHE* 5.3 3.1 - - + -
160B VAL* 3.9 41.7 - - + +
164B ASP* 6.4 0.2 - - - -
175B TYR* 4.5 22.4 - - + +
183B ARG* 2.9 30.6 + - + +
184B ALA* 3.8 7.2 - - - +
186B VAL* 1.3 78.4 - - + +
188B ILE* 1.3 57.9 + - + +
190B LEU* 3.5 11.1 - - + +
191B ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR* 3.3 43.1 - - + +
105B PHE* 4.3 16.4 - - + -
108B SER* 3.7 38.4 - - - +
157B ASN* 5.0 5.4 - - - +
160B VAL* 6.1 1.1 - - + -
184B ALA 2.9 14.8 + - - +
185B GLY* 3.0 7.8 + - - +
187B MET* 1.3 74.1 - - - +
189B GLY* 1.3 66.9 + - - +
191B ALA* 3.1 6.0 + - - +
192B TRP* 3.0 35.7 + - + +
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Residues in contact with GLY 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLY 2.9 13.5 + - - -
186B VAL* 3.8 2.7 - - - -
188B ILE* 1.3 76.9 - - - +
190B LEU* 1.3 63.0 + - - +
192B TRP* 3.5 5.3 + - - +
193B VAL* 2.9 31.4 + - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TRP* 5.6 4.3 - - + -
209A PHE* 3.6 37.5 - - + -
186B VAL* 2.9 17.9 + - + +
187B MET* 3.5 10.5 - - + +
189B GLY* 1.3 76.4 - - - +
191B ALA* 1.3 57.0 + - - +
193B VAL* 3.2 14.7 + - + +
194B ILE* 2.9 53.1 + - + +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 5.3 2.5 - - - +
156B MET* 4.0 33.7 - - + +
157B ASN* 5.3 5.2 - - - +
160B VAL* 5.0 10.8 - - + -
187B MET 2.9 18.2 + - - +
188B ILE* 3.1 6.9 + - - +
190B LEU* 1.3 72.5 - - - +
192B TRP* 1.3 71.7 + - + +
194B ILE* 3.0 8.5 + - - +
195B SER* 2.9 24.4 + - - -
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Residues in contact with TRP 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER* 3.3 22.8 + - - -
111B CYS* 4.7 8.3 - - + -
112B ALA* 4.1 37.7 - - + -
115B ILE* 4.6 18.6 - - + -
149B VAL* 4.6 12.9 - - + +
150B ALA* 4.8 9.9 - - + -
153B ALA* 3.9 25.3 + - + +
157B ASN* 4.2 6.1 + - - -
188B ILE* 3.0 37.1 + - + +
189B GLY* 3.9 5.6 - - - +
191B ALA* 1.3 77.1 - - + +
193B VAL* 1.3 66.2 + - + +
195B SER* 2.8 18.8 + - - -
196B PHE* 2.9 15.8 + - - +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLY 2.9 21.4 + - - +
190B LEU* 3.2 16.8 - - + +
192B TRP* 1.3 77.2 - - + +
194B ILE* 1.3 68.5 + - + +
196B PHE* 3.0 6.7 + - + +
197B VAL* 2.9 41.1 + - + +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B MET* 3.9 27.1 - - + -
190B LEU* 2.9 46.4 + - + +
191B ALA* 3.4 5.6 - - - +
193B VAL* 1.3 74.9 - - + +
195B SER* 1.3 57.6 + - - +
197B VAL* 3.4 6.9 + - - +
198B LEU* 2.9 55.2 + - + +
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.9 22.0 - - - -
152B ASN* 2.8 32.7 + - - +
153B ALA* 3.1 20.7 + - - -
156B MET* 3.5 6.6 - - - -
191B ALA 2.9 6.2 + - - -
192B TRP 2.8 11.3 + - - -
194B ILE* 1.3 73.1 - - - +
196B PHE* 1.3 61.1 + - - -
198B LEU* 2.8 21.4 + - - +
199B TRP* 2.9 17.2 + - - -
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Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.7 24.4 - - + +
192B TRP 2.9 13.9 + - - +
193B VAL* 3.6 9.4 - - + +
195B SER* 1.3 72.5 - - - +
197B VAL* 1.3 72.8 + - + +
200B ALA* 2.9 62.6 + - + +
201B PRO* 3.0 7.4 - - + +
204B LEU* 5.8 3.8 - - + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 6.0 6.7 - - + -
193B VAL* 2.9 34.9 + - + +
194B ILE* 3.5 7.4 - - - +
196B PHE* 1.3 88.9 - - + +
198B LEU* 1.3 66.2 + - + +
201B PRO* 3.0 29.4 - - + +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 5.0 17.3 - - + -
152B ASN* 5.0 11.0 - - - +
156B MET* 5.3 2.2 - - - -
194B ILE* 2.9 41.2 + - + +
195B SER* 2.8 6.9 + - - +
197B VAL* 1.3 85.5 - - + +
199B TRP* 1.3 74.1 + - + +
201B PRO* 4.5 0.7 - - - -
202B ALA* 4.5 9.6 - - - +
224B PHE* 5.9 0.2 - - - -
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Residues in contact with TRP 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.8 40.4 - + + -
149B VAL* 3.8 16.6 - - + +
152B ASN* 3.2 37.7 + - + +
195B SER 2.9 20.7 + - - +
197B VAL 3.3 0.2 - - - -
198B LEU* 1.3 88.9 - - + +
200B ALA* 1.3 66.6 + - - +
201B PRO* 3.3 2.2 - - - -
202B ALA* 3.1 5.5 + - - +
203B ILE* 2.9 39.9 + - + +
222B ILE* 4.5 2.9 - - + -
224B PHE* 4.2 25.8 - + - -
225B LEU* 5.1 2.5 - - + -
234B THR* 3.7 29.4 - - + -
238B ALA* 4.4 6.7 - - + -
2000B 0HK 3.3 28.5 - - + +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER* 4.4 15.5 - - - -
149B VAL* 4.1 6.1 - - + +
196B PHE* 2.9 57.1 + - + +
199B TRP* 1.3 74.5 - - - +
201B PRO* 1.3 63.9 - - + +
203B ILE* 4.6 0.2 - - - -
204B LEU* 2.9 39.3 + - + +
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Residues in contact with PRO 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 3.0 12.8 - - + +
197B VAL* 3.0 35.2 - - + +
198B LEU 4.5 0.2 - - - -
199B TRP 3.3 3.4 - - - -
200B ALA* 1.3 90.7 - - + +
202B ALA* 1.3 57.9 + - - +
204B LEU* 5.1 2.2 - - + -
205B PHE* 2.9 42.5 + - + +
206B TRP 3.9 0.2 + - - -
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU 4.5 11.0 - - - +
199B TRP 3.1 6.9 + - - +
201B PRO* 1.3 81.0 - - - +
203B ILE* 1.3 60.1 + - - +
206B TRP* 2.7 41.5 + - + +
224B PHE* 3.5 26.2 - - + -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 4.1 17.5 - - + +
144B LEU* 4.0 17.5 - - + +
145B SER* 3.4 41.3 - - - +
148B TYR* 4.2 10.8 - - + -
199B TRP* 2.9 28.3 + - + +
200B ALA 3.8 2.5 - - - +
202B ALA* 1.3 80.0 - - - +
204B LEU* 1.3 68.1 + - - +
206B TRP* 3.8 5.2 + - - +
207B GLN* 4.7 3.8 + - - +
222B ILE* 3.9 33.7 - - + -
223B GLN* 5.6 4.0 + - - +
224B PHE* 4.0 11.2 - - + -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 3.6 41.7 - - + +
142B LEU* 4.6 11.9 - - + +
145B SER* 4.3 11.4 - - - +
196B PHE* 5.8 3.1 - - + -
200B ALA* 2.9 36.1 + - + +
201B PRO* 4.3 1.3 - - + +
203B ILE* 1.3 76.0 - - - +
205B PHE* 1.3 81.1 + - + +
207B GLN* 3.2 33.9 + - - +
208B TYR* 4.2 0.2 - - - -
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO* 2.9 23.1 + - + +
204B LEU* 1.3 92.3 - - + +
206B TRP* 1.3 63.9 + - - +
207B GLN 3.1 3.1 - - - -
208B TYR* 3.2 23.3 + + + -
209B PHE* 2.9 24.3 + - + +
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Residues in contact with TRP 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 5.7 5.6 - - + -
201B PRO 3.9 0.8 + - - -
202B ALA* 2.7 28.8 + - + +
203B ILE 4.2 2.9 - - - +
204B LEU 3.4 1.0 - - - -
205B PHE* 1.3 78.3 - - - +
207B GLN* 1.3 56.9 + - - +
209B PHE* 3.3 31.7 + + + +
210B VAL* 2.9 48.9 + - + +
223B GLN* 3.6 36.0 - - + +
224B PHE* 3.5 40.0 - + + +
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Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 3.7 21.8 + - - -
203B ILE 4.7 2.8 + - - +
204B LEU 3.2 20.0 + - - +
206B TRP* 1.3 80.5 - - - +
208B TYR* 1.3 90.7 + - + +
210B VAL 3.4 0.7 + - - -
211B GLY* 2.9 24.1 + - - -
212B LYS 3.1 21.4 + - - +
213B ARG* 3.0 37.3 + - + +
223B GLN* 3.1 25.6 + - - +
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU 4.0 6.7 - - - -
205B PHE* 3.2 24.9 + + + +
207B GLN* 1.3 108.1 + - + +
209B PHE* 1.3 64.3 + - - +
211B GLY* 3.7 11.0 + - - +
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Residues in contact with PHE 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 4.1 26.7 - - + -
187A MET* 5.2 11.7 - - + -
190A LEU* 3.9 30.3 - - + -
205B PHE 2.9 16.9 + - - +
206B TRP* 3.5 41.7 - + + +
208B TYR* 1.3 77.6 - - - +
210B VAL* 1.3 71.2 + - + +
211B GLY* 3.5 0.7 + - - -
----------------------------------------------------------
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 5.2 10.1 + - - +
206B TRP* 2.9 57.1 + - + +
207B GLN 3.9 3.4 - - - +
209B PHE* 1.3 81.5 - - + +
211B GLY* 1.3 58.2 + - - +
212B LYS* 3.7 18.3 + - + +
214B THR* 5.4 2.9 - - - +
223B GLN* 4.3 5.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN 2.9 10.5 + - - -
208B TYR* 3.7 10.0 + - - -
209B PHE 3.3 2.6 - - - -
210B VAL* 1.3 78.1 - - - +
212B LYS* 1.3 59.2 + - - +
----------------------------------------------------------
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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