Contacts of the helix formed by residues 291 - 321 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A FAD 3.6 40.0 + + + +
283B THR* 2.9 45.1 + - - -
284B PHE* 3.9 5.7 - - - +
286B LYS* 3.3 40.5 - - + +
288B LEU* 3.3 20.2 + - - +
290B GLU* 1.3 76.5 - - - +
292B GLN* 1.3 55.0 + - - +
293B GLY 2.9 1.3 - - - -
294B ILE* 2.7 30.6 + - + +
295B SER* 3.1 8.3 + - - -
292D GLN* 3.3 14.6 - - - +
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Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU 3.4 6.3 + - - -
291B HIS* 1.3 69.6 - - - +
293B GLY* 1.3 62.4 + - - +
295B SER* 4.0 9.4 - - - -
296B PHE* 3.1 46.3 + - + -
384C ILE* 4.0 8.7 - - - +
2399C FAD 3.1 37.7 + - - -
291D HIS* 3.5 13.4 + - - +
292D GLN* 3.3 17.1 + - + +
293D GLY* 2.6 33.0 - - - +
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Residues in contact with GLY 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLN* 5.8 0.7 - - - -
399A FAD 5.0 0.7 - - - -
291B HIS 2.7 1.6 + - - -
292B GLN* 1.3 74.2 - - - +
294B ILE* 1.3 61.4 + - - -
296B PHE* 3.6 6.1 + - - +
297B LEU* 3.4 16.5 + - - +
292D GLN* 2.7 34.4 + - - +
293D GLY* 5.2 2.2 - - - -
296D PHE* 4.1 22.3 - - - -
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLN* 4.3 12.3 - - + -
399A FAD 3.6 51.6 - - + +
278B ALA* 4.6 6.5 - - + -
288B LEU* 3.2 37.5 - - + +
289B ALA* 4.4 4.7 - - - -
291B HIS* 2.7 8.9 + - + +
293B GLY* 1.3 70.9 - - - -
295B SER* 1.3 63.6 + - - +
297B LEU* 3.0 21.6 + - + +
298B LEU* 2.9 38.0 + - + +
350B VAL* 5.2 9.4 - - + -
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA 2.9 25.6 + - - -
290B GLU 4.6 0.9 - - - -
291B HIS 3.1 9.3 + - - -
292B GLN* 3.6 15.2 - - - -
294B ILE* 1.3 77.6 - - - +
296B PHE* 1.3 64.5 + - - +
298B LEU* 3.3 10.3 + - - +
299B ALA* 2.9 28.8 + - - +
384C ILE* 6.1 1.3 - - - -
387C ALA* 3.6 20.8 - - - +
391C ILE* 5.4 2.1 - - - +
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Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLN* 3.1 50.6 + - + +
293B GLY* 3.8 6.3 - - - +
295B SER* 1.3 78.4 - - - +
297B LEU* 1.3 67.4 + - - +
299B ALA* 3.7 5.9 - - - +
300B ASP* 2.9 36.1 + - - +
380C GLN* 4.0 36.1 - - + -
383C ARG* 4.2 20.3 - - + -
384C ILE* 3.9 18.2 - - + -
2399C FAD 4.1 8.3 - + - -
293D GLY* 4.0 20.2 - - - -
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLN* 5.0 13.2 - - - +
293B GLY 3.4 9.8 + - - +
294B ILE* 3.0 24.6 + - + +
296B PHE* 1.3 81.1 - - - +
298B LEU* 1.3 64.5 + - + +
300B ASP* 3.2 7.6 + - + +
301B MET* 3.0 35.3 + - + +
346B ASP* 3.8 35.9 - - + +
349B GLN* 5.1 4.9 - - + -
350B VAL* 3.8 27.8 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.3 4.5 - - + +
274B ALA* 4.7 14.4 - - + +
275B THR* 4.3 23.8 - - + +
278B ALA* 4.3 20.0 - - + -
289B ALA* 4.5 2.5 - - + -
294B ILE* 2.9 26.0 + - + +
295B SER* 3.4 11.9 - - - +
297B LEU* 1.3 77.9 - - + +
299B ALA* 1.3 56.6 + - - +
301B MET* 3.1 22.5 + - - +
302B ALA* 2.9 28.5 + - - +
350B VAL* 4.9 7.0 - - + -
387C ALA* 5.4 2.9 - - + -
390C HIS* 4.5 12.4 - - + +
391C ILE* 4.1 28.0 - - + -
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B SER 2.9 14.4 + - - +
296B PHE 3.7 4.9 - - - +
297B LEU 3.3 0.2 - - - -
298B LEU* 1.3 75.4 - - - +
300B ASP* 1.3 64.3 + - - +
302B ALA* 3.2 4.6 + - - +
303B MET* 3.0 25.7 + - - +
383C ARG* 3.4 37.2 - - + +
386C ILE* 4.0 18.7 - - + +
387C ALA* 4.0 12.5 - - - +
390C HIS* 5.9 0.4 - - - -
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Residues in contact with ASP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 2.9 26.7 + - - +
297B LEU* 3.7 9.1 - - + +
299B ALA* 1.3 76.9 - - - +
301B MET* 1.3 63.2 + - + +
303B MET* 3.5 13.0 - - - +
304B LYS* 3.1 41.9 + - - +
383C ARG* 2.9 35.1 + - - +
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Residues in contact with MET 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.8 20.2 - - + -
274B ALA* 4.5 8.5 - - + -
297B LEU* 3.0 26.9 + - + +
298B LEU* 3.1 26.7 + - - +
300B ASP* 1.3 75.6 - - + +
302B ALA* 1.3 66.6 + - - +
304B LYS* 3.2 3.1 + - - +
305B VAL* 3.1 28.3 + - - +
343B LEU* 3.5 52.8 - - + +
346B ASP* 3.8 22.4 - - + +
347B ALA* 3.7 22.7 - - + +
350B VAL* 5.1 0.4 - - - -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.1 14.5 - - + +
298B LEU 2.9 12.0 + - - +
299B ALA* 3.5 9.6 - - - +
301B MET* 1.3 75.0 - - - +
303B MET* 1.3 63.9 + - - +
305B VAL* 3.0 4.9 + - - +
306B GLU* 3.0 27.8 + - - +
327C TYR* 3.8 17.3 - - - +
331C ILE* 4.9 0.2 - - - -
386C ILE* 4.3 12.3 - - + -
390C HIS* 4.0 21.3 - - + +
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Residues in contact with MET 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ALA 3.0 13.7 + - - +
300B ASP* 3.5 15.5 - - - +
302B ALA* 1.3 77.1 - - - +
304B LYS* 1.3 64.8 + - + +
306B GLU* 3.4 2.1 + - - +
307B LEU* 3.1 39.1 + - + +
331C ILE* 3.9 31.9 - - + +
334C ALA* 3.9 8.7 - - + -
335C TYR* 4.3 29.6 - - - -
383C ARG* 3.8 29.6 - - - +
386C ILE* 3.6 26.2 - - + -
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASP* 3.1 27.6 + - - +
301B MET* 3.2 5.3 + - - +
303B MET* 1.3 76.3 - - + +
305B VAL* 1.3 66.1 + - - +
307B LEU* 5.8 0.2 - - + -
308B ALA* 3.1 24.9 + - - +
335B TYR* 3.8 21.3 - - - +
339B ILE* 3.6 23.6 - - + +
342B GLN* 2.7 40.5 + - - +
343B LEU* 3.8 17.1 - - + +
346B ASP* 5.0 7.1 + - - -
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 4.2 12.0 - - + +
267B ALA* 4.1 13.2 - - + +
268B GLN* 3.4 31.6 - - - +
271B LEU* 4.1 13.2 - - + -
301B MET 3.2 5.6 - - - +
302B ALA 3.0 7.5 + - - +
304B LYS* 1.3 76.7 - - - +
306B GLU* 1.3 65.6 + - + +
308B ALA* 3.4 2.9 + - - +
309B ARG* 3.1 34.2 + - - +
339B ILE* 4.6 4.9 - - - -
343B LEU* 3.1 35.0 - - + -
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLN* 6.0 0.2 - - - -
302B ALA 3.0 12.6 + - - +
303B MET 3.8 4.0 - - - +
305B VAL* 1.3 80.1 - - + +
307B LEU* 1.3 61.1 + - + +
309B ARG* 3.3 29.7 + - - +
310B LEU* 3.3 29.8 + - + +
327C TYR* 2.7 42.6 + - - +
328C TYR* 4.2 19.0 + - + -
331C ILE* 3.8 20.4 - - + -
393C ARG* 3.6 13.7 + - - -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 3.1 29.0 + - + +
304B LYS* 5.8 0.4 - - + -
305B VAL 3.2 0.2 - - - -
306B GLU* 1.3 76.5 - - - +
308B ALA* 1.3 65.3 + - - +
309B ARG 3.2 0.2 - - - -
310B LEU* 3.4 8.6 + - + +
311B SER* 3.1 22.2 + - - -
335B TYR* 3.9 24.2 - - + +
307C LEU* 3.7 24.3 - - + +
311C SER* 3.6 32.1 - - - +
331C ILE* 4.5 9.0 - - + -
335C TYR* 3.6 43.5 - - + -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 3.4 23.7 - - + +
304B LYS 3.1 18.7 + - - +
305B VAL 3.9 2.5 - - - +
307B LEU* 1.3 74.0 - - - +
309B ARG* 1.3 65.8 + - - +
311B SER* 2.8 24.4 + - - -
312B TYR* 3.4 10.0 + - - +
335B TYR* 3.8 15.2 - - + -
336B ALA* 4.1 7.4 - - - +
339B ILE* 3.8 17.5 - - + -
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Residues in contact with ARG 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLU* 3.1 40.7 + - - +
264B VAL* 4.0 5.1 - - + +
268B GLN* 2.7 34.1 + - - +
305B VAL* 3.1 26.8 + - - +
306B GLU* 3.3 33.5 + - - +
307B LEU 3.2 0.2 - - - -
308B ALA* 1.3 78.1 - - - +
310B LEU* 1.3 63.2 + - + +
312B TYR* 3.3 20.1 - - + +
313B GLN* 3.2 44.9 + - - +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.1 14.1 - - + -
306B GLU* 3.3 20.6 + - + +
307B LEU* 3.8 10.1 - - + +
308B ALA 3.4 0.2 - - - -
309B ARG* 1.3 78.8 - - + +
311B SER* 1.3 63.6 + - - +
313B GLN* 3.3 22.9 + - - +
314B ARG* 3.0 25.3 + - - +
14C PHE* 4.9 2.1 - - + -
310C LEU* 3.8 43.1 - - + +
311C SER* 4.1 9.2 - - - +
314C ARG* 4.0 34.3 - - + +
328C TYR* 6.1 1.6 - - + -
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU 3.1 9.0 + - - -
308B ALA* 2.8 22.9 + - - -
309B ARG 3.2 0.2 - - - -
310B LEU* 1.3 77.8 - - - +
312B TYR* 1.3 58.5 + - - +
314B ARG* 3.6 3.3 + - - +
315B ALA* 3.3 16.5 + - - +
328B TYR* 4.3 2.8 - - - +
331B ILE* 4.8 3.1 - - - -
332B ALA* 3.2 37.4 + - - +
335B TYR* 5.0 1.7 - - - -
307C LEU* 3.5 27.6 - - - -
310C LEU* 4.0 10.5 - - - +
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Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B CYS* 3.4 35.2 + - + -
82B LEU* 4.7 10.2 - - + +
85B GLU* 2.5 34.9 + - - +
257B PRO* 3.9 18.9 - - - +
260B ALA* 4.2 4.9 - - + -
261B ALA* 3.6 28.9 - - + -
264B VAL* 4.1 7.6 - - + -
308B ALA 3.4 11.8 + - - +
309B ARG* 3.3 30.8 + - + +
310B LEU 3.3 0.4 - - - -
311B SER* 1.3 76.6 + - - +
313B GLN* 1.3 87.4 + - + +
314B ARG 3.1 2.5 - - - -
315B ALA* 3.1 4.0 + - - +
316B ALA* 2.8 37.2 + - + +
332B ALA* 3.8 13.9 - - + -
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Residues in contact with GLN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.5 2.4 - - - -
78B ILE* 4.8 4.6 - - + +
82B LEU* 5.6 3.6 - - + +
309B ARG* 3.2 30.1 + - - +
310B LEU* 3.3 36.7 + - - +
312B TYR* 1.3 99.5 + - + +
314B ARG* 1.3 57.5 + - - +
316B ALA* 3.9 4.3 - - - +
317B TRP* 3.0 31.0 + - - +
12C PHE* 3.4 44.2 - - + +
14C PHE* 3.6 11.4 - - + -
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU 3.0 17.3 + - - +
311B SER 3.7 5.8 - - - +
313B GLN* 1.3 78.8 - - - +
315B ALA* 1.3 56.5 + - - +
317B TRP* 3.9 8.6 - - - +
318B GLU* 2.5 57.3 + - - +
323B ARG* 5.1 2.0 - - - +
328B TYR* 3.3 49.5 + - + -
14C PHE* 3.5 48.6 + - + +
310C LEU* 4.1 22.0 - - + +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PRO* 4.2 7.4 - - + -
311B SER 3.3 6.9 + - - +
312B TYR* 3.1 9.9 + - - +
314B ARG* 1.3 76.7 - - - +
316B ALA* 1.3 64.8 + - - +
318B GLU* 3.5 3.2 - - - +
319B ILE 3.3 9.4 + - - -
325B ASN* 2.8 25.9 + - - +
328B TYR* 3.6 16.4 - - - +
329B ALA* 3.6 35.7 - - - +
332B ALA* 4.5 2.0 - - + -
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 3.6 22.0 - - + +
78B ILE* 3.7 24.0 - - + -
81B CYS* 4.3 8.7 - - + -
257B PRO* 4.4 2.2 - - + +
312B TYR* 2.8 21.1 + - + +
313B GLN* 3.9 4.3 - - - +
315B ALA* 1.3 70.0 - - - +
317B TRP* 1.3 61.3 + - - +
318B GLU 3.0 1.3 - - - -
319B ILE* 2.8 14.4 - - - +
320B ASP* 2.8 29.3 + - - +
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Residues in contact with TRP 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 3.7 23.0 - - + +
313B GLN 3.0 16.9 + - - +
314B ARG* 3.9 6.5 - - - +
316B ALA* 1.3 79.1 - - - +
318B GLU* 1.3 74.3 + - - +
320B ASP* 3.8 3.4 - - + +
321B SER* 2.9 42.9 + - - -
323B ARG* 2.9 44.4 - - - -
12C PHE* 3.1 34.3 + - + -
13C SER* 3.5 5.9 - - - +
14C PHE* 3.8 46.9 - + + -
15C GLU* 3.6 24.9 - - + -
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ARG* 2.5 53.9 + - - +
315B ALA* 3.5 10.1 - - - +
316B ALA 3.0 0.6 - - - -
317B TRP* 1.3 89.9 - - - +
319B ILE* 1.3 60.7 + - - +
321B SER* 3.4 6.1 + - - -
323B ARG* 3.0 60.3 + - - +
324B ARG 3.9 10.8 - - - +
325B ASN* 3.7 18.6 - - + -
328B TYR* 4.1 17.8 - - + -
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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
----------------------------------------------------------
77B ILE* 3.5 27.6 - - + -
253B ASP* 3.9 23.1 - - + +
254B LYS* 4.0 25.4 - - + -
315B ALA 3.3 8.5 + - - +
316B ALA* 2.8 24.5 - - - +
318B GLU* 1.3 74.9 - - - +
320B ASP* 1.3 62.3 + - - +
321B SER 3.0 4.7 - - - -
322B GLY* 2.9 15.2 + - - -
323B ARG 3.5 16.1 + - - +
324B ARG* 5.1 2.0 - - - -
325B ASN* 3.6 21.5 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
76B GLY* 3.8 8.9 - - - -
77B ILE* 2.8 35.5 + - - +
78B ILE* 3.1 35.7 + - + +
79B ASP* 5.3 0.7 - - - +
316B ALA 2.8 17.4 + - - +
317B TRP* 3.8 9.0 - - + +
319B ILE* 1.3 76.8 - - - +
321B SER* 1.3 59.6 + - - +
322B GLY 3.2 1.3 + - - -
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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 TRP* 2.9 35.7 + - - -
318B GLU 3.6 7.2 - - - -
319B ILE 3.0 1.0 - - - -
320B ASP* 1.3 78.9 - - - +
322B GLY* 1.3 54.7 + - - +
323B ARG* 3.1 40.8 + - - +
----------------------------------------------------------
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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