Contacts of the helix formed by residues 210 - 234 (chain C) in PDB entry 1OJ7
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 210 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ASN* 3.7 4.0 - - - -
1C LEU* 3.7 23.1 - - + -
208C VAL* 2.8 13.8 + - + +
209C ASP* 1.3 70.7 - - - +
211C LYS* 1.3 59.4 + - - +
212C ILE 3.4 2.2 - - - -
213C HIS* 3.4 31.1 + - + +
214C ASP* 3.0 33.2 + - - +
260C VAL* 4.0 9.2 - - + -
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B THR* 3.6 28.0 - - + +
226B GLU* 4.0 18.8 - - + -
227B ASP* 2.8 42.9 + - + +
230B LYS* 4.2 6.7 - - - +
240B VAL* 5.7 0.2 - - - +
243B ASN* 3.0 14.8 + - - +
-2C LYS* 6.3 0.7 - - - +
209C ASP* 2.7 36.8 + - - +
210C ALA* 1.3 71.6 - - - +
212C ILE* 1.3 61.2 + - - +
214C ASP* 3.4 7.3 + - - +
215C ARG* 3.0 34.2 + - + +
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLY 4.1 1.8 - - - +
220B ILE* 3.8 20.2 - - + +
223B THR* 3.6 25.6 - - + +
243B ASN* 4.3 5.9 + - - +
246B TRP* 3.8 26.2 - - + +
247B ALA* 3.8 41.5 - - + +
250B GLN* 4.1 6.3 - - + -
210C ALA 3.4 0.4 - - - -
211C LYS* 1.3 73.3 - - - +
213C HIS* 1.3 68.4 + - - +
215C ARG* 3.1 3.6 + - - -
216C PHE* 2.9 55.5 + - + +
255C LEU* 6.1 0.2 - - + -
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Residues in contact with HIS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TRP* 3.6 31.4 + + - -
1C LEU* 3.6 24.2 - - + +
4C PHE* 4.7 2.0 - + - -
203C TYR* 5.5 0.2 - - - -
210C ALA* 3.4 23.4 - - + +
212C ILE* 1.3 75.6 - - - +
214C ASP* 1.3 60.6 + - - +
216C PHE* 3.8 5.6 - - - +
217C ALA* 2.9 31.9 + - - +
255C LEU 3.8 14.7 + - - -
256C ILE* 3.4 31.6 - - - +
258C ALA* 2.7 31.9 + - - +
260C VAL* 3.7 11.9 - - + -
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Residues in contact with ASP 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2C LYS* 4.2 6.6 + - - -
203C TYR* 3.4 10.5 - - - -
208C VAL 4.1 11.3 - - - +
210C ALA* 3.0 22.7 + - - +
211C LYS* 3.7 7.8 - - - +
213C HIS* 1.3 79.8 - - - +
215C ARG* 1.3 57.0 + - - +
217C ALA* 3.4 1.2 + - - +
218C GLU* 2.9 37.7 + - - +
303C LYS* 2.8 30.0 + - - -
306C GLN* 3.2 31.0 + - - +
310C ARG* 4.7 2.7 - - - +
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Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ARG 4.8 5.0 - - - +
216B PHE* 5.0 0.2 - - - -
219B GLY* 3.6 39.0 - - - +
222B LEU* 3.7 42.4 - - - +
223B THR* 4.1 4.1 + - - +
211C LYS* 3.0 21.2 + - + +
212C ILE* 3.8 3.6 - - - +
214C ASP* 1.3 76.1 - - - +
216C PHE* 1.3 61.1 + - + +
218C GLU* 3.8 11.0 + - - +
219C GLY* 2.8 26.2 + - - -
310C ARG* 3.5 49.0 - - - +
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Residues in contact with PHE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 3.3 77.0 - + + -
219B GLY* 5.1 0.2 - - - -
220B ILE* 4.1 12.6 - - + -
250B GLN* 3.9 24.0 - - + -
255B LEU* 4.7 0.9 - - + -
256B ILE* 5.1 1.8 - - + -
212C ILE* 2.9 43.4 + - + +
213C HIS* 3.8 4.3 - - - +
215C ARG* 1.3 79.8 - - + +
217C ALA* 1.3 64.1 + - - +
219C GLY 3.1 0.9 + - - -
220C ILE* 3.0 30.2 + - - +
255C LEU* 3.8 28.7 - - + -
256C ILE* 3.8 11.9 - - + -
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Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C THR* 3.5 16.7 - - + +
203C TYR* 3.8 33.0 - - + -
213C HIS 2.9 18.8 + - - +
214C ASP 3.7 3.8 - - - +
216C PHE* 1.3 76.7 - - - +
218C GLU* 1.3 62.6 + - - +
220C ILE* 3.2 8.1 + - - +
221C LEU* 3.1 27.7 + - - +
256C ILE* 4.2 10.9 - - + +
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Residues in contact with GLU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR* 2.6 35.5 + - + +
214C ASP 2.9 20.4 + - - +
215C ARG* 3.8 14.9 + - - +
217C ALA* 1.3 75.2 - - - +
219C GLY* 1.3 56.5 + - - +
221C LEU* 3.3 3.0 + - - +
222C LEU* 2.9 43.3 + - + +
306C GLN* 2.7 24.3 + - - -
310C ARG* 3.0 45.4 + - + +
311C VAL* 4.2 14.1 - - + +
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Residues in contact with GLY 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 4.3 5.2 - - - -
215B ARG* 3.7 30.1 - - - +
216B PHE* 4.8 1.6 - - - -
215C ARG 2.8 18.5 + - - -
216C PHE 3.1 3.3 + - - -
218C GLU* 1.3 74.9 - - - +
220C ILE* 1.3 62.4 + - - +
222C LEU* 3.9 2.1 - - - +
223C THR* 2.8 30.4 + - - -
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Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 3.8 19.5 - - + +
216B PHE* 4.1 7.0 - - + -
199C THR* 3.4 19.7 - - + +
216C PHE 3.0 19.7 + - - +
217C ALA* 3.5 6.5 - - - +
219C GLY* 1.3 77.5 - - - +
221C LEU* 1.3 56.1 + - - +
223C THR* 3.2 3.5 + - - -
224C LEU* 2.9 45.0 + - + +
247C ALA* 3.8 16.6 - - + +
250C GLN* 3.8 35.9 - - + +
251C ALA* 3.8 5.6 - - + +
256C ILE* 4.1 22.7 - - + -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C PHE* 3.6 49.5 - - + +
199C THR* 3.8 14.6 - - + +
200C VAL* 3.8 13.9 - - + -
203C TYR* 4.0 16.6 - - + -
217C ALA 3.1 20.9 + - - +
218C GLU 3.7 3.6 - - - +
220C ILE* 1.3 76.4 - - - +
222C LEU* 1.3 56.5 + - - +
224C LEU* 3.4 4.5 + - + +
225C ILE* 3.0 35.9 + - - +
307C TYR* 3.9 24.2 - - + -
311C VAL* 4.0 21.8 - - + -
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ARG* 3.7 40.4 - - - +
218C GLU* 2.9 30.8 + - + +
219C GLY* 3.9 3.4 - - - +
221C LEU* 1.3 75.6 - - - +
223C THR* 1.3 57.5 + - - +
225C ILE* 3.4 8.3 + - + +
226C GLU* 3.0 45.9 + - + +
310C ARG 3.8 20.2 - - - +
311C VAL* 3.4 30.1 - - - +
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Residues in contact with THR 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LYS* 3.6 37.9 + - + +
212B ILE* 3.7 18.3 - - + +
215B ARG* 4.2 3.6 - - - +
219C GLY 2.8 22.2 + - - -
220C ILE 3.2 4.5 + - - -
222C LEU* 1.3 74.1 - - - +
224C LEU* 1.3 59.4 + - - +
226C GLU* 3.8 8.8 + - - +
227C ASP* 2.8 30.7 + - - +
243C ASN* 4.0 29.6 - - + +
244C VAL* 5.4 0.8 - - - +
247C ALA* 4.3 2.9 - - + -
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C VAL* 4.0 17.2 - - + +
195C ALA* 3.8 17.7 - - + -
196C PHE* 3.5 46.7 - - + +
220C ILE* 2.9 33.3 + - + +
221C LEU* 3.8 4.7 - - - +
223C THR* 1.3 76.1 - - - +
225C ILE* 1.3 58.3 + - - +
228C GLY* 2.8 30.0 + - - +
244C VAL* 4.4 25.4 - - + +
247C ALA* 3.8 22.0 - - + -
248C ALA* 5.6 0.2 - - + -
333C PHE* 3.5 8.0 - - - -
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C PHE* 3.9 18.2 - - + -
221C LEU 3.0 18.8 + - - +
222C LEU* 3.7 7.6 - - + +
223C THR 3.3 0.2 - - - -
224C LEU* 1.3 75.7 - - - +
226C GLU* 1.3 64.1 + - + +
229C PRO* 3.2 19.2 - - - +
311C VAL* 3.4 37.9 - - + +
312C TRP* 3.4 43.1 - - + -
333C PHE* 3.7 15.1 - - + -
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Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LYS* 3.3 29.8 - - - +
215B ARG* 3.0 31.2 + - - -
310B ARG* 5.0 3.9 + - - -
222C LEU* 3.0 31.2 + - + +
223C THR* 3.8 6.3 + - - +
224C LEU 3.3 0.2 - - - -
225C ILE* 1.3 82.7 - - + +
227C ASP* 1.3 70.8 + - - +
229C PRO* 3.9 4.7 - - - +
230C LYS* 3.8 22.1 - - - +
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Residues in contact with ASP 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASP* 4.4 0.2 - - - +
211B LYS* 3.0 30.2 + - - -
223C THR 2.8 15.0 + - - +
226C GLU* 1.3 72.0 - - - +
228C GLY* 1.3 67.4 + - - +
229C PRO* 3.4 2.2 - - - -
230C LYS* 3.1 24.5 + - - +
231C ALA 3.0 18.7 + - - -
240C VAL* 3.5 24.6 - - + +
243C ASN* 2.9 37.8 + - + +
244C VAL* 3.7 16.0 - - + +
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Residues in contact with GLY 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL* 5.2 0.2 - - - +
192C VAL* 4.0 25.5 - - - +
224C LEU* 2.8 18.8 + - - -
227C ASP* 1.3 75.7 - - - +
229C PRO* 1.3 65.1 - - - +
231C ALA* 3.1 18.2 + - - +
232C LEU* 3.6 9.0 + - - +
244C VAL* 3.9 8.1 - - - +
337C LEU* 4.1 7.6 - - - +
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Residues in contact with PRO 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU 3.6 3.1 - - - +
225C ILE 3.2 25.1 - - - +
226C GLU 3.9 4.0 - - - +
227C ASP 3.6 2.2 - - - -
228C GLY* 1.3 89.6 - - - +
230C LYS* 1.3 61.2 + - + +
232C LEU* 3.2 17.0 + - + +
233C LYS* 3.2 35.5 + - - +
333C PHE* 4.0 18.2 - - + -
336C GLN* 6.5 0.7 - - + -
337C LEU* 3.9 13.2 - - + -
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Residues in contact with LYS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LYS* 4.4 10.7 - - - +
226C GLU* 3.8 19.3 + - - +
227C ASP* 3.1 31.8 + - - +
229C PRO* 1.3 78.6 - - + +
231C ALA* 1.3 53.4 + - - +
233C LYS* 4.4 8.5 - - + +
234C GLU* 2.6 54.9 + - - +
240C VAL* 3.7 24.4 - - + +
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL* 4.0 18.1 - - + +
192C VAL* 5.5 0.4 - - + -
227C ASP 3.0 11.8 + - - +
228C GLY 3.1 11.6 + - - +
230C LYS* 1.3 76.0 - - - +
232C LEU* 1.3 60.9 + - - +
234C GLU 4.3 0.7 - - - -
235C PRO* 3.4 23.9 - - - +
240C VAL* 3.4 10.3 - - + +
241C ARG* 3.8 31.1 + - - +
244C VAL* 4.2 13.2 - - + -
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C PRO* 3.5 41.0 - - + +
188C VAL* 3.8 20.4 - - + -
189C ALA* 4.0 5.2 - - + +
192C VAL* 6.4 0.2 - - + -
228C GLY 3.6 8.3 + - - +
229C PRO* 3.2 8.9 + - + +
230C LYS 3.2 0.4 - - - -
231C ALA* 1.3 78.8 - - - +
233C LYS* 1.3 63.6 + - + +
234C GLU 3.4 0.2 - - - -
235C PRO* 4.0 8.5 - - - +
336C GLN 4.8 3.1 - - - +
337C LEU* 3.5 50.0 - - + +
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Residues in contact with LYS 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PRO* 3.2 34.5 + - - +
230C LYS* 3.2 8.4 + - + +
232C LEU* 1.3 79.5 - - + +
234C GLU* 1.3 69.0 + - + +
235C PRO* 3.5 7.1 - - - +
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C LYS* 2.6 45.3 + - + +
231C ALA* 3.9 1.7 - - - +
233C LYS* 1.3 82.5 - - + +
235C PRO* 1.3 66.1 - - - +
236C GLU 3.1 4.1 + - - -
237C ASN* 2.8 49.7 + - + +
240C VAL* 4.7 0.3 - - - +
241C ARG* 4.3 5.0 - - - -
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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