Contacts of the helix formed by residues 287 - 314 (chain F) in PDB entry 6C3P
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 ILE 287 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F ALA* 1.3 78.0 - - + +
288F TRP* 1.3 69.4 + - + +
289F GLN 3.1 2.7 - - - -
290F ALA* 3.1 11.1 + - + +
291F LEU* 2.9 27.8 + - + +
394F LYS* 6.3 1.6 - - - +
607F VAL* 3.6 30.1 - - + -
610F LEU* 4.5 19.7 - - + -
611F SER* 4.7 20.4 - - - +
614F LEU* 5.7 12.3 - - + -
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Residues in contact with TRP 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F ALA* 4.9 11.4 - - + +
287F ILE* 1.3 79.1 - - + +
289F GLN* 1.3 60.2 + - + +
291F LEU* 3.6 15.7 - - + +
292F SER* 2.9 32.8 + - - -
432F PHE* 6.6 0.2 - + - -
603F ALA 5.4 0.2 - - - -
604F LEU* 3.5 47.3 - - + -
607F VAL* 3.2 41.2 - - + +
608F GLN 5.9 0.2 - - - -
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Residues in contact with GLN 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F ALA* 5.4 3.8 - - + -
286F ALA 3.6 31.6 + - - +
287F ILE 3.1 0.4 - - - -
288F TRP* 1.3 78.4 - - + +
290F ALA* 1.3 57.4 + - - +
292F SER* 2.6 22.3 + - - -
293F HIS* 2.9 17.8 + - - +
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F GLU* 4.5 2.7 - - - +
269F ALA* 4.5 18.4 - - + +
272F ALA* 4.3 21.6 - - + +
286F ALA 4.1 1.7 + - - +
287F ILE* 3.1 14.9 + - + +
289F GLN* 1.3 75.8 - - - +
291F LEU* 1.3 67.0 + - - +
293F HIS* 3.3 7.0 + - - +
294F ALA* 2.9 26.1 + - - +
394F LYS* 6.0 4.0 - - - +
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Residues in contact with LEU 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 2.9 16.1 + - + +
288F TRP* 3.6 19.7 - - + +
290F ALA* 1.3 76.0 - - - +
292F SER* 1.3 67.7 + - - +
294F ALA* 3.0 6.4 + - - +
295F PHE* 2.9 48.9 + - + +
299F LEU* 5.2 2.7 - - + -
387F LEU* 3.7 39.9 - - + -
391F ILE* 5.8 1.6 - - + -
428F LEU* 6.4 1.1 - - + -
432F PHE* 4.1 22.9 - - + -
607F VAL* 6.6 0.4 - - + -
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Residues in contact with SER 292 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F TRP 2.9 17.3 + - - -
289F GLN* 2.6 26.2 + - - -
291F LEU* 1.3 79.5 - - - +
293F HIS* 1.3 63.1 + - - +
295F PHE 2.9 0.2 + - - -
296F GLY* 2.9 31.7 + - - +
299F LEU* 6.4 0.7 - - - -
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Residues in contact with HIS 293 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F GLU* 4.1 17.2 + - + +
271F ASP* 3.7 28.0 - - + +
272F ALA* 4.3 10.8 + - + +
275F ARG* 6.4 1.1 - - + -
289F GLN 2.9 16.0 + - - +
290F ALA* 3.7 7.2 - - - +
292F SER* 1.3 79.8 + - - +
294F ALA* 1.3 59.4 + - - +
295F PHE 3.7 0.2 + - - -
297F ARG* 5.6 3.6 + - - -
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Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F GLN* 4.8 9.2 - - + +
265F ARG* 4.8 9.4 - - + +
268F GLU* 3.4 25.1 - - + +
290F ALA 2.9 17.6 + - - +
291F LEU* 3.5 6.3 - - - +
293F HIS* 1.3 76.7 - - - +
295F PHE* 1.3 62.8 + - + +
297F ARG* 5.6 5.4 + - - +
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Residues in contact with PHE 295 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F LEU* 2.9 34.6 + - + +
292F SER 2.9 0.6 + - - -
294F ALA* 1.3 84.2 - - + +
296F GLY* 1.3 65.2 + - - +
297F ARG* 3.1 7.0 + - - -
298F ARG* 3.5 22.7 + - + +
299F LEU* 3.8 30.2 + - + -
383F THR* 3.2 54.3 - - + -
386F ASN* 4.6 13.2 - - + -
387F LEU* 4.8 15.9 - - + -
432F PHE* 4.9 7.2 - + - -
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Residues in contact with GLY 296 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F SER* 2.9 20.9 + - - -
293F HIS 4.9 0.4 + - - -
295F PHE* 1.3 77.1 - - - +
297F ARG* 1.3 58.3 + - - +
298F ARG 3.3 0.2 - - - -
299F LEU* 3.3 12.8 + - - +
300F VAL* 2.9 37.3 + - - +
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Residues in contact with ARG 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F HIS 5.6 3.4 + - - -
294F ALA 5.6 5.3 + - - +
295F PHE* 4.7 4.5 - - - +
296F GLY* 1.3 77.5 - - - +
298F ARG* 1.3 63.7 + - + +
300F VAL* 3.1 13.1 - - + +
301F LEU* 2.9 29.8 + - - +
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Residues in contact with ARG 298 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F PHE* 3.5 16.0 + - + +
296F GLY 3.3 0.4 - - - -
297F ARG* 1.3 85.9 - - + +
299F LEU* 1.3 58.4 + - - +
301F LEU* 3.2 12.0 + - + +
302F SER 3.0 23.7 + - - -
379F VAL* 3.5 18.7 - - + +
382F GLU* 3.1 35.7 + - - -
383F THR* 3.4 23.1 - - + +
386F ASN* 4.5 7.2 - - - +
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Residues in contact with LEU 299 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F LEU* 5.2 3.6 - - + -
292F SER* 6.4 0.9 - - - -
295F PHE* 3.8 34.3 + - + +
296F GLY* 3.3 12.9 + - - +
297F ARG 3.3 0.4 - - - -
298F ARG* 1.3 78.9 - - - +
300F VAL* 1.3 59.3 + - + +
302F SER* 3.2 6.2 + - - -
303F SER* 2.8 32.4 + - - +
380F ALA* 5.2 4.5 - - + -
383F THR* 3.8 28.5 - - + +
432F PHE* 4.0 15.9 - - + +
435F CYS* 3.7 36.9 - - + -
436F PRO* 4.8 2.2 - - + +
439F TRP* 5.9 2.0 - - + -
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Residues in contact with VAL 300 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F GLY* 2.9 20.9 + - - +
297F ARG* 3.1 22.2 - - + +
299F LEU* 1.3 77.6 - - + +
301F LEU* 1.3 52.7 + - - +
303F SER* 3.6 9.4 - - - +
304F THR* 2.6 40.1 + - - +
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Residues in contact with LEU 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F ARG 2.9 15.3 + - - +
298F ARG* 3.3 13.9 - - + +
299F LEU 3.1 0.2 - - - -
300F VAL* 1.3 76.6 - - - +
302F SER* 1.3 67.4 + - - +
304F THR* 3.2 7.8 + - - -
305F PHE* 3.0 60.0 + - + -
379F VAL* 3.8 18.2 - - + -
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Residues in contact with SER 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F ARG 3.0 8.6 + - - -
299F LEU* 3.6 9.4 - - - -
301F LEU* 1.3 75.4 - - - +
303F SER* 1.3 63.8 + - - +
305F PHE* 3.2 8.7 + - - +
306F ARG 3.0 6.6 + - - -
376F SER* 2.1 56.4 + - - -
379F VAL* 3.5 24.5 - - - -
380F ALA* 3.5 16.9 + - - +
436F PRO* 4.0 5.5 - - - +
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Residues in contact with SER 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 2.8 20.9 + - - +
300F VAL* 3.6 11.2 - - - -
301F LEU 3.2 0.2 - - - -
302F SER* 1.3 75.2 - - - +
304F THR* 1.3 55.2 + - - +
306F ARG* 2.6 25.7 + - - +
307F ILE* 2.8 28.3 + - - +
435F CYS* 5.7 0.3 - - - -
436F PRO* 3.4 32.0 + - - +
439F TRP* 4.6 14.9 - - - +
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Residues in contact with THR 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F VAL* 2.6 27.6 + - - +
301F LEU* 3.2 7.9 + - - -
303F SER* 1.3 71.5 - - - +
305F PHE* 1.3 68.2 + - + +
307F ILE* 3.9 8.6 - - + +
308F LEU* 2.9 33.1 + - + +
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Residues in contact with PHE 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F LEU* 3.0 47.5 + - + -
302F SER* 3.2 7.9 - - - +
304F THR* 1.3 82.3 - - + +
306F ARG* 1.3 57.7 - - - +
308F LEU* 3.9 4.9 - - + +
309F ALA* 2.9 30.5 + - - +
372F PHE* 4.0 12.5 - + + +
375F ALA* 3.4 36.1 - - + -
376F SER* 3.5 15.5 - - - +
379F VAL* 3.7 13.2 - - + -
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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
----------------------------------------------------------
302F SER 3.0 6.3 + - - +
303F SER* 2.6 17.4 + - - +
305F PHE* 1.3 72.5 - - - +
307F ILE* 1.3 56.3 + - - +
309F ALA* 3.5 2.9 - - - +
310F ASP* 2.9 40.7 + - - +
373F LEU* 3.9 22.8 + - - +
376F SER* 2.9 34.2 + - - +
377F TYR* 4.1 26.9 - - - +
433F PHE 5.2 2.6 + - - -
436F PRO* 3.8 16.8 - - + +
437F ASN* 3.6 35.1 + - - +
440F ALA* 3.5 24.0 - - + -
592F LEU* 5.6 3.4 - - - +
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Residues in contact with ILE 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F SER* 2.8 46.5 + - - +
304F THR* 3.9 9.2 - - + +
306F ARG* 1.3 69.4 - - - +
308F LEU* 1.3 68.8 + - - +
310F ASP* 2.5 22.4 - - - +
311F LEU* 2.9 22.9 + - + +
439F TRP* 4.6 5.4 - - + +
440F ALA* 4.0 29.6 - - + +
443F VAL* 4.2 32.1 - - + -
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Residues in contact with LEU 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F THR* 2.9 24.8 + - + +
305F PHE* 3.9 6.1 - - + +
307F ILE* 1.3 77.8 - - - +
309F ALA* 1.3 67.5 + - - +
311F LEU* 3.8 5.4 - - - +
312F LEU* 2.9 28.7 + - + +
372F PHE* 3.6 35.4 - - + -
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Residues in contact with ALA 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F PHE 2.9 19.0 + - - +
306F ARG 3.5 3.8 - - - +
307F ILE 3.2 0.2 - - - -
308F LEU* 1.3 76.3 - - - +
310F ASP* 1.3 57.7 + - - +
312F LEU* 2.8 17.9 + - - -
369F GLN* 2.2 52.5 + - - +
372F PHE* 3.8 14.8 - - + -
373F LEU* 3.6 17.7 - - + +
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Residues in contact with ASP 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ARG* 2.9 23.9 + - - +
307F ILE* 2.5 33.4 - - - +
309F ALA* 1.3 73.6 - - - +
311F LEU* 1.3 62.3 + - - +
313F GLY* 3.7 1.2 - - - -
314F PHE* 2.8 28.8 + - - +
369F GLN* 3.5 8.2 + - - +
373F LEU* 5.4 2.5 - - + -
440F ALA* 4.1 17.3 - - - +
443F VAL* 6.0 0.7 - - - +
444F GLN* 3.4 47.0 + - - +
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Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ILE* 2.9 24.3 + - + +
308F LEU* 3.8 4.7 - - - +
310F ASP* 1.3 82.1 + - - +
312F LEU* 1.3 66.8 + - - +
314F PHE* 3.1 20.5 - - + +
315F ALA* 3.7 3.1 + - - +
443F VAL* 6.1 4.7 - - + -
444F GLN* 6.4 1.8 - - - +
447F VAL* 3.6 40.8 - - + -
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Residues in contact with LEU 312 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F LEU* 2.9 17.9 + - + +
309F ALA 2.8 13.1 + - - +
311F LEU* 1.3 67.9 - - - +
313F GLY* 1.3 52.4 + - - +
314F PHE 3.0 3.6 - - - -
315F ALA* 2.6 42.3 + - + +
365F ALA* 3.7 38.5 - - + +
368F LEU* 4.0 23.8 - - + -
369F GLN* 4.1 8.5 - - - +
372F PHE* 4.8 10.1 - - + -
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Residues in contact with GLY 313 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F ALA 2.9 2.6 + - - -
310F ASP* 3.7 4.3 - - - -
312F LEU* 1.3 69.7 - - - +
314F PHE* 1.3 55.1 + - - +
315F ALA 3.0 0.2 - - - -
316F GLY* 2.9 23.0 + - - -
317F PRO* 4.2 2.1 - - - +
365F ALA* 5.8 2.7 - - - -
366F LEU* 5.0 10.8 - - - +
369F GLN* 2.8 37.3 - - - +
370F ARG* 5.8 0.2 - - - -
585F ILE* 4.9 9.5 - - - +
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Residues in contact with PHE 314 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F ASP 2.8 16.1 + - - +
311F LEU* 3.1 18.8 - - + +
312F LEU 2.9 0.4 + - - -
313F GLY* 1.3 71.5 - - - +
315F ALA* 1.3 55.6 + - - +
316F GLY 3.0 8.9 + - - -
317F PRO* 3.3 15.7 - - + +
318F LEU* 4.8 6.0 - - + +
444F GLN* 5.0 13.5 - - + -
447F VAL* 3.4 28.5 - - + -
448F GLY* 3.3 35.0 - - - -
451F LEU* 3.3 36.6 - - + +
582F LEU* 4.0 23.5 - - + +
585F ILE* 5.4 13.2 - - + -
586F LEU* 6.1 2.7 - - + -
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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