Contacts of the helix formed by residues 210 - 237 (chain B) in PDB entry 4BPW
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 PRO 210 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.8 1.3 - - + -
170B SER* 4.0 9.2 - - - +
173B LEU* 3.8 33.4 - - + -
178B LEU* 6.0 0.2 - - + -
181B GLU* 4.2 10.5 - - + +
182B SER 3.8 2.2 - - - +
183B ILE* 3.9 18.8 - - + -
184B TYR* 4.5 1.2 - - - -
200B VAL* 5.1 1.3 - - + -
208B TYR 3.8 7.2 - - - +
209B VAL* 1.3 93.2 - - + +
211B LEU* 1.3 61.6 + - - +
212B LYS* 3.3 8.7 - - + +
213B ASP* 3.4 28.3 - - - +
214B ILE* 3.2 22.3 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LYS* 3.7 46.7 - - + +
140B ILE* 3.9 25.6 - - + -
141B GLN* 5.9 0.2 - - + -
144B LEU* 5.0 0.9 - - + -
181B GLU* 4.1 14.7 + - + +
182B SER* 3.4 21.1 + - - +
184B TYR* 3.6 29.2 - - + +
210B PRO* 1.3 72.4 - - - +
212B LYS* 1.3 65.3 + - - +
213B ASP 3.1 1.0 + - - -
214B ILE* 3.4 23.0 - - + +
215B VAL* 3.2 22.7 - - + +
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Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 5.4 9.6 - - - +
172B SER* 3.5 36.6 + - - +
173B LEU* 5.1 4.5 - - + -
181B GLU* 3.6 25.6 + - - +
210B PRO* 3.3 5.1 - - + -
211B LEU* 1.3 81.0 - - - +
213B ASP* 1.3 65.2 + - - +
215B VAL* 3.8 16.0 - - - +
216B ALA* 4.5 2.4 + - - +
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Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B SER* 3.9 9.4 + - - -
172B SER* 3.0 32.1 + - - -
194B LEU* 3.9 20.9 - - + +
199B LYS 4.4 5.2 - - - +
209B VAL* 3.6 18.6 - - + +
210B PRO* 3.4 24.7 + - + +
211B LEU 3.1 0.6 - - - -
212B LYS* 1.3 79.0 - - - +
214B ILE* 1.3 61.9 + - - +
215B VAL 3.0 5.4 - - - -
216B ALA* 3.2 19.5 + - + +
217B ILE* 3.5 12.3 + - - +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 5.3 1.6 - - + -
144B LEU* 4.0 22.7 - - + +
151B PHE* 3.5 34.3 - - + -
184B TYR* 3.9 20.2 - - + -
186B ILE* 3.8 20.9 - - + -
209B VAL* 3.7 4.0 - - + +
210B PRO 3.2 13.7 + - - +
211B LEU* 3.4 34.5 - - + +
213B ASP* 1.3 74.6 - - - +
215B VAL* 1.3 69.7 + - + +
217B ILE* 3.5 22.9 + - + +
218B ILE* 3.8 11.4 + - + +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 5.2 10.3 - - + +
132B PHE* 4.4 33.4 - - + +
133B SER* 6.0 0.7 - - - +
140B ILE* 6.1 5.2 - - + -
211B LEU* 3.2 22.4 - - + +
212B LYS* 3.8 13.2 - - - +
213B ASP 3.0 0.4 - - - -
214B ILE* 1.3 81.6 - - + +
216B ALA* 1.3 58.7 + - - +
217B ILE 3.0 0.7 + - - -
218B ILE* 3.1 13.4 - - - +
219B LEU* 2.9 40.0 + - + +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 5.9 4.9 - - - +
194B LEU* 5.6 7.9 - - + -
212B LYS 4.5 2.0 + - - +
213B ASP* 3.2 15.0 + - + +
215B VAL* 1.3 78.0 - - - +
217B ILE* 1.3 61.7 + - - +
219B LEU* 3.6 17.7 - - + -
220B ASN* 3.0 36.9 + - - +
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 5.0 12.8 - - + -
151B PHE* 5.7 2.5 - - + -
186B ILE* 4.0 26.5 - - + -
190B ASP 3.8 25.4 - - - +
191B ALA* 4.6 10.8 - - + -
193B ASP* 6.0 0.4 - - - -
194B LEU* 4.7 10.3 - - + -
209B VAL* 4.5 11.2 - - + -
213B ASP 3.7 11.2 - - - +
214B ILE* 3.5 21.8 - - + +
215B VAL 3.0 1.0 + - - -
216B ALA* 1.3 79.9 - - + +
218B ILE* 1.3 68.1 - - + +
220B ASN* 3.2 4.7 + - - +
221B GLU* 3.1 23.7 + - + +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 6.2 0.2 - - - -
132B PHE* 3.5 33.9 - - + -
140B ILE* 6.3 4.0 - - + -
143B PHE* 3.8 22.9 - - + -
144B LEU* 4.3 23.8 - - + -
147B SER* 5.6 9.2 - - - -
149B LEU* 6.0 2.5 - - + -
151B PHE* 5.4 4.5 - - + -
214B ILE* 3.9 8.7 - - + +
215B VAL* 3.1 19.7 - - + +
217B ILE* 1.3 80.0 - - + +
219B LEU* 1.3 59.8 + - - +
221B GLU* 3.7 17.8 - - - +
222B PHE* 2.9 32.1 + - - +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 3.3 58.7 - - + +
128B LEU* 3.7 29.6 - - + -
129B ARG* 3.7 43.1 - - + +
215B VAL* 2.9 25.0 + - + +
216B ALA* 3.6 18.4 - - + +
218B ILE* 1.3 79.5 - - + +
220B ASN* 1.3 62.6 + - - +
222B PHE* 4.0 2.8 - - - +
223B ARG* 3.5 5.7 + - - +
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Residues in contact with ASN 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 5.9 0.5 - - - +
193B ASP* 3.4 35.9 + - - +
216B ALA* 3.0 27.4 + - - +
217B ILE* 3.7 5.3 - - - +
218B ILE 3.1 0.2 - - - -
219B LEU* 1.3 83.1 - - - +
221B GLU* 1.3 60.0 + - - +
222B PHE 3.2 2.0 - - - -
223B ARG* 3.1 24.4 + - - +
224B ALA* 2.8 28.8 + - - +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER* 6.0 2.3 - - - -
149B LEU* 5.3 9.0 - - - +
217B ILE* 3.1 17.6 + - + +
218B ILE* 3.3 19.5 + - - +
220B ASN* 1.3 75.6 - - - +
222B PHE* 1.3 57.8 + - - +
224B ALA* 3.4 8.0 + - + +
225B LYS* 3.0 60.7 + - + +
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Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 3.9 47.1 - + + -
30B LEU* 6.3 2.0 - - + -
103B HIS* 4.9 4.3 - + - -
124B GLU* 5.1 7.2 - - + -
125B MET* 3.4 33.2 - - + -
128B LEU* 4.6 22.9 - - + -
218B ILE 2.9 18.1 + - - +
219B LEU* 4.0 4.5 - - - +
221B GLU* 1.3 73.9 - - - +
223B ARG* 1.3 54.9 + - - +
225B LYS* 3.2 9.4 + - + -
226B LEU* 2.8 62.0 + - + +
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Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.8 21.3 - - + +
122B GLN* 4.3 20.6 - - - +
125B MET* 3.6 41.6 - - + +
126B ASP* 5.8 0.6 + - - -
219B LEU 3.5 10.0 + - - +
220B ASN* 3.1 24.2 + - - +
222B PHE* 1.3 78.6 - - - +
224B ALA* 1.3 60.2 + - - +
226B LEU* 3.6 2.3 - - - +
227B SER* 2.8 32.2 + - - -
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASN 2.8 15.1 + - - +
221B GLU* 3.6 9.9 - - + +
222B PHE 3.1 0.2 - - - -
223B ARG* 1.3 76.7 - - - +
225B LYS* 1.3 67.1 + - + +
227B SER* 3.3 3.9 + - - -
228B LYS* 3.1 38.9 + - + +
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Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 5.6 11.3 - - + +
221B GLU* 3.0 48.1 + - + +
222B PHE* 3.8 8.3 - - + +
224B ALA* 1.3 77.6 - - + +
226B LEU* 1.3 57.5 + - - +
228B LYS* 3.9 5.4 + - - +
229B ALA* 3.2 27.5 + - - +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 4.1 14.6 - - + +
107B ARG* 3.7 35.4 - - - +
120B PHE* 5.0 3.4 - - + -
121B ILE* 4.1 20.4 - - + -
124B GLU* 4.9 5.2 - - + -
125B MET* 4.1 13.0 - - + -
222B PHE* 2.8 44.9 + - + +
223B ARG 3.6 3.8 - - - +
225B LYS* 1.3 75.5 - - - +
227B SER* 1.3 60.9 + - - +
228B LYS 3.1 1.6 - - - -
229B ALA* 3.1 4.6 + - + +
230B LEU* 2.8 49.8 + - + +
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 3.8 16.2 + - - +
121B ILE* 3.6 26.7 - - - +
223B ARG* 2.8 24.4 + - - -
224B ALA* 4.0 4.9 - - - -
226B LEU* 1.3 73.5 - - - +
228B LYS* 1.3 60.3 + - - +
230B LEU* 4.2 3.0 - - - +
231B ALA* 3.3 26.0 + - - +
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Residues in contact with LYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 3.1 24.7 + - + +
225B LYS* 4.3 4.7 - - - +
227B SER* 1.3 79.0 - - - +
229B ALA* 1.3 63.3 + - - +
231B ALA* 3.5 5.7 + - - +
232B LEU* 3.2 23.6 + - - +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 4.8 17.7 - - - +
225B LYS 3.2 19.6 + - - +
226B LEU* 3.1 7.0 + - + +
228B LYS* 1.3 74.1 - - - +
230B LEU* 1.3 64.0 + - - +
232B LEU* 3.6 5.6 + - - +
233B THR* 2.9 27.8 + - - -
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 3.5 52.9 - - + +
110B TYR 5.5 2.0 - - - +
111B CYS* 3.8 8.0 - - + +
117B ARG* 4.3 22.9 - - + +
120B PHE* 3.9 24.2 - - + -
121B ILE* 3.9 26.2 - - + -
226B LEU* 2.8 28.2 + - + +
227B SER 4.2 3.4 - - - +
229B ALA* 1.3 76.1 - - + +
231B ALA* 1.3 64.5 + - - +
233B THR* 3.3 8.0 + - - +
234B ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 4.1 23.5 - - - +
227B SER 3.3 17.9 + - - +
228B LYS* 3.8 7.9 - - - +
229B ALA 3.4 0.2 - - - -
230B LEU* 1.3 79.8 - - - +
232B LEU* 1.3 60.2 + - - +
234B ALA* 3.5 4.4 + - - +
235B ARG* 3.4 27.7 + - + +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LYS 3.2 14.0 + - - +
229B ALA* 3.9 6.1 - - - +
230B LEU 3.2 0.2 - - - -
231B ALA* 1.3 77.8 - - - +
233B THR* 1.3 58.3 + - - +
234B ALA 3.1 0.2 - - - -
235B ARG* 5.8 0.4 - - - -
236B SER* 2.5 55.2 + - - +
238D PRO* 6.2 3.6 - - + -
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Residues in contact with THR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 5.4 12.1 + - + +
108B LEU* 4.4 14.8 - - + -
111B CYS* 4.6 10.2 - - - -
229B ALA 2.9 15.2 + - - -
230B LEU* 3.3 11.4 + - - +
232B LEU* 1.3 79.1 - - - +
234B ALA* 1.3 60.5 + - - +
236B SER* 4.1 2.9 - - - -
237B LEU* 3.1 44.4 + - + +
240B VAL* 5.6 0.5 - - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B CYS* 3.0 40.8 - - + +
112B GLN* 5.0 1.1 - - - -
117B ARG* 5.1 1.3 - - - +
230B LEU 3.1 11.7 + - - +
231B ALA* 3.5 11.9 - - - +
232B LEU 3.1 0.4 - - - -
233B THR* 1.3 82.3 - - - +
235B ARG* 1.3 77.3 + - + +
237B LEU* 3.8 11.8 - - - +
239B ALA* 5.1 4.2 + - - -
240B VAL* 5.8 1.4 + - - +
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Residues in contact with ARG 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B CYS 4.0 11.1 + - - -
112B GLN* 3.2 24.2 + - - +
113B SER 5.2 0.4 - - - -
114B GLU* 4.6 11.1 + - - +
117B ARG* 5.0 8.8 - - - +
231B ALA 3.4 14.7 + - - +
232B LEU* 5.1 0.4 - - - +
234B ALA* 1.3 84.8 - - + +
236B SER* 1.3 64.5 + - - +
237B LEU 3.8 2.3 - - - +
114D GLU* 3.8 23.6 + - - +
117D ARG* 4.1 25.4 - - - +
231D ALA* 5.7 6.1 - - - +
234D ALA* 5.7 8.3 - - + +
235D ARG* 3.1 48.2 + - + +
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 2.5 43.7 + - - +
233B THR* 4.1 3.6 + - - -
235B ARG* 1.3 76.1 - - - +
237B LEU* 1.3 80.3 + - - +
238B PRO* 3.6 3.1 - - - +
235D ARG* 4.6 12.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.2 7.0 - - + -
233B THR* 3.1 44.9 + - + +
234B ALA 3.8 7.0 - - - +
235B ARG 3.5 7.0 - - - +
236B SER* 1.3 89.5 + - - +
238B PRO* 1.3 66.3 - - + +
239B ALA 2.6 16.4 + - - +
240B VAL* 3.4 33.9 - - + +
95C LYS* 5.9 7.4 - - + -
96C LEU 5.1 3.4 - - - +
235D ARG* 5.1 3.8 + - - -
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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