Contacts of the helix formed by residues 293 - 322 (chain B) in PDB entry 3PRJ
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 LEU 293 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ALA* 4.1 13.9 - - + +
240A LEU* 3.9 38.4 - - + +
243A ALA* 4.2 9.4 - - + -
309A TYR* 3.7 20.9 - - - +
313A ARG* 5.8 0.9 - - - -
288B CYS* 2.8 18.5 + - + +
289B GLU 4.4 0.2 + - - -
291B LEU* 4.1 22.0 - - + +
292B ASN* 1.3 85.0 - - - +
294B PRO* 1.3 65.0 - - - +
295B GLU* 3.2 5.6 + - - +
296B VAL* 3.4 17.6 + - + -
297B ALA* 3.0 21.3 + - - +
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Residues in contact with PRO 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLU* 5.4 7.2 - - + -
292B ASN* 3.4 18.2 - - - +
293B LEU* 1.3 88.3 - - - +
295B GLU* 1.3 74.8 + - - +
297B ALA* 3.4 7.4 - - + +
298B ARG* 2.8 54.1 + - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLN* 4.3 1.6 - - - +
305A ASP 6.4 0.2 - - - -
306A MET* 3.5 6.6 - - + +
309A TYR* 3.3 60.8 + - + -
312A ARG* 4.3 11.5 + - - +
293B LEU* 4.3 0.9 - - - -
294B PRO* 1.3 98.2 - - - +
296B VAL* 1.3 60.9 + - - +
298B ARG* 3.7 24.8 + - - +
299B TYR* 3.2 22.2 + - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 3.8 30.5 - - - +
237A ILE* 5.7 0.2 - - - -
239A ALA* 4.0 16.8 - - + -
240A LEU* 5.1 6.1 - - + -
306A MET* 3.7 14.8 - - + -
309A TYR* 4.2 7.4 - - + -
288B CYS* 3.5 23.3 - - - -
293B LEU* 3.8 18.6 - - + +
294B PRO 3.3 0.2 - - - -
295B GLU* 1.3 75.1 - - - +
297B ALA* 1.3 65.3 + - - +
299B TYR* 3.2 2.9 + - - +
300B TRP* 3.2 39.0 + - + +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 3.6 25.9 - - + +
288B CYS* 3.7 18.1 - - + +
289B GLU* 4.1 20.4 - - + +
293B LEU 3.0 17.5 + - - +
294B PRO* 3.2 10.1 + - + +
296B VAL* 1.3 78.5 - - - +
298B ARG* 1.3 61.9 + - - +
300B TRP* 3.4 0.7 + - - -
301B GLN* 3.2 22.6 + - - +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLN* 4.0 22.8 + - - +
294B PRO* 2.8 41.7 + - - +
295B GLU* 3.7 30.9 - - - +
297B ALA* 1.3 71.9 - - - +
299B TYR* 1.3 65.9 + - - +
301B GLN* 3.7 14.9 + - + +
302B GLN* 3.7 17.2 + - - +
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLN* 3.2 12.9 + - + +
232A SER* 3.7 6.0 - - - -
233A SER* 2.6 51.3 + - - -
236A SER* 4.2 5.6 - - - -
302A GLN* 3.3 52.5 - - + +
303A VAL* 4.1 4.7 - - + -
306A MET* 3.6 24.7 - - + -
229B GLN* 3.2 20.5 + - - -
295B GLU 3.2 14.9 + - - +
296B VAL 3.2 8.3 + - - +
298B ARG* 1.3 78.5 - - - +
300B TRP* 1.3 84.1 + + - +
302B GLN* 3.4 18.7 + - - +
303B VAL* 4.5 2.4 + - - +
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Residues in contact with TRP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A SER* 3.6 26.9 - - - -
236A SER* 3.0 26.0 + - - -
237A ILE* 4.0 11.2 - - + +
225B ALA* 3.5 32.5 - - + -
226B PHE* 3.8 29.8 - + - -
229B GLN* 3.7 22.7 - - + -
281B VAL* 3.3 21.2 - - + +
284B LEU* 3.6 29.5 - - + +
285B VAL* 4.2 11.9 - - + -
288B CYS* 5.4 0.4 - - - -
296B VAL* 3.2 33.3 + - + +
297B ALA* 5.4 0.2 - - - -
299B TYR* 1.3 83.7 - + - +
301B GLN* 1.3 66.9 + - - +
302B GLN 3.0 2.5 - - - -
303B VAL* 3.0 29.7 + - + +
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 5.5 2.8 + - - -
281B VAL* 4.7 1.8 - - - -
282B LEU* 4.4 13.4 - - - +
285B VAL* 3.7 26.7 - - + +
297B ALA 3.2 18.9 + - - +
298B ARG* 3.8 10.8 - - + +
299B TYR 3.3 0.2 - - - -
300B TRP* 1.3 76.4 - - - +
302B GLN* 1.3 65.2 + - - +
304B ILE* 2.9 33.0 + - - +
305B ASP* 3.1 40.3 + - - +
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Residues in contact with GLN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU 4.3 2.1 - - - +
298A ARG* 3.9 24.7 + - - +
299A TYR* 3.3 45.5 + - + +
302A GLN* 3.5 30.8 - - + +
298B ARG 3.7 6.2 + - - +
299B TYR 3.4 10.9 + - - +
300B TRP 3.0 0.8 - - - -
301B GLN* 1.3 80.8 - - - +
303B VAL* 1.3 61.1 + - - +
305B ASP* 3.6 27.6 + - - +
306B MET* 2.9 29.3 + - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TYR* 4.2 7.6 - - + -
228B ALA* 3.7 35.4 - - + -
229B GLN* 3.8 24.9 - - + +
232B SER* 2.7 34.0 + - - +
272B PHE* 4.1 7.1 - - + -
281B VAL* 4.5 9.6 - - + -
299B TYR 5.0 1.3 - - - +
300B TRP* 3.0 37.8 + - + +
302B GLN* 1.3 76.3 - - + +
304B ILE* 1.3 61.7 + - - +
307B ASN* 3.3 10.4 + - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 4.4 8.5 - - + -
278B GLN* 3.9 37.5 - - + +
281B VAL* 3.6 39.7 - - + -
282B LEU* 4.6 16.8 - - + -
301B GLN* 2.9 27.8 + - - +
303B VAL* 1.3 77.0 - - - +
305B ASP* 1.3 59.4 + - - +
307B ASN* 3.2 6.1 + - + +
308B ASP* 2.9 45.7 + - - +
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 6.4 0.2 - - - -
301B GLN* 3.1 35.9 + - - +
302B GLN* 3.2 33.0 + - - +
304B ILE* 1.3 73.6 - - - +
306B MET* 1.3 60.7 + - - +
308B ASP* 3.4 11.5 + - - +
309B TYR* 2.9 29.5 + - - +
312B ARG* 5.3 0.9 + - - -
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 3.5 28.9 - - + +
296A VAL* 3.6 19.3 - - + +
299A TYR* 3.7 21.5 - - + -
232B SER* 3.3 34.5 - - - +
235B ASN* 4.6 5.4 - - + -
236B SER* 3.6 25.4 - - - +
302B GLN* 2.9 18.0 + - - +
305B ASP* 1.3 73.9 - - - +
307B ASN* 1.3 56.0 + - - +
309B TYR* 3.2 19.4 + - + +
310B GLN* 2.7 35.9 + - - +
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Residues in contact with ASN 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B SER* 3.8 2.8 + - - -
235B ASN* 4.3 6.0 + - - +
271B GLY* 3.3 8.9 - - - -
272B PHE* 2.9 73.5 + - + +
278B GLN* 5.3 4.2 + - - +
303B VAL 3.3 12.2 + - - +
304B ILE* 3.2 10.9 + - + +
306B MET* 1.3 80.3 - - - +
308B ASP* 1.3 63.7 + - - +
310B GLN* 3.1 14.7 + - - +
311B ARG* 3.2 32.5 + - - +
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Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLN* 5.1 4.5 - - - +
304B ILE* 2.9 36.3 + - - +
305B ASP* 3.6 13.2 - - - +
307B ASN* 1.3 76.8 + - - +
309B TYR* 1.3 62.0 + - - +
311B ARG* 3.2 23.6 + - - +
312B ARG* 3.0 39.3 + - - +
352B TYR* 6.0 1.2 - - - -
356B TYR* 5.0 2.8 + - - +
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 3.6 22.9 - - - +
295A GLU* 3.3 54.4 + - + -
296A VAL* 4.2 16.4 - - + -
239B ALA* 4.2 3.5 - - + +
305B ASP 2.9 18.6 + - - +
306B MET* 3.5 19.5 - - - +
308B ASP* 1.3 74.6 - - - +
310B GLN* 1.3 65.5 + - - +
312B ARG* 3.9 22.1 - - + +
313B ARG* 2.9 64.3 + - + +
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASN* 3.0 38.8 + - + +
238B SER* 3.2 17.2 + - - -
239B ALA* 5.1 0.3 - - - +
269B SER 2.8 29.5 + - - +
270B VAL* 3.7 10.3 - - - +
271B GLY* 4.8 0.4 - - - -
306B MET* 2.7 18.7 + - - +
307B ASN* 3.1 13.6 + - - +
309B TYR* 1.3 76.8 - - - +
311B ARG* 1.3 60.7 + - - +
313B ARG* 2.4 33.5 + - - +
314B PHE* 3.3 22.9 + - - +
462B ILE* 3.6 11.6 - - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL 3.4 17.9 - - - +
271B GLY* 4.6 0.6 - - - -
272B PHE 3.0 24.6 + - - -
278B GLN* 4.2 13.9 + - - -
307B ASN* 3.2 26.1 + - - +
308B ASP* 3.2 17.9 + - - +
310B GLN* 1.3 73.2 - - - +
312B ARG* 1.3 60.8 + - - +
314B PHE* 3.2 6.3 + - - +
315B ALA* 2.9 28.3 + - - +
347B GLU* 3.1 23.0 + - - +
349B SER* 2.9 25.9 + - - +
352B TYR* 3.3 46.7 - - + -
353B ILE* 3.6 15.0 - - + +
356B TYR* 4.8 10.8 - - + +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 4.5 11.3 + - - +
305B ASP 5.3 0.6 + - - -
308B ASP* 3.0 36.1 + - - +
309B TYR* 3.8 31.7 - - + +
311B ARG* 1.3 78.3 - - - +
313B ARG* 1.3 59.4 + - - +
315B ALA* 3.4 7.3 + - - +
316B SER* 2.9 27.9 + - - -
356B TYR* 3.6 36.2 + - + +
98F MET* 4.8 9.5 - - + +
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 5.7 0.9 - - - -
238B SER* 3.1 20.0 + - - -
239B ALA* 3.6 23.0 + - - +
242B GLU* 2.6 45.3 + - - +
309B TYR* 2.9 52.9 + - + +
310B GLN* 2.4 36.6 + - - +
312B ARG* 1.3 73.0 - - - +
314B PHE* 1.3 61.4 + - - +
316B SER* 3.3 8.1 + - - -
317B ARG* 3.0 35.6 + - + +
462B ILE* 5.0 2.9 - - - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.4 27.6 - - + -
310B GLN 3.3 10.8 + - - +
311B ARG 3.2 8.0 + - - +
313B ARG* 1.3 79.1 - - - +
315B ALA* 1.3 66.1 + - - +
317B ARG* 3.1 26.1 + - + +
318B ILE* 3.2 30.1 + - + +
353B ILE* 3.8 11.4 - - + -
412B VAL* 3.9 12.1 - - + -
413B ILE 5.0 1.3 - - - -
414B CYS* 5.3 0.9 - - - -
439B PHE* 3.8 29.8 - + + -
440B ASP 4.3 3.4 - - - -
441B GLY* 3.6 33.2 - - - -
460B GLU 5.3 1.6 - - - -
461B THR 5.4 0.9 - - - -
462B ILE* 3.6 28.0 - - + -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG 2.9 13.6 + - - +
312B ARG* 3.5 10.1 - - - +
313B ARG 3.3 0.2 - - - -
314B PHE* 1.3 75.6 - - - +
316B SER* 1.3 57.5 + - - +
318B ILE* 3.0 27.5 + - - +
319B ILE* 3.1 20.0 + - + +
353B ILE* 4.4 11.9 - - + +
356B TYR* 3.9 37.7 - - + -
357B LEU* 4.7 2.5 - - + +
98F MET* 5.3 0.7 - - + -
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG 2.9 16.3 + - - -
313B ARG* 3.3 9.2 + - - -
315B ALA* 1.3 75.0 - - - +
317B ARG* 1.3 60.4 + - - +
319B ILE* 3.9 11.6 - - - +
320B ASP* 2.9 35.1 + - - +
98F MET* 4.1 23.1 - - - -
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLU* 3.3 34.2 + - - +
313B ARG* 3.0 25.0 + - + +
314B PHE* 3.1 21.0 + - + +
316B SER* 1.3 75.9 - - - +
318B ILE* 1.3 66.1 + - - +
320B ASP* 3.3 6.6 + - - +
321B SER* 3.1 27.5 + - - -
439B PHE* 4.2 10.1 - - + -
460B GLU* 3.5 40.0 + - - +
461B THR 2.7 32.9 + - - +
462B ILE* 4.1 4.0 - - - +
464B LYS 4.2 4.3 + - - -
466B VAL* 4.2 25.0 - - - +
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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 PHE* 3.2 36.8 + - + +
315B ALA* 3.0 8.8 + - - +
317B ARG* 1.3 78.4 - - - +
319B ILE* 1.3 63.2 + - - +
320B ASP 3.2 0.9 + - - -
321B SER* 3.2 10.7 + - - -
322B LEU* 3.2 27.5 + - + +
331B ILE* 4.9 2.9 - - + -
353B ILE* 4.4 11.2 - - + -
357B LEU* 4.0 20.4 - - + -
410B ALA* 5.2 1.8 - - + -
412B VAL* 3.8 27.8 - - + -
439B PHE* 3.5 39.5 - - + -
----------------------------------------------------------
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA* 3.1 25.7 + - + +
316B SER* 4.1 9.6 - - - +
317B ARG 3.4 0.2 - - - -
318B ILE* 1.3 75.4 - - - +
320B ASP* 1.3 59.0 + - - +
322B LEU* 3.4 12.1 + - - +
324B ASN* 2.9 51.5 + - - +
325B THR 4.7 1.1 - - - +
326B VAL* 4.8 8.1 - - + -
356B TYR 4.7 5.6 - - - +
357B LEU* 4.0 20.0 - - + -
360B GLU* 3.8 42.6 - - + +
98F MET* 4.1 19.3 - - + -
----------------------------------------------------------
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B SER* 2.9 23.5 + - - +
317B ARG* 3.6 7.0 - - - +
318B ILE 3.1 0.2 - - - -
319B ILE* 1.3 72.2 - - - +
321B SER* 1.3 55.5 + - - +
322B LEU 3.0 4.3 - - - -
323B PHE* 2.8 26.2 + - - -
324B ASN* 4.2 17.1 + - - +
135F ARG* 4.4 18.6 + - - -
142F ARG* 4.6 4.2 + - - -
----------------------------------------------------------
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ARG 3.1 8.0 + - - -
318B ILE 3.2 1.3 + - - -
320B ASP* 1.3 76.8 - - - +
322B LEU* 1.3 58.4 + - - +
323B PHE* 3.3 9.5 + - - -
437B PHE* 3.6 34.6 - - - -
439B PHE* 3.6 22.0 - - - -
460B GLU* 3.1 29.3 + - - -
142F ARG* 3.7 18.5 + - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 3.2 23.2 + - + +
319B ILE 3.9 3.8 - - - +
320B ASP 3.0 2.0 - - - -
321B SER* 1.3 83.7 - - - +
323B PHE* 1.3 73.5 + - - +
324B ASN 3.3 2.0 - - - -
325B THR* 3.0 18.2 + - - +
326B VAL* 3.4 28.7 - - + -
329B LYS* 3.4 26.2 + - + +
331B ILE* 4.0 21.1 - - + -
409B HIS* 5.0 7.6 - - + +
410B ALA* 4.6 11.7 - - + -
437B PHE* 3.6 29.4 - - + -
439B PHE* 4.9 1.3 - - + -
----------------------------------------------------------
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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