Contacts of the helix formed by residues 284 - 316 (chain C) in PDB entry 2VT4
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 ARG 284 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C GLU* 1.3 73.9 + - + +
286C HIS* 3.0 6.7 - - - +
287C LYS* 2.8 64.0 + - - +
288C ALA* 3.5 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ARG* 1.3 79.8 - - - +
286C HIS* 1.3 67.1 + - + +
288C ALA* 3.3 14.5 + - - +
289C LEU* 2.9 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ALA* 3.2 42.3 + - + +
237C GLN* 4.4 13.9 + - + +
238C ILE* 5.2 8.9 - - + +
284C ARG 2.9 3.7 + - - +
285C GLU* 1.3 86.1 - - + +
287C LYS* 1.3 56.6 + - + +
289C LEU* 3.0 12.1 + - + +
290C LYS* 2.6 37.7 + - - +
405C SOG 3.0 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ARG* 2.8 57.6 + - - +
286C HIS* 1.3 77.9 - - + +
288C ALA* 1.3 56.6 + - - +
290C LYS* 3.3 3.1 + - - -
291C THR* 2.9 27.1 + - - -
345C ARG* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ARG 3.5 3.4 + - - +
285C GLU* 3.3 18.7 + - - +
286C HIS 3.1 0.2 - - - -
287C LYS* 1.3 76.7 - - - +
289C LEU* 1.3 68.9 + - + +
291C THR* 3.3 7.8 + - - -
292C LEU* 3.2 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ARG* 3.5 41.5 - - + +
143C ILE* 4.0 27.8 - - + -
230C VAL* 4.1 14.6 - - + -
234C ALA* 4.5 12.8 - - + -
285C GLU* 2.9 19.3 + - + +
286C HIS* 3.0 16.1 + - + +
288C ALA* 1.3 78.1 - - + +
290C LYS* 1.3 61.6 + - - +
292C LEU* 3.3 10.9 + - + +
293C GLY 3.1 16.6 + - - -
405C SOG 3.3 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C HIS 2.6 20.2 + - - +
287C LYS* 3.7 6.7 - - - +
289C LEU* 1.3 71.4 - - - +
291C THR* 1.3 66.6 + - - +
293C GLY* 3.0 3.1 + - - -
294C ILE* 2.9 41.5 + - + +
345C ARG* 3.8 25.6 - - - +
405C SOG 3.3 62.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LYS 2.9 11.7 + - - -
288C ALA* 3.3 11.3 + - - +
290C LYS* 1.3 75.4 - - - +
292C LEU* 1.3 61.7 + - + +
294C ILE* 3.0 7.7 + - - +
295C ILE* 2.9 31.9 + - + +
342C ILE* 4.4 10.5 - - + +
343C TYR* 4.2 27.8 - - + -
345C ARG* 2.9 36.9 + - - +
346C SER* 5.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C THR* 4.2 19.5 - - + -
80C ILE* 4.3 23.6 - - + -
135C ILE* 4.1 21.8 - - + -
139C ARG* 4.1 26.0 - - + -
288C ALA* 3.2 17.5 + - + +
289C LEU* 3.6 12.6 - - + +
290C LYS 3.2 0.6 - - - -
291C THR* 1.3 84.1 - - + +
293C GLY* 1.3 62.2 + - - +
295C ILE* 3.4 10.8 - - + +
296C MET* 3.0 41.3 + - + +
343C TYR* 5.6 0.7 - - + -
405C SOG 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU 3.1 7.8 + - - -
290C LYS 3.0 7.6 + - - -
292C LEU* 1.3 75.4 - - - +
294C ILE* 1.3 57.8 + - - +
296C MET* 3.2 9.5 + - - +
297C GLY* 2.8 26.2 + - - -
405C SOG 3.9 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LYS* 2.9 34.2 + - + +
291C THR* 3.0 6.7 + - - +
293C GLY* 1.3 72.6 - - - +
295C ILE* 1.3 66.8 + - - +
297C GLY* 3.0 1.7 + - - +
298C VAL* 2.9 32.9 + - + +
342C ILE* 3.6 28.0 - - + -
345C ARG* 4.0 37.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 5.6 2.0 - - + -
83C LEU* 4.2 12.1 - - + -
132C LEU* 3.8 25.1 - - + -
135C ILE* 5.8 0.7 - - + -
291C THR* 2.9 23.9 + - + +
292C LEU* 3.4 14.8 - - + +
294C ILE* 1.3 71.7 - - - +
296C MET* 1.3 61.5 + - - +
298C VAL* 4.2 1.4 - - - +
299C PHE* 3.2 22.2 + - - +
335C ASN* 5.1 0.7 - - - +
339C ASN* 3.4 29.8 - - - +
342C ILE* 3.7 31.9 - - + -
343C TYR* 3.7 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.8 20.6 - - + +
135C ILE* 3.8 25.1 - - + -
136C ALA* 3.7 16.4 - - + -
223C MET* 3.7 37.1 - - + +
227C ALA* 4.3 8.3 - - - -
292C LEU* 3.0 19.2 + - + +
293C GLY* 3.5 8.3 - - - +
295C ILE* 1.3 76.7 - - - +
297C GLY* 1.3 62.2 + - - +
299C PHE* 3.2 7.6 + - - +
300C THR* 3.0 27.8 + - - -
405C SOG 3.0 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLY 2.8 18.8 + - - -
294C ILE* 3.0 2.9 + - - -
296C MET* 1.3 70.0 - - - +
298C VAL* 1.3 64.7 + - - +
300C THR* 3.2 8.7 + - - -
301C LEU* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ILE* 2.9 24.8 + - + +
295C ILE 4.2 2.7 - - - +
297C GLY* 1.3 72.9 - - - +
299C PHE* 1.3 67.4 + - - +
301C LEU* 3.9 10.5 - - + +
302C CYS* 3.0 25.1 + - - -
335C ASN* 3.5 15.5 - - - +
338C MET* 3.5 32.3 - - + -
339C ASN* 6.0 0.9 - - - +
342C ILE* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C VAL* 4.3 10.5 - - + -
128C SER* 3.7 23.8 - - - -
129C ILE* 3.7 45.1 - - + -
132C LEU* 3.6 18.4 - - + -
216C PHE* 3.8 20.0 - + - -
220C LEU* 5.3 0.4 - - + -
223C MET* 5.4 0.4 - - + -
295C ILE 3.2 15.6 + - - +
296C MET 3.2 10.5 + - - +
298C VAL* 1.3 78.4 - - - +
300C THR* 1.3 67.5 + - - +
302C CYS 3.4 0.3 + - - -
303C TRP* 3.1 50.3 + + - +
335C ASN* 3.4 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PHE* 5.4 1.6 - - + -
220C LEU* 3.9 23.0 - - + +
223C MET* 3.8 18.0 - - - +
224C ILE* 4.7 10.3 - - + +
296C MET 3.0 14.8 + - - -
297C GLY* 3.7 9.0 - - - -
298C VAL 3.2 0.2 - - - -
299C PHE* 1.3 81.5 - - - +
301C LEU* 1.3 59.6 + - + +
303C TRP* 5.3 0.4 - - - -
304C LEU* 2.8 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C GLY* 3.0 24.9 + - - +
298C VAL* 3.9 9.9 - - + +
300C THR* 1.3 79.1 - - + +
302C CYS* 1.3 58.1 + - - +
304C LEU* 5.0 0.7 - - - -
305C PRO* 2.9 30.2 - - - +
331C LEU* 4.1 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 3.0 28.7 + - - +
299C PHE 3.9 1.8 - - - +
301C LEU* 1.3 80.2 - - - +
303C TRP* 1.3 59.2 + - + +
305C PRO* 4.3 1.3 - - - +
306C PHE* 5.4 0.5 + - - +
328C PHE 4.3 2.9 - - - +
331C LEU* 3.5 34.7 - - - +
332C GLY* 3.3 21.2 + - - -
335C ASN* 3.7 16.6 - - + +
338C MET* 3.5 39.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C VAL* 3.4 29.9 - - + +
216C PHE* 3.9 18.8 - - + -
299C PHE* 3.1 52.9 + + + +
302C CYS* 1.3 78.1 - - - +
304C LEU* 1.3 68.3 + - - +
305C PRO* 3.4 2.7 - - - -
306C PHE* 3.2 33.9 + + + +
307C PHE* 3.3 29.9 + + - -
329C ASN* 3.7 18.6 - - - -
332C GLY* 3.3 42.0 + - - -
333C TYR* 4.0 7.6 - + - -
335C ASN* 4.4 6.9 - - + +
400C P32 3.6 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PHE* 3.6 27.8 - - + -
217C TYR* 4.3 10.5 - - + +
220C LEU* 4.7 8.5 - - + -
300C THR* 2.8 35.9 + - + +
301C LEU* 5.0 0.7 - - - -
303C TRP* 1.3 78.2 - - - +
305C PRO* 1.3 69.0 - - + +
307C PHE 3.1 1.4 + - - -
308C LEU* 2.9 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LEU* 2.9 29.2 - - - +
302C CYS 4.3 1.3 - - - +
303C TRP 3.5 3.1 - - - +
304C LEU* 1.3 87.5 - - + +
306C PHE* 1.3 56.4 + - - +
308C LEU* 3.3 8.5 + - + +
309C VAL* 2.9 33.4 + - - +
328C PHE* 3.7 41.3 - - + +
331C LEU* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C CYS 5.4 0.2 + - - -
303C TRP* 3.2 29.8 + + + +
304C LEU 3.1 0.6 - - - -
305C PRO* 1.3 80.3 - - - +
307C PHE* 1.3 74.3 + + - +
309C VAL* 3.4 5.9 + - + +
310C ASN* 2.9 36.8 + - - +
325C PHE* 4.0 34.9 - + - -
328C PHE* 4.1 22.1 + - + +
329C ASN* 3.6 38.6 - - + -
400C P32 3.5 49.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C VAL* 4.3 9.6 - - + -
212C SER* 3.8 20.8 - - - -
216C PHE* 3.4 59.2 - + + -
217C TYR* 2.9 23.3 + - + +
303C TRP* 3.3 37.5 + + - -
304C LEU 3.1 3.7 + - - +
306C PHE* 1.3 82.1 - + - +
308C LEU* 1.3 64.0 - - - +
310C ASN* 3.3 8.0 - - - +
311C ILE* 3.3 19.4 + - - +
400C P32 3.6 52.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C TYR* 3.5 17.7 + - + +
304C LEU* 2.9 45.0 + - + +
305C PRO* 3.5 7.6 - - + +
307C PHE* 1.3 73.1 - - - +
309C VAL* 1.3 66.3 + - + +
310C ASN 3.0 1.1 - - - -
311C ILE* 3.0 15.9 + - + +
312C VAL* 3.1 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PRO 2.9 19.5 + - - +
306C PHE* 3.7 7.9 - - + +
308C LEU* 1.3 77.5 - - + +
310C ASN* 1.3 61.8 + - - +
312C VAL* 3.9 7.8 - - + +
313C ASN* 3.2 25.2 + - + +
320C VAL* 4.3 30.3 - - + -
324C LEU* 5.3 0.4 - - + -
325C PHE* 3.3 36.3 - - + -
328C PHE* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ALA* 4.2 3.4 + - - +
212C SER* 3.7 18.4 + - - +
306C PHE* 2.9 25.4 + - - +
307C PHE* 3.3 14.2 - - + +
308C LEU 3.0 0.2 - - - -
309C VAL* 1.3 79.6 - - - +
311C ILE* 1.3 62.3 + - + +
313C ASN* 3.6 8.7 - - - +
314C VAL* 3.4 16.8 - - - +
325C PHE* 3.6 25.2 - - - -
400C P32 3.2 46.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ALA 5.6 0.4 - - - +
209C ILE* 5.3 11.2 - - + -
212C SER* 4.2 13.7 - - - +
213C ILE* 5.7 4.7 - - + -
217C TYR* 3.1 45.5 - - + +
307C PHE 3.5 4.5 - - - +
308C LEU* 3.0 8.5 + - + +
310C ASN* 1.3 76.9 - - - +
312C VAL* 1.3 67.8 + - + +
314C VAL* 2.8 27.9 + - + +
315C PHE* 3.6 27.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C LEU* 3.1 20.1 + - + +
309C VAL* 3.9 7.6 - - - +
311C ILE* 1.3 74.7 - - - +
313C ASN* 1.3 65.4 + - - +
315C PHE* 2.9 24.1 + - - +
316C ASN* 3.1 11.2 + - + +
319C LEU* 4.1 31.9 - - + -
320C VAL* 4.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C VAL* 3.2 17.0 + - - +
310C ASN 3.6 7.6 - - - +
312C VAL* 1.3 81.7 - - - +
314C VAL* 1.3 62.0 + - + +
315C PHE 3.2 0.7 + - - -
316C ASN 3.5 12.1 + - - +
317C ARG* 3.1 52.4 + - - +
320C VAL* 4.5 13.5 + - - +
322C ASP* 5.8 2.0 + - - -
325C PHE* 3.7 27.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ARG* 2.9 61.2 + - + +
208C ALA* 3.7 27.8 - - + -
209C ILE* 3.7 31.4 - - + -
310C ASN 3.4 17.3 - - - +
311C ILE* 2.8 20.5 + - + +
313C ASN* 1.3 71.6 - - + +
315C PHE* 1.3 64.7 + - + +
317C ARG* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ARG* 4.2 10.1 + - - +
209C ILE* 4.9 9.2 - - + -
311C ILE* 3.9 28.3 - - + -
312C VAL* 2.9 12.6 + - - +
313C ASN 4.0 0.2 - - - -
314C VAL* 1.3 96.5 - - + +
316C ASN* 1.3 62.8 + - + +
317C ARG 4.1 0.8 + - - -
148D ARG* 6.3 1.3 - - - -
152D LEU* 5.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C VAL* 3.1 10.0 + - + +
313C ASN* 3.7 7.8 - - - +
315C PHE* 1.3 83.3 - - + +
317C ARG* 1.3 66.2 + - - +
318C ASP* 3.0 7.7 + - - +
319C LEU* 3.1 53.9 + - + +
----------------------------------------------------------
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