Contacts of the helix formed by residues 249 - 281 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TRP* 4.1 8.3 - - - -
236C GLN 5.1 1.5 + - - -
237C LEU* 4.6 3.8 - - - -
240C MET* 3.5 15.6 - - - +
245C SER 2.8 13.6 + - - -
248C ILE* 1.3 95.0 + - - +
250C PRO* 1.3 64.8 - - - +
251C LYS 3.2 2.9 - - - +
252C VAL* 2.9 34.5 + - - +
253C TRP* 3.3 13.2 + - - -
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Residues in contact with PRO 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C SER 3.7 0.8 - - - +
246C ARG 3.8 15.7 - - - +
247C TRP* 3.4 20.2 - - - +
248C ILE 3.5 2.7 - - - +
249C SER* 1.3 91.8 - - - +
251C LYS* 1.3 65.7 + - + +
253C TRP* 3.4 11.0 - - + +
254C LYS* 3.1 24.7 + - - +
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Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C SER 3.2 1.0 - - - -
250C PRO* 1.3 86.5 - - + +
252C VAL* 1.3 62.4 + - + +
254C LYS* 3.4 17.0 - - + +
255C GLU* 2.9 29.5 + - - +
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C SER* 3.9 12.3 - - - -
236C GLN* 3.7 40.2 - - + +
237C LEU* 3.5 28.5 - - + -
249C SER* 2.9 30.2 + - - +
251C LYS* 1.3 75.2 - - + +
253C TRP* 1.3 65.0 - - - +
255C GLU* 3.1 13.0 + - - +
256C HIS* 2.9 21.8 + - - +
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Residues in contact with TRP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 4.5 3.4 - - + -
115C PRO* 3.8 35.0 - - + -
118C ALA* 3.9 11.9 - - + -
237C LEU* 3.4 33.8 - - + +
242C ARG* 3.8 47.1 - - + +
245C SER* 3.0 42.9 + - - -
246C ARG* 3.8 8.2 - - - +
249C SER 3.3 13.8 + - - -
250C PRO* 3.4 11.2 - - + +
252C VAL* 1.3 79.0 - - - +
254C LYS* 1.3 60.9 + - - +
256C HIS* 3.3 1.7 + - - +
257C PHE* 3.1 65.5 + + + +
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Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C PRO 3.1 14.2 + - - +
251C LYS* 3.4 21.1 - - + +
252C VAL 3.2 0.2 - - - -
253C TRP* 1.3 78.0 - - - +
255C GLU* 1.3 63.8 + - - +
256C HIS 3.2 0.2 + - - -
257C PHE* 3.4 3.5 + - - +
258C GLU* 3.1 46.4 + - - +
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C VAL* 3.8 33.1 - - + +
232C LYS* 5.6 3.9 - - - +
233C SER* 5.0 4.4 - - - -
236C GLN* 4.5 13.2 + - - +
251C LYS 2.9 11.5 + - - +
252C VAL* 3.3 16.5 - - - +
254C LYS* 1.3 75.6 - - - +
256C HIS* 1.3 57.3 + - - +
258C GLU* 3.5 9.1 + - - +
259C ALA* 2.9 29.5 + - - +
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Residues in contact with HIS 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO* 3.6 33.6 + - + +
116C TRP* 3.8 6.6 - + - -
230C MET* 3.6 6.5 + - + -
233C SER* 2.9 30.7 + - - +
234C THR* 3.3 31.6 + - - -
237C LEU* 4.0 13.2 - - + -
252C VAL 2.9 15.4 + - - +
253C TRP* 3.6 5.2 - - - +
254C LYS 3.2 0.2 - - - -
255C GLU* 1.3 73.5 - - - +
257C PHE* 1.3 70.5 + + - +
259C ALA* 3.4 4.9 + - - +
260C TRP* 2.8 68.0 + + - -
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Residues in contact with PHE 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO 4.0 3.8 - - - -
118C ALA* 3.9 8.7 - - + -
119C TYR* 3.4 50.2 - + + -
122C HIS* 3.8 40.4 - + + -
123C ARG* 5.5 3.4 - - - +
242C ARG* 4.5 11.0 - - - -
253C TRP* 3.1 48.5 + + + +
254C LYS* 4.1 3.4 - - - +
256C HIS* 1.3 87.3 - + - +
258C GLU* 1.3 55.3 + - - +
260C TRP 3.4 0.3 + - - -
261C ASP* 2.7 41.6 + - - +
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C LYS* 3.1 43.0 + - - +
255C GLU* 3.6 9.3 - - - +
257C PHE* 1.3 75.2 - - - +
259C ALA* 1.3 64.8 + - - +
261C ASP* 3.2 14.5 + - + +
262C CYS* 3.1 22.3 + - - +
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ALA* 3.6 29.6 - - - +
229C VAL* 3.8 9.9 - - + -
230C MET* 3.8 17.7 - - + +
255C GLU 2.9 19.0 + - - +
256C HIS 3.5 4.5 - - - +
258C GLU* 1.3 73.2 - - - +
260C TRP* 1.3 65.1 + - - +
262C CYS* 3.1 5.6 + - - +
263C ILE* 3.0 27.5 + - - +
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Residues in contact with TRP 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C TRP* 3.6 27.7 - + - +
119C TYR* 3.5 37.9 - + + -
120C ARG* 3.5 35.1 - - - +
230C MET* 3.4 35.0 - - + -
256C HIS* 2.8 63.2 + + - +
259C ALA* 1.3 72.7 - - - +
261C ASP* 1.3 53.0 + - - +
262C CYS 3.1 0.3 + - - -
263C ILE* 3.2 26.3 + - + +
264C PHE* 2.7 60.1 + + - +
309C MET* 5.4 0.9 - - + -
313C ALA* 4.6 11.4 - - + -
602C 1CA 5.1 1.3 - - + -
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Residues in contact with ASP 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C TYR* 2.5 37.2 + - - -
123C ARG* 3.0 31.7 + - - -
257C PHE 2.7 24.6 + - - +
258C GLU* 3.2 16.3 + - + +
260C TRP* 1.3 73.3 - - - +
262C CYS* 1.3 57.4 + - - +
264C PHE* 3.2 2.6 + - - +
265C GLN* 3.0 29.0 + - - +
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Residues in contact with CYS 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ASN* 4.0 27.4 - - - -
223C PHE* 4.6 3.1 - - - -
226C ALA* 3.7 21.5 - - + -
258C GLU 3.1 8.6 + - - +
259C ALA* 3.1 9.2 + - - +
261C ASP* 1.3 77.5 - - - +
263C ILE* 1.3 63.1 + - - +
265C GLN* 3.5 10.5 + - - +
266C TYR* 3.2 21.5 + - - +
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 4.0 24.4 - - + -
226C ALA* 3.9 15.9 - - + +
227C LEU* 4.2 15.9 - - + +
230C MET* 3.9 25.4 - - + -
259C ALA 3.0 17.0 + - - +
260C TRP* 3.6 35.7 - - + +
262C CYS* 1.3 77.0 - - - +
264C PHE* 1.3 61.4 + - - +
266C TYR* 3.1 4.7 + - - +
267C GLY 3.0 19.4 + - - -
309C MET* 3.8 10.5 - - - +
312C THR* 6.1 0.4 - - + +
313C ALA* 4.0 24.2 - - + +
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Residues in contact with PHE 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C TYR* 3.5 26.5 - + - +
120C ARG* 3.5 33.2 - - - -
125C HIS* 3.3 41.7 - + + +
126C LYS 5.9 1.1 - - - -
260C TRP* 2.7 45.3 + + - +
261C ASP 3.8 3.6 - - - +
263C ILE* 1.3 73.5 - - - +
265C GLN* 1.3 56.5 + - - +
268C ASP* 2.9 30.8 + - - +
306C ALA* 6.1 3.8 - - - -
309C MET* 3.6 43.1 - - + +
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Residues in contact with GLN 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ASP 3.0 15.6 + - - +
262C CYS* 3.7 9.3 - - - +
263C ILE 3.2 0.2 - - - -
264C PHE* 1.3 75.6 - - - +
266C TYR* 1.3 66.7 + - - +
268C ASP* 4.1 4.2 - - - +
269C ASN* 3.1 24.8 + - + +
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Residues in contact with TYR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE* 3.4 15.1 - - + +
201C ASN* 4.1 3.8 + - - -
209C LEU* 3.4 28.8 - - + +
211C LEU* 5.4 0.5 - - - +
219C ALA* 4.3 23.8 - - + -
220C SER* 5.1 3.1 - - - -
223C PHE* 3.6 59.2 - + + -
262C CYS* 3.2 12.8 + - - +
263C ILE 3.1 8.2 + - - +
265C GLN* 1.3 78.4 - - - +
267C GLY* 1.3 63.5 + - - +
269C ASN* 3.4 7.1 + - - +
270C CYS* 3.2 36.8 + - - -
312C THR* 4.0 17.0 - - + -
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Residues in contact with GLY 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C PHE* 5.0 1.7 - - - -
263C ILE 3.0 10.7 + - - -
266C TYR* 1.3 80.6 - - - +
268C ASP* 1.3 65.4 + - - +
270C CYS* 3.1 6.6 + - - +
271C ILE* 3.0 23.0 + - - +
308C SER 6.4 0.2 - - - -
309C MET* 3.5 25.8 - - - -
312C THR* 4.4 12.3 - - - -
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Residues in contact with ASP 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C PHE* 2.9 21.8 + - + +
265C GLN* 4.1 4.9 - - - +
267C GLY* 1.3 74.4 - - - +
269C ASN* 1.3 65.9 + - - +
271C ILE* 3.0 9.5 + - - +
272C GLN* 2.9 55.5 + - - +
305C LYS* 4.7 6.1 + - - +
309C MET* 3.4 6.7 - - + +
----------------------------------------------------------
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Residues in contact with ASN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C GLN* 3.1 18.8 + - + +
266C TYR* 3.6 8.7 + - - +
267C GLY 3.2 0.2 - - - -
268C ASP* 1.3 81.1 - - - +
270C CYS* 1.3 68.9 + - - +
272C GLN* 4.0 4.5 - - - +
273C LYS* 3.2 44.0 + - - +
496E LEU* 5.0 10.2 - - - +
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Residues in contact with CYS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ASN* 3.5 27.6 - - - +
205C PHE* 3.7 30.2 - - + +
207C GLU* 6.2 0.5 - - - +
209C LEU* 5.8 3.1 - - - -
266C TYR* 3.2 35.1 + - - -
267C GLY* 3.1 9.7 + - - +
269C ASN* 1.3 86.6 - - - +
271C ILE* 1.3 62.3 + - - +
273C LYS* 3.5 16.2 + - - +
274C ILE* 3.3 21.1 + - - +
312C THR* 5.2 0.4 - - - -
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C PHE* 4.3 6.1 - - + -
267C GLY 3.0 13.5 + - - +
268C ASP* 3.0 12.7 + - - +
270C CYS* 1.3 76.6 - - - +
272C GLN* 1.3 77.0 + - - +
274C ILE* 3.0 17.7 - - + +
275C TYR* 2.8 33.6 + - + +
290C VAL* 4.6 2.7 - - + -
294C LEU* 5.3 4.7 - - + -
301C LEU* 5.8 2.2 - - + -
304C ILE* 4.2 9.2 - - + +
305C LYS* 3.5 51.4 - - + +
308C SER* 3.7 25.4 - - - +
309C MET* 6.4 0.4 - - + -
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Residues in contact with GLN 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ASP* 2.9 53.4 + - - +
269C ASN* 4.0 5.2 - - - +
271C ILE* 1.3 81.8 - - - +
273C LYS* 1.3 64.3 + - - +
275C TYR* 3.8 16.3 - - - +
276C GLN* 3.2 24.1 + - - +
305C LYS* 3.3 26.1 + - - +
496E LEU* 4.0 21.6 - - + +
----------------------------------------------------------
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Residues in contact with LYS 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ASN* 6.2 0.2 - - - +
207C GLU* 3.1 39.9 + - + +
209C LEU* 5.7 8.1 - - - +
269C ASN* 3.2 41.5 + - - +
270C CYS* 3.5 15.0 - - - +
272C GLN* 1.3 80.7 - - - +
274C ILE* 1.3 62.9 + - - +
276C GLN* 3.9 1.6 - - - +
277C GLU* 3.2 27.1 + - - +
184E LEU* 4.2 11.1 - - - +
185E THR* 3.4 48.0 + - + +
496E LEU* 4.5 6.0 - - + +
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C PHE* 3.7 31.9 - - + +
207C GLU* 5.8 0.2 - - - +
270C CYS 3.3 10.4 + - - +
271C ILE* 3.0 29.8 - - + +
273C LYS* 1.3 79.7 - - - +
275C TYR* 1.3 63.3 + - - +
277C GLU* 3.3 1.9 + - - +
278C LEU* 3.0 32.7 + - + +
290C VAL* 4.2 2.7 - - + -
291C ALA* 3.8 30.3 - - + +
294C LEU* 3.6 15.0 - - + -
181E ARG* 3.2 40.8 - - - +
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Residues in contact with TYR 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 2.8 21.4 + - + +
272C GLN* 3.8 17.9 - - - +
273C LYS 3.3 0.2 - - - -
274C ILE* 1.3 79.8 - - + +
276C GLN* 1.3 56.3 + - - +
278C LEU* 3.6 3.0 + - - +
279C ALA* 3.1 27.5 + - + +
294C LEU* 4.0 18.4 - - + -
301C LEU* 3.3 47.0 - - + +
305C LYS* 6.4 0.2 - - - -
476E LEU* 3.6 28.3 - - + -
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Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C GLN 3.2 15.0 + - - +
273C LYS 3.9 2.9 - - - +
275C TYR* 1.3 77.8 - - - +
277C GLU* 1.3 67.1 + - - +
279C ALA* 3.3 7.6 + - - +
280C PHE* 3.4 21.0 - - + -
185E THR* 3.8 6.4 - - + +
474E GLU 3.3 12.5 + - - -
475E THR* 3.9 1.6 - - - +
476E LEU* 3.2 48.3 + - + +
477E THR* 4.7 1.7 + - - -
496E LEU* 2.9 38.4 + - + +
497E LEU 3.7 0.2 - - - -
498E THR* 2.9 31.0 + - - +
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Residues in contact with GLU 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLU* 3.7 14.6 - - - +
273C LYS 3.2 10.1 + - - +
274C ILE 3.3 4.5 + - - +
276C GLN* 1.3 76.9 - - - +
278C LEU* 1.3 62.9 + - - +
280C PHE 3.2 1.7 + - - -
281C ASN 3.2 14.2 + - - +
179E ASN* 6.1 0.5 - - - +
181E ARG* 2.7 52.4 + - - +
183E SER* 4.0 19.5 + - - +
184E LEU 4.0 2.9 - - - -
185E THR* 2.6 40.8 + - - +
498E THR* 4.0 12.1 - - + +
500E ARG* 3.1 27.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 3.0 21.9 + - + +
275C TYR* 4.1 3.8 - - - +
277C GLU* 1.3 75.4 - - - +
279C ALA* 1.3 61.2 + - - +
280C PHE 3.2 0.2 - - - -
281C ASN 3.7 10.0 + - - +
282C ARG* 4.1 13.7 - - - +
283C PRO* 3.7 29.6 - - + -
291C ALA* 3.8 24.7 - - + +
294C LEU* 3.6 42.6 - - + -
295C LEU* 4.4 14.7 - - + +
181E ARG* 3.9 18.4 - - - -
----------------------------------------------------------
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C TYR* 3.1 21.9 + - + +
276C GLN* 3.6 7.9 - - - +
277C GLU 3.2 0.6 - - - -
278C LEU* 1.3 76.7 - - - +
280C PHE* 1.3 63.9 + - + +
476E LEU* 4.1 28.0 - - + -
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Residues in contact with PHE 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLN* 3.4 22.0 - - + -
277C GLU 3.2 2.0 + - - +
279C ALA* 1.3 83.2 - - + +
281C ASN* 1.3 61.5 + - - +
331E ALA 5.4 3.1 - - - -
334E PRO* 6.3 3.4 - - + -
474E GLU* 3.5 49.8 - - + +
475E THR* 3.2 41.5 - - - -
476E LEU* 4.1 15.3 - - + -
478E GLN* 4.9 6.3 - - - -
498E THR* 6.1 0.2 - - - -
500E ARG* 3.9 6.5 - - - +
----------------------------------------------------------
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Residues in contact with ASN 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLU 3.2 11.4 + - - +
278C LEU* 3.7 10.0 + - - +
279C ALA 3.6 1.2 - - - -
280C PHE* 1.3 81.3 - - - +
282C ARG* 1.3 66.6 + - - +
283C PRO* 3.5 28.1 - - - +
181E ARG* 5.4 1.2 - - - +
500E ARG* 3.8 35.2 + - - +
----------------------------------------------------------
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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