Contacts of the helix formed by residues 244 - 276 (chain B) in PDB entry 5VBL
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 244 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.5 32.6 - - + +
133B ARG* 6.1 0.8 - - - +
227B THR 6.1 0.4 - - - -
228B ILE* 3.6 44.2 - - - +
243B ARG* 1.3 66.5 - - - +
245B ARG* 1.3 63.2 + - - +
246B LEU 3.6 1.8 - - - -
247B LEU* 4.2 21.7 - - + +
248B SER* 3.2 23.9 + - - -
1002B LYS* 5.8 0.2 - - - +
1054B GLU* 2.8 55.3 + - + +
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ARG* 3.0 64.4 + - + +
244B ARG* 1.3 72.8 + - - +
246B LEU* 1.4 66.5 + - + +
248B SER* 3.2 13.8 + - - -
249B ILE* 3.2 33.7 + - + +
312B PHE 5.2 3.3 - - - +
314B PRO* 3.7 30.7 - - + +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.5 43.7 - - + +
63B SER* 5.2 1.8 - - - +
64B ALA* 3.8 24.9 - - + +
127B ARG* 3.5 38.1 - - - +
244B ARG* 4.6 0.2 - - - +
245B ARG* 1.4 76.5 - - + +
247B LEU* 1.4 60.7 + - - +
249B ILE* 3.4 8.2 + - + +
250B ILE* 3.1 30.2 + - + +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 3.8 23.2 - - + +
131B ILE* 4.2 9.4 - - + -
221B TYR* 4.6 13.2 - - + -
224B ILE* 3.8 24.9 - - + -
228B ILE* 3.8 28.7 - - + -
244B ARG* 4.0 24.5 + - + +
245B ARG 3.3 0.4 - - - -
246B LEU* 1.4 77.7 - - - +
248B SER* 1.4 57.1 + - - +
250B ILE* 3.4 3.7 + - + +
251B VAL* 2.9 50.8 + - + +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ARG 3.2 13.7 + - - -
245B ARG* 3.2 17.0 + - - -
247B LEU* 1.4 77.2 - - - +
249B ILE* 1.4 61.7 + - - +
251B VAL* 4.1 5.2 - - - +
252B VAL* 3.3 26.0 + - - +
312B PHE* 5.1 13.3 - - - +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.5 15.9 - - - +
68B ILE* 5.7 4.0 - - + -
245B ARG* 3.2 24.6 + - + +
246B LEU* 3.7 7.2 - - + +
247B LEU 3.4 0.2 - - - -
248B SER* 1.4 76.0 - - - +
250B ILE* 1.3 63.5 + - + +
252B VAL* 3.2 13.4 - - + +
253B LEU* 3.2 28.8 + - + +
308B LEU 5.8 0.4 - - - +
309B TYR* 3.8 34.5 - - + -
312B PHE* 4.0 11.4 - - + +
313B ASP* 3.4 44.9 - - + +
314B PRO* 4.4 7.9 - - + -
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 4.6 8.5 - - + -
68B ILE* 6.3 0.4 - - + -
120B LEU* 4.9 0.7 - - + +
123B LEU* 3.7 47.6 - - + +
124B SER* 3.9 27.1 - - - +
127B ARG* 3.7 32.3 - - + +
246B LEU* 3.1 21.9 + - + +
247B LEU* 4.0 4.5 - - + +
249B ILE* 1.3 75.2 - - + +
251B VAL* 1.4 65.6 + - + +
253B LEU* 3.1 11.6 + - + +
254B VAL* 3.0 27.6 + - + +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR* 3.8 36.1 - - + +
247B LEU* 2.9 34.8 + - + +
248B SER* 4.1 6.5 - - - +
249B ILE 3.5 0.4 - - - -
250B ILE* 1.4 72.0 - - + +
252B VAL* 1.4 58.5 + - - +
254B VAL* 3.2 8.0 + - - +
255B VAL* 2.9 40.5 + - + +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER 3.3 13.6 + - - +
249B ILE* 3.2 18.8 - - + +
251B VAL* 1.4 78.5 - - + +
253B LEU* 1.4 51.4 + - + +
255B VAL* 4.0 8.5 - - + +
256B THR* 2.7 40.4 + - + +
308B LEU* 3.9 23.6 - - + +
312B PHE* 3.8 48.0 - - + -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 5.6 1.1 - - + -
71B LEU* 4.6 4.3 - - + -
120B LEU* 3.8 14.6 - - + +
123B LEU* 4.4 18.8 - - + -
249B ILE* 3.2 30.9 + - + +
250B ILE* 3.1 14.5 + - + +
252B VAL* 1.4 76.3 - - + +
254B VAL* 1.4 56.6 + - - +
256B THR* 3.1 14.7 + - - -
257B PHE* 3.2 18.5 + - - +
301B ASN* 5.2 0.2 - - - +
305B ASN* 3.3 38.3 - - + +
308B LEU* 4.2 11.4 - - + -
309B TYR* 3.6 37.0 - - + +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.8 15.5 - - + -
124B SER* 4.1 14.4 - - - +
214B PHE* 4.0 21.1 - - + -
217B MET* 3.8 39.5 - - + -
218B LEU* 6.4 0.2 - - + -
250B ILE* 3.0 22.5 + - + +
251B VAL* 3.2 8.5 + - - +
253B LEU* 1.4 74.4 - - - +
255B VAL* 1.4 56.8 + - + +
257B PHE* 3.2 3.0 + - + +
258B ALA* 2.8 32.9 + - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 2.9 32.7 + - + +
252B VAL* 4.0 10.1 - - + +
254B VAL* 1.4 76.7 - - + +
256B THR* 1.4 59.2 + - + +
258B ALA* 3.4 6.8 + - - +
259B LEU* 3.1 45.5 + - + +
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 2.7 30.6 + - + +
253B LEU 3.1 13.2 + - - -
255B VAL* 1.4 73.2 - - + +
257B PHE* 1.4 57.7 + - - +
259B LEU* 3.3 9.3 + - + +
260B CYS* 2.9 35.1 + - - -
301B ASN* 3.9 4.5 + - - -
304B LEU* 4.1 19.3 - - + -
305B ASN* 4.8 1.4 + - - -
308B LEU* 3.4 37.3 - - + +
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET 5.2 1.6 - - - -
116B SER* 4.3 16.2 - - - -
117B ALA* 3.8 26.2 - - + -
120B LEU* 3.6 23.8 - - + -
209B GLY 4.5 2.7 - - - -
210B PHE* 4.0 30.5 - + - -
213B PRO* 5.7 0.2 - - + -
214B PHE* 5.3 7.2 - + + -
217B MET* 4.1 20.9 - - + -
253B LEU 3.2 16.7 + - - +
254B VAL 3.4 4.9 - - - +
256B THR* 1.4 78.7 + - - +
258B ALA* 1.4 59.3 + - + +
260B CYS 3.4 0.3 + - - -
261B LYS* 2.9 67.4 + - + +
301B ASN* 3.4 23.3 + - - +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 4.5 9.0 - - + -
214B PHE* 3.8 32.3 - - + -
254B VAL 2.8 20.8 + - - +
255B VAL* 3.6 7.9 - - - +
257B PHE* 1.4 77.1 - - - +
259B LEU* 1.4 56.3 + - + +
262B MET* 3.0 36.2 + - - +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL* 3.1 41.1 + - + +
256B THR* 3.3 9.2 + - + +
258B ALA* 1.4 76.0 - - + +
260B CYS* 1.3 61.9 + - - +
262B MET* 5.1 1.3 - - - -
263B PRO* 3.5 15.5 - - - +
297B ILE* 3.9 7.5 - - - +
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Residues in contact with CYS 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 2.9 22.7 + - - +
257B PHE 3.9 1.1 - - - +
259B LEU* 1.3 80.4 - - - +
261B LYS* 1.3 60.1 + - + +
263B PRO* 3.9 3.5 - - - +
264B TYR 4.9 0.2 + - - -
294B CYS 4.3 0.3 - - - +
297B ILE* 3.4 41.4 - - - +
298B SER* 3.4 21.8 - - - -
300B VAL* 5.5 1.6 - - - -
301B ASN* 3.7 27.6 - - + +
304B LEU* 4.0 20.9 - - - -
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Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 4.9 12.2 - - - +
113B MET* 5.2 13.9 - - + +
116B SER* 4.7 8.3 + - - -
209B GLY 6.1 0.2 - - - +
210B PHE* 3.7 19.1 - - + -
257B PHE* 2.9 48.2 + - + +
260B CYS* 1.3 75.0 - - - +
262B MET* 1.4 62.5 + - - +
263B PRO 3.5 0.7 - - - -
264B TYR* 3.3 5.3 + - + +
265B HIS* 3.2 41.3 + - + +
298B SER* 3.2 37.8 + - - +
301B ASN* 3.2 29.0 - - - +
302B SER* 5.3 2.0 + - - +
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Residues in contact with MET 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 3.7 30.6 - - + -
214B PHE* 5.7 5.4 - - - -
258B ALA* 3.0 23.0 + - - +
259B LEU* 5.0 1.3 - - - +
261B LYS* 1.4 75.0 - - - +
263B PRO* 1.4 62.3 - - + +
265B HIS* 3.4 1.4 + - - +
266B LEU* 2.9 59.2 + - + +
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Residues in contact with PRO 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU 3.5 17.3 - - - +
260B CYS 3.9 2.0 - - - +
261B LYS 3.7 2.2 - - - -
262B MET* 1.4 91.6 - - + +
264B TYR* 1.4 56.7 + - - +
266B LEU* 4.5 6.5 - - + -
267B VAL* 3.0 37.6 + - + +
294B CYS* 3.7 21.8 - - - +
297B ILE* 3.6 28.9 - - + -
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Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A 200 2.7 27.0 + - + -
109B ILE* 5.9 2.0 - - + +
110B PHE* 4.3 10.9 - - - -
113B MET* 4.3 11.0 - - + -
261B LYS* 3.3 8.1 + - + +
263B PRO* 1.4 78.6 - - - +
265B HIS* 1.3 96.5 + + - +
267B VAL* 4.3 1.8 - - - +
268B LYS* 3.3 42.4 + - + +
291B PHE* 3.8 25.9 - + - -
294B CYS* 3.8 24.3 - - - +
295B THR* 3.6 25.4 - - + -
298B SER* 4.1 18.6 - - - -
299B TYR* 5.7 6.3 - + - -
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Residues in contact with HIS 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 3.9 29.3 - - + +
205B SER* 5.6 0.2 - - - -
206B THR* 3.3 36.0 + - + +
209B GLY 4.7 1.2 + - - -
210B PHE* 3.7 44.3 - + + +
261B LYS* 3.2 35.5 + - + +
262B MET* 4.1 2.2 - - - +
264B TYR* 1.3 100.2 - + - +
266B LEU* 1.4 57.3 + - - +
268B LYS* 4.0 4.1 - - - +
269B THR* 2.7 37.4 + - - -
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B MET* 2.9 45.3 + - + +
263B PRO* 3.9 6.7 - - + +
265B HIS* 1.4 74.1 - - - +
267B VAL* 1.4 63.2 + - + +
269B THR* 3.3 4.6 + - - -
270B LEU* 2.9 58.7 + - + +
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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
----------------------------------------------------------
15A NLE 4.1 2.9 - - + -
263B PRO* 3.0 22.4 + - + +
264B TYR 4.3 2.2 - - - +
266B LEU* 1.4 78.3 - - + +
268B LYS* 1.4 57.1 + - - +
270B LEU* 3.4 3.1 + - + +
271B TYR* 3.0 27.2 + - - +
287B LEU* 3.6 47.3 - - + +
290B ILE* 3.9 12.8 - - + -
291B PHE* 3.7 22.9 - - + -
294B CYS* 3.8 18.8 - - - -
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A NLE 4.2 25.6 + - + -
17A 200 2.9 34.0 + - - +
110B PHE* 4.6 1.2 - - - -
198B GLU* 4.6 12.8 - - - -
202B GLY* 5.8 5.2 - - - +
206B THR* 5.5 8.3 - - - +
264B TYR* 3.3 37.1 + - + +
265B HIS* 4.0 5.8 - - - +
267B VAL* 1.4 75.7 - - - +
269B THR* 1.4 59.1 - - - +
271B TYR* 3.4 7.5 + - - +
272B MET* 3.2 41.6 + - + +
291B PHE* 4.5 4.7 - - + -
1102B OLC 2.9 31.0 + - - -
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Residues in contact with THR 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 5.9 5.4 - - + -
206B THR* 4.0 20.3 + - - +
265B HIS 2.7 23.6 + - - -
266B LEU* 3.3 6.9 + - - -
268B LYS* 1.4 70.8 - - - +
270B LEU* 1.4 59.5 + - + +
272B MET* 3.1 8.8 + - + +
273B LEU* 2.8 52.5 + - + +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 2.9 49.7 + - + +
267B VAL* 3.7 5.4 - - + +
268B LYS 3.4 0.2 - - - -
269B THR* 1.4 79.3 - - + +
271B TYR* 1.3 56.2 + - - +
273B LEU* 3.7 6.6 - - + +
274B GLY* 3.2 23.9 + - - -
279B TRP* 4.2 10.8 - - - +
283B PHE* 3.7 31.4 - - + -
284B ASP* 5.2 0.2 - - - +
287B LEU* 4.0 24.7 - - + +
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Residues in contact with TYR 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 4.5 8.8 - - + +
13A LYS 2.7 34.1 + - - -
14A OIC 4.5 2.7 - - - -
15A NLE 3.6 44.2 - - + -
21B TYR* 5.2 2.8 - + - -
24B TRP* 5.0 0.6 - + - -
267B VAL 3.0 17.8 + - - +
268B LYS 3.4 6.7 - - - +
269B THR 3.2 0.2 - - - -
270B LEU* 1.3 75.5 - - - +
272B MET* 1.4 76.5 + - + +
274B GLY* 3.7 5.0 + - - -
275B SER* 3.8 13.5 + - - -
284B ASP* 4.4 22.9 - - + +
287B LEU* 4.1 14.8 - - + +
288B MET* 3.3 36.1 - - + +
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Residues in contact with MET 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A OIC 5.5 2.7 - - + -
15A NLE 6.0 1.6 - - + +
198B GLU* 3.4 35.7 - - + +
199B VAL* 3.9 40.4 - - + -
202B GLY* 5.5 4.9 - - - -
203B VAL* 5.1 9.9 - - + +
268B LYS* 3.2 29.3 + - + +
269B THR* 3.1 10.0 + - - +
271B TYR* 1.4 87.8 - - + +
273B LEU* 1.4 65.3 - - + +
274B GLY 3.0 9.6 + - - -
275B SER* 3.3 17.8 + - - -
276B LEU* 3.4 18.7 + - - +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 6.1 0.2 - - + -
203B VAL* 5.4 8.7 - - + -
269B THR* 2.8 42.4 + - + +
270B LEU* 3.7 7.9 - - + +
272B MET* 1.4 77.3 - - + +
274B GLY* 1.3 55.2 + - - +
276B LEU* 4.6 15.7 - - + -
277B LEU* 3.4 51.4 - - + +
279B TRP* 3.5 12.0 + - + +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU 3.2 15.7 + - - -
271B TYR 3.7 2.9 + - - -
272B MET 3.0 1.8 + - - -
273B LEU* 1.3 78.2 - - - +
275B SER* 1.3 60.1 + - - +
276B LEU 3.3 0.9 - - - -
278B HIS* 3.2 7.9 + - - -
279B TRP* 2.8 45.9 + - - +
284B ASP* 4.6 10.7 - - - +
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 6.0 6.5 - - - -
271B TYR 3.8 12.1 + - - -
272B MET* 3.3 11.6 + - - -
274B GLY* 1.3 74.3 - - - +
276B LEU* 1.3 67.0 + - - +
278B HIS* 4.0 19.2 + - - +
284B ASP* 4.9 2.1 + - - -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 3.8 35.2 - - + -
199B VAL* 3.8 25.8 - - + -
272B MET* 3.4 22.8 + - + +
273B LEU* 4.6 16.8 - - + +
274B GLY 3.3 0.2 - - - -
275B SER* 1.3 81.9 + - - +
277B LEU* 1.3 61.6 + - + +
278B HIS* 3.3 16.9 + - - -
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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