Contacts of the helix formed by residues 249 - 281 (chain B) in PDB entry 4DVQ
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 249 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 3.4 14.3 + - - -
236B GLN* 6.4 0.2 - - - -
237B LEU* 4.9 6.5 - - - -
240B MET* 4.8 6.3 - - - -
245B SER* 2.9 14.7 + - - -
248B ILE* 1.3 91.7 + - - +
250B PRO* 1.3 59.0 - - - +
251B LYS* 3.1 4.3 - - - -
252B VAL* 2.9 44.7 + - - +
253B TRP* 3.3 7.4 + - - -
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Residues in contact with PRO 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B SER 3.7 0.6 - - - -
246B ARG 3.5 17.5 - - - +
247B TRP* 3.3 22.2 - - - +
248B ILE 3.4 2.9 - - - +
249B SER* 1.3 90.0 - - - +
251B LYS* 1.3 71.2 + - + +
253B TRP* 3.1 20.4 + - + +
254B LYS* 3.2 23.1 + - + +
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B SER* 3.1 1.9 + - - -
250B PRO* 1.3 82.2 - - + +
252B VAL* 1.3 65.8 + - + +
254B LYS* 3.4 6.7 + - - +
255B GLU* 3.0 28.7 + - - +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 5.4 3.4 - - - +
233B SER* 4.2 12.0 - - - +
236B GLN* 3.6 37.9 - - + +
237B LEU* 3.4 30.5 - - + -
249B SER* 2.9 29.8 + - - +
251B LYS* 1.3 79.6 - - + +
253B TRP* 1.3 58.6 + - - +
255B GLU* 3.5 14.4 - - - +
256B HIS* 3.0 21.5 + - - +
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Residues in contact with TRP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 4.8 2.9 - - + -
115B PRO* 4.0 26.0 - - + -
118B ALA* 3.8 18.8 - - + -
237B LEU* 3.6 32.5 - - + +
242B ARG* 3.9 29.2 - - + -
245B SER* 3.0 46.9 + - - -
246B ARG* 3.8 9.0 - - + +
249B SER 3.3 8.3 + - - -
250B PRO* 3.1 12.6 + - + +
252B VAL* 1.3 77.1 - - - +
254B LYS* 1.3 72.7 + - - +
256B HIS* 3.1 3.6 + - - +
257B PHE* 2.9 67.1 + + - +
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B HIS* 5.6 5.1 - - - -
250B PRO* 3.2 19.3 + - + +
251B LYS* 3.4 7.1 + - - +
253B TRP* 1.3 88.9 - - - +
255B GLU* 1.3 56.9 + - - +
257B PHE* 4.0 25.1 - - + +
258B GLU* 2.9 50.5 + - - +
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 5.8 1.4 + - - -
229B VAL* 3.7 26.5 - - + +
232B LYS* 3.9 23.0 + - - +
233B SER* 4.0 14.3 - - - -
236B GLN* 4.1 6.4 + - - +
251B LYS* 3.0 19.7 + - - +
252B VAL* 3.5 16.2 + - - +
254B LYS* 1.3 76.5 - - - +
256B HIS* 1.3 59.5 - - - +
258B GLU* 4.0 7.7 - - - +
259B ALA* 3.0 24.8 + - - +
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Residues in contact with HIS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 3.4 40.6 + - + +
116B TRP* 3.8 1.5 - + - -
230B MET* 3.5 11.1 + - + -
233B SER* 3.1 32.3 + - - +
234B THR* 3.1 22.4 + - - -
237B LEU* 4.0 13.0 - - + +
252B VAL 3.0 18.2 + - - +
253B TRP* 3.5 4.7 - - - +
255B GLU* 1.3 76.0 - - - +
257B PHE* 1.3 66.9 + - + +
259B ALA* 3.5 4.4 + - - +
260B TRP* 3.0 62.0 + + - -
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO 4.2 3.4 - - - -
118B ALA* 4.0 6.1 - - + -
119B TYR* 3.5 48.1 - + + -
122B HIS* 3.8 40.4 - + + -
123B ARG* 5.9 1.8 - - - +
242B ARG* 5.9 2.5 - - - -
253B TRP* 2.9 49.8 + + - +
254B LYS* 4.1 26.7 - - + +
256B HIS* 1.3 85.8 - - - +
258B GLU* 1.3 54.2 + - + +
260B TRP 3.2 0.9 + - - -
261B ASP* 2.7 42.4 + - - +
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LYS* 2.9 35.3 + - + +
255B GLU* 4.0 5.7 - - - +
257B PHE* 1.3 74.4 - - + +
259B ALA* 1.3 65.5 + - - +
261B ASP* 3.3 14.1 + - - +
262B CYS* 3.0 22.2 + - - +
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA* 3.6 28.2 - - + +
229B VAL* 4.3 9.6 - - + -
230B MET* 3.7 18.2 - - - +
255B GLU 3.0 18.8 + - - +
256B HIS 3.6 5.2 - - - +
258B GLU* 1.3 75.2 - - - +
260B TRP* 1.3 62.4 + - - +
262B CYS* 3.1 6.5 + - - +
263B ILE* 3.0 26.9 + - - +
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Residues in contact with TRP 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 3.4 38.2 - + - +
119B TYR* 3.5 37.7 - + + -
120B ARG* 3.5 30.2 - - - +
230B MET* 3.4 29.5 - - + +
256B HIS* 3.0 58.1 + + - -
257B PHE 3.6 0.9 - - - +
259B ALA* 1.3 76.7 - - - +
261B ASP* 1.3 56.0 + - - +
263B ILE* 3.2 24.8 + - + -
264B PHE* 2.8 57.0 + + - -
309B MET* 4.5 3.8 - - + -
313B ALA* 4.7 7.0 - - + -
602B 1CA 4.8 4.9 - - - -
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Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 2.6 29.8 + - - -
123B ARG* 3.0 36.9 + - - -
257B PHE* 2.7 23.8 + - - +
258B GLU* 3.5 20.3 - - + +
259B ALA 3.3 0.2 - - - -
260B TRP* 1.3 70.0 - - - +
262B CYS* 1.3 58.1 + - - +
264B PHE* 3.5 1.4 + - - +
265B GLN* 3.0 29.0 + - - +
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Residues in contact with CYS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN* 4.0 36.8 - - - -
223B PHE* 4.6 3.4 - - - -
226B ALA* 3.8 10.3 - - + -
258B GLU 3.0 12.9 + - - +
259B ALA* 3.1 7.8 + - - +
261B ASP* 1.3 77.2 - - - +
263B ILE* 1.3 62.6 + - - +
265B GLN* 3.2 11.8 + - - +
266B TYR* 3.0 22.2 + - - +
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 4.1 21.2 - - + -
226B ALA* 3.9 15.3 - - + +
227B LEU* 4.1 21.8 - - + +
230B MET* 3.8 29.4 - - + -
259B ALA 3.0 19.2 + - - +
260B TRP* 3.2 25.8 + - + +
262B CYS* 1.3 76.0 - - - +
264B PHE* 1.3 57.3 + - - +
266B TYR* 3.3 4.5 + - - +
267B GLY 2.9 22.7 + - - -
309B MET* 3.3 25.4 - - + +
312B THR* 5.8 0.6 - - + +
313B ALA* 4.0 16.4 - - + -
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Residues in contact with PHE 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 3.6 22.7 - + - +
120B ARG* 3.8 29.2 - - - -
125B HIS* 3.7 38.8 - + + +
260B TRP* 2.8 54.4 + + - +
261B ASP 4.0 2.9 - - - +
263B ILE* 1.3 71.7 - - - +
265B GLN* 1.3 57.8 + - - +
267B GLY 3.6 0.2 - - - -
268B ASP* 2.7 40.1 + - + +
306B ALA* 6.0 4.0 - - - -
309B MET* 3.6 40.9 - - + +
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Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ASP 3.0 15.0 + - - +
262B CYS* 3.2 14.9 + - - +
264B PHE* 1.3 74.8 - - - +
266B TYR* 1.3 66.7 + - - +
268B ASP* 4.0 4.5 - - - +
269B ASN* 3.2 29.7 + - - +
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 3.5 14.9 - - - +
201B ASN* 4.6 2.4 + - - -
209B LEU* 3.4 28.5 - - + +
211B LEU* 5.3 1.0 - - - +
219B ALA* 4.0 28.5 - - + -
220B SER* 4.9 3.4 - - - -
223B PHE* 3.7 56.1 - + + -
262B CYS* 3.0 13.4 + - - +
263B ILE 3.5 7.2 - - - +
265B GLN* 1.3 83.2 - - - +
267B GLY* 1.3 62.7 + - - +
269B ASN* 3.5 11.3 + - - +
270B CYS* 3.5 27.3 + - - -
312B THR* 4.1 15.7 - - + -
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Residues in contact with GLY 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PHE* 4.8 1.0 - - - -
263B ILE 2.9 11.1 + - - -
264B PHE 3.6 0.2 - - - -
266B TYR* 1.3 79.4 - - - +
268B ASP* 1.3 65.3 + - - +
270B CYS* 3.5 7.3 + - - +
271B ILE* 3.2 28.1 + - - +
309B MET* 3.6 23.6 - - - -
312B THR* 4.5 12.3 - - - -
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 2.7 24.8 + - + +
265B GLN* 4.0 4.9 - - - +
267B GLY* 1.3 71.8 - - - +
269B ASN* 1.3 55.6 + - - +
271B ILE* 2.9 15.3 + - + +
272B GLN* 2.6 69.6 + - - +
305B LYS* 4.3 19.4 + - - -
309B MET* 4.6 1.2 - - - -
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Residues in contact with ASN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLN* 3.2 26.9 + - - +
266B TYR* 3.7 5.9 + - - +
267B GLY 3.3 0.2 - - - -
268B ASP* 1.3 79.7 + - - +
270B CYS* 1.3 66.1 + - - +
272B GLN* 3.8 12.4 - - - +
273B LYS* 3.2 47.2 + - - +
496D LEU* 4.9 10.9 - - - +
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Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASN* 3.7 24.7 - - - +
205B PHE* 3.6 30.6 - - + +
209B LEU* 5.8 2.7 - - - -
266B TYR* 3.5 33.6 + - - -
267B GLY* 3.5 9.4 + - - +
268B ASP 3.2 0.2 - - - -
269B ASN* 1.3 81.6 - - - +
271B ILE* 1.3 60.2 + - - +
273B LYS* 3.4 16.9 + - - +
274B ILE* 3.3 23.9 + - - +
312B THR* 5.2 1.1 - - - -
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PHE* 4.3 8.1 - - + -
267B GLY 3.2 19.0 + - - +
268B ASP* 2.9 15.0 + - - +
270B CYS* 1.3 73.8 - - - +
272B GLN* 1.3 60.8 + - + +
273B LYS 3.1 1.8 - - - -
274B ILE* 3.2 8.3 - - + +
275B TYR* 2.9 35.5 + - + +
290B VAL* 5.8 2.0 - - + -
294B LEU* 5.9 4.3 - - + -
301B LEU* 5.4 5.6 - - + -
304B ILE* 6.3 1.8 - - + -
305B LYS* 3.7 59.9 - - + +
308B SER* 4.0 20.4 - - - +
309B MET* 4.7 7.0 - - + +
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASP* 2.6 47.4 + - - +
269B ASN* 3.8 12.4 - - - +
271B ILE* 1.3 73.9 - - + +
273B LYS* 1.3 62.2 + - - +
275B TYR* 4.0 6.1 - - - +
276B GLN* 3.2 23.7 + - - +
496D LEU* 3.9 30.9 - - + +
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASN* 5.4 1.6 - - - +
207B GLU* 2.7 45.8 + - + +
209B LEU* 4.5 12.5 - - - +
269B ASN* 3.2 43.1 + - - +
270B CYS* 3.6 13.4 - - - +
271B ILE 3.1 0.6 - - - -
272B GLN* 1.3 77.3 - - - +
274B ILE* 1.3 66.7 - - - +
276B GLN* 3.2 4.5 + - - +
277B GLU* 3.1 29.7 + - - +
181D ARG* 6.0 0.4 - - - +
184D LEU* 4.9 2.5 - - - -
185D THR* 3.6 44.1 + - + +
496D LEU* 5.0 4.9 - - + -
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PHE* 3.5 32.8 - - + +
270B CYS 3.3 12.3 + - - +
271B ILE* 3.2 17.5 - - + +
273B LYS* 1.3 76.7 - - - +
275B TYR* 1.3 69.6 + - - +
277B GLU* 3.3 3.0 + - - +
278B LEU* 3.0 36.8 + - + +
290B VAL* 4.5 3.6 - - + -
291B ALA* 4.1 23.8 - - + +
294B LEU* 4.1 13.2 - - + -
181D ARG* 3.3 45.3 - - - +
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Residues in contact with TYR 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE* 2.9 25.7 + - + +
272B GLN* 4.0 6.3 - - - +
274B ILE* 1.3 79.4 - - + +
276B GLN* 1.3 60.9 + - - +
278B LEU* 3.4 3.3 + - + +
279B ALA* 3.1 26.8 + - + +
294B LEU* 4.4 17.0 - - + -
301B LEU* 4.0 42.1 - - + +
305B LYS* 6.2 1.8 - - - -
476D LEU* 3.5 33.7 - - + -
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLN 3.2 15.7 + - - +
273B LYS 3.2 4.3 + - - +
275B TYR* 1.3 78.8 - - - +
277B GLU* 1.3 63.5 + - - +
278B LEU 3.5 0.2 + - - -
279B ALA* 3.5 6.4 + - - +
280B PHE* 3.3 23.8 - - + -
185D THR* 4.0 7.7 - - + +
474D GLU 3.3 12.5 + - - -
475D THR* 3.6 7.3 - - - +
476D LEU* 3.0 47.3 + - + +
477D THR* 4.5 2.9 + - - -
496D LEU* 2.9 34.0 + - + +
497D LEU 3.9 0.2 - - - -
498D THR* 3.0 29.0 + - - +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 3.6 14.0 - - - +
273B LYS 3.1 15.1 + - - +
274B ILE 3.3 3.6 + - - +
276B GLN* 1.3 78.5 - - - +
278B LEU* 1.3 56.9 + - - +
280B PHE* 5.5 0.2 - - - -
281B ASN 3.1 25.9 + - - +
181D ARG* 2.7 49.0 + - - +
183D SER* 3.6 26.6 + - - +
185D THR* 2.8 40.1 + - - +
498D THR* 3.9 6.7 - - + -
500D ARG* 3.1 20.3 + - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 3.0 28.0 + - + +
275B TYR* 4.1 3.8 - - + +
277B GLU* 1.3 72.3 - - - +
279B ALA* 1.3 66.2 + - - +
280B PHE 3.1 2.2 + - - -
281B ASN 3.4 16.3 + - - +
282B ARG* 3.8 12.4 - - + +
283B PRO* 3.3 34.5 - - + -
291B ALA* 4.0 19.7 - - + +
294B LEU* 4.0 37.0 - - + -
295B LEU* 4.5 17.5 - - + -
181D ARG* 4.0 15.5 - - - -
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TYR* 3.1 22.1 + - + +
276B GLN 3.7 7.0 - - - +
277B GLU 3.4 0.4 - - - -
278B LEU* 1.3 77.8 - - - +
280B PHE* 1.3 60.2 + - + +
476D LEU* 3.8 28.9 - - + -
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Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLN* 3.3 21.8 - - + -
277B GLU 3.5 1.4 + - - +
278B LEU 3.1 1.0 - - - -
279B ALA* 1.3 80.8 - - + +
281B ASN* 1.3 63.5 + - - +
282B ARG* 6.0 0.2 - - - -
331D ALA 5.6 3.8 - - - -
334D PRO* 6.2 4.9 - - + -
474D GLU* 3.7 45.9 - - + +
475D THR* 3.0 48.2 - - - -
476D LEU* 3.8 16.6 - - + -
478D GLN* 5.2 5.4 - - - -
498D THR* 6.1 0.2 - - - -
500D ARG* 3.7 5.6 - - - +
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU 3.1 14.9 + - - +
278B LEU* 3.4 12.2 + - - +
280B PHE* 1.3 81.6 + - - +
282B ARG* 1.3 75.5 + - - +
283B PRO* 3.3 19.8 - - - +
284B GLN* 5.0 2.9 + - - +
181D ARG* 5.4 0.7 - - - -
500D ARG* 3.7 37.3 + - - +
----------------------------------------------------------
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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