Contacts of the helix formed by residues 202 - 232 (chain D) in PDB entry 6H25
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 SER 202 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLY 4.1 9.9 - - - -
231C LYS* 4.9 15.0 - - - +
232C LEU* 3.6 8.7 - - - -
201D TYR* 1.3 82.9 - - - +
203D ASP* 1.3 69.8 + - - +
204D THR* 3.6 10.2 + - - -
205D GLU* 3.4 25.6 + - - +
206D LEU 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLY 4.5 2.6 + - - -
232C LEU* 3.6 7.5 - - + +
249C GLN* 4.4 21.3 + - - +
252C MET* 3.8 36.7 - - + +
202D SER* 1.3 76.2 - - - +
204D THR* 1.3 80.0 + - - +
206D LEU* 3.2 12.3 + - + +
207D GLN* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D SER* 3.6 10.0 + - - -
203D ASP* 1.3 92.2 + - - +
205D GLU* 1.3 65.7 + - - +
207D GLN* 3.2 8.5 + - - +
208D GLN* 3.0 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LEU* 4.4 26.9 - - + +
163D GLY* 5.2 4.8 - - - -
178D ARG* 2.7 32.5 + - - -
201D TYR* 3.3 26.0 - - + +
202D SER* 3.4 25.9 + - - +
203D ASP 3.3 0.2 - - - -
204D THR* 1.3 80.7 + - - +
206D LEU* 1.3 55.3 + - - +
208D GLN* 3.4 10.6 + - - +
209D CYS* 2.9 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 4.1 13.7 - - + -
235C LEU* 3.7 27.1 - - + -
248C LEU* 4.8 18.2 - - + -
249C GLN* 6.0 2.5 - - - +
252C MET* 5.8 4.5 - - + -
181D LEU* 3.7 13.5 - - + -
183D PHE* 3.7 30.5 - - + -
192D LEU* 6.1 0.2 - - + -
201D TYR* 3.7 21.9 - - + +
202D SER 3.1 8.0 + - - +
203D ASP* 3.2 14.6 - - + +
205D GLU* 1.3 77.1 - - - +
207D GLN* 1.3 60.8 + - - +
209D CYS* 3.4 4.4 + - - +
210D LEU* 2.9 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLY* 4.1 25.6 - - - +
248C LEU* 5.7 1.4 - - - +
249C GLN* 2.8 33.8 + - - +
203D ASP 2.9 11.4 + - - +
204D THR* 3.2 11.4 + - - +
206D LEU* 1.3 78.2 - - - +
208D GLN* 1.3 59.0 + - + +
210D LEU* 3.3 17.9 + - - +
211D ALA* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D GLY 5.3 4.3 - - - +
165D LEU* 4.3 15.0 - - + +
204D THR* 3.0 22.9 + - - +
205D GLU* 3.8 9.4 - - - +
206D LEU 3.3 0.2 - - - -
207D GLN* 1.3 75.3 - - + +
209D CYS* 1.3 61.3 + - - +
211D ALA* 3.3 6.6 + - - +
212D ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D CYS* 3.0 31.4 - - - +
159D LEU* 2.9 38.8 - - - -
165D LEU* 3.9 17.7 - - - -
167D LEU* 5.3 0.2 - - - +
181D LEU* 4.8 3.8 - - + -
183D PHE* 4.5 8.7 - - + -
205D GLU 2.9 24.1 + - - +
206D LEU* 3.8 5.8 - - - +
208D GLN* 1.3 76.5 - - - +
210D LEU* 1.3 57.7 + - - +
212D ALA* 3.5 1.6 + - - +
213D ALA* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLY* 4.4 19.1 - - - +
248C LEU* 4.9 5.4 - - + -
183D PHE* 4.5 17.2 - - + -
185D LEU* 5.1 7.2 - - + -
190D ARG 5.9 0.4 - - - +
192D LEU* 3.7 35.9 - - + +
206D LEU* 2.9 20.7 + - + +
207D GLN* 3.5 23.6 - - - +
209D CYS* 1.3 77.0 - - - +
211D ALA* 1.3 57.4 + - - +
213D ALA* 3.3 8.1 + - + +
214D GLN* 2.9 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D GLN 3.0 13.1 + - - +
208D GLN* 3.3 9.6 + - - +
210D LEU* 1.3 77.0 - - - +
212D ALA* 1.3 61.3 + - - +
214D GLN* 3.1 22.5 + - - +
215D ALA* 3.1 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D CYS* 5.4 5.2 - - + -
165D LEU* 3.8 24.7 - - + -
167D LEU* 3.8 22.3 - - + +
208D GLN 3.0 16.7 + - - +
209D CYS 3.9 1.8 - - - +
211D ALA* 1.3 74.8 - - - +
213D ALA* 1.3 56.4 + - - +
215D ALA* 3.3 7.9 + - - +
216D ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL* 3.7 27.1 - - + +
157D CYS* 6.3 0.4 - - + -
167D LEU* 4.6 3.5 - - + +
183D PHE* 4.6 11.7 - - + -
185D LEU* 3.8 15.5 - - + +
209D CYS 2.9 18.6 + - - +
210D LEU* 3.4 10.1 - - + +
212D ALA* 1.3 74.9 - - - +
214D GLN* 1.3 59.6 + - - +
216D ALA* 3.4 3.3 + - - +
217D SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C THR* 6.3 1.4 - - - +
185D LEU* 3.8 15.3 - - + -
189D GLU 5.7 0.2 + - - -
190D ARG* 3.5 35.0 + - + +
210D LEU* 2.9 36.7 + - + +
211D ALA* 3.1 14.0 + - - +
213D ALA* 1.3 77.7 - - - +
215D ALA* 1.3 61.0 + - - +
217D SER* 2.4 24.5 + - - +
218D GLN* 3.0 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D LEU* 6.0 1.1 - - + -
211D ALA 3.1 11.8 + - - +
212D ALA* 3.3 9.8 + - - +
214D GLN* 1.3 76.4 - - - +
216D ALA* 1.3 61.9 + - - +
218D GLN* 3.1 22.9 + - - +
219D HIS* 3.2 22.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 3.7 25.7 - - + +
155D VAL* 3.7 20.6 - - + -
167D LEU* 4.0 15.7 - - + +
212D ALA 3.0 16.1 + - - +
213D ALA* 3.8 4.3 - - - +
215D ALA* 1.3 76.5 - - - +
217D SER* 1.3 57.2 + - - +
219D HIS* 3.2 7.1 + - - +
220D VAL* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D CYS* 3.9 25.6 - - - -
155D VAL* 4.6 1.7 - - - +
185D LEU* 3.9 14.3 - - - +
190D ARG* 3.8 14.4 - - - +
213D ALA 2.9 14.6 + - - -
214D GLN* 2.4 27.0 + - - -
216D ALA* 1.3 75.3 - - - +
218D GLN* 1.3 57.9 + - - +
220D VAL 3.8 0.2 - - - -
221D PHE* 2.9 46.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ARG* 3.5 34.0 + - - +
214D GLN 3.0 6.6 + - - +
215D ALA* 3.1 15.7 + - - +
217D SER* 1.3 83.4 + - - +
219D HIS* 1.3 68.6 + - + +
221D PHE* 3.4 3.4 + - - +
222D ARG* 3.1 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER* 6.0 5.7 + - - -
28D LEU* 4.6 12.8 - - + -
31D PHE* 6.0 2.9 - - + -
215D ALA* 3.2 25.3 + - + -
216D ALA* 3.2 11.2 + - - +
218D GLN* 1.3 84.8 - - + +
220D VAL* 1.3 62.8 + - + +
222D ARG* 3.2 18.8 + - - +
223D PHE* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 4.6 3.8 - - + -
31D PHE* 3.6 35.2 - - + -
47D PHE* 5.4 3.1 - - + -
135D ASN* 4.2 11.2 - - - +
153D CYS* 3.7 17.7 - - + -
154D GLY 5.4 1.3 - - - +
155D VAL* 4.6 14.4 - - + -
216D ALA 3.0 19.0 + - - +
217D SER 4.0 2.7 - - - +
219D HIS* 1.3 76.0 - - - +
221D PHE* 1.3 57.7 + - - +
223D PHE* 3.0 13.0 + - + +
224D TYR* 2.9 50.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 4.4 6.2 - - + +
152D PHE* 3.7 10.3 - - - -
153D CYS* 3.6 42.6 - - + -
185D LEU 3.8 2.0 - - - -
186D ASP 3.2 34.5 - - - -
187D SER* 3.5 21.1 - - - -
190D ARG* 4.7 11.9 - - - +
217D SER* 2.9 35.6 + - - +
218D GLN* 3.9 4.7 - - - +
220D VAL* 1.3 73.6 - - - +
222D ARG* 1.3 65.0 + - - +
224D TYR* 3.5 22.4 + + - +
225D ARG* 3.5 18.7 + - - +
29G LEU* 4.6 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D GLN* 3.1 34.3 + - - +
219D HIS* 3.6 22.2 + - - +
220D VAL 3.2 0.2 - - - -
221D PHE* 1.3 77.4 - - - +
223D PHE* 1.3 61.7 + - - +
225D ARG* 3.2 8.5 + - + +
226D GLU* 3.1 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 3.6 56.3 - + + -
32D ALA* 4.3 0.7 - - - -
33D CYS* 3.8 30.5 - - + -
47D PHE* 4.5 11.0 - + - -
219D HIS 3.0 12.0 + - - +
220D VAL* 3.0 15.7 + - + +
222D ARG* 1.3 74.8 - - - +
224D TYR* 1.3 66.3 + + - +
226D GLU* 3.6 17.8 + - + +
227D SER* 3.3 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 5.6 4.0 - + - -
135D ASN* 3.2 23.6 + - + -
138D CYS* 3.6 21.7 - - - +
139D MET* 3.5 41.8 - - + +
142D VAL* 6.1 0.2 - - + -
151D LEU* 4.5 20.2 - - + -
152D PHE 3.0 19.5 + - - -
153D CYS* 3.8 3.4 - - + -
220D VAL* 2.9 43.3 + - + -
221D PHE* 3.5 33.7 - + - +
223D PHE* 1.3 79.8 - + - +
225D ARG* 1.3 58.2 + - - +
227D SER* 3.3 5.1 + - - -
228D LEU* 3.0 37.0 + - + +
29G LEU* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D PHE 3.5 5.3 + - - +
222D ARG* 3.2 11.9 + - + +
224D TYR* 1.3 79.2 - - - +
226D GLU* 1.3 57.8 + - - +
228D LEU* 3.4 1.8 + - - +
229D GLN* 3.0 54.6 + - + +
26G GLN* 4.5 14.1 + - - -
27G VAL* 4.6 11.8 + - + +
29G LEU* 3.7 38.5 - - + +
32G GLU* 4.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D ARG* 3.1 21.2 + - + +
223D PHE* 4.0 20.4 - - + +
224D TYR 3.2 0.2 - - - -
225D ARG* 1.3 77.7 - - - +
227D SER* 1.3 57.9 + - - +
229D GLN* 3.3 8.4 + - - +
230D ARG* 2.9 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D CYS* 4.4 13.7 + - - +
35D GLN* 6.0 0.9 - - - -
139D MET* 4.9 15.0 - - - -
223D PHE* 3.3 37.2 + - - -
224D TYR* 3.9 3.4 - - - -
226D GLU* 1.3 77.7 - - - +
228D LEU* 1.3 58.9 + - - +
230D ARG* 3.1 14.4 + - - +
231D ARG* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLN* 3.4 30.5 - - - +
139D MET* 4.4 11.9 - - + -
142D VAL* 4.2 25.1 - - + -
151D LEU* 5.4 2.5 - - + -
224D TYR* 3.0 23.0 + - + +
225D ARG* 4.0 4.9 - - - +
226D GLU 3.3 0.4 - - - -
227D SER* 1.3 77.2 - - - +
229D GLN* 1.3 61.4 + - - +
231D ARG* 3.8 6.8 + - + +
232D TYR* 3.8 30.4 + - + -
27G VAL* 4.0 11.2 - - + +
28G VAL 5.5 0.7 - - - +
29G LEU* 3.8 26.2 - - + -
30G PRO* 4.8 4.5 - - + -
83G CYS* 4.3 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D ARG* 3.0 46.5 + - + +
226D GLU* 3.8 7.0 - - - +
228D LEU* 1.3 76.7 - - - +
230D ARG* 1.3 61.9 + - - +
231D ARG 3.2 0.8 + - - -
232D TYR 3.6 15.1 + - - +
233D SER* 4.2 4.0 + - - -
26G GLN* 5.7 4.0 + - - +
27G VAL* 4.1 35.8 + - + +
85G ARG* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D GLU* 2.9 44.6 + - + +
227D SER* 3.1 15.8 + - - +
229D GLN* 1.3 75.4 - - - +
231D ARG* 1.3 63.5 + - - +
233D SER* 3.5 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLN* 3.2 22.8 + - + +
36D ASN* 4.0 23.7 - - - +
143D ASP* 2.4 35.6 + - - -
227D SER 3.0 14.1 + - - +
228D LEU* 4.2 8.7 - - + +
229D GLN 3.2 0.4 - - - -
230D ARG* 1.3 81.2 - - - +
232D TYR* 1.3 85.7 + - + +
233D SER* 2.8 12.0 + - - -
234D LYS 4.6 1.0 + - - -
83G CYS* 5.6 1.2 - - - -
105G GLN* 3.0 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 3.8 19.8 + - + +
229D GLN 3.6 9.2 + - - +
230D ARG 3.5 0.6 - - - -
231D ARG* 1.3 114.4 + - + +
233D SER* 1.3 60.0 + - - +
234D LYS 3.6 3.3 - - - +
27G VAL* 4.1 20.6 - - + -
83G CYS* 3.1 33.2 + - + -
84G GLY* 3.6 29.2 - - - -
85G ARG* 2.6 43.4 + - + +
103G ASP 4.8 3.6 - - - -
104G SER* 4.0 12.0 - - - -
105G GLN* 4.3 16.4 + - + -
----------------------------------------------------------
Back to top of page
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