Contacts of the helix formed by residues 283 - 314 (chain C) in PDB entry 4LML
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 GLN 283 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU* 3.1 33.0 + - + +
279C LYS 4.5 0.2 + - - -
281C GLU* 4.3 11.7 + - + +
282C SER* 1.3 78.9 - - - +
284C PRO* 1.4 61.8 - - - +
285C ALA* 3.0 12.7 + - + +
286C ARG* 3.1 51.5 + - + +
287C ALA* 3.2 8.0 + - - +
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Residues in contact with PRO 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU 5.2 0.2 - - - +
279C LYS* 4.9 17.3 - - + +
282C SER* 3.3 12.6 - - - +
283C GLN* 1.4 85.2 - - - +
285C ALA* 1.3 65.5 + - + +
286C ARG 3.2 0.2 - - - -
287C ALA* 3.5 13.5 - - + -
288C ALA* 2.9 28.4 + - + +
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLN* 3.0 9.8 - - + +
284C PRO* 1.3 81.0 - - - +
286C ARG* 1.3 59.2 + - - +
288C ALA* 4.9 0.9 - - - +
289C SER* 3.4 18.9 + - - -
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Residues in contact with ARG 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU* 3.4 24.4 - - + +
283C GLN* 3.1 34.6 + - - +
285C ALA* 1.3 77.8 - - - +
287C ALA* 1.3 60.6 + - - +
289C SER* 3.1 8.0 + - - -
290C ILE* 2.9 45.8 + - + +
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C THR* 6.2 2.0 - - + -
275C GLN* 3.6 29.6 - - + +
278C LEU* 3.4 17.2 - - + +
279C LYS* 4.5 10.1 - - + +
283C GLN 3.2 5.6 + - - +
284C PRO* 3.2 20.5 + - + -
286C ARG* 1.3 80.2 - - - +
288C ALA* 1.3 61.2 + - - +
290C ILE* 4.2 2.4 - - - +
291C THR* 3.0 25.6 + - - -
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLN* 5.4 0.4 - - - -
284C PRO* 2.9 16.0 + - + +
285C ALA 4.9 0.9 - - - +
287C ALA* 1.3 76.0 - - - +
289C SER* 1.3 57.8 + - - +
291C THR* 3.9 4.9 - - - -
292C ARG* 2.9 31.4 + - - +
295C ARG* 5.7 1.7 + - - -
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Residues in contact with SER 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ALA 3.4 15.3 + - - -
286C ARG* 3.1 16.7 + - - -
288C ALA* 1.3 76.1 - - - +
290C ILE* 1.3 66.9 + - - +
292C ARG* 3.2 7.2 + - - +
293C ALA* 3.0 23.4 + - - +
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Residues in contact with ILE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C GLU* 4.5 18.8 - - + -
274C VAL* 3.6 23.6 - - + -
275C GLN* 5.8 3.6 - - + -
278C LEU* 3.6 25.6 - - + -
286C ARG* 2.9 27.5 + - + +
287C ALA 4.2 3.6 - - - +
289C SER* 1.3 73.0 - - - +
291C THR* 1.3 65.2 + - - +
293C ALA* 3.0 11.2 + - - +
294C SER* 2.9 24.2 + - - +
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Residues in contact with THR 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ALA 5.0 0.9 - - - +
215C PHE* 3.0 40.6 - - + +
217C SER 5.3 2.2 - - - +
271C GLU* 3.5 22.3 + - - +
275C GLN* 2.3 35.0 + - - +
287C ALA 3.0 12.2 + - - -
288C ALA* 3.9 6.1 - - - -
289C SER 3.3 0.2 - - - -
290C ILE* 1.3 78.2 - - - +
292C ARG* 1.3 55.8 + - - +
294C SER* 3.1 4.0 + - - -
295C ARG* 2.9 33.7 + - - +
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Residues in contact with ARG 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C TRP* 6.3 0.2 - - - -
288C ALA 2.9 20.2 + - - +
289C SER* 3.2 8.0 + - - +
291C THR* 1.3 76.3 - - - +
293C ALA* 1.3 62.2 + - - +
295C ARG* 3.5 51.2 + - - +
296C ILE* 4.1 25.0 + - - +
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C SER 3.0 12.7 + - - +
290C ILE* 3.3 11.4 - - - +
292C ARG* 1.3 76.7 - - - +
294C SER* 1.3 64.2 + - - +
296C ILE* 3.3 6.1 + - - +
297C ALA* 3.0 26.8 + - + +
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Residues in contact with SER 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C PHE* 3.6 26.9 - - - -
271C GLU* 3.4 24.4 + - - +
290C ILE* 2.9 15.2 + - - +
291C THR 3.2 9.2 - - - -
293C ALA* 1.3 76.5 - - - +
295C ARG* 1.3 62.4 + - - +
296C ILE 2.9 1.9 + - - -
297C ALA* 4.2 3.1 - - - -
298C PHE* 3.0 43.3 + - - +
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TYR* 3.9 34.8 + - - -
215C PHE* 3.1 35.4 + - + -
216C TRP* 3.5 60.3 + - + +
288C ALA 5.7 1.4 + - - -
291C THR* 2.9 21.2 + - - +
292C ARG* 3.6 53.2 - - - +
293C ALA 3.3 0.8 - - - -
294C SER* 1.3 75.1 - - - +
296C ILE* 1.3 63.3 + - + +
299C PRO* 3.9 14.6 - - - +
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Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ARG* 4.1 26.0 + - - +
293C ALA* 3.3 6.2 + - - +
294C SER 3.0 0.2 - - - -
295C ARG* 1.3 83.0 - - + +
297C ALA* 1.3 68.8 + - - +
298C PHE 3.3 1.6 - - - -
299C PRO* 3.1 14.4 - - - +
300C VAL* 3.2 31.4 - - + +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ALA* 3.0 22.8 + - + +
294C SER* 4.1 4.0 - - - +
296C ILE* 1.3 79.8 - - - +
298C PHE* 1.3 68.3 + - + +
300C VAL* 3.1 10.0 + - - +
301C VAL* 3.0 32.0 + - + +
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Residues in contact with PHE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TRP* 3.9 29.5 - + + -
215C PHE* 3.4 32.5 - + + -
264C PHE* 4.4 8.4 - + + -
267C VAL* 3.8 39.9 - - + -
268C ALA* 4.0 16.2 - - + -
271C GLU* 4.6 5.6 - - + -
294C SER* 3.0 41.3 + - - +
297C ALA* 1.3 78.2 - - + +
299C PRO* 1.4 70.0 - - + +
301C VAL* 3.3 7.6 + - + +
302C PHE* 3.2 19.8 + - - +
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Residues in contact with PRO 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TRP* 4.0 35.0 - - + +
215C PHE* 5.6 1.3 - - + -
294C SER 4.0 0.9 - - - +
295C ARG* 3.9 14.6 - - - +
296C ILE* 3.1 19.7 - - - +
298C PHE* 1.4 89.0 - - + +
300C VAL* 1.3 56.1 + - + +
302C PHE* 3.5 2.8 + - + +
303C LEU* 3.0 32.1 + - - +
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Residues in contact with VAL 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ILE* 3.2 32.1 + - + +
297C ALA* 3.1 12.0 + - - +
299C PRO* 1.3 76.7 - - + +
301C VAL* 1.3 69.3 + - + +
303C LEU* 4.0 3.8 - - - +
304C LEU* 3.0 35.3 + - + +
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C PHE* 3.4 25.8 - - + -
297C ALA* 3.0 20.9 + - + +
298C PHE* 3.7 8.5 - - + +
300C VAL* 1.3 78.1 - - + +
302C PHE* 1.3 52.2 + - - +
304C LEU* 3.4 7.3 + - - +
305C ALA* 2.7 42.9 + - + +
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Residues in contact with PHE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 3.5 25.6 - - + -
208C LEU* 3.3 28.3 - - + -
209C PHE* 4.3 17.0 - + - -
212C TRP* 3.8 15.9 - + + -
257C ILE* 6.1 0.9 - - + -
260C MET* 4.6 3.8 - - + -
261C ILE* 3.9 20.6 - - + -
264C PHE* 3.3 33.3 - + + -
298C PHE 3.2 3.6 + - - +
299C PRO* 3.6 7.6 - - + +
301C VAL* 1.3 77.2 - - - +
303C LEU* 1.3 60.3 + - + +
304C LEU 3.0 0.3 + - - -
305C ALA* 3.1 1.3 + - - -
306C ASN* 2.8 75.0 + - - +
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PRO 3.0 14.1 + - - +
300C VAL* 4.2 3.6 - - - +
302C PHE* 1.3 86.6 - - + +
304C LEU* 1.3 64.9 + - + +
306C ASN* 4.0 5.5 - - - +
307C ILE* 3.2 48.8 + - + +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C VAL* 3.0 25.0 + - + +
301C VAL* 3.5 7.9 - - + +
302C PHE 3.0 0.6 - - - -
303C LEU* 1.3 78.1 - - + +
305C ALA* 1.3 55.2 + - - +
306C ASN 3.1 1.3 - - - -
307C ILE* 2.8 16.4 + - + +
308C ILE* 2.7 53.0 + - + +
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C MET* 3.4 31.7 - - + +
264C PHE* 4.8 3.4 - - + -
301C VAL* 2.7 25.6 + - + +
302C PHE 3.8 0.2 - - - +
304C LEU* 1.3 73.1 - - - +
306C ASN* 1.3 57.7 + - - +
308C ILE* 3.5 12.0 - - - +
309C LEU* 2.8 32.1 + - - +
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Residues in contact with ASN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 5.7 0.5 - - - +
253C TYR* 4.2 14.0 + - - +
257C ILE* 4.5 16.6 - - - +
260C MET* 4.1 10.4 - - - +
302C PHE* 2.8 78.0 + - - +
303C LEU* 4.0 7.4 - - - +
305C ALA* 1.3 73.2 - - - +
307C ILE* 1.3 53.0 + - + +
309C LEU* 3.4 3.0 + - - +
310C ALA* 2.6 38.0 + - - +
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Residues in contact with ILE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LEU* 3.2 35.8 + - + +
304C LEU* 2.8 19.8 + - + +
306C ASN* 1.3 73.8 - - + +
308C ILE* 1.3 70.8 + - + +
310C ALA* 3.8 6.5 - - + +
311C PHE* 3.0 25.9 + - + +
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LEU* 2.7 49.0 + - + +
305C ALA* 3.5 11.0 - - - +
307C ILE* 1.3 79.6 - - + +
309C LEU* 1.3 67.5 + - + +
311C PHE* 3.9 4.9 - - - +
312C LEU* 3.1 33.0 + - + +
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Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C TYR* 4.0 7.0 - - + -
256C ALA* 3.7 26.0 - - + +
257C ILE* 3.8 13.2 - - + +
260C MET* 3.4 27.8 - - + -
305C ALA 2.8 19.3 + - - +
306C ASN* 3.6 4.7 - - - +
308C ILE* 1.3 76.7 - - + +
310C ALA* 1.3 64.4 + - - +
312C LEU* 2.9 25.9 + - + +
313C PHE* 3.1 36.9 + - + -
----------------------------------------------------------
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C TYR* 3.7 24.1 - - + +
306C ASN 2.6 22.8 + - - +
307C ILE* 3.8 7.9 - - + +
308C ILE 3.4 0.2 - - - -
309C LEU* 1.3 72.3 - - - +
311C PHE* 1.3 62.7 + - - +
314C PHE* 2.9 33.9 + - + +
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Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C ILE* 3.0 18.3 + - + +
308C ILE* 3.9 3.6 - - - +
310C ALA* 1.3 76.4 - - - +
312C LEU* 1.3 69.3 + - + +
313C PHE 2.9 7.4 + - - -
315C GLY* 3.1 34.6 + - - +
316C PHE* 3.1 57.9 + + + +
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C ILE* 3.1 25.0 + - + +
309C LEU* 2.9 20.2 + - + +
311C PHE* 1.3 88.8 - - + +
313C PHE* 1.3 63.8 + - + +
316C PHE* 3.9 33.2 - - + +
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Residues in contact with PHE 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ARG* 3.9 26.0 - - + -
117C ARG* 4.1 15.7 + - + +
251C MET* 3.2 28.7 - - + -
252C THR 3.2 20.2 - - - -
253C TYR* 3.4 28.7 - + + -
256C ALA* 4.0 13.9 - - + -
309C LEU* 3.1 30.4 + - + +
311C PHE 2.9 2.0 + - - -
312C LEU* 1.3 83.5 - - + +
314C PHE* 1.3 81.6 + - + +
316C PHE* 3.3 13.4 - - - +
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Residues in contact with PHE 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ARG* 3.7 52.0 + - + +
120C PHE* 3.8 43.5 - + + -
253C TYR* 3.6 37.5 - + + -
310C ALA* 2.9 28.0 + - + +
313C PHE* 1.3 78.4 - - + +
315C GLY* 1.3 58.0 + - - +
316C PHE* 3.1 11.4 + - - +
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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