Contacts of the helix formed by residues 293 - 318 (chain B) in PDB entry 3R29
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 PRO 293 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU 3.8 5.4 - - - +
292B LEU* 1.3 100.5 - - + +
294B LEU* 1.3 66.2 + - - +
295B ASP* 4.3 5.6 - - + +
296B ASP* 2.9 21.2 + - + +
297B GLN 3.0 7.4 + - - -
384B SER* 4.2 19.7 - - - +
385B ASN* 5.6 6.7 - - + +
388B GLU* 5.4 0.2 - - - +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU 3.3 1.2 + - - -
293B PRO* 1.3 72.2 - - - +
295B ASP* 1.3 58.3 + - - +
297B GLN* 3.4 23.3 - - - +
298B VAL* 2.9 17.8 - - - +
2346D ARG* 3.5 40.2 - - + +
2349D LEU* 4.6 22.2 - - + +
2350D MET* 4.3 28.5 - - + -
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PRO* 3.0 3.2 - - + +
294B LEU* 1.3 77.1 - - - +
296B ASP* 1.3 65.0 + - - +
298B VAL* 2.5 33.3 + - - +
299B ILE* 3.4 13.3 + - + +
384B SER* 5.1 6.1 - - - +
2342D GLU* 5.2 3.3 - - - +
2346D ARG* 2.9 33.6 + - - -
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.7 9.4 - - + -
293B PRO* 2.9 21.3 + - + +
295B ASP* 1.3 78.8 - - - +
297B GLN* 1.3 67.2 + - - +
298B VAL 2.6 5.8 + - - -
299B ILE* 3.4 10.0 + - - +
300B LEU* 3.1 29.3 + - + +
383B LEU* 3.8 14.1 - - + +
384B SER* 2.7 44.8 + - - -
385B ASN 2.9 25.9 + - - +
389B VAL* 5.6 0.7 - - + -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 4.2 6.9 - - - +
289B PHE* 3.5 35.0 - - + +
290B SER* 3.2 32.8 + - - +
292B LEU* 2.1 38.2 + - + +
293B PRO 3.0 15.2 + - - -
294B LEU* 3.4 20.1 - - - +
296B ASP* 1.3 77.7 - - - +
298B VAL* 1.3 56.7 + - - +
300B LEU* 3.7 2.4 + - - +
301B LEU* 2.8 32.2 + - - +
2349D LEU* 3.8 22.9 - - + +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU 2.9 17.9 - - - +
295B ASP* 2.5 37.5 - - - +
296B ASP 2.6 8.9 + - - -
297B GLN* 1.3 68.3 - - - +
299B ILE* 1.3 68.1 + - + +
300B LEU 3.0 1.1 - - - -
301B LEU* 2.9 16.7 + - - +
302B ARG* 3.0 20.3 + - + +
2342D GLU* 4.4 30.1 - - + +
2345D ILE* 4.1 29.2 - - + +
2346D ARG* 4.8 13.2 - - + +
2349D LEU* 5.0 3.6 - - + -
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP* 3.4 15.5 + - + +
296B ASP* 3.9 13.2 - - - +
298B VAL* 1.3 77.6 - - + +
300B LEU* 1.3 58.7 + - - +
302B ARG* 3.2 9.3 + - - +
303B ALA* 2.8 29.5 + - + +
380B SER* 3.6 23.8 - - - +
381B LYS* 3.3 38.1 - - - +
382B GLY 2.8 33.2 - - - +
383B LEU* 3.8 13.7 - - + -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 5.1 1.8 - - + -
292B LEU* 4.0 26.7 - - + -
296B ASP* 3.1 17.1 + - + +
297B GLN* 3.9 5.6 - - - +
298B VAL 3.0 1.2 - - - -
299B ILE* 1.3 75.7 - - - +
301B LEU* 1.3 59.2 + - + +
303B ALA* 4.2 2.4 - - + +
304B GLY* 3.0 25.5 + - - -
375B LEU* 3.3 42.9 - - + +
376B PHE* 4.3 7.0 - - + -
377B ASN* 3.7 26.0 - - + +
380B SER* 4.0 9.4 - - - +
383B LEU* 4.0 15.7 - - + -
389B VAL* 4.2 14.4 - - + -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.5 46.9 - - + +
280B VAL* 4.1 9.6 - - + -
282B TRP* 6.3 0.2 - - + -
283B ALA* 4.1 8.1 - - + -
289B PHE* 3.5 25.1 - - + -
297B GLN* 2.8 24.5 - - + +
298B VAL 2.9 7.4 + - - +
300B LEU* 1.3 76.6 - - + +
302B ARG* 1.3 60.4 + - - +
304B GLY* 3.8 0.7 - - - +
305B TRP* 3.0 36.4 + - + +
308B LEU* 5.4 0.4 - - - -
375B LEU* 3.9 13.0 - - + -
2345D ILE* 4.4 26.2 - - + -
2349D LEU* 5.0 4.7 - - + -
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B VAL* 3.0 16.9 + - + +
299B ILE* 3.3 12.8 - - - +
301B LEU* 1.3 78.3 - - - +
303B ALA* 1.3 65.2 + - - +
305B TRP* 3.6 14.2 + - - +
306B ASN 5.3 0.2 + - - -
381B LYS* 4.9 16.4 - - - +
2341D LEU* 3.3 43.3 - - + +
2342D GLU* 4.1 21.2 + - - +
2345D ILE* 5.6 10.7 - - + +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 2.8 15.1 + - + +
300B LEU* 4.2 2.9 - - - +
302B ARG* 1.3 79.8 - - - +
304B GLY* 1.3 59.3 + - - +
305B TRP 3.6 0.2 + - - -
306B ASN* 5.0 2.1 + - - +
307B GLU* 5.7 3.8 + - - +
377B ASN* 5.8 2.9 - - + +
380B SER* 3.2 29.2 - - - +
381B LYS 5.9 0.2 - - - +
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU 3.0 19.0 + - - -
303B ALA* 1.3 77.3 - - - +
305B TRP* 1.3 68.2 + - - +
306B ASN 3.1 2.0 + - - -
307B GLU* 3.3 6.1 + - - +
308B LEU* 3.0 37.7 + - - +
374B VAL* 4.6 16.4 - - - -
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA* 3.9 7.0 - - + -
275B GLN* 3.6 37.8 + - + +
276B LEU* 3.4 49.1 - - + -
279B LEU* 4.3 23.5 - - + +
280B VAL* 5.6 1.6 - - + -
301B LEU* 3.0 27.3 + - + +
302B ARG* 3.6 11.9 - - - +
303B ALA 3.3 2.4 - - - -
304B GLY* 1.3 78.1 - - - +
306B ASN* 1.3 77.4 + - - +
308B LEU* 3.7 2.3 - - - +
309B LEU* 3.1 30.4 + - + +
2341D LEU* 5.8 3.8 - - + -
2345D ILE* 4.5 15.9 - - + -
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Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 5.0 1.5 + - - +
304B GLY 3.1 1.0 + - - -
305B TRP* 1.3 86.8 - - - +
307B GLU* 1.3 56.7 + - + +
309B LEU* 3.1 6.5 + - - +
310B ILE* 2.7 48.8 + - + +
429B GLY* 3.3 27.2 + - - +
432B CYS* 4.4 9.7 - - - +
433B LEU* 3.9 25.1 - - + +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 5.7 4.3 - - - -
304B GLY* 3.3 4.4 + - - +
306B ASN* 1.3 75.8 - - + +
308B LEU* 1.3 54.8 + - - +
310B ILE* 2.5 26.6 + - - +
311B ALA* 2.6 20.9 + - - -
374B VAL* 3.3 31.0 - - + +
377B ASN* 5.6 0.7 + - - -
425B LEU* 3.6 36.4 - - + +
426B ARG* 3.1 54.4 + - - +
429B GLY* 4.7 7.3 - - - -
430B LEU* 5.9 0.5 - - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 4.1 26.7 - - + -
282B TRP* 4.4 12.3 - - + -
300B LEU 4.8 1.3 - - - +
301B LEU* 5.3 0.4 - - + +
304B GLY* 3.0 31.5 + - - +
305B TRP 3.7 2.7 - - - +
307B GLU* 1.3 76.6 - - - +
309B LEU* 1.3 58.7 + - - +
311B ALA 3.8 0.2 + - - -
312B SER* 3.0 24.8 + - - -
371B ARG* 3.1 61.9 + - + +
374B VAL* 3.9 14.1 - - + +
375B LEU* 4.0 26.0 - - + +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ILE* 5.5 11.4 - - + -
275B GLN* 3.8 45.8 - - + +
278B THR* 5.9 4.9 - - + -
279B LEU* 3.9 16.4 - - + -
305B TRP* 3.1 25.4 + - + +
306B ASN* 3.4 6.7 - - - +
307B GLU 2.8 1.6 + - - -
308B LEU* 1.3 76.9 - - - +
310B ILE* 1.3 64.1 + - + +
312B SER* 3.7 9.2 - - - -
313B PHE* 3.1 40.1 + - + -
316B ARG* 6.3 0.4 - - - +
327B ALA* 6.3 2.9 - - + -
371B ARG* 5.7 0.9 - - - +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN* 2.7 29.0 + - + +
307B GLU* 2.5 13.2 + - - +
309B LEU* 1.3 72.1 - - + +
311B ALA* 1.3 67.6 + - - +
312B SER 2.9 2.8 + - - -
313B PHE* 3.1 37.3 + - + -
314B SER* 2.8 25.8 + - - +
349B VAL* 4.7 3.6 - - + -
353B LEU* 4.2 8.1 - - + -
425B LEU* 3.8 18.6 - - + -
428B ILE* 4.4 9.9 - - + +
429B GLY* 4.3 16.6 - - - -
432B CYS* 3.8 30.3 - - + -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU 2.6 18.9 + - - +
308B LEU* 3.9 4.9 - - - +
310B ILE* 1.3 73.9 - - - +
312B SER* 1.3 57.0 + - - +
314B SER* 3.2 7.7 - - - -
315B HIS* 3.0 26.3 + - - +
353B LEU* 5.9 0.2 - - - -
357B MET* 3.7 12.4 - - + +
367B LEU* 4.1 9.8 - - + +
370B LEU* 6.3 1.8 - - + -
371B ARG* 4.2 21.5 - - + +
425B LEU* 3.9 24.6 - - + +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLU* 5.0 1.4 + - - -
308B LEU 3.0 5.5 + - - -
309B LEU* 3.7 11.2 - - - -
310B ILE 2.9 1.0 + - - -
311B ALA* 1.3 74.8 - - - +
313B PHE* 1.3 66.0 + - - -
315B HIS* 3.3 3.3 + - - +
316B ARG* 3.0 39.6 + - - +
367B LEU* 4.7 9.0 - - - +
371B ARG* 2.3 44.7 + - - +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ILE* 5.1 12.8 - - + -
309B LEU* 3.1 31.9 - - + -
310B ILE* 3.1 41.4 + - + -
312B SER* 1.3 80.0 - - - +
314B SER* 1.3 60.1 + - - +
316B ARG* 3.2 27.9 + - - +
317B SER* 2.5 34.7 + - - -
324B ILE* 4.1 35.0 - - + -
325B LEU 3.6 7.6 - - - +
326B LEU* 4.7 13.0 - - + -
349B VAL* 4.4 23.8 - - + -
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 2.8 30.7 + - - +
311B ALA* 3.2 8.9 - - - -
313B PHE* 1.3 78.5 - - - +
315B HIS* 1.3 64.4 + - - +
317B SER* 3.0 12.4 + - - -
318B ILE* 3.4 4.3 + - - +
349B VAL* 3.8 11.2 - - - +
353B LEU* 4.0 12.0 - - - +
354B VAL* 3.4 29.6 - - - +
357B MET* 3.6 21.7 - - - +
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Residues in contact with HIS 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA 3.0 4.3 + - - +
312B SER 3.3 1.7 + - - +
314B SER* 1.3 80.7 - - - +
316B ARG* 1.3 52.4 + - - +
318B ILE* 2.4 60.0 - - + +
357B MET* 3.6 9.6 - - - -
362B MET* 3.1 45.1 + - + +
363B ASP* 3.7 11.6 - - - -
364B LYS* 4.1 16.8 + - + -
367B LEU* 3.3 58.3 - - + -
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLU* 6.0 1.8 - - - +
244B PRO* 4.4 24.0 - - - +
309B LEU* 6.3 0.6 - - - +
312B SER* 3.0 36.0 + - - +
313B PHE* 3.4 21.8 - - - +
314B SER 3.2 0.2 - - - -
315B HIS* 1.3 77.4 - - - +
317B SER* 1.3 57.0 + - - +
318B ILE* 3.2 2.6 - - - +
319B ALA* 3.3 18.7 + - - +
325B LEU* 2.6 65.6 + - + +
326B LEU 5.0 2.5 - - - -
327B ALA* 3.2 34.9 - - - +
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PHE 2.5 24.0 + - - -
314B SER 3.0 7.1 + - - -
316B ARG* 1.3 72.5 - - - +
318B ILE* 1.3 65.0 + - - +
319B ALA 2.8 0.9 - - - +
320B VAL* 2.9 32.3 + - - +
323B GLY 3.4 22.9 - - - -
324B ILE* 3.3 9.2 - - - +
325B LEU* 3.2 20.1 + - - -
354B VAL* 3.8 13.2 - - - +
358B ARG* 3.7 4.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B SER 3.4 4.8 + - - +
315B HIS* 2.4 58.1 - - + +
316B ARG* 3.9 3.6 - - - +
317B SER* 1.3 76.4 - - - +
319B ALA* 1.3 77.5 + - + +
320B VAL* 3.2 1.7 + - - -
354B VAL* 4.1 9.6 - - - +
357B MET* 4.1 17.0 - - + +
358B ARG* 3.5 51.8 + - + +
361B GLN* 6.3 0.4 - - - -
362B MET* 5.6 1.8 - - + +
364B LYS* 6.1 2.9 - - - -
----------------------------------------------------------
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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