Contacts of the helix formed by residues 292 - 325 (chain F) in PDB entry 6O81
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 292 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F LEU* 5.9 0.2 - - - +
290F SER 5.0 3.4 - - - +
291F LYS* 1.3 80.5 - - - +
293F GLU* 1.3 65.7 + - - +
294F GLU* 4.6 17.1 + - - +
295F GLU* 4.1 22.9 - - + +
296F ALA* 3.3 20.6 + - - +
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Residues in contact with GLU 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F TYR* 3.7 6.8 - - - +
241F THR* 3.5 12.6 + - - -
242F THR* 3.3 43.9 + - - +
248F LEU* 5.2 7.7 - - + +
292F ARG* 1.3 75.6 - - - +
294F GLU* 1.3 60.7 + - + +
296F ALA* 3.4 3.8 + - - +
297F LYS* 2.9 47.8 + - + +
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Residues in contact with GLU 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F ARG* 4.6 18.7 + - - +
293F GLU* 1.3 77.5 - - + +
295F GLU* 1.3 71.0 + - - +
297F LYS* 3.7 16.8 - - + +
298F SER* 2.9 33.8 + - - -
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Residues in contact with GLU 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F LYS* 3.9 17.5 - - - +
292F ARG* 4.1 23.5 - - + +
293F GLU 3.2 0.4 - - - -
294F GLU* 1.3 92.3 - - - +
296F ALA* 1.3 56.9 + - - +
298F SER* 2.9 9.8 + - - +
299F GLU* 2.9 63.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 296 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F LEU* 5.0 14.4 - - + -
287F VAL* 5.1 14.5 - - + +
288F GLY 5.9 0.2 - - - +
291F LYS* 4.5 15.0 - - + -
292F ARG 3.3 19.9 + - - +
293F GLU* 3.9 2.7 - - - +
295F GLU* 1.3 79.4 + - - +
297F LYS* 1.3 61.0 + - - +
299F GLU* 3.6 9.3 - - - +
300F LEU* 2.9 37.9 + - + +
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Residues in contact with LYS 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F ILE* 3.4 39.8 - - + +
238F GLN* 3.9 13.8 + - - +
240F TYR* 3.3 30.7 + - + +
248F LEU* 5.1 7.2 - - + -
293F GLU* 2.9 42.2 + - + +
294F GLU* 3.7 13.0 - - - +
296F ALA* 1.3 77.2 - - - +
298F SER* 1.3 56.4 + - - +
300F LEU* 3.3 5.0 + - + +
301F ARG* 2.9 37.3 + - - +
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Residues in contact with SER 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLU* 2.9 18.5 + - - -
295F GLU* 2.9 20.3 + - - +
297F LYS* 1.3 73.0 - - - +
299F GLU* 1.3 61.5 + - - +
301F ARG* 3.4 8.4 + - - +
302F ALA* 2.9 31.2 + - - +
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Residues in contact with GLU 299 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F VAL* 5.4 3.4 - - + +
291F LYS* 2.7 38.9 + - - +
295F GLU* 2.9 46.6 + - - +
296F ALA* 3.6 6.7 - - - +
298F SER* 1.3 79.4 + - - +
300F LEU* 1.3 58.8 + - + +
302F ALA* 3.5 4.9 + - - +
303F ALA* 2.9 29.6 + - - +
306F ARG* 4.7 2.3 + - - -
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Residues in contact with LEU 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F ILE* 4.1 22.0 - - + -
248F LEU* 4.3 13.9 - - + -
252F LEU* 4.3 13.7 - - + -
280F LEU* 4.9 3.8 - - + -
283F GLU* 4.2 29.4 - - + +
284F ILE* 3.7 33.4 - - + -
287F VAL* 4.3 13.9 - - + -
296F ALA* 2.9 22.8 + - + +
297F LYS* 3.8 6.1 - - + +
298F SER 3.3 0.2 - - - -
299F GLU* 1.3 74.6 - - + +
301F ARG* 1.3 60.6 + - - +
303F ALA* 3.3 3.8 + - + +
304F ILE* 2.9 36.9 + - + +
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Residues in contact with ARG 301 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F GLN* 2.9 55.5 + - + +
235F GLN* 4.9 3.8 - - - +
237F ILE* 4.1 17.9 - - + -
238F GLN* 3.6 35.8 + - - +
297F LYS* 2.9 23.7 + - - +
298F SER* 3.8 7.9 - - - +
299F GLU 3.3 0.2 - - - -
300F LEU* 1.3 76.4 - - - +
302F ALA* 1.3 56.8 + - - +
304F ILE* 3.4 7.1 + - - +
305F ASP* 2.9 43.3 + - - +
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Residues in contact with ALA 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F SER 2.9 19.3 + - - +
299F GLU* 3.9 5.6 - - - +
301F ARG* 1.3 75.7 - - - +
303F ALA* 1.3 56.6 + - - +
305F ASP* 3.7 7.4 - - - +
306F ARG* 2.9 55.5 + - + +
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Residues in contact with ALA 303 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F PHE* 4.7 4.8 - - + -
283F GLU* 4.0 27.6 - - + +
299F GLU 2.9 18.6 + - - +
300F LEU* 3.7 8.5 - - + +
301F ARG 3.3 0.2 - - - -
302F ALA* 1.3 74.2 - - - +
304F ILE* 1.3 60.3 + - + +
306F ARG* 3.6 19.8 - - - +
307F TYR* 2.9 31.8 + - - +
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Residues in contact with ILE 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F LEU* 3.9 32.3 - - + +
233F LEU* 4.7 7.4 - - + -
234F GLN* 3.4 32.5 - - + +
237F ILE* 3.8 19.3 - - + -
279F PHE* 5.5 5.8 - - + -
280F LEU* 3.7 36.8 - - + -
283F GLU* 6.4 0.9 - - + -
300F LEU 2.9 21.0 + - - +
301F ARG 3.8 3.6 - - - +
303F ALA* 1.3 75.5 - - + +
305F ASP* 1.3 56.7 + - - +
307F TYR* 3.4 6.8 + - + +
308F VAL* 2.9 30.9 + - + +
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Residues in contact with ASP 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F ARG* 4.2 10.9 + - - -
234F GLN* 2.5 31.1 + - - +
301F ARG* 2.9 29.0 + - - +
302F ALA* 3.7 7.9 - - - +
304F ILE* 1.3 75.6 - - - +
306F ARG* 1.3 58.0 + - + +
308F VAL* 3.4 7.0 - - - +
309F GLN* 2.9 31.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 306 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F GLU 4.7 1.8 + - - -
302F ALA* 2.9 42.9 + - - +
303F ALA* 3.6 25.0 - - - +
305F ASP* 1.3 76.7 - - + +
307F TYR* 1.3 57.9 + - - +
309F GLN* 3.5 5.8 - - - +
310F GLU* 3.0 37.9 + - - +
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Residues in contact with TYR 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F CYS* 5.5 0.4 - - - -
230F LEU* 4.1 26.9 - - + -
275F ASN* 4.5 3.5 + - - +
276F ALA* 4.5 14.5 + - + -
279F PHE* 3.4 56.2 - + + +
303F ALA 2.9 19.7 + - - +
304F ILE* 3.7 5.8 - - + +
306F ARG* 1.3 76.8 - - - +
308F VAL* 1.3 60.0 + - - +
310F GLU* 3.7 10.0 - - - +
311F LYS* 3.0 70.3 + - + +
441F TYR* 3.6 31.9 - + + +
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Residues in contact with VAL 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F CYS* 5.7 1.3 - - - -
227F ILE* 4.0 19.3 - - + -
230F LEU* 3.8 24.0 - - + -
231F ARG* 3.9 28.5 - - - +
304F ILE* 2.9 21.3 + - + +
305F ASP* 3.4 10.8 - - - +
307F TYR* 1.3 80.0 - - - +
309F GLN* 1.3 62.2 + - + +
311F LYS* 5.1 0.7 - - - -
312F ILE* 2.9 54.3 + - + +
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Residues in contact with GLN 309 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F ASP 2.9 20.7 + - - +
306F ARG* 3.5 8.7 - - - +
307F TYR 3.2 0.2 - - - -
308F VAL* 1.3 77.0 - - - +
310F GLU* 1.3 64.6 + - - +
313F VAL* 3.0 59.1 + - + +
314F LEU* 4.8 6.5 - - + +
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Residues in contact with GLU 310 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ARG* 3.0 22.9 + - - +
307F TYR* 3.7 12.1 - - - +
309F GLN* 1.3 76.5 - - - +
311F LYS* 1.3 80.9 + - + +
312F ILE 3.0 2.6 + - - -
314F LEU* 3.0 45.4 + - + +
315F ALA 3.2 9.2 + - - -
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Residues in contact with LYS 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F PHE* 5.7 4.0 - - - -
307F TYR* 3.0 50.9 + - + +
308F VAL* 3.8 1.3 - - - -
310F GLU* 1.3 88.6 - - + +
312F ILE* 1.3 68.8 + - - +
315F ALA* 4.3 14.8 - - - +
439F GLU* 4.3 1.4 - - + +
440F THR* 5.5 8.3 - - - +
441F TYR* 3.6 42.2 - - + +
503F GLU* 5.6 5.4 - - - +
519F LYS* 5.0 26.3 + - - +
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Residues in contact with ILE 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F ASN* 4.0 17.9 - - + +
226F CYS* 5.8 1.6 - - + -
227F ILE* 4.3 22.9 - - + -
308F VAL* 2.9 39.2 + - + +
310F GLU 3.0 0.8 + - - -
311F LYS* 1.3 86.3 - - - +
313F VAL* 1.3 75.3 + - + +
314F LEU 3.5 1.1 - - - -
315F ALA* 3.7 1.6 + - - +
316F ALA* 2.9 33.1 + - + +
344F ARG* 5.6 1.1 - - - +
439F GLU* 4.6 6.8 - - - +
441F TYR* 3.4 30.3 - - + +
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Residues in contact with VAL 313 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F VAL 5.4 0.2 - - - +
309F GLN* 3.0 48.2 + - - +
312F ILE* 1.3 86.4 - - + +
314F LEU* 1.3 71.6 + - + +
316F ALA* 3.8 0.7 - - - +
317F GLN* 2.9 39.8 + - - +
344F ARG* 4.0 22.6 + - - +
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Residues in contact with LEU 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F GLN* 3.9 9.4 - - + +
310F GLU* 3.0 31.8 + - + +
313F VAL* 1.3 93.5 - - + +
315F ALA* 1.3 61.8 + - - +
317F GLN* 3.4 17.3 + - + +
318F ALA* 3.0 30.5 + - - +
321F ARG* 5.3 0.2 + - - -
503F GLU* 5.3 0.7 - - - -
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Residues in contact with ALA 315 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F GLU 3.2 11.8 + - - +
311F LYS* 4.3 9.9 - - - +
312F ILE 4.0 4.5 - - - +
313F VAL 3.3 0.2 - - - -
314F LEU* 1.3 77.7 - - - +
316F ALA* 1.3 57.6 + - - +
318F ALA* 3.4 0.9 + - - +
319F ILE* 2.9 37.1 + - + +
439F GLU* 3.7 25.1 - - + -
440F THR 5.6 0.2 - - - +
503F GLU* 3.8 31.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 316 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F ILE* 2.9 21.4 + - + +
313F VAL 3.8 0.2 - - - +
315F ALA* 1.3 76.1 - - - +
317F GLN* 1.3 55.7 + - - +
319F ILE* 3.8 1.0 - - - +
320F SER* 2.5 39.4 + - - -
341F LEU* 3.9 25.9 - - + +
344F ARG* 3.6 30.1 - - - +
439F GLU* 4.8 4.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F VAL* 2.9 26.9 + - - +
314F LEU* 3.8 20.2 - - + +
316F ALA* 1.3 76.2 - - - +
318F ALA* 1.3 56.4 + - - +
320F SER* 3.4 5.1 + - - -
321F ARG* 2.9 40.5 + - + +
344F ARG* 3.4 25.4 - - - +
348F GLU* 4.5 9.9 - - - +
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Residues in contact with ALA 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F LEU 3.0 18.3 + - - +
317F GLN* 1.3 73.0 - - - +
319F ILE* 1.3 60.8 + - - +
321F ARG* 3.3 27.6 + - - +
322F PHE* 2.9 39.0 + - + -
503F GLU* 3.7 31.6 - - + +
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Residues in contact with ILE 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F ALA 2.9 22.2 + - - +
316F ALA 3.9 2.7 - - - +
318F ALA* 1.3 74.8 - - - +
320F SER* 1.3 57.7 + - - +
322F PHE* 3.3 3.4 + - - +
323F ALA* 2.9 28.8 + - - +
341F LEU* 4.1 19.7 - - + -
345F ILE* 3.7 23.8 - - + -
437F CYS* 4.1 7.9 - - + -
438F CYS 3.8 16.8 - - - +
439F GLU* 4.2 11.2 - - + -
501F ILE* 3.3 39.3 - - + +
502F THR* 3.6 17.5 - - - -
503F GLU* 4.2 3.1 - - - +
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Residues in contact with SER 320 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F ALA 2.5 24.5 + - - -
317F GLN 3.8 2.7 - - - -
319F ILE* 1.3 79.4 - - - +
321F ARG* 1.3 57.2 + - - +
323F ALA* 3.4 1.7 + - - +
324F TYR* 2.9 29.3 + - - +
341F LEU* 4.8 0.9 - - - +
344F ARG* 4.4 4.9 - - - +
345F ILE* 3.6 35.0 + - - +
348F GLU* 3.3 35.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F LEU 5.3 0.2 + - - -
317F GLN* 2.9 24.5 + - + +
318F ALA* 3.5 29.0 - - - +
319F ILE 3.3 0.2 - - - -
320F SER* 1.3 77.2 - - - +
322F PHE* 1.3 79.3 + - + +
324F TYR* 3.4 16.2 + - + +
325F GLN* 3.6 14.4 + - - +
348F GLU* 5.4 4.3 - - - +
----------------------------------------------------------
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Residues in contact with PHE 322 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F ALA* 2.9 25.9 + - + +
319F ILE* 3.8 4.0 - - - +
321F ARG* 1.3 95.4 - - + +
323F ALA* 1.3 59.4 + - - +
325F GLN* 3.4 27.7 - - - +
326F LYS* 3.9 2.9 + - - +
501F ILE* 4.0 14.1 - - + +
502F THR 3.3 17.3 - - - -
503F GLU* 3.2 27.8 - - - -
504F LEU 4.6 2.7 - - - -
505F GLY* 3.5 23.3 - - - -
506F MET* 3.3 27.6 - - + +
237H ARG* 6.2 0.4 - - - -
----------------------------------------------------------
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Residues in contact with ALA 323 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F ILE 2.9 16.7 + - - +
320F SER 3.9 4.0 - - - +
321F ARG 3.3 0.2 - - - -
322F PHE* 1.3 75.3 - - - +
324F TYR* 1.3 64.6 + - - +
325F GLN 3.3 0.9 - - - -
326F LYS* 3.3 6.1 + - - +
327F ILE* 3.2 34.9 + - + +
345F ILE* 4.0 28.7 - - + -
349F ALA* 6.1 0.2 - - - -
402F LEU* 5.3 3.6 - - + -
435F LEU* 6.1 1.1 - - + -
501F ILE* 4.5 18.1 - - + +
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Residues in contact with TYR 324 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F SER 2.9 17.9 + - - +
321F ARG* 3.7 10.8 - - + +
322F PHE 3.4 0.8 - - - -
323F ALA* 1.3 78.1 - - - +
325F GLN* 1.3 63.5 + - + +
326F LYS 3.2 1.5 + - - -
327F ILE* 3.5 17.4 - - - +
348F GLU* 6.2 0.7 - - + -
349F ALA* 4.5 14.1 - - - -
352F GLU* 3.3 50.8 + - + -
353F GLY* 4.9 1.6 - - - -
354F ARG* 3.5 50.4 + - + -
----------------------------------------------------------
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Residues in contact with GLN 325 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F ARG 3.6 9.9 + - - +
322F PHE* 3.4 32.8 - - - +
324F TYR* 1.3 81.6 - - + +
326F LYS* 1.3 59.9 + - - +
327F ILE 4.9 0.4 - - - -
354F ARG* 4.6 8.3 + - - +
506F MET* 3.4 24.5 - - + +
----------------------------------------------------------
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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