Contacts of the helix formed by residues 291 - 321 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN* 3.7 16.4 + - - +
283C THR* 3.2 26.2 + - - -
284C PHE* 4.2 8.3 - - + -
286C LYS* 3.4 26.9 + - + +
287C LEU 3.6 17.7 - - - -
288C LEU* 3.1 18.0 + - - +
290C GLU* 1.3 79.7 - - - +
292C GLN* 1.3 67.3 + - - +
293C GLY 3.1 0.2 - - - -
294C ILE* 2.9 17.0 + - + +
295C SER* 3.0 11.8 + - - -
3399D FAD 3.5 48.4 + + + +
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Residues in contact with GLN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A HIS* 3.4 22.4 + - - +
292A GLN* 3.7 14.4 + - + +
293A GLY* 2.8 28.8 + - - +
384B ILE* 3.1 22.2 - - + +
1399B FAD 3.0 29.0 + - - -
290C GLU 3.6 4.8 + - - -
291C HIS* 1.3 70.6 - - - +
293C GLY* 1.3 64.0 + - - +
295C SER* 4.0 7.4 - - - -
296C PHE* 3.1 44.5 + - + -
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Residues in contact with GLY 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN* 2.6 34.4 + - - +
293A GLY* 5.2 1.6 - - - -
296A PHE* 4.0 23.6 - - - -
292C GLN* 1.3 75.5 - - - +
294C ILE* 1.3 62.0 + - - +
296C PHE* 3.6 5.2 + - - +
297C LEU* 3.4 16.3 + - - +
380D GLN* 5.8 1.6 - - - -
3399D FAD 5.1 0.2 - - - -
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN* 4.2 0.2 + - - -
278C ALA* 4.8 2.9 - - + -
288C LEU* 3.1 44.0 - - + +
289C ALA* 4.3 0.9 - - - -
291C HIS* 2.9 3.7 + - + -
293C GLY* 1.3 74.2 - - - +
295C SER* 1.3 60.3 + - - +
297C LEU* 3.1 18.9 + - + +
298C LEU* 2.9 50.3 + - + +
350C VAL* 4.9 10.3 - - + -
380D GLN* 4.6 11.4 - - + -
3399D FAD 3.7 50.5 - - + +
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Residues in contact with SER 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ILE* 5.6 3.1 - - - -
387B ALA* 3.7 19.8 - - - +
391B ILE* 5.1 3.0 - - - +
289C ALA 2.8 26.1 + - - -
290C GLU 4.7 0.7 - - - -
291C HIS 3.0 7.9 + - - -
292C GLN* 3.5 15.7 - - - -
294C ILE* 1.3 77.6 - - - +
296C PHE* 1.3 65.6 + - - +
298C LEU* 3.3 10.3 + - - +
299C ALA* 2.9 28.4 + - - +
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Residues in contact with PHE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLY* 4.2 21.8 - - - -
380B GLN* 3.6 38.4 - - + -
383B ARG* 3.9 21.8 - - + -
384B ILE* 3.2 35.0 - - + -
1399B FAD 4.3 6.3 - + - -
292C GLN* 3.1 32.1 + - + +
293C GLY* 3.9 5.2 - - - +
295C SER* 1.3 77.7 - - - +
297C LEU* 1.3 60.1 + - - +
299C ALA* 3.7 5.1 - - - +
300C ASP* 2.9 40.0 + - - +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLY 3.4 11.7 + - - +
294C ILE* 3.1 22.1 + - + +
296C PHE* 1.3 78.9 - - - +
298C LEU* 1.3 63.1 + - + +
300C ASP* 3.4 6.9 + - + +
301C MET* 3.0 35.2 + - + +
346C ASP* 3.7 34.8 - - + +
349C GLN* 5.2 4.3 - - + -
350C VAL* 3.5 31.4 - - + -
380D GLN* 4.7 13.5 - - - +
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ALA* 5.5 1.1 - - + -
390B HIS* 4.6 11.1 - - + -
391B ILE* 4.1 27.6 - - + -
271C LEU* 4.1 4.8 - - + +
274C ALA* 4.7 13.7 - - + +
275C THR* 4.3 18.4 - - + +
278C ALA* 4.1 20.2 - - + -
279C LEU* 6.4 0.2 - - + -
289C ALA* 4.3 4.7 - - + -
294C ILE* 2.9 34.1 + - + +
295C SER* 3.6 5.6 - - - +
297C LEU* 1.3 79.6 - - + +
299C ALA* 1.3 62.3 + - - +
301C MET* 3.2 19.9 + - - +
302C ALA* 3.0 24.1 + - - +
350C VAL* 4.6 13.7 - - + -
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ARG* 3.7 35.7 - - + +
386B ILE* 3.8 24.0 - - + +
387B ALA* 4.0 8.2 - - - +
390B HIS* 5.8 0.2 - - - -
295C SER 2.9 16.6 + - - +
296C PHE* 3.7 4.5 - - - +
297C LEU 3.3 0.2 - - - -
298C LEU* 1.3 77.6 - - - +
300C ASP* 1.3 62.3 + - - +
301C MET 3.2 0.2 + - - -
302C ALA* 3.4 2.0 + - - +
303C MET* 3.0 25.2 + - - +
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ARG* 3.1 40.2 + - - +
296C PHE* 2.9 26.1 + - - +
297C LEU* 3.8 8.0 - - + +
299C ALA* 1.3 77.0 - - - +
301C MET* 1.3 58.6 - - + +
303C MET* 3.9 15.3 - - - +
304C LYS* 3.1 42.8 + - - +
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Residues in contact with MET 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ALA 4.6 0.2 - - - +
271C LEU* 3.6 22.2 - - + -
274C ALA* 4.2 16.4 - - + -
297C LEU* 3.0 32.3 + - + +
298C LEU* 3.5 22.4 - - - +
299C ALA 3.1 0.2 - - - -
300C ASP* 1.3 75.6 - - - +
302C ALA* 1.3 65.5 + - - +
304C LYS* 3.2 14.4 + - - +
305C VAL* 3.2 10.2 + - - +
343C LEU* 3.5 59.5 - - + +
346C ASP* 3.9 28.0 - - + +
347C ALA* 4.0 7.6 - - + +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 4.0 15.5 - - - +
386B ILE* 4.6 5.6 - - + -
390B HIS* 4.1 21.1 - - + +
271C LEU* 3.7 15.4 - - + +
298C LEU 3.0 15.9 + - - +
299C ALA 3.8 4.3 - - - +
301C MET* 1.3 76.3 - - - +
303C MET* 1.3 63.0 + - - +
305C VAL* 2.7 31.4 + - + +
306C GLU* 3.1 10.8 + - - +
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Residues in contact with MET 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 3.6 36.2 - - + +
334B ALA* 4.1 25.6 - - - -
335B TYR* 3.9 31.9 - - + -
338B ASP* 4.9 2.5 - - - +
383B ARG* 4.2 12.1 - - - +
386B ILE* 4.5 7.8 - - + +
299C ALA 3.0 18.4 + - - +
300C ASP* 3.9 25.4 - - - +
301C MET 3.3 0.2 - - - -
302C ALA* 1.3 78.1 - - - +
304C LYS* 1.3 70.1 + - + +
306C GLU* 3.3 3.5 + - - +
307C LEU* 3.1 33.4 + - + +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ASP* 3.1 28.1 + - - +
301C MET* 3.2 8.3 + - - +
303C MET* 1.3 84.9 - - + +
305C VAL* 1.3 63.2 + - - +
307C LEU* 4.5 1.6 - - - -
308C ALA* 3.1 24.8 + - - +
335C TYR* 3.7 25.5 - - - +
339C ILE* 3.8 18.8 - - + +
342C GLN* 2.6 37.0 + - - +
343C LEU* 3.9 17.1 - - + +
346C ASP* 5.1 6.5 + - - -
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Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 5.5 0.2 - - - +
264C VAL* 4.2 14.6 - - + +
267C ALA* 4.7 2.5 - - + -
268C GLN* 3.5 31.6 - - + +
271C LEU* 3.7 14.8 - - + -
301C MET 3.2 6.7 + - - +
302C ALA* 2.7 36.6 - - - +
304C LYS* 1.3 72.0 - - - +
306C GLU* 1.3 71.1 + - + +
308C ALA* 3.4 2.3 + - - +
309C ARG* 3.1 39.0 + - - +
339C ILE* 4.4 8.9 - - - +
343C LEU* 4.5 11.2 - - + +
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 2.6 41.9 + - + +
328B TYR* 4.2 19.2 + - + -
331B ILE* 3.8 19.3 - - + -
393B ARG* 3.9 9.2 + - - -
268C GLN* 5.5 1.4 - - - +
302C ALA 3.1 12.2 + - - +
303C MET 3.4 7.4 - - - +
305C VAL* 1.3 78.9 - - - +
307C LEU* 1.3 62.0 + - + +
309C ARG* 3.3 27.2 + - - +
310C LEU* 3.1 33.5 + - + +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 3.7 30.0 - - + +
311B SER* 3.5 33.0 - - - +
331B ILE* 4.5 8.3 - - + -
335B TYR* 3.6 44.2 - - + -
303C MET* 3.1 30.4 + - + +
304C LYS* 3.9 0.7 - - - +
305C VAL 3.3 0.2 - - - -
306C GLU* 1.3 81.0 - - + +
308C ALA* 1.3 60.5 + - - +
310C LEU* 3.5 10.1 + - + +
311C SER 3.2 15.6 + - - -
335C TYR* 3.9 23.6 - - + +
----------------------------------------------------------
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C VAL* 4.0 12.2 - - + +
304C LYS 3.1 18.4 + - - +
305C VAL 3.9 3.1 - - - +
306C GLU 3.3 0.2 - - - -
307C LEU* 1.3 73.0 - - - +
309C ARG* 1.3 66.1 + - - +
311C SER* 2.7 23.7 + - - -
312C TYR* 3.3 10.6 + - - +
335C TYR* 3.8 17.7 - - + -
336C ALA* 4.0 12.9 - - - +
339C ILE* 3.9 19.5 - - + -
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Residues in contact with ARG 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLU* 2.8 34.6 + - - -
264C VAL* 4.1 4.2 - - + +
268C GLN* 3.2 30.7 + - - +
305C VAL* 3.1 34.8 + - - +
306C GLU* 3.3 33.6 + - - +
308C ALA* 1.3 78.2 - - - +
310C LEU* 1.3 64.8 + - + +
312C TYR* 3.2 25.0 - - + +
313C GLN* 3.1 48.8 + - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.8 2.2 - - + -
310B LEU* 3.8 46.3 - - + +
311B SER* 4.0 11.0 - - - +
314B ARG* 4.1 31.2 - - + +
328B TYR* 6.2 1.8 - - + -
14C PHE* 4.7 7.4 - - + -
306C GLU* 3.1 22.2 + - + +
307C LEU* 3.7 16.4 - - + +
308C ALA 3.2 0.4 - - - -
309C ARG* 1.3 79.7 - - + +
311C SER* 1.3 62.2 + - - +
313C GLN* 3.3 23.4 + - - +
314C ARG* 3.0 24.4 + - - +
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Residues in contact with SER 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 3.6 27.4 - - - -
310B LEU* 4.1 10.3 - - - +
307C LEU 3.2 2.8 + - - -
308C ALA* 2.7 24.5 + - - +
310C LEU* 1.3 80.8 - - - +
312C TYR* 1.3 56.0 + - - +
314C ARG* 3.6 3.0 + - - +
315C ALA* 3.1 20.6 + - - +
328C TYR* 4.4 2.9 - - - +
331C ILE* 4.7 4.5 - - - -
332C ALA* 3.4 35.8 + - - +
335C TYR* 4.8 2.5 - - - +
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Residues in contact with TYR 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE 5.3 0.4 - - - -
81C CYS* 3.3 36.0 + - + -
82C LEU* 4.3 16.2 - - + +
85C GLU* 2.4 35.8 + - - +
257C PRO* 3.9 17.9 - - - +
260C ALA* 4.2 12.1 - - + -
261C ALA* 3.9 12.1 - - + -
264C VAL* 3.8 18.8 - - + -
308C ALA 3.3 7.0 + - - +
309C ARG* 3.2 40.1 - - + +
310C LEU 3.3 0.4 - - - -
311C SER* 1.3 78.8 + - - +
313C GLN* 1.3 75.4 + - + +
314C ARG 3.2 0.4 - - - -
315C ALA* 3.8 2.7 - - - +
316C ALA* 2.8 31.9 + - - +
332C ALA* 3.8 6.1 - - + -
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Residues in contact with GLN 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.8 42.8 - - + -
14B PHE* 3.8 6.7 - - + -
14C PHE* 4.5 6.3 - - - -
78C ILE* 5.1 5.1 - - + +
82C LEU* 5.4 4.9 - - + +
309C ARG* 3.1 36.4 + - - +
310C LEU* 3.4 33.6 + - - +
312C TYR* 1.3 93.1 + - + +
314C ARG* 1.3 57.9 + - - +
316C ALA* 3.4 3.7 + - - +
317C TRP* 2.9 31.9 + - - +
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Residues in contact with ARG 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 3.4 43.9 + - + +
310B LEU* 4.0 22.9 - - + +
310C LEU 3.0 16.2 + - - +
311C SER* 3.7 5.6 - - - +
313C GLN* 1.3 77.9 - - - +
315C ALA* 1.3 61.8 + - - +
317C TRP* 3.3 22.9 - - - +
318C GLU* 2.7 43.5 + - - +
328C TYR* 3.7 43.7 + - + -
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C PRO* 4.0 11.2 - - + -
311C SER 3.1 16.1 + - - +
312C TYR* 3.3 6.5 + - - +
314C ARG* 1.3 76.4 - - - +
316C ALA* 1.3 66.1 + - - +
318C GLU* 3.6 1.8 + - - +
319C ILE 3.4 8.0 + - - -
325C ASN* 2.9 22.5 + - - +
328C TYR* 3.7 35.0 - - - +
329C ALA* 3.7 11.4 - - - +
332C ALA* 4.4 2.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 3.8 20.2 - - + +
78C ILE* 3.7 33.2 - - + +
81C CYS* 4.0 7.9 - - + -
257C PRO* 4.3 2.4 - - + +
312C TYR 2.8 18.2 + - - +
313C GLN* 3.7 5.6 - - - +
315C ALA* 1.3 74.2 - - - +
317C TRP* 1.3 66.7 + - - +
319C ILE* 3.1 5.8 - - - +
320C ASP* 2.9 24.9 + - - +
----------------------------------------------------------
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Residues in contact with TRP 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 2.8 40.1 + - + -
13B SER* 3.6 7.3 - - - +
14B PHE* 3.7 51.1 - + + -
15B GLU* 4.3 11.2 - - + -
78C ILE* 3.9 18.9 - - + +
313C GLN 2.9 18.8 + - - +
314C ARG* 3.3 35.0 - - - +
316C ALA* 1.3 75.9 - - - +
318C GLU* 1.3 66.6 + - - +
320C ASP* 3.2 3.3 + - + +
321C SER* 2.8 49.2 + - - -
323C ARG* 3.5 34.8 - - - -
----------------------------------------------------------
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ARG* 2.7 52.6 + - - +
315C ALA* 3.6 7.9 - - - +
316C ALA 3.2 0.2 - - - -
317C TRP* 1.3 84.1 - - - +
319C ILE* 1.3 60.9 + - - +
321C SER* 3.3 9.9 + - - -
322C GLY 3.6 0.2 + - - -
323C ARG* 3.2 62.4 + - - +
324C ARG 4.1 6.2 - - - +
325C ASN* 3.6 24.9 - - + -
328C TYR* 4.1 15.7 - - + -
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Residues in contact with ILE 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 4.0 22.7 - - + -
253C ASP* 5.0 4.7 - - + +
254C LYS* 3.4 33.7 - - + -
315C ALA 3.4 3.5 + - - +
316C ALA* 3.1 14.4 - - - +
318C GLU* 1.3 76.1 - - - +
320C ASP* 1.3 63.6 + - - +
322C GLY* 2.9 22.8 + - - -
323C ARG 3.2 19.1 - - - +
324C ARG* 4.9 2.2 - - - -
325C ASN* 3.4 34.3 - - - +
----------------------------------------------------------
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Residues in contact with ASP 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS* 5.2 1.0 + - - -
76C GLY* 3.8 8.6 - - - -
77C ILE* 3.0 28.9 + - - +
78C ILE* 2.8 43.9 + - + +
316C ALA 2.9 17.1 + - - +
317C TRP* 3.3 8.5 - - + +
319C ILE* 1.3 79.5 - - - +
321C SER* 1.3 57.6 + - - +
322C GLY* 3.0 4.7 + - - -
----------------------------------------------------------
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Residues in contact with SER 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TRP* 2.8 41.8 + - - -
318C GLU 3.6 1.3 - - - -
319C ILE 3.1 0.8 - - - -
320C ASP* 1.3 75.1 - - - +
322C GLY* 1.3 59.6 + - - +
323C ARG* 3.5 36.0 - - - +
----------------------------------------------------------
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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