Contacts of the helix formed by residues 258 - 287 (chain A) in PDB entry 2PPQ
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 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 4.9 5.4 - - - +
256A PRO 4.0 0.8 + - - -
257A LEU* 1.3 75.8 - - - +
259A GLU* 1.3 64.3 + - - +
260A ALA* 3.4 10.3 + - - +
261A GLU* 2.8 38.9 + - - +
262A LEU* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU 5.6 0.2 - - - +
258A SER* 1.3 73.1 - - - +
260A ALA* 1.3 56.5 + - - +
262A LEU* 3.4 17.0 + - + +
263A GLU* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASP 5.4 2.2 - - - +
185A LEU* 3.7 19.7 - - + +
258A SER* 3.2 9.0 + - - +
259A GLU* 1.3 78.3 - - - +
261A GLU* 1.3 62.6 + - - +
263A GLU* 3.7 9.3 - - - +
264A ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.2 9.2 - - + -
186A PRO* 3.5 31.8 - - + +
220A LEU* 4.3 0.2 - - - +
221A ALA* 4.1 32.2 + - + +
255A ARG* 3.1 36.1 + - - -
256A PRO 4.3 0.7 - - - +
257A LEU* 3.4 19.3 - - + +
258A SER* 2.8 43.6 + - - +
260A ALA* 1.3 74.8 - - - +
262A LEU* 1.3 64.4 + - - +
264A ALA* 3.2 13.0 + - - +
265A LEU* 3.3 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A GLN* 4.6 5.8 - - - +
257A LEU* 3.7 40.2 - - + +
258A SER 3.0 19.8 + - - +
259A GLU* 3.9 19.7 - - - +
260A ALA 3.4 0.2 - - - -
261A GLU* 1.3 75.8 - - - +
263A GLU* 1.3 64.1 + - - +
265A LEU* 3.2 23.4 + - + +
266A PRO* 3.8 3.8 - - - +
314A VAL* 3.9 35.4 + - + +
319A LEU* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU* 3.0 23.7 + - - +
260A ALA* 3.7 7.8 - - - +
262A LEU* 1.3 78.5 - - - +
264A ALA* 1.3 58.3 + - - +
266A PRO* 3.5 12.9 - - - +
267A LEU* 5.3 0.5 + - - +
314A VAL 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 4.6 8.3 - - + -
185A LEU* 3.6 26.9 - - + -
260A ALA 3.1 18.6 + - - +
261A GLU 3.7 4.7 - - - +
262A LEU 3.2 0.8 - - - -
263A GLU* 1.3 76.3 - - - +
265A LEU* 1.3 63.3 + - - +
266A PRO* 3.4 0.9 - - - -
267A LEU* 3.2 11.3 + - + +
268A LEU* 2.9 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 3.6 34.5 - - + +
224A VAL* 4.1 15.7 - - + -
225A SER* 4.3 8.5 - - - +
228A LEU* 4.0 12.8 - - + -
248A LEU* 4.1 25.4 - - + -
257A LEU* 5.0 3.1 - - + -
261A GLU 3.3 4.8 + - - +
262A LEU* 3.2 22.3 + - + +
264A ALA* 1.3 76.7 - - - +
266A PRO* 1.4 63.6 - - + +
268A LEU* 3.7 3.3 - - + +
269A SER* 2.7 38.4 + - - -
314A VAL* 3.8 23.6 - - + -
317A TYR* 4.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU 3.8 4.7 - - - +
263A GLU 3.5 15.7 - - - +
264A ALA 3.5 0.7 - - - -
265A LEU* 1.4 93.2 - - + +
267A LEU* 1.3 60.7 + - - +
269A SER* 3.3 2.4 + - - -
270A ARG* 3.0 30.2 + - - +
308A HIS* 3.9 11.4 - - - +
311A ILE* 3.6 40.6 - - + +
312A ALA 5.4 1.1 - - - -
313A ASN* 5.2 3.4 - - - +
314A VAL 5.2 4.0 - - - +
317A TYR* 3.3 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.9 16.8 - - + +
177A LEU* 3.7 24.2 - - + +
180A HIS* 3.6 35.7 - - + +
181A TRP* 3.7 8.1 - - + -
182A PRO* 4.0 19.7 - - + -
263A GLU 5.3 0.4 + - - +
264A ALA* 3.2 11.9 + - - +
266A PRO* 1.3 79.0 - - - +
268A LEU* 1.3 64.4 + - - +
270A ARG* 3.2 27.6 + - - +
271A GLY 3.0 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TRP* 3.6 31.9 - - + -
182A PRO* 3.7 23.8 - - + -
185A LEU* 4.1 4.7 - - + -
219A LEU* 4.1 11.0 - - + -
221A ALA* 3.6 38.8 - - + +
222A TYR* 3.8 6.8 - - + +
225A SER* 3.2 20.9 + - - +
264A ALA* 2.9 36.8 + - + +
265A LEU* 3.8 6.3 - - - +
267A LEU* 1.3 76.9 - - - +
269A SER* 1.3 57.5 + - - +
271A GLY* 3.2 2.6 + - - -
272A SER* 2.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 3.4 14.8 + - - -
228A LEU* 3.8 13.7 - - - +
229A ASN* 3.1 9.8 - - - +
265A LEU 2.7 24.1 + - - -
266A PRO 3.6 1.8 - - - -
268A LEU* 1.3 73.9 - - - +
270A ARG* 1.3 60.5 + - - +
272A SER* 3.6 8.7 - - - -
273A ALA* 2.9 27.4 + - - +
308A HIS* 3.4 34.8 - - - -
317A TYR* 3.6 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 2.8 44.9 + - - +
176A TYR* 3.4 31.4 + - - -
177A LEU* 4.0 6.2 - - + +
266A PRO 3.0 20.9 + - - +
267A LEU* 3.2 26.8 + - - +
269A SER* 1.3 75.0 - - - +
271A GLY* 1.3 59.4 + - - +
273A ALA* 3.4 1.0 + - - +
274A LEU* 2.9 25.5 + - - +
305A LEU* 3.3 26.5 - - + +
308A HIS* 3.7 17.3 - - + -
309A ARG* 3.6 35.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP* 3.5 34.7 - - - -
177A LEU* 3.8 10.2 - - - +
181A TRP* 3.8 8.5 - - - -
222A TYR* 4.2 0.2 - - - -
267A LEU 3.0 9.9 + - - -
268A LEU 3.2 4.7 + - - -
270A ARG* 1.3 78.4 - - - +
272A SER* 1.3 55.9 + - - +
274A LEU* 3.2 3.5 + - - +
275A ARG 3.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 3.6 16.6 - - - -
225A SER* 2.9 24.7 + - - -
226A ILE* 3.5 31.9 - - - -
229A ASN* 2.9 23.2 + - - -
268A LEU 2.9 13.3 + - - -
269A SER* 3.5 1.0 + - - -
271A GLY* 1.3 68.8 - - - +
273A ALA* 1.3 63.9 + - - +
275A ARG* 3.2 8.2 + - - +
276A PHE* 3.1 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASN* 3.5 16.3 + - - +
269A SER 2.9 19.8 + - - +
270A ARG 3.7 3.8 - - - +
272A SER* 1.3 77.4 + - - +
274A LEU* 1.3 58.7 + - - +
276A PHE 3.4 0.5 + - - -
277A PHE* 3.0 23.6 + - - +
301A TYR* 3.5 36.8 - - + +
304A LYS* 4.3 2.2 - - + -
305A LEU* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP* 4.0 18.2 - - + -
170A ILE* 4.1 26.2 - - + -
173A GLU* 5.2 2.2 - - + -
174A ILE* 4.1 25.6 - - + +
177A LEU* 3.7 22.2 - - + -
270A ARG 2.9 18.1 + - - +
271A GLY 3.6 4.0 - - - +
272A SER 3.2 0.4 - - - -
273A ALA* 1.3 76.8 - - - +
275A ARG* 1.3 56.4 + - - +
277A PHE* 3.3 23.5 + - + +
278A LEU* 2.8 51.8 + - + +
305A LEU* 3.8 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.2 56.2 - - + +
148A TRP* 3.4 23.5 - - + +
151A LEU* 5.0 0.5 - - - +
192A ALA 4.8 6.2 + - - -
193A ASP* 5.1 1.8 + - - -
214A PHE* 3.7 21.8 - - - -
222A TYR* 3.8 12.1 - - - +
226A ILE* 5.6 1.3 - - - +
271A GLY 3.0 10.5 + - - +
272A SER 3.2 7.8 + - - +
274A LEU* 1.3 76.7 - - - +
276A PHE* 1.3 103.5 + - - +
278A LEU* 3.4 3.7 + - - +
279A THR* 2.8 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA 4.2 8.5 - - - -
193A ASP* 4.1 6.3 - - - -
195A PHE* 3.4 37.5 - + - -
226A ILE* 3.8 31.6 - - + -
229A ASN* 5.5 2.0 - - + -
272A SER* 3.1 25.7 + - - -
275A ARG* 1.3 115.0 - - - +
277A PHE* 1.3 66.1 + - - +
279A THR* 3.4 4.2 + - - -
280A ARG* 3.1 34.1 + - - +
301A TYR* 3.7 35.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TRP* 4.2 1.1 - + - -
166A LEU* 3.8 37.2 - - + -
170A ILE* 3.6 29.4 - - + -
273A ALA 3.0 14.9 + - - +
274A LEU* 3.4 20.4 - - + +
276A PHE* 1.3 74.9 - - - +
278A LEU* 1.3 69.9 + - + +
280A ARG* 3.7 2.7 - - - +
281A LEU* 2.7 58.2 + - + +
298A PRO* 3.4 33.4 - - + +
299A LEU* 4.9 1.6 - - + -
301A TYR* 3.6 13.7 - - + +
302A LEU* 4.1 18.6 - - + +
305A LEU* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP* 3.3 49.6 - - + +
151A LEU* 4.1 17.7 - - + +
152A TRP* 3.7 42.8 - - + +
155A SER* 4.9 1.7 + - - -
170A ILE* 5.0 0.7 - - + -
174A ILE* 4.5 1.8 - - + -
274A LEU* 2.8 39.1 + - + +
275A ARG* 3.8 4.3 - - - +
276A PHE 3.2 0.2 - - - -
277A PHE* 1.3 86.0 - - + +
279A THR* 1.3 62.8 + - - +
281A LEU* 3.7 5.4 - - + +
282A TYR* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.2 11.4 - - + -
151A LEU* 3.7 26.9 - - + -
275A ARG* 2.8 40.2 + - - +
276A PHE* 3.4 6.9 + - - -
278A LEU* 1.3 77.1 - - - +
280A ARG* 1.3 56.1 + - - +
282A TYR* 3.2 6.4 + - - +
283A ASP* 2.8 45.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 6.2 0.6 - - - -
276A PHE* 3.1 28.2 + - - +
277A PHE 3.8 2.2 - - - +
279A THR* 1.3 77.3 + - - +
281A LEU* 1.3 59.2 + - - +
283A ASP* 3.5 7.0 + - - +
284A TRP* 2.9 31.2 + - - +
296A LYS* 3.7 52.6 - - + +
297A ASP* 2.9 35.4 + - - +
298A PRO* 3.9 15.6 - - + +
300A GLU* 2.8 31.1 + - - +
301A TYR* 3.6 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TRP* 3.5 33.7 - - + -
155A SER* 3.8 19.1 - - - -
159A ALA* 4.1 12.6 - - + -
162A VAL* 3.6 32.1 - - + -
166A LEU* 4.7 3.8 - - + -
277A PHE* 2.7 38.6 + - + +
278A LEU* 3.7 6.7 - - + +
279A THR 3.3 0.2 - - - -
280A ARG* 1.3 73.8 - - - +
282A TYR* 1.3 61.8 + - - +
284A TRP* 3.2 1.7 + - - +
285A LEU* 3.0 40.9 + - + +
298A PRO* 3.7 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.9 21.5 - - + -
154A LYS* 3.9 43.4 + - + -
155A SER* 3.8 20.8 + - - +
278A LEU 3.0 17.4 + - - +
279A THR 3.2 3.1 + - - +
281A LEU* 1.3 76.1 - - - +
283A ASP* 1.3 71.7 + - - +
285A LEU* 3.5 4.5 + - + +
286A THR* 2.8 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 2.8 27.3 + - - +
280A ARG* 3.9 7.2 + - - +
282A TYR* 1.3 88.1 - - - +
284A TRP* 1.3 61.0 + - - +
286A THR* 3.4 7.9 - - - +
287A THR* 2.8 37.1 + - + +
295A LYS* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 5.4 3.4 + - - +
162A VAL* 3.6 35.6 - - + +
280A ARG 2.9 19.1 + - - +
281A LEU* 3.2 5.1 + - - +
283A ASP* 1.3 78.6 - - - +
285A LEU* 1.3 68.4 + - + +
287A THR* 3.1 19.7 + - - +
295A LYS* 3.4 62.9 + - + +
296A LYS 3.5 19.7 - - - +
297A ASP* 4.2 15.7 - - + -
298A PRO* 3.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS 5.4 0.4 - - - +
155A SER* 3.6 45.3 - - - +
158A ARG* 3.0 78.3 + - + +
161A GLU* 4.1 6.7 - - + +
162A VAL* 4.4 8.5 - - + -
281A LEU* 3.0 26.9 + - + +
282A TYR* 4.0 4.7 - - + +
284A TRP* 1.3 89.2 - - + +
286A THR* 1.3 58.8 + - - +
287A THR 3.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 5.3 0.2 - - - +
282A TYR* 2.8 53.4 + - + +
283A ASP* 3.3 19.7 - - - +
285A LEU* 1.3 78.9 - - - +
287A THR* 1.3 63.3 + - + +
288A PRO* 3.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 2.8 28.8 + - + +
284A TRP 3.1 9.4 + - - +
285A LEU 4.5 2.9 - - - +
286A THR* 1.3 80.8 - - + +
288A PRO* 1.4 74.8 + - + +
289A ALA* 3.5 1.9 + - - -
291A ALA* 6.1 0.7 - - - -
293A VAL* 4.7 19.1 - - + -
295A LYS* 3.1 38.9 + - + +
----------------------------------------------------------
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