Contacts of the helix formed by residues 291 - 321 (chain D) in PDB entry 1UDY
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 HIS 291 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B GLN* 3.5 18.1 + - - +
2399C FAD 3.3 36.4 + + + +
283D THR* 2.8 41.2 + - - -
284D PHE* 4.1 9.0 - - + -
286D LYS* 3.9 28.7 - - + +
287D LEU 4.2 2.5 - - - -
288D LEU* 2.9 25.4 + - - +
289D ALA 4.5 0.2 - - - -
290D GLU* 1.3 77.6 - - - +
292D GLN* 1.3 60.9 + - - +
294D ILE* 2.8 23.2 + - + +
295D SER* 3.0 10.7 + - - -
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Residues in contact with GLN 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ILE* 3.8 11.1 - - - +
399A FAD 3.0 26.2 + - - -
291B HIS* 3.3 22.9 - - - +
292B GLN* 3.3 14.3 + - + +
293B GLY* 2.7 27.4 + - - +
290D GLU 3.4 5.8 + - - +
291D HIS* 1.3 72.0 - - - +
293D GLY* 1.3 63.2 + - - +
295D SER* 3.6 9.0 - - - +
296D PHE* 3.0 52.3 + - + -
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Residues in contact with GLY 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLN* 2.6 38.5 - - - +
293B GLY* 5.1 1.8 - - - -
296B PHE* 4.0 19.8 - - - -
380C GLN* 5.8 1.6 - - - +
2399C FAD 5.2 0.2 - - - -
292D GLN* 1.3 75.5 - - - +
294D ILE* 1.3 60.0 + - - +
296D PHE* 3.8 6.6 + - - +
297D LEU* 3.4 18.4 + - - +
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Residues in contact with ILE 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C GLN* 4.5 9.4 - - + -
2399C FAD 3.5 51.8 - - + +
278D ALA* 4.6 3.6 - - + -
288D LEU* 3.3 43.3 - - + +
289D ALA* 4.3 5.2 - - - +
291D HIS* 2.8 4.4 + - + +
293D GLY* 1.3 76.5 - - - +
295D SER* 1.3 64.4 + - - +
296D PHE 3.2 0.2 - - - -
297D LEU* 3.2 20.1 + - + +
298D LEU* 3.0 37.7 + - + +
350D VAL* 5.3 6.7 - - + -
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Residues in contact with SER 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ILE* 5.6 1.6 - - - +
387A ALA* 3.6 21.4 - - - +
391A ILE* 5.3 3.4 - - - -
289D ALA 3.8 20.6 + - - -
291D HIS 3.0 8.6 + - - -
292D GLN* 3.2 16.9 + - - +
294D ILE* 1.3 77.5 - - - +
296D PHE* 1.3 68.8 + - - +
298D LEU* 3.2 11.2 + - - +
299D ALA* 2.9 29.6 + - - +
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Residues in contact with PHE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLN* 3.6 45.8 - - + -
383A ARG* 4.1 19.4 - - + +
384A ILE* 3.8 15.7 - - + -
399A FAD 4.2 3.4 - + - -
293B GLY* 4.1 17.7 - - - -
292D GLN* 3.0 52.3 + - + +
293D GLY* 3.8 6.1 - - - +
295D SER* 1.3 88.1 + - - +
297D LEU* 1.3 60.1 + - - +
299D ALA* 3.3 7.7 + - - +
300D ASP* 3.0 30.8 + - - +
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Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C GLN* 5.1 11.0 - - - +
2399C FAD 6.1 0.2 - - - +
293D GLY 3.4 10.3 + - - +
294D ILE* 3.2 22.1 + - + +
296D PHE* 1.3 78.7 - - - +
298D LEU* 1.3 64.6 + - + +
300D ASP* 3.2 9.2 + - + +
301D MET* 3.0 35.6 + - + +
346D ASP* 3.4 38.6 - - + +
349D GLN* 5.1 4.3 - - + -
350D VAL* 3.8 28.9 - - + -
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Residues in contact with LEU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ALA* 5.7 1.6 - - + -
390A HIS* 4.7 10.2 - - + -
391A ILE* 4.0 28.3 - - + -
271D LEU* 4.1 5.7 - - + +
274D ALA* 4.9 5.4 - - + -
275D THR* 4.6 19.7 - - + +
278D ALA* 4.0 24.2 - - + -
289D ALA* 4.8 2.0 - - + -
294D ILE* 3.0 28.9 + - + +
295D SER* 3.6 9.9 - - - +
297D LEU* 1.3 78.2 - - + +
299D ALA* 1.3 58.1 + - - +
301D MET* 3.3 21.1 + - - +
302D ALA* 2.9 28.9 + - - +
350D VAL* 4.4 15.9 - - + -
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Residues in contact with ALA 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ARG* 3.4 36.1 - - + +
386A ILE* 3.6 24.9 - - + +
387A ALA* 3.9 7.4 - - - +
390A HIS* 6.0 0.4 - - - -
295D SER 2.9 14.4 + - - +
296D PHE 3.5 7.2 - - - +
297D LEU 3.2 0.2 - - - -
298D LEU* 1.3 77.9 - - - +
300D ASP* 1.3 56.2 + - - +
302D ALA* 3.4 3.9 + - - +
303D MET* 3.0 29.0 + - - +
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Residues in contact with ASP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ARG* 3.1 38.1 + - - +
296D PHE* 3.0 20.1 + - - +
297D LEU* 3.2 10.5 + - + +
299D ALA* 1.3 73.8 - - - +
301D MET* 1.3 66.0 + - + +
303D MET* 3.3 12.9 + - - +
304D LYS* 3.2 39.8 + - - +
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Residues in contact with MET 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D LEU* 3.8 13.0 - - + -
274D ALA* 4.2 12.8 - - + -
297D LEU* 3.0 34.1 + - + +
298D LEU* 3.5 24.0 - - - +
299D ALA 3.3 0.2 - - - -
300D ASP* 1.3 78.0 - - + +
302D ALA* 1.3 62.2 + - - +
304D LYS* 3.3 16.7 + - - +
305D VAL* 3.3 17.5 + - - +
343D LEU* 3.6 55.3 - - + +
346D ASP* 4.1 16.2 - - + +
347D ALA* 4.0 20.2 - - + +
350D VAL* 5.0 0.2 - - - -
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Residues in contact with ALA 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 4.1 10.4 + - + +
331A ILE* 5.4 0.4 - - - -
386A ILE* 4.5 6.3 - - + -
390A HIS* 4.0 23.8 - - + +
271D LEU* 3.5 23.0 - - + +
298D LEU 2.9 16.4 + - - +
299D ALA* 3.6 7.6 - - - +
301D MET* 1.3 77.3 - - - +
303D MET* 1.3 60.9 + - - +
305D VAL* 3.3 4.2 + - - +
306D GLU* 3.3 27.6 + - - +
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Residues in contact with MET 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 3.5 35.9 - - + +
334A ALA* 4.1 3.1 - - + -
335A TYR* 4.3 33.0 - - - -
383A ARG* 3.8 24.5 - - - +
386A ILE* 3.9 21.0 - - + +
299D ALA 3.0 13.2 + - - +
300D ASP* 3.4 31.6 - - - +
302D ALA* 1.3 76.8 - - - +
304D LYS* 1.3 63.1 + - + +
306D GLU* 3.5 2.1 + - - +
307D LEU* 3.2 31.5 + - + +
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Residues in contact with LYS 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ASP* 3.2 27.5 + - - +
301D MET* 3.3 8.6 + - - +
303D MET* 1.3 76.8 - - + +
305D VAL* 1.3 59.6 + - - +
307D LEU* 3.1 2.9 + - - +
308D ALA* 2.8 31.4 + - - +
335D TYR* 4.0 19.6 - - - +
339D ILE* 3.8 29.4 - - + -
342D GLN* 2.4 41.9 + - - +
343D LEU* 4.0 11.6 - - + +
346D ASP* 5.1 6.3 + - - -
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 4.3 13.8 - - + +
267D ALA* 3.9 19.1 - - + -
268D GLN* 3.4 26.7 - - + +
271D LEU* 4.0 12.3 - - + -
301D MET 3.3 13.8 + - - +
302D ALA 3.3 6.0 + - - +
304D LYS* 1.3 75.0 - - - +
306D GLU* 1.3 59.4 + - + +
308D ALA* 3.2 2.0 + - - +
309D ARG* 2.9 45.1 + - - +
339D ILE* 4.3 6.5 - - - -
343D LEU* 3.7 21.5 - - + -
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Residues in contact with GLU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A TYR* 2.7 47.2 + - + +
328A TYR* 3.9 23.8 + - + -
331A ILE* 4.0 12.8 - - + -
393A ARG* 4.4 5.4 + - - -
268D GLN* 5.7 0.4 - - - +
302D ALA 3.3 10.2 + - - +
303D MET 3.8 6.7 - - - +
305D VAL* 1.3 76.3 - - + +
307D LEU* 1.3 62.3 - - + +
309D ARG* 3.6 27.2 + - - +
310D LEU* 3.1 33.6 + - + +
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 4.5 20.5 - - + +
310A LEU* 5.4 0.3 - - - +
311A SER* 3.8 26.7 - - - -
331A ILE* 3.8 15.3 - - + -
335A TYR* 3.4 50.0 - - + -
303D MET* 3.2 21.1 + - + +
304D LYS 3.1 4.8 + - - +
306D GLU* 1.3 80.6 - - + +
308D ALA* 1.3 64.2 + - - +
310D LEU* 3.3 10.5 + - + +
311D SER* 3.0 22.3 + - - -
335D TYR* 3.9 19.5 - - + +
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 4.1 10.0 - - + +
304D LYS 2.8 20.1 + - - +
305D VAL 3.7 2.7 - - - +
307D LEU* 1.3 72.7 - - - +
309D ARG* 1.3 63.5 + - - +
311D SER* 2.7 21.5 + - - -
312D TYR* 3.3 9.7 + - - +
335D TYR* 3.8 10.9 - - + -
336D ALA* 4.0 18.7 - - + +
339D ILE* 3.6 28.5 - - + -
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Residues in contact with ARG 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D GLU* 2.5 43.0 + - - +
264D VAL* 4.0 7.7 - - + +
268D GLN* 3.0 30.3 + - - +
305D VAL* 2.9 31.2 + - - +
306D GLU* 3.6 31.2 + - - +
308D ALA* 1.3 78.1 - - - +
310D LEU* 1.3 65.0 + - + +
311D SER 3.2 0.3 + - - -
312D TYR* 3.4 16.5 + - - +
313D GLN* 3.2 48.0 + - - +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.8 1.8 - - + -
310A LEU* 3.5 53.1 - - + +
311A SER* 3.9 13.2 - - - +
314A ARG* 3.9 23.8 - - + +
328A TYR* 6.4 0.4 - - + -
14D PHE* 4.0 19.7 - - + -
306D GLU* 3.1 19.8 + - + +
307D LEU* 3.5 12.1 - - + +
309D ARG* 1.3 77.9 - - + +
311D SER* 1.3 62.4 + - - +
313D GLN* 3.4 24.9 + - - +
314D ARG* 3.2 16.8 + - - +
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Residues in contact with SER 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 4.0 22.9 - - - -
310A LEU* 3.9 9.4 - - - +
307D LEU 3.0 13.3 + - - -
308D ALA* 2.7 22.8 + - - -
309D ARG 3.1 0.2 - - - -
310D LEU* 1.3 75.4 - - - +
312D TYR* 1.3 64.3 + - - +
314D ARG* 3.1 6.1 + - - +
315D ALA* 3.1 17.5 + - - +
328D TYR* 4.7 1.0 - - - +
331D ILE* 5.2 0.4 - - - -
332D ALA* 3.1 36.0 + - - +
335D TYR* 4.9 2.5 - - - -
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Residues in contact with TYR 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ILE* 5.2 2.9 - - + -
81D CYS* 3.5 37.8 + - + -
82D LEU* 4.6 8.8 - - + +
85D GLU* 2.5 31.5 + - - +
257D PRO* 3.7 20.2 - - - +
260D ALA* 4.0 11.4 - - + -
261D ALA* 3.5 29.2 - - + -
264D VAL* 3.7 15.9 - - + -
308D ALA 3.3 3.1 + - - +
309D ARG* 3.5 29.6 - - + +
311D SER* 1.3 80.3 + - - +
313D GLN* 1.3 75.6 + - + +
315D ALA* 3.8 3.3 - - - +
316D ALA* 2.9 29.3 + - + +
332D ALA* 3.6 8.3 - - + -
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Residues in contact with GLN 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.1 42.9 - - + -
14A PHE* 3.7 10.9 - - + -
14D PHE* 4.2 6.9 - - - -
78D ILE* 4.3 12.1 - - + +
82D LEU* 5.1 3.4 - - + +
309D ARG* 3.2 29.7 + - - +
310D LEU* 3.5 34.5 - - - +
311D SER 3.1 0.8 - - - -
312D TYR* 1.3 101.6 + - + +
314D ARG* 1.3 61.2 + - - +
316D ALA* 3.9 1.4 - - - +
317D TRP* 3.1 25.5 + - - +
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Residues in contact with ARG 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.4 52.0 + - + +
310A LEU* 4.0 24.2 - - + +
310D LEU 3.2 9.9 + - - +
311D SER* 3.1 9.9 + - - +
313D GLN* 1.3 81.1 - - - +
315D ALA* 1.3 60.8 + - - +
317D TRP* 4.0 7.5 - - - +
318D GLU* 2.6 47.2 + - - +
328D TYR* 3.5 48.4 + - + -
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D PRO* 3.7 12.8 - - + -
311D SER 3.1 11.8 + - - +
312D TYR* 3.8 5.6 - - - +
314D ARG* 1.3 76.2 - - - +
316D ALA* 1.3 64.7 + - - +
318D GLU* 3.6 1.4 + - - +
319D ILE 3.6 6.1 + - - -
325D ASN* 2.7 25.6 + - - -
328D TYR* 3.5 40.6 - - - +
329D ALA* 3.7 11.7 - - - +
332D ALA* 4.3 1.6 - - + -
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ILE* 3.9 12.6 - - + -
78D ILE* 3.6 36.3 - - + +
81D CYS* 4.2 7.6 - - - -
257D PRO* 4.1 2.6 - - + +
312D TYR 2.9 16.8 + - - +
313D GLN 3.9 3.1 - - - +
315D ALA* 1.3 75.8 - - - +
317D TRP* 1.3 62.8 + - - +
319D ILE* 2.9 28.5 - - - +
320D ASP* 3.0 11.6 + - - -
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Residues in contact with TRP 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 2.9 39.5 + - + -
13A SER* 3.5 10.6 - - - +
14A PHE* 3.7 54.7 - + + -
15A GLU* 3.7 24.0 - - + -
78D ILE* 4.9 5.5 - - + +
313D GLN 3.1 16.3 + - - +
314D ARG* 4.0 7.0 - - - +
316D ALA* 1.3 80.8 - - - +
318D GLU* 1.3 77.7 + - - +
320D ASP* 3.5 9.3 + - + +
321D SER* 2.7 44.9 + - - -
323D ARG* 3.8 18.4 - - - -
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D ARG* 2.6 49.9 + - - +
315D ALA 3.8 0.7 - - - +
316D ALA 3.2 0.6 - - - -
317D TRP* 1.3 86.9 - - - +
319D ILE* 1.3 59.2 + - - +
321D SER* 3.6 6.6 + - - -
323D ARG* 3.1 71.0 + - + +
324D ARG 4.3 3.4 - - - +
325D ASN* 3.8 25.1 - - + -
328D TYR* 4.1 19.3 - - + -
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Residues in contact with ILE 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ILE* 3.6 26.9 - - + -
253D ASP* 5.3 2.9 - - + +
254D LYS* 4.2 32.5 - - + -
315D ALA 3.6 5.3 + - - +
316D ALA* 2.9 26.2 + - - +
318D GLU* 1.3 75.7 - - - +
320D ASP* 1.3 63.1 + - - +
321D SER 3.0 2.0 - - - -
322D GLY* 2.8 21.3 + - - -
323D ARG 3.5 20.9 - - - +
324D ARG* 4.8 2.2 - - - -
325D ASN* 3.5 26.4 - - - +
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Residues in contact with ASP 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D HIS* 5.2 0.9 + - - -
76D GLY* 3.9 6.5 - - - -
77D ILE* 3.0 32.7 + - - +
78D ILE* 3.0 39.3 + - - +
316D ALA 3.0 15.8 + - - +
317D TRP* 4.0 8.9 - - + +
318D GLU 3.5 0.2 - - - -
319D ILE* 1.3 77.6 - - - +
321D SER* 1.3 60.0 + - - +
322D GLY 3.1 1.5 + - - -
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Residues in contact with SER 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D TRP* 2.7 42.5 + - - -
318D GLU 3.6 8.1 - - - -
319D ILE 3.0 0.4 - - - -
320D ASP* 1.3 76.3 - - - +
322D GLY* 1.3 61.4 + - - +
323D ARG* 3.6 24.7 - - - +
----------------------------------------------------------
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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