Contacts of the helix formed by residues 264 - 293 (chain F) in PDB entry 6PB4
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 LYS 264 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F LEU* 5.5 11.4 - - + -
263F PRO* 1.3 75.3 - - + +
265F GLN* 1.3 65.0 + - - +
266F PHE 3.1 0.9 - - - -
267F ASP* 2.9 34.0 + - - +
268F TYR* 3.1 31.4 + - + +
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Residues in contact with GLN 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F TYR 4.5 1.2 + - - -
147F GLN* 3.4 18.1 - - - +
150F ARG* 3.2 28.6 + - - +
161F LEU* 4.3 7.6 - - + +
165F PHE* 3.4 33.4 - - + -
263F PRO 2.5 8.3 + - - +
264F LYS* 1.3 74.1 - - - +
266F PHE* 1.3 79.2 + - + +
268F TYR* 3.3 24.3 - - + +
269F LEU* 3.0 43.9 - - - +
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Residues in contact with PHE 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F VAL* 5.1 8.7 - - + -
143F TYR 5.3 0.9 - - - -
144F LEU* 4.2 20.6 - - + -
165F PHE* 4.7 3.1 - + - -
256F PHE* 3.9 29.6 - + - -
259F PHE* 5.8 3.4 - - + -
260F ARG 4.6 7.6 - - - -
261F LEU* 5.1 6.7 - - + -
262F VAL* 3.2 50.0 - - + +
263F PRO 3.4 1.5 + - - -
264F LYS 2.9 1.2 + - - -
265F GLN* 1.3 93.1 - - + +
267F ASP* 1.3 57.2 + - - +
268F TYR 3.2 0.4 - - - -
269F LEU* 2.9 24.2 + - + +
270F VAL* 2.6 42.6 + - + +
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Residues in contact with ASP 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F PRO* 5.5 1.5 - - - +
264F LYS* 2.9 26.0 + - - +
266F PHE* 1.3 76.7 - - - +
268F TYR* 1.3 52.5 + - + +
270F VAL* 2.9 9.7 + - - +
271F ASN* 2.4 50.6 + - - +
274F ARG* 5.1 4.9 + - - +
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Residues in contact with TYR 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F LYS* 3.1 49.2 + - + +
265F GLN* 3.3 17.5 - - + +
267F ASP* 1.3 77.5 - - + +
269F LEU* 1.3 54.5 + - + +
271F ASN* 2.9 14.4 + - + +
272F SER* 2.6 42.7 + - - +
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Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F VAL* 5.7 6.5 - - + -
143F TYR* 3.5 42.1 - - + +
147F GLN* 3.6 22.0 - - - +
265F GLN* 3.0 45.3 - - - +
266F PHE* 2.9 31.9 + - + +
268F TYR* 1.3 79.4 - - + +
270F VAL* 1.3 58.8 + - + +
272F SER* 3.3 20.8 - - - +
273F MET* 3.3 19.8 + - + +
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Residues in contact with VAL 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F VAL* 5.1 9.6 - - + -
134F VAL* 4.7 11.2 - - + -
266F PHE* 2.6 24.0 + - + +
267F ASP* 3.4 10.8 - - - +
269F LEU* 1.3 70.6 - - + +
271F ASN* 1.3 55.8 + - - +
272F SER 3.1 1.3 - - - -
273F MET* 2.9 20.7 + - + +
274F ARG* 2.5 60.7 + - + +
365F MET* 4.7 21.8 - - + -
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Residues in contact with ASN 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F ASP* 2.4 44.2 + - - +
268F TYR* 3.3 16.5 - - + +
270F VAL* 1.3 70.8 - - - +
272F SER* 1.3 56.4 + - - +
274F ARG* 2.5 41.5 + - - +
275F VAL* 2.8 45.5 + - + +
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Residues in contact with SER 272 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F TYR* 4.1 21.7 - - - -
268F TYR* 2.6 25.9 + - - +
269F LEU* 3.3 20.7 - - - +
271F ASN* 1.3 74.1 - - - +
273F MET* 1.3 59.0 + - - +
275F VAL* 4.7 1.6 - - - +
276F MET* 3.2 27.7 + - - +
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Residues in contact with MET 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F VAL* 6.3 0.2 - - + -
133F SER* 4.4 6.3 - - - +
134F VAL* 3.9 34.1 - - + +
137F TYR* 3.3 52.2 + - + +
140F ALA* 5.4 11.2 - - + +
143F TYR* 5.7 2.2 - - + -
269F LEU* 3.3 23.3 - - + +
270F VAL* 2.9 22.0 + - + +
272F SER* 1.3 78.3 - - - +
274F ARG* 1.3 64.2 + - - +
275F VAL 3.4 0.4 - - - -
276F MET* 4.2 4.3 - - - +
277F MET* 3.7 17.8 + - - +
362F ASN* 4.6 6.1 + - - -
365F MET* 5.5 14.6 - - + +
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Residues in contact with ARG 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F ASP* 5.1 4.4 + - - +
270F VAL* 2.5 41.9 + - + +
271F ASN* 2.5 38.2 + - - +
273F MET* 1.3 72.1 - - - +
275F VAL* 1.3 67.7 + - + +
277F MET* 3.4 29.8 - - + +
278F ASP* 3.5 17.0 + - - +
365F MET* 5.5 9.6 - - + +
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Residues in contact with VAL 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F ASN* 2.8 26.8 + - + +
272F SER* 4.7 2.9 - - - +
274F ARG* 1.3 80.3 - - + +
276F MET* 1.3 66.8 + - + +
278F ASP* 2.9 28.3 + - + +
279F ARG* 3.2 20.3 + - + +
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Residues in contact with MET 276 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F SER 3.2 21.4 + - - +
273F MET* 4.5 4.5 - - - +
274F ARG 3.4 0.4 - - - -
275F VAL* 1.3 79.1 - - + +
277F MET* 1.3 67.5 + - - +
279F ARG* 2.9 57.1 + - - +
280F VAL* 3.2 17.1 + - + +
347F ILE* 3.7 10.3 - - + -
350F GLU* 3.4 24.7 - - + +
351F THR* 3.5 25.6 - - + -
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Residues in contact with MET 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F MET 3.7 7.8 + - - +
274F ARG* 3.4 24.8 + - + +
275F VAL 3.2 0.2 - - - -
276F MET* 1.3 77.2 - - - +
278F ASP* 1.3 74.1 + - - +
279F ARG 2.9 6.8 + - - -
280F VAL* 3.0 7.2 + - - +
281F ARG* 2.9 34.0 + - + +
358F VAL* 5.7 4.0 - - - -
362F ASN* 3.4 48.0 - - - +
363F ARG* 6.0 0.7 - - - -
365F MET* 5.5 7.2 - - + -
366F SER* 5.1 8.1 - - - +
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Residues in contact with ASP 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F ARG* 3.5 19.8 - - - +
275F VAL* 2.9 14.5 + - + +
277F MET* 1.3 89.4 - - - +
279F ARG* 1.3 51.9 + - - +
281F ARG* 4.2 25.0 + - - +
282F THR* 2.5 28.6 + - - -
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Residues in contact with ARG 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F VAL* 3.5 17.7 - - + +
276F MET* 2.9 52.0 + - + +
277F MET 2.9 0.2 + - - -
278F ASP* 1.3 79.4 - - - +
280F VAL* 1.3 61.7 + - + +
281F ARG 3.3 0.9 - - - -
282F THR* 2.9 9.8 + - - -
283F GLN* 2.8 31.8 + - - +
343F LYS* 3.7 25.3 - - - +
347F ILE* 4.2 16.7 - - + +
350F GLU* 3.6 20.3 + - - +
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Residues in contact with VAL 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F MET* 3.2 11.2 + - + +
277F MET* 3.0 6.7 + - - +
279F ARG* 1.3 78.1 - - + +
281F ARG* 1.3 62.6 + - - +
283F GLN* 2.9 21.0 + - + -
284F GLU* 2.9 38.9 + - + +
347F ILE* 5.0 16.8 - - + -
351F THR* 6.5 0.4 - - + -
355F ILE* 5.8 7.2 - - + -
358F VAL* 5.1 18.4 - - + -
359F LYS* 5.6 3.4 - - - -
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Residues in contact with ARG 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F MET* 2.9 25.7 + - + +
278F ASP* 4.2 22.5 + - - +
280F VAL* 1.3 76.6 - - - +
282F THR* 1.3 62.4 + - - +
284F GLU* 4.5 9.4 - - - +
285F ARG* 3.2 22.0 + - + +
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Residues in contact with THR 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F ASP 2.5 26.0 + - - -
279F ARG* 2.9 15.0 + - - -
281F ARG* 1.3 75.9 - - - +
283F GLN* 1.3 70.3 + - - +
285F ARG* 3.0 6.1 + - - +
286F LEU* 2.9 24.3 + - + +
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Residues in contact with GLN 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F ARG* 2.8 23.1 + - - +
280F VAL* 2.9 15.5 + - + +
282F THR* 1.3 79.7 - - - +
284F GLU* 1.3 65.5 + - + +
286F LEU* 3.0 11.5 + - - +
287F ILE* 3.0 38.9 + - + +
340F ALA 4.8 4.2 - - - +
343F LYS* 3.8 31.8 - - - +
344F LEU* 4.6 15.4 + - + +
347F ILE* 3.4 31.5 - - + +
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Residues in contact with GLU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F VAL* 2.9 34.4 + - + +
281F ARG* 4.5 7.5 - - - +
283F GLN* 1.3 75.9 - - + +
285F ARG* 1.3 59.8 + - - +
287F ILE* 3.0 12.6 + - + +
288F MET* 2.9 39.8 + - + +
306F PHE* 5.6 7.0 - - + -
307F THR* 5.3 2.6 - - - +
310F GLU* 5.3 5.9 - - - +
355F ILE* 5.7 0.3 - - - +
359F LYS* 3.4 32.5 + - - -
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Residues in contact with ARG 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F ARG* 3.2 20.2 + - + +
282F THR* 3.0 5.4 + - - +
284F GLU* 1.3 78.5 - - - +
286F LEU* 1.3 64.3 + - - +
288F MET* 3.2 42.2 - - - +
289F LYS* 3.0 46.3 + - - +
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Residues in contact with LEU 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F THR* 2.9 15.0 + - + +
283F GLN* 3.3 15.9 - - - +
285F ARG* 1.3 75.7 - - - +
287F ILE* 1.3 68.1 + - + +
289F LYS* 3.0 24.0 + - + +
290F LEU* 3.2 36.9 + - + +
340F ALA* 5.7 6.1 - - + -
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Residues in contact with ILE 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F GLN* 3.1 36.8 - - + +
284F GLU* 3.0 11.1 + - + +
286F LEU* 1.3 80.7 - - + +
288F MET* 1.3 63.5 + - - +
290F LEU* 3.0 11.9 + - - +
291F CYS* 2.8 38.1 + - - -
302F PHE* 4.2 6.1 - - + -
306F PHE* 3.8 41.5 - - + -
340F ALA* 4.9 22.4 - - + +
341F LEU* 6.5 0.2 - - - -
344F LEU* 4.8 11.2 - - + -
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Residues in contact with MET 288 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F GLU* 2.9 23.2 + - + +
285F ARG* 3.2 35.0 - - - +
287F ILE* 1.3 74.5 - - - +
289F LYS* 1.3 58.4 + - - +
291F CYS 3.0 0.5 + - - -
292F VAL* 2.6 60.4 + - + +
299F LYS* 3.6 26.7 - - - +
302F PHE* 4.4 10.5 - - + -
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Residues in contact with LYS 289 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F ARG* 3.0 45.6 + - - +
286F LEU* 3.0 15.7 + - + +
288F MET* 1.3 78.4 - - - +
290F LEU* 1.3 68.5 + - + +
292F VAL* 5.3 0.4 - - - -
293F GLU* 3.3 36.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 290 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F LEU* 3.6 39.5 - - + +
287F ILE* 3.0 13.0 + - + +
289F LYS* 1.3 86.9 - - + +
291F CYS* 1.3 66.6 + - - +
293F GLU* 4.4 1.9 + - - +
294F GLN* 4.4 12.0 - - - +
333F VAL* 5.6 5.4 - - - +
336F GLU* 5.7 10.5 - - + +
339F ARG* 6.2 1.3 - - - +
340F ALA* 4.9 14.8 - - + -
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Residues in contact with CYS 291 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 2.8 28.7 + - - +
290F LEU* 1.3 84.5 - - - +
292F VAL* 1.3 64.5 + - - +
293F GLU 3.4 0.5 + - - -
294F GLN* 3.4 7.3 + - - +
295F CYS* 3.4 28.6 + - - -
302F PHE* 3.4 36.1 - - + -
306F PHE* 6.0 1.1 - - - -
315F TRP* 6.2 2.5 - - - -
333F VAL* 6.3 1.3 - - - -
337F VAL* 4.7 23.6 - - - -
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Residues in contact with VAL 292 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F MET* 2.6 49.0 + - + +
289F LYS* 5.3 0.2 - - - -
291F CYS* 1.3 72.4 - - - +
293F GLU* 1.3 68.4 + - + +
294F GLN* 3.0 2.8 + - - -
295F CYS* 4.2 4.4 + - - +
297F MET 4.9 0.3 - - - +
298F PRO* 3.5 27.3 - - - +
299F LYS* 3.8 23.1 - - + +
302F PHE* 3.8 27.1 - - + -
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Residues in contact with GLU 293 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F LYS* 3.3 35.3 + - + +
290F LEU 5.0 2.0 - - - +
291F CYS 3.3 1.2 - - - -
292F VAL* 1.3 81.1 - - + +
294F GLN* 1.3 60.1 + - + +
----------------------------------------------------------
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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