Contacts of the helix formed by residues 255 - 288 (chain B) in PDB entry 4EA3
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 ASP 255 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLU* 3.5 16.1 + - - +
254B LYS* 1.3 76.5 + - - +
256B ARG* 1.3 64.0 + - - +
257B ASN 3.0 0.9 - - - -
258B LEU* 2.9 41.0 + - + +
259B ARG* 3.0 27.3 + - - +
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLU 5.4 3.2 + - - +
254B LYS* 2.8 19.0 - - + +
255B ASP* 1.3 77.4 - - - +
257B ASN* 1.3 53.3 + - - +
259B ARG* 3.3 13.7 + - - +
260B ARG* 2.6 68.4 + - - +
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Residues in contact with ASN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LYS* 3.2 43.6 + - - +
255B ASP 3.0 0.4 - - - -
256B ARG* 1.3 76.2 - - - +
258B LEU* 1.3 58.9 + - + +
260B ARG* 2.9 9.3 + - - +
261B ILE* 2.5 55.7 + - + +
324B GLU* 6.1 1.7 - - - +
325B ASN* 6.0 0.5 + - - -
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.6 15.6 + - - +
151B ALA* 3.6 40.4 - - + +
152B ILE* 4.3 15.0 - - + -
155B PRO* 6.0 4.5 - - + -
162B ARG* 6.1 0.9 - - - +
255B ASP* 2.9 39.4 + - + +
257B ASN* 1.3 73.8 - - + +
259B ARG* 1.3 53.9 + - + +
261B ILE* 4.6 2.4 - - + +
262B THR* 2.7 42.8 + - - -
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Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 5.8 2.9 - - + -
242B LEU* 3.8 40.6 - - + +
255B ASP* 3.0 25.4 + - + +
256B ARG* 3.5 14.8 - - - +
258B LEU* 1.3 76.0 - - + +
260B ARG* 1.3 59.5 + - - +
262B THR* 3.7 5.8 - - - +
263B ARG* 2.8 51.7 + - - +
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Residues in contact with ARG 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ARG* 2.6 58.0 + - - +
257B ASN* 3.5 8.3 - - - +
259B ARG* 1.3 72.0 - - + +
261B ILE* 1.3 60.2 + - + +
263B ARG* 3.4 16.1 + - - +
264B LEU* 3.0 27.0 + - - +
322B LEU* 4.4 16.3 - - - +
324B GLU* 4.2 32.1 + - - -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 3.9 25.4 - - + +
148B ARG* 3.4 34.5 - - - +
162B ARG* 5.9 0.9 - - - +
257B ASN* 2.5 40.4 + - + +
258B LEU* 4.6 1.1 - - - +
260B ARG* 1.3 70.8 - - + +
262B THR* 1.3 63.5 + - - +
264B LEU* 3.3 11.8 + - + +
265B VAL* 3.1 22.3 + - - +
323B ASP* 5.7 5.8 - - - +
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.5 23.8 + - - +
152B ILE* 3.8 15.4 - - + +
235B TYR* 3.1 32.2 + - + +
238B MET* 3.2 32.5 - - + -
258B LEU 2.7 25.5 + - - -
259B ARG* 3.7 6.1 - - - +
261B ILE* 1.3 74.7 - - - +
263B ARG* 1.3 66.2 + - - +
265B VAL 3.3 0.9 + - - -
266B LEU* 3.2 8.8 + - - +
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Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 2.8 38.9 + - - +
260B ARG* 3.6 15.9 - - - +
261B ILE 3.3 0.2 - - - -
262B THR* 1.3 77.7 - - - +
264B LEU* 1.3 61.7 + - - +
266B LEU* 3.4 9.8 + - + +
267B VAL* 3.2 33.9 + - + +
322B LEU* 5.0 8.3 - - + -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 5.3 8.1 - - + -
90B ILE* 4.4 19.7 - - + -
144B MET* 6.2 1.3 - - + -
260B ARG 3.0 13.6 + - - +
261B ILE* 3.3 16.6 - - + +
263B ARG* 1.3 74.5 - - - +
265B VAL* 1.3 68.3 + - + +
267B VAL* 3.0 15.1 + - + +
268B VAL* 3.1 23.9 + - + +
318B LEU* 4.0 13.2 - - + +
319B TYR* 4.3 15.3 - - + -
322B LEU* 3.5 39.5 - - + +
323B ASP* 3.8 27.6 - - + +
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 4.5 11.0 - - + -
141B LEU* 4.8 0.9 - - + +
144B MET* 4.0 41.7 - - + -
145B SER* 4.2 15.0 - - - +
148B ARG* 3.6 24.2 - - + -
235B TYR* 3.2 16.8 - - - +
261B ILE 3.1 14.3 + - - +
262B THR 3.3 2.0 + - - +
264B LEU* 1.3 81.4 - - + +
266B LEU* 1.3 60.5 + - - +
268B VAL* 3.4 7.9 + - - +
269B VAL* 3.1 28.8 + - + +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 5.7 1.8 - - + -
235B TYR* 3.1 49.9 + - + +
262B THR 3.2 8.9 + - - +
263B ARG* 3.7 9.6 - - + +
264B LEU 3.1 0.8 - - - -
265B VAL* 1.3 77.9 - - - +
267B VAL* 1.3 57.9 + - + +
269B VAL* 3.3 11.2 + - + +
270B ALA* 2.9 30.2 + - + +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ARG* 3.3 19.1 - - + +
264B LEU* 3.0 7.7 + - + +
266B LEU* 1.3 75.7 - - + +
268B VAL* 1.3 61.4 + - + +
270B ALA* 3.2 6.5 + - + +
271B VAL* 2.8 45.0 + - + +
318B LEU* 4.0 21.1 - - + -
322B LEU* 3.7 25.8 - - + -
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.4 9.6 - - + -
141B LEU* 3.6 22.7 - - + -
144B MET* 5.6 6.1 - - + -
264B LEU* 3.1 24.6 + - + +
265B VAL* 3.6 9.2 - - - +
267B VAL* 1.3 75.3 - - - +
269B VAL* 1.3 58.0 + - - +
271B VAL* 3.9 1.7 - - - +
272B PHE* 3.0 28.8 + - + +
311B ASN* 5.0 0.2 + - - -
315B ASN* 3.5 22.6 - - - +
318B LEU* 4.3 18.8 - - + -
319B TYR* 4.0 23.8 - - + +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 4.0 28.7 - - + -
145B SER* 4.4 9.6 - - - +
228B VAL* 5.9 2.5 - - + -
231B ILE* 4.2 33.2 - - + -
235B TYR* 5.5 0.7 - - + -
265B VAL* 3.1 19.8 + - + +
266B LEU* 3.6 13.2 - - + +
268B VAL* 1.3 73.6 - - - +
270B ALA* 1.3 68.5 + - - +
272B PHE* 3.1 6.4 + - - +
273B VAL* 2.8 42.4 + - + +
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 2.9 16.7 + - + +
267B VAL* 3.4 13.0 - - + +
269B VAL* 1.3 77.3 - - - +
271B VAL* 1.3 58.7 + - + +
273B VAL* 3.3 5.3 + - - +
274B GLY* 2.8 27.7 + - - -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B VAL* 2.8 32.9 + - + +
268B VAL 3.9 3.4 - - - +
270B ALA* 1.3 74.4 - - + +
272B PHE* 1.3 63.6 + - - +
274B GLY* 3.4 2.5 + - - -
275B CYS* 3.1 24.9 + - - -
311B ASN* 3.8 14.1 - - - +
314B LEU* 3.9 24.0 - - + -
315B ASN* 5.6 0.2 - - - +
318B LEU* 3.9 30.5 - - + -
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Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 5.7 1.1 - - - -
134B MET* 3.9 15.7 - - - -
137B SER* 3.5 33.9 - - - -
138B THR* 3.7 22.4 - - + -
141B LEU* 3.8 23.1 - - + -
224B PHE* 4.4 12.6 - + - -
228B VAL* 6.3 0.9 - - + -
268B VAL* 3.0 21.4 + - + +
269B VAL 3.5 3.4 - - - +
271B VAL* 1.3 74.5 - - - +
273B VAL* 1.3 75.9 + - + +
275B CYS* 3.0 11.8 + - - -
276B TRP* 3.1 43.5 + + - +
311B ASN* 3.2 31.0 - - - +
315B ASN* 6.1 1.1 - - - -
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 6.1 0.2 - - + -
224B PHE* 3.9 15.5 - - + -
228B VAL* 4.1 28.0 - - + -
269B VAL* 2.8 37.9 + - + +
270B ALA* 3.8 5.6 - - - +
272B PHE* 1.3 82.3 - - + +
274B GLY* 1.3 61.9 + - - +
277B THR* 2.6 44.2 + - - +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 2.8 16.8 + - - -
271B VAL* 3.8 2.9 - - - -
272B PHE 3.1 0.4 - - - -
273B VAL* 1.3 79.4 - - - +
275B CYS* 1.3 58.7 + - - +
277B THR* 4.8 1.7 - - - -
278B PRO* 3.6 17.2 - - - +
307B LEU* 4.5 4.9 - - - +
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Residues in contact with CYS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B VAL* 3.1 24.5 + - - +
272B PHE 3.0 5.6 + - - +
274B GLY* 1.3 78.1 - - - +
276B TRP* 1.3 60.7 + - + +
277B THR 3.6 0.4 - - - -
278B PRO* 4.2 5.2 - - - +
279B VAL* 4.5 1.6 - - - +
304B CYS 4.3 4.0 - - - +
307B LEU* 3.8 37.2 - - - +
308B GLY* 3.5 18.8 + - - -
311B ASN* 3.8 28.9 - - + -
314B LEU* 4.1 20.9 - - - -
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Residues in contact with TRP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 5.0 0.2 - - - -
133B ASN* 4.1 15.5 - - - +
134B MET* 3.4 36.3 - - + -
224B PHE* 4.2 15.0 - - + -
272B PHE* 3.1 53.7 + + + +
273B VAL 4.0 0.2 - - - -
275B CYS* 1.3 79.6 - - + +
277B THR* 1.3 60.8 + - - +
278B PRO* 3.6 1.6 - - - -
279B VAL* 3.7 25.7 + - + +
280B GLN* 2.9 36.4 + - + +
305B THR 4.6 4.0 - - - -
308B GLY* 3.2 43.2 + - - -
309B TYR* 3.9 24.9 - + - -
311B ASN* 3.9 6.9 + - - -
312B SER* 5.6 1.1 - - - -
1501B 0NN 3.8 19.3 - + + -
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 3.4 21.8 - - + -
273B VAL* 2.6 30.3 + - - +
274B GLY* 4.8 1.1 - - - -
276B TRP* 1.3 76.0 - - - +
278B PRO* 1.3 74.2 - - + +
280B GLN* 3.2 3.4 + - + +
281B VAL* 3.0 35.3 + - + +
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Residues in contact with PRO 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLY 3.6 16.8 - - - +
275B CYS 4.2 4.3 - - - +
276B TRP 3.7 1.8 - - - -
277B THR* 1.3 97.3 - - + +
279B VAL* 1.3 60.7 + - + +
281B VAL* 4.0 2.8 - - + +
282B PHE* 3.0 41.4 + - + -
304B CYS* 3.9 25.8 - - + -
307B LEU* 4.6 14.6 - - + -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B CYS 4.5 6.3 - - - +
276B TRP* 3.7 30.9 + - + +
277B THR 3.2 0.4 - - - -
278B PRO* 1.3 74.6 - - + +
280B GLN* 1.3 61.3 + - - +
282B PHE* 3.2 7.4 + - + +
283B VAL* 2.8 47.5 + - + +
304B CYS* 2.8 39.5 - - + +
305B THR* 3.8 14.6 - - - +
1501B 0NN 3.9 18.2 - - + +
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Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B MET* 3.8 16.1 - - - +
220B PHE* 3.8 30.3 - - + -
223B SER* 3.5 21.1 + - - -
224B PHE* 3.5 37.9 - - + +
276B TRP* 2.9 28.9 + - + +
277B THR* 3.2 7.2 + - - +
279B VAL* 1.3 78.2 - - + +
281B VAL* 1.3 58.0 + - + +
283B VAL* 3.9 4.4 - - - +
284B LEU* 2.9 29.1 + - - +
1501B 0NN 3.6 26.3 - - + -
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 4.9 13.0 - - + -
277B THR* 3.0 28.7 + - + +
278B PRO* 4.0 4.9 - - + +
280B GLN* 1.3 72.5 - - + +
282B PHE* 1.3 72.6 + - + +
284B LEU* 3.2 14.0 + - + +
285B ALA* 2.8 29.6 + - + +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PRO* 3.0 27.2 + - + +
279B VAL* 3.6 5.4 - - - +
281B VAL* 1.3 86.1 - - + +
283B VAL* 1.3 54.0 + - + +
285B ALA* 2.8 10.7 + - + +
286B GLN* 2.8 38.9 + - + +
300B ILE* 4.3 15.7 - - + -
301B LEU* 4.8 25.1 - - + -
304B CYS* 3.6 36.3 - - + -
----------------------------------------------------------
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA* 5.1 2.1 - - - +
219B ILE* 6.5 0.2 - - + -
279B VAL* 2.8 32.3 + - + +
280B GLN* 3.9 3.8 - - - +
282B PHE* 1.3 73.2 - - + +
284B LEU* 1.3 62.6 + - - +
286B GLN* 3.3 21.1 + - + +
287B GLY* 3.1 19.4 + - - -
1501B 0NN 3.6 46.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA* 3.3 37.3 - - + +
217B ILE* 4.1 14.1 - - + +
220B PHE* 3.9 38.8 - - + -
280B GLN 2.9 19.2 + - - +
281B VAL* 3.3 12.6 - - + +
282B PHE 3.1 0.2 - - - -
283B VAL* 1.3 78.2 - - - +
285B ALA* 1.3 61.6 + - - +
287B GLY* 3.2 11.3 + - - -
288B LEU* 3.4 28.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL* 2.8 14.8 + - + +
282B PHE* 2.8 14.4 + - + +
284B LEU* 1.3 73.9 - - - +
286B GLN* 1.3 65.6 + - - +
288B LEU* 2.9 22.8 + - - +
289B GLY 3.3 0.2 + - - -
290B VAL* 3.1 41.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 2.8 18.6 + - + +
283B VAL* 3.3 29.2 + - - +
285B ALA* 1.3 72.0 - - + +
287B GLY* 1.3 62.0 + - - +
289B GLY* 3.1 14.9 + - - -
290B VAL 3.3 18.1 - - - +
291B GLN* 3.6 26.3 + - - +
292B PRO* 4.1 9.6 - - + +
301B LEU* 3.6 30.1 - - + +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY* 3.5 8.9 - - - -
213B PRO* 3.5 21.8 - - - +
216B ALA* 3.8 20.0 - - - -
283B VAL 3.1 12.3 + - - -
284B LEU 3.2 5.4 + - - -
285B ALA 3.1 0.4 - - - -
286B GLN* 1.3 76.3 - - - +
288B LEU* 1.3 60.2 + - - +
289B GLY 3.2 1.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PRO* 3.8 36.6 - - + +
216B ALA* 4.8 3.6 - - + -
217B ILE* 6.3 2.9 - - + -
284B LEU* 3.4 28.9 - - + +
285B ALA* 2.9 15.4 + - - +
287B GLY* 1.3 75.3 - - - +
289B GLY* 1.3 57.0 + - - +
290B VAL* 3.4 11.8 + - + +
----------------------------------------------------------
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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