Contacts of the helix formed by residues 227 - 260 (chain D) in PDB entry 2E52
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 LYS 227 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU* 3.9 39.3 + - + +
220D MET* 3.6 26.6 - - + -
226D ASP* 1.3 73.7 - - - +
228D ASP* 1.3 57.2 + - - +
230D LEU* 3.3 1.0 + - - +
231D ASN* 2.8 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASP* 3.3 9.2 + - - +
227D LYS* 1.3 82.7 - - - +
229D THR* 1.3 58.0 + - - +
231D ASN* 3.6 7.8 - - - +
232D GLN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LEU* 4.4 13.2 - - + -
225D ILE* 3.9 16.8 - - + -
226D ASP* 2.7 28.7 + - - -
228D ASP* 1.3 75.3 - - - +
230D LEU* 1.3 65.7 + - - +
232D GLN* 2.9 38.1 + - - +
233D LEU* 3.0 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU* 3.5 25.1 - - + -
171D HIS* 5.3 1.8 - - + -
174D ILE* 3.6 32.8 - - + -
216D ASN* 4.0 20.6 - - + +
219D PHE* 4.3 19.3 - - + -
220D MET* 3.6 23.8 - - + -
225D ILE* 3.9 11.2 - - + +
226D ASP 3.0 15.8 + - - +
227D LYS 3.9 3.1 - - - +
229D THR* 1.3 75.7 - - - +
231D ASN* 1.3 56.8 + - - +
233D LEU* 3.2 2.9 + - - -
234D LEU* 2.9 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ASN* 4.8 4.0 - - - +
297C LEU* 3.5 25.0 - - - +
299C LEU* 3.6 18.7 - - + +
227D LYS* 2.8 25.8 + - + +
228D ASP* 3.6 9.0 - - - +
230D LEU* 1.3 73.1 - - - +
232D GLN* 1.3 64.1 + - - +
234D LEU* 3.4 2.9 + - - +
235D GLN* 2.9 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LEU* 6.0 0.8 - - - +
228D ASP 2.9 19.7 + - - +
229D THR* 2.9 34.4 + - - +
231D ASN* 1.3 77.2 + - - +
233D LEU* 1.3 77.1 + - - +
235D GLN* 3.5 7.0 + - - +
236D LYS* 2.7 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 3.8 43.7 - - + +
177D GLN* 4.2 21.1 - - + -
178D LEU* 4.0 27.8 - - + -
225D ILE* 5.6 0.2 - - + -
229D THR* 3.0 25.2 + - + +
230D LEU* 3.9 3.8 - - - +
232D GLN* 1.3 83.0 - - - +
234D LEU* 1.3 64.7 + - - +
236D LYS* 3.4 30.9 + - + +
237D GLU* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU* 3.9 38.6 - - + +
299C LEU* 4.0 16.2 - - + -
145D PHE* 4.9 10.8 - - + -
146D PHE* 4.8 12.1 - - + -
170D GLU* 4.5 17.5 - - + -
171D HIS* 5.4 6.1 - - + +
174D ILE* 3.8 18.6 - - + -
216D ASN* 4.5 7.2 - - - +
230D LEU* 2.9 34.7 + - + +
231D ASN 3.9 3.8 - - - +
233D LEU* 1.3 73.3 - - - +
235D GLN* 1.3 58.8 - - - +
237D GLU* 3.1 8.0 + - + +
238D ILE* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ASN* 4.8 5.1 - - - +
297C LEU* 3.9 22.9 - - + +
231D ASN* 2.9 41.4 + - - +
232D GLN* 3.7 6.7 - - - +
233D LEU 3.3 0.2 - - - -
234D LEU* 1.3 75.7 - - - +
236D LYS* 1.3 57.7 + - + +
238D ILE* 3.3 17.7 + - - +
239D ASN* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D GLN* 2.7 49.8 + - + +
233D LEU* 3.6 23.4 - - + +
235D GLN* 1.3 79.2 - - - +
237D GLU* 1.3 62.4 + - + +
239D ASN* 3.3 14.4 + - - +
240D PHE* 3.0 45.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 3.3 44.4 - - - +
146D PHE* 5.0 3.6 - - + -
170D GLU* 4.1 39.7 - - + +
173D ALA* 3.9 14.4 - - - +
174D ILE* 5.0 5.0 - - + +
233D LEU* 3.1 20.2 + - - +
234D LEU* 3.1 13.2 + - + +
236D LYS* 1.3 73.9 - - - +
238D ILE* 1.3 60.9 + - - +
240D PHE* 3.3 7.5 + - - +
241D ILE* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ILE* 3.4 40.5 - - + +
292C LYS* 4.2 20.4 - - + -
297C LEU* 3.8 25.8 - - + -
146D PHE* 3.6 23.6 - - + -
234D LEU 2.9 18.7 + - - +
235D GLN* 3.5 19.5 - - - +
237D GLU* 1.3 74.1 - - - +
239D ASN* 1.3 63.2 + - - +
241D ILE* 3.1 10.1 + - - +
242D GLU* 2.8 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D GLN* 3.0 29.6 + - - +
236D LYS* 3.7 14.5 - - - +
237D GLU 3.3 0.2 - - - -
238D ILE* 1.3 81.3 - - - +
240D PHE* 1.3 58.0 + - + +
242D GLU* 3.3 14.3 + - - +
243D GLU* 3.0 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 3.6 54.1 - - + +
236D LYS* 3.0 41.9 + - + -
237D GLU* 3.6 8.3 - - - +
239D ASN* 1.3 72.0 - - + +
241D ILE* 1.3 63.8 + - + +
243D GLU* 3.4 21.0 + - - +
244D ARG* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C PHE* 3.9 16.4 - - + -
288C ILE* 3.7 19.1 - - + -
291C ILE* 3.7 10.3 - - + -
44D ARG 5.5 4.5 - - - +
48D ILE* 4.2 24.0 - - + -
114D LEU* 4.4 3.9 - - + +
146D PHE* 3.9 31.6 - - + -
170D GLU* 3.9 15.7 - - - +
237D GLU* 2.9 22.3 + - + +
238D ILE* 3.1 8.7 + - - +
240D PHE* 1.3 75.6 - - + +
242D GLU* 1.3 58.7 + - - +
244D ARG* 3.2 8.2 + - - +
245D SER* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ILE* 3.8 24.3 - - + +
291C ILE* 5.7 0.2 - - + -
292C LYS* 2.8 40.2 + - - +
238D ILE* 2.8 18.6 + - + +
239D ASN* 3.6 15.4 - - - +
241D ILE* 1.3 78.1 - - - +
243D GLU* 1.3 61.4 + - + +
245D SER* 2.5 26.6 + - - +
246D LEU* 3.5 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ASN* 3.0 24.8 + - - +
240D PHE* 3.7 27.4 - - - +
242D GLU* 1.3 75.0 - - + +
244D ARG* 1.3 64.2 + - - +
246D LEU* 3.3 28.4 + - + +
247D ILE* 4.0 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 3.6 36.2 - - - +
9D LEU* 5.5 0.4 - - - +
45D SER* 3.0 31.1 + - - +
48D ILE* 2.7 48.2 + - + +
50D PRO* 3.7 18.6 - - - +
114D LEU* 4.5 1.3 - - + -
240D PHE 2.9 14.3 + - - +
241D ILE* 3.2 11.2 + - - +
243D GLU* 1.3 76.8 - - - +
245D SER* 1.3 61.9 + - - +
246D LEU 3.1 1.0 + - - -
247D ILE* 3.2 22.7 + - - +
248D GLU* 2.7 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ILE* 3.8 8.2 - - - +
288C ILE* 3.6 25.5 - - - +
114D LEU* 3.6 23.8 - - - -
241D ILE 2.9 13.2 + - - -
242D GLU* 2.5 23.4 + - - +
244D ARG* 1.3 76.7 - - - +
246D LEU* 1.3 61.0 + - - +
248D GLU* 3.2 2.2 + - - +
249D LYS* 2.9 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLU* 3.6 21.1 - - + +
243D GLU* 3.6 17.3 - - + +
244D ARG 3.1 0.8 + - - -
245D SER* 1.3 78.4 + - - +
247D ILE* 1.3 64.6 + - + +
249D LYS* 3.5 27.3 + - - +
250D GLU* 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLU 4.3 7.9 - - - +
244D ARG* 3.4 16.4 - - - +
246D LEU* 1.3 80.4 - - + +
248D GLU* 1.3 73.2 + - + +
250D GLU* 3.3 26.8 + - - +
251D TYR* 3.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ILE* 4.4 8.3 - - + -
48D ILE* 4.8 2.7 - - + -
49D LEU 4.6 1.8 - - - -
50D PRO* 3.6 9.5 - - - +
51D GLU* 2.8 53.6 + - + +
52D ALA* 4.4 1.6 + - - +
114D LEU* 4.2 9.9 - - + -
244D ARG* 2.7 57.4 + - + +
245D SER* 3.2 9.3 + - - +
247D ILE* 1.3 84.9 - - - +
249D LYS* 1.3 61.5 + - - +
251D TYR* 3.4 18.9 + - - +
252D TRP* 3.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ILE* 4.0 25.3 - - + +
284C ILE* 3.7 30.7 - - + -
285C ASP* 2.9 34.6 + - - +
288C ILE* 6.2 0.8 - - - +
245D SER* 2.9 32.3 + - - +
246D LEU* 3.7 26.3 - - - +
248D GLU* 1.3 73.6 - - - +
250D GLU* 1.3 65.5 + - + +
252D TRP* 3.1 15.5 + - - +
253D LYS* 3.1 15.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D LEU* 3.1 21.5 + - - +
247D ILE* 3.6 21.3 - - - +
248D GLU 3.3 0.2 - - - -
249D LYS* 1.3 74.6 - - + +
251D TYR* 1.3 66.3 + - - +
253D LYS* 3.4 30.6 + - + +
254D LYS* 3.0 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D GLU* 3.5 28.6 + - + -
52D ALA* 3.6 37.8 + - + +
247D ILE 3.4 9.6 + - - +
248D GLU* 3.5 12.6 - - - +
249D LYS 3.2 0.6 - - - -
250D GLU* 1.3 78.5 - - - +
252D TRP* 1.3 84.8 + + - +
254D LYS* 3.3 13.7 + - + +
255D GLN* 3.1 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ILE* 4.5 7.2 - - + -
277C MET* 3.5 40.3 - - + +
280C LYS* 3.3 46.8 - - + +
281C ILE* 3.7 22.9 - - + -
284C ILE* 4.4 8.1 - - + -
51D GLU* 2.8 41.8 + - + +
113D ARG* 5.9 2.5 - - - -
248D GLU 3.8 13.2 - - - -
249D LYS 3.1 3.2 + - - +
251D TYR* 1.3 102.1 - + - +
253D LYS* 1.3 61.6 + - - +
255D GLN* 3.8 6.9 - - + +
256D ILE* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ILE* 3.9 15.5 - - + +
249D LYS* 3.1 13.6 + - + +
250D GLU* 3.5 38.3 + - + +
252D TRP* 1.3 75.9 - - - +
254D LYS* 1.3 63.7 + - - +
256D ILE* 3.4 7.7 + - + +
257D ASN* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D GLU* 3.0 34.2 + - - +
251D TYR* 3.5 13.5 - - + +
253D LYS* 1.3 77.6 - - + +
255D GLN* 1.3 61.4 + - - +
257D ASN* 3.3 7.2 + - - +
258D ILE* 2.9 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C MET* 3.7 19.7 - - - -
251D TYR* 3.1 60.2 + - + +
252D TRP* 3.2 7.4 + - + +
254D LYS* 1.3 73.5 - - - +
256D ILE* 1.3 67.6 + - - +
258D ILE* 3.2 31.4 + - - +
259D ILE* 3.0 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 4.3 8.5 - - + +
277C MET* 3.6 37.4 - - + -
278C SER* 4.2 17.9 - - - +
281C ILE* 4.1 20.0 - - + -
252D TRP 2.9 21.4 + - - +
253D LYS* 3.7 7.2 - - + +
255D GLN* 1.3 77.3 - - - +
257D ASN* 1.3 58.6 + - - +
259D ILE* 3.3 3.3 + - - +
260D LYS* 3.0 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LYS 3.2 10.5 + - - +
254D LYS* 3.7 8.9 - - - +
255D GLN 3.2 0.4 - - - -
256D ILE* 1.3 78.2 - - - +
258D ILE* 1.3 65.8 + - - +
260D LYS* 3.1 20.8 + - - +
261D ASN* 2.8 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D LYS* 2.9 25.9 + - + +
255D GLN* 3.5 38.4 - - - +
257D ASN* 1.3 77.3 - - - +
259D ILE* 1.3 64.4 + - + +
261D ASN* 3.2 19.3 + - - +
262D PHE* 3.6 31.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ILE* 3.8 22.3 - - + +
271C LEU* 3.9 30.3 - - + -
272C LEU* 3.8 24.0 - - + +
275C ILE* 5.2 5.2 - - + -
277C MET* 3.3 34.5 - - + -
255D GLN* 3.0 14.6 + - + +
256D ILE 3.6 7.0 - - - +
258D ILE* 1.3 75.7 - - + +
260D LYS* 1.3 62.9 + - - +
261D ASN 3.1 1.6 - - - -
262D PHE* 3.1 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ARG* 6.2 0.2 - - - -
268C ILE* 5.1 7.7 - - + +
272C LEU* 4.4 21.3 - - + -
256D ILE* 3.0 35.5 + - + +
257D ASN* 3.1 19.5 + - - +
259D ILE* 1.3 77.2 - - - +
261D ASN* 1.3 58.2 + - - +
262D PHE 3.4 1.7 + - - +
----------------------------------------------------------
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