Contacts of the helix formed by residues 289 - 319 (chain B) in PDB entry 5UNG
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 289 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 3.7 1.7 - - - +
288B ASN* 1.3 74.7 - - - +
290B CYS* 1.3 63.1 + - - +
291B GLU* 3.6 28.1 + - - +
292B VAL* 3.2 22.8 + - - +
293B ILE* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS* 2.0 61.6 - - + +
288B ASN 3.4 5.2 + - - -
289B SER* 1.3 68.8 + - - +
291B GLU* 1.3 68.9 + - - +
292B VAL 3.3 0.2 - - - -
293B ILE* 3.9 0.8 - - - +
294B ALA* 2.9 33.1 + - - +
1047B LYS* 4.4 4.3 - - - -
1048B LEU* 4.7 20.2 - - - -
1051B LYS* 5.0 10.1 - - - +
1110B SER 4.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER* 3.2 14.7 + - - +
290B CYS* 1.3 90.2 + - - +
292B VAL* 1.3 61.2 + - + +
294B ALA* 4.1 4.5 - - - +
295B VAL* 3.3 26.2 + - - +
1051B LYS* 4.6 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 5.7 5.6 - - + -
287B ILE* 3.9 21.3 - - + -
289B SER* 3.2 26.3 + - - +
291B GLU* 1.3 76.0 - - + +
293B ILE* 1.4 62.3 + - - +
295B VAL* 3.2 9.8 + - + +
296B ILE* 3.1 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS* 3.8 23.8 - - + -
36B SER 5.1 0.4 - - - +
279B ASP* 6.0 1.6 - - - +
282B ALA* 4.3 13.7 - - + -
287B ILE* 3.7 31.0 - - + +
288B ASN 3.9 5.6 - - - -
289B SER 3.2 17.6 + - - +
290B CYS 3.5 3.6 + - - +
292B VAL* 1.4 72.4 - - - +
294B ALA* 1.4 63.3 + - - +
296B ILE* 3.3 12.6 + - + +
297B ASP* 3.1 24.3 + - - +
1047B LYS* 3.8 25.8 - - - +
1107B GLY 5.3 0.2 - - - +
1108B SER* 3.7 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS* 4.7 2.2 - - - +
36B SER* 4.5 20.1 - - - +
37B GLN* 4.4 17.0 - - - +
290B CYS 2.9 19.0 + - - +
291B GLU* 4.1 6.7 - - - +
292B VAL 3.4 0.2 - - - -
293B ILE* 1.4 75.4 - - - +
295B VAL* 1.4 61.7 + - + +
297B ASP* 3.5 4.6 + - - +
298B LEU* 3.3 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 5.8 2.5 - - + -
291B GLU 3.3 16.6 + - - +
292B VAL* 3.2 11.5 + - - +
294B ALA* 1.4 74.2 - - + +
296B ILE* 1.4 60.5 + - + +
298B LEU* 3.4 16.1 + - + +
299B ALA* 3.0 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 3.8 44.2 - - + +
278B LEU* 3.8 33.9 - - + +
279B ASP* 4.3 17.9 - - + +
282B ALA* 5.7 1.1 - - + -
287B ILE* 5.1 2.7 - - + -
292B VAL* 3.1 36.6 + - + +
293B ILE* 3.3 16.6 + - + +
295B VAL* 1.4 76.3 - - + +
297B ASP* 1.3 59.1 + - - +
299B ALA* 4.0 0.9 - - - +
300B LEU* 3.1 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 3.4 24.4 - - - -
279B ASP* 4.7 6.1 - - - +
293B ILE* 3.1 20.3 + - - +
294B ALA 3.7 5.6 - - - +
295B VAL 3.3 0.2 - - - -
296B ILE* 1.3 80.8 - - - +
298B LEU* 1.4 59.9 + - - +
300B LEU* 3.7 6.4 - - - +
301B PRO* 3.4 18.2 - - - +
1108B SER* 3.0 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA* 3.3 23.9 + - + +
295B VAL* 3.7 17.0 - - + +
297B ASP* 1.4 76.8 - - - +
299B ALA* 1.3 65.1 - - + +
301B PRO* 3.4 8.2 - - - +
302B PHE* 3.3 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 4.0 21.1 - - + -
295B VAL* 3.0 25.5 + - + +
296B ILE 4.2 0.2 - - - +
298B LEU* 1.3 80.5 - - + +
300B LEU* 1.4 63.0 + - - +
301B PRO 3.6 0.2 - - - -
302B PHE* 3.2 13.7 + - - +
303B ALA* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 5.1 9.6 - - + -
275B LEU* 4.0 26.5 - - + +
276B THR* 5.1 5.8 - - - +
279B ASP* 5.5 5.6 - - + +
296B ILE* 3.1 30.6 + - + +
297B ASP* 3.7 6.7 - - - +
299B ALA* 1.4 76.3 - - - +
301B PRO* 1.4 63.1 - - + +
303B ALA* 3.1 7.3 + - - +
304B ILE* 2.9 53.4 + - + +
1201B 8ES 5.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.7 26.0 - - + -
51B TYR* 2.9 28.7 + - - +
104B TYR* 4.0 20.6 - - + +
108B TYR* 4.4 7.6 - - - +
297B ASP 3.4 17.0 - - - +
298B LEU* 3.4 14.8 - - - +
300B LEU* 1.4 87.8 - - + +
302B PHE* 1.4 53.6 + - - +
304B ILE* 4.1 7.4 - - + -
305B LEU 3.2 13.2 + - - -
1201B 8ES 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA* 4.9 13.9 - - + -
47B ILE* 3.7 29.2 - - + -
50B LEU* 4.7 20.9 - - + -
298B LEU* 3.3 31.2 - - + -
299B ALA* 3.2 10.0 + - - +
300B LEU 3.2 0.6 - - - -
301B PRO* 1.4 73.7 - - + +
303B ALA* 1.4 63.3 + - - +
305B LEU* 3.4 13.3 - - + +
306B LEU* 3.2 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B CYS 4.3 0.5 - - - +
271B PRO* 4.2 4.7 - - + -
272B PHE* 3.8 36.0 + - + +
275B LEU* 3.7 22.7 - - + -
299B ALA 3.0 12.2 + - - +
300B LEU* 3.4 8.7 - - + +
302B PHE* 1.4 74.7 - - - +
304B ILE* 1.4 62.3 + - - +
306B LEU* 3.4 22.8 + - - +
307B GLY* 3.4 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.5 17.7 - - - +
269B TRP* 6.3 0.4 - - - -
272B PHE* 3.7 26.0 - - + -
300B LEU* 2.9 44.3 + - + +
301B PRO* 3.8 0.7 - - + +
303B ALA* 1.4 74.4 - - - +
305B LEU* 1.4 62.6 + - - +
307B GLY* 3.1 13.4 + - - -
308B PHE* 3.3 22.4 + - + -
1201B 8ES 3.6 73.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 5.9 1.1 - - + -
50B LEU* 3.6 53.6 - - + +
51B TYR* 3.6 28.5 - - + -
54B ILE* 3.8 22.4 - - + -
97B LEU* 4.9 3.6 - - + -
301B PRO 3.2 15.3 + - - +
302B PHE* 3.4 19.5 - - + +
303B ALA 3.3 0.2 - - - -
304B ILE* 1.4 76.3 - - - +
306B LEU* 1.4 51.0 + - + +
308B PHE* 3.2 11.7 + - - +
309B THR* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.7 26.5 - - + +
268B CYS* 3.3 40.9 - - - +
271B PRO* 4.1 20.2 - - + -
302B PHE* 3.2 22.9 + - + +
303B ALA* 3.4 14.8 - - - +
304B ILE 3.3 0.4 - - - -
305B LEU* 1.4 74.1 - - + +
307B GLY* 1.3 62.7 + - - +
309B THR* 3.2 20.2 + - + +
310B ASN 3.3 2.6 + - - -
1203B OLA 6.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 5.2 1.1 - - - +
268B CYS 3.4 8.1 + - - -
269B TRP* 3.4 48.0 - - - -
303B ALA 3.4 4.5 + - - -
304B ILE 3.1 9.9 + - - -
306B LEU* 1.3 78.6 - - - +
308B PHE* 1.4 58.5 + - - +
310B ASN* 3.4 13.9 - - - +
311B SER* 4.2 4.5 + - - -
1201B 8ES 4.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 4.8 2.0 - + - -
54B ILE* 4.3 8.1 - - + -
93B LEU* 3.3 48.0 - - + -
94B LEU* 3.4 13.5 - - + +
96B THR* 3.9 2.5 - - - -
97B LEU* 3.7 38.6 - - + -
100B TRP* 3.7 21.3 - + - -
124B LEU* 3.7 2.5 - - + -
304B ILE* 3.3 32.5 + - + -
305B LEU* 3.2 10.4 + - - +
307B GLY* 1.4 71.7 - - - +
309B THR* 1.4 63.0 + - - +
310B ASN 3.2 0.7 - - - -
311B SER* 3.2 22.4 + - - -
312B CYS* 3.7 1.4 - - - -
1201B 8ES 3.4 39.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.7 27.1 - - + +
268B CYS* 4.3 7.2 - - - -
305B LEU* 2.7 22.7 + - - +
306B LEU* 3.2 18.8 + - + +
308B PHE* 1.4 75.0 - - - +
310B ASN* 1.4 58.8 + - - +
312B CYS* 2.9 28.1 + - + +
313B VAL* 3.1 22.3 + - + +
1203B OLA 4.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B SER* 5.0 1.2 + - - -
135B ILE* 3.6 26.3 - - - +
264B ALA* 3.4 35.0 + - - +
265B PHE* 4.0 8.4 - - - +
268B CYS* 3.7 19.2 - - + +
269B TRP* 3.7 19.4 + - + +
306B LEU 3.3 5.1 + - - -
307B GLY 3.4 13.7 - - - +
308B PHE 3.2 0.6 - - - -
309B THR* 1.4 76.5 - - - +
311B SER* 1.3 55.8 + - - +
313B VAL* 3.3 5.8 + - - +
314B ASN* 3.0 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN* 3.0 24.1 + - - -
90B ASP* 2.9 35.4 + - - +
93B LEU* 3.4 22.4 - - - +
94B LEU* 3.8 20.9 - - - -
131B SER* 4.2 2.4 + - - -
307B GLY 4.5 2.9 + - - -
308B PHE 3.2 14.3 + - - -
310B ASN* 1.3 76.5 - - - +
312B CYS* 1.4 55.1 + - - +
314B ASN* 3.8 0.7 - - - +
315B PRO* 3.3 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.7 41.1 - - + -
57B ILE* 4.9 10.1 - - + -
58B GLY* 3.7 17.7 - - - +
61B VAL* 4.0 8.7 - - + +
94B LEU* 3.8 3.1 - - - -
308B PHE 3.7 15.5 - - - -
309B THR* 2.9 14.1 + - + +
311B SER* 1.4 74.6 - - - +
313B VAL* 1.3 62.3 + - + +
315B PRO* 3.4 7.5 - - - +
316B PHE* 3.2 27.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 4.2 13.0 - - + -
268B CYS* 4.7 3.4 - - - -
309B THR* 3.1 24.0 + - + +
310B ASN* 3.3 10.7 + - - +
312B CYS* 1.3 79.6 - - + +
314B ASN* 1.4 62.4 + - - +
316B PHE* 3.2 12.9 + - + +
317B LEU* 3.1 46.2 + - + +
1203B OLA 3.9 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.8 14.2 - - + +
90B ASP* 3.1 38.0 + - - +
131B SER* 3.8 1.4 + - - -
135B ILE* 3.5 29.8 - - - +
310B ASN* 3.0 33.6 + - - +
311B SER* 3.8 1.4 - - - +
313B VAL* 1.4 75.2 - - - +
315B PRO* 1.4 64.4 - - + +
316B PHE 3.3 0.2 + - - -
317B LEU* 3.4 3.9 + - - +
318B TYR* 3.2 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.9 12.6 - - + +
62B ASN* 3.4 33.7 - - - +
65B VAL* 3.8 17.3 - - + -
87B ALA* 6.1 0.2 - - + -
311B SER 3.3 14.8 - - - +
312B CYS 3.4 11.9 - - - +
314B ASN* 1.4 90.3 - - + +
316B PHE* 1.3 54.9 + - + +
318B TYR* 5.5 0.2 - - + -
319B CYS* 3.0 13.8 + - + +
320B PHE* 2.9 47.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 5.9 3.6 - - + -
61B VAL* 3.7 31.4 - - + -
312B CYS* 3.2 26.5 - - + -
313B VAL* 3.2 11.3 + - + +
315B PRO* 1.3 78.5 - - + +
317B LEU* 1.3 61.8 + - + +
318B TYR 3.5 0.3 + - - -
320B PHE* 3.8 24.2 - + + -
321B VAL* 2.8 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.7 11.6 + - - -
257B MET* 5.6 1.0 - - - +
260B ALA* 3.7 42.6 - - + +
261B VAL* 4.0 23.6 - - + +
264B ALA* 3.8 18.6 - - + -
313B VAL* 3.1 31.2 + - + +
314B ASN* 4.2 4.5 - - - +
316B PHE* 1.3 78.6 - - + +
318B TYR* 1.3 65.6 + - + +
321B VAL* 5.0 6.5 - - + +
322B GLY* 3.4 17.8 + - - +
1203B OLA 5.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 3.7 26.6 - - + +
86B LEU* 3.8 22.4 - - + -
135B ILE* 3.4 30.9 + - + +
138B MET* 3.7 39.0 - - + +
139B SER* 5.1 1.8 + - - -
142B ARG* 4.1 16.2 + - - +
261B VAL* 3.5 37.3 + - + +
314B ASN* 3.2 45.1 + - - +
315B PRO* 5.5 0.2 - - + -
317B LEU* 1.3 85.1 - - + +
319B CYS* 1.3 59.7 + - + +
322B GLY* 3.1 24.5 - - - +
323B ASN* 4.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.8 35.2 - - + -
68B LEU* 5.1 11.9 - - - -
73B LYS* 5.4 10.3 - - - -
83B ILE* 3.8 20.9 - - + -
315B PRO* 3.0 13.2 + - + +
318B TYR* 1.3 77.9 - - - +
320B PHE* 1.3 74.2 + - + +
323B ASN* 3.3 29.7 - - - +
----------------------------------------------------------
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