Contacts of the helix formed by residues 284 - 315 (chain D) in PDB entry 5J0Z
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 284 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU* 3.2 23.8 + - + +
282D GLU* 3.3 31.2 - - - +
283D SER* 1.3 78.2 - - - +
285D PRO* 1.4 52.6 - - - +
286D ALA* 2.6 21.7 + - + -
287D ARG* 2.6 59.7 + - + +
288D ALA* 3.1 8.0 + - - -
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Residues in contact with PRO 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU 4.6 2.2 - - - +
280D LYS* 4.7 22.0 - - + +
283D SER* 3.3 14.8 - - - -
284D GLN* 1.4 87.2 - - - +
286D ALA* 1.3 60.4 + - - +
288D ALA* 3.9 10.2 - - + +
289D ALA* 3.1 27.4 + - - +
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D GLN* 2.6 6.8 + - + +
285D PRO* 1.3 75.3 - - - +
287D ARG* 1.3 51.2 + - - +
289D ALA* 3.4 1.6 - - - +
290D SER* 2.8 39.6 + - - +
293D ARG* 4.8 4.2 + - - +
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Residues in contact with ARG 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU* 3.9 15.2 - - + +
284D GLN* 2.6 48.5 + - + +
286D ALA* 1.3 72.0 - - - +
288D ALA* 1.3 66.2 + - - +
290D SER* 3.3 16.2 + - - -
291D ILE* 3.3 22.3 + - + +
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D GLN* 3.7 26.8 - - + +
279D LEU* 3.5 33.3 - - + +
280D LYS* 4.4 6.5 - - + +
284D GLN 3.1 6.9 + - - +
285D PRO* 3.9 14.4 - - + +
287D ARG* 1.3 80.5 - - - +
289D ALA* 1.3 58.0 + - + +
290D SER 3.2 0.2 + - - -
291D ILE* 3.2 7.6 + - - +
292D THR* 3.1 23.4 + - - -
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Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR* 5.3 9.4 - - + -
276D GLN* 5.4 1.8 - - + +
285D PRO 3.1 16.4 + - - +
286D ALA 3.4 3.1 - - - +
288D ALA* 1.3 75.8 - - + +
290D SER* 1.3 61.1 + - - +
292D THR* 3.7 21.5 - - + -
293D ARG* 3.0 36.6 + - - +
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Residues in contact with SER 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA* 2.8 24.4 + - - +
287D ARG* 3.4 11.6 - - - -
288D ALA 3.1 0.6 - - - -
289D ALA* 1.3 75.8 - - - +
291D ILE* 1.3 56.2 + - - +
293D ARG* 3.1 18.0 + - - +
294D ALA* 2.8 34.9 + - - +
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Residues in contact with ILE 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D GLU* 4.0 25.6 - - + +
275D VAL* 3.9 29.4 - - + -
276D GLN* 5.7 1.6 - - + +
279D LEU* 3.9 13.9 - - + -
287D ARG* 3.4 22.0 - - + +
288D ALA 3.3 6.3 - - - +
290D SER* 1.3 77.8 - - - +
292D THR* 1.3 64.5 + - - +
294D ALA* 2.8 20.1 + - - +
295D SER* 2.8 18.4 + - - +
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Residues in contact with THR 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D PHE* 3.5 28.3 + - - +
218D SER 5.1 0.2 - - - +
219D THR* 5.2 3.6 - - + -
272D GLU* 2.6 26.3 + - - -
276D GLN* 2.7 30.4 + - - +
288D ALA 3.1 9.5 + - - -
289D ALA* 3.7 22.4 - - + +
290D SER 3.3 0.4 - - - -
291D ILE* 1.3 80.3 - - - +
293D ARG* 1.3 63.9 + - + +
295D SER* 3.5 5.3 - - - -
296D ARG* 3.4 33.1 + - - +
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Residues in contact with ARG 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA* 4.8 4.2 + - - +
289D ALA* 3.0 33.9 + - + +
290D SER* 3.1 14.6 + - - +
292D THR* 1.3 77.6 - - + +
294D ALA* 1.3 67.9 + - - +
296D ARG* 3.2 53.5 - - - +
297D ILE* 4.1 6.9 + - - +
278E TYR* 5.7 1.3 - - - -
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Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D SER 2.8 13.9 + - - +
291D ILE* 2.8 13.4 + - - +
293D ARG* 1.3 73.6 - - - +
295D SER* 1.3 54.6 + - - +
297D ILE* 2.7 31.4 + - - +
298D ALA* 3.0 15.0 + - + +
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Residues in contact with SER 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D PHE* 3.7 28.3 - - - -
272D GLU* 3.5 18.4 - - - +
291D ILE* 2.8 19.2 + - - +
292D THR 3.5 9.9 - - - -
294D ALA* 1.3 70.3 - - - +
296D ARG* 1.3 54.5 + - - +
297D ILE 2.7 12.8 + - - -
298D ALA* 3.0 20.9 + - - +
299D PHE* 3.1 27.8 + - - +
300D PRO* 3.8 0.2 - - - +
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Residues in contact with ARG 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D PHE* 3.1 32.6 + - + -
217D TRP* 3.4 71.2 - - + +
219D THR* 6.0 2.4 - - - +
292D THR* 3.4 20.1 + - - +
293D ARG* 3.2 45.6 - - - +
294D ALA 3.0 0.2 + - - -
295D SER* 1.3 76.2 - - - +
297D ILE* 1.3 67.4 + - + +
300D PRO* 3.6 17.7 - - - +
278E TYR* 3.8 28.7 + - - -
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Residues in contact with ILE 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ARG 4.4 6.1 - - - +
294D ALA* 2.7 10.7 + - - +
295D SER 2.7 2.4 + - - -
296D ARG* 1.3 87.3 - - + +
298D ALA* 1.3 66.2 + - - +
299D PHE 3.1 2.7 + - - -
300D PRO* 3.3 5.1 - - - +
301D VAL* 3.0 41.7 + - + +
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Residues in contact with ALA 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ALA* 3.0 10.2 + - + +
295D SER* 3.0 18.4 + - - +
297D ILE* 1.3 76.0 - - - +
299D PHE* 1.3 65.4 + - + +
301D VAL* 3.7 4.4 - - - +
302D VAL* 2.8 43.9 + - + +
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Residues in contact with PHE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TRP* 3.5 28.0 - + + -
216D PHE* 3.4 37.9 - + + -
265D PHE* 3.9 16.7 - + - -
268D VAL* 3.4 29.4 - - + -
269D ALA* 3.7 26.5 - - + -
272D GLU* 4.5 5.4 - - + -
295D SER* 3.1 31.6 + - - +
298D ALA* 1.3 83.4 - - + +
300D PRO* 1.3 73.1 - - + +
301D VAL 3.1 0.3 + - - -
302D VAL* 3.8 2.6 - - - -
303D PHE* 2.9 25.1 + - - +
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Residues in contact with PRO 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TRP* 3.9 31.6 - - + -
216D PHE* 5.5 1.1 - - + -
295D SER 3.8 1.8 - - - +
296D ARG* 3.6 22.9 - - - +
297D ILE* 3.3 8.5 - - - +
299D PHE* 1.3 95.0 - - + +
301D VAL* 1.3 56.7 + - + +
303D PHE* 3.7 0.9 - - - +
304D LEU* 3.1 36.2 + - + +
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ILE* 3.0 38.7 + - + +
298D ALA* 3.7 5.6 - - - +
300D PRO* 1.3 72.1 - - + +
302D VAL* 1.3 74.3 + - + +
303D PHE 3.0 1.1 - - - -
304D LEU* 2.8 18.7 + - - +
305D LEU* 2.9 32.0 + - + +
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Residues in contact with VAL 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D PHE* 3.9 19.1 - - + -
298D ALA* 2.8 32.0 + - + +
299D PHE* 4.0 2.5 - - - +
301D VAL* 1.3 78.8 - - + +
303D PHE* 1.3 56.5 + - - +
305D LEU* 3.7 12.8 - - + +
306D ALA* 2.9 33.1 + - + +
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Residues in contact with PHE 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D LEU* 3.6 27.8 - - + -
209D LEU* 3.6 24.7 - - + -
210D PHE* 4.8 5.6 - + - -
213D TRP* 4.0 16.4 - + + -
258D ILE* 5.8 1.1 - - + -
261D MET* 3.3 27.8 - - + -
262D ILE* 4.2 15.0 - - + -
265D PHE* 3.3 27.7 - + + -
299D PHE 2.9 17.7 + - - +
300D PRO 3.7 4.5 - - - +
301D VAL 2.9 0.8 + - - -
302D VAL* 1.3 75.0 - - - +
304D LEU* 1.3 69.7 + - + +
306D ALA* 4.1 0.6 - - - +
307D ASN* 2.8 52.5 + - - +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D PRO* 3.1 20.7 + - + +
301D VAL* 2.8 9.2 + - - +
303D PHE* 1.3 80.8 - - + +
305D LEU* 1.3 67.3 + - + +
307D ASN* 4.6 4.1 - - + +
308D ILE* 3.3 36.1 + - + +
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D VAL* 2.9 33.5 + - + +
302D VAL* 3.7 14.6 - - + +
304D LEU* 1.3 77.2 - - + +
306D ALA* 1.3 54.0 + - + +
308D ILE* 2.8 12.0 + - - +
309D ILE* 2.7 46.3 + - + +
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Residues in contact with ALA 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D MET* 4.0 19.8 - - - +
265D PHE* 5.0 2.2 - - + -
302D VAL* 2.9 24.0 + - + +
303D PHE* 4.1 1.6 - - - +
305D LEU* 1.3 78.2 - - - +
307D ASN* 1.3 59.1 + - - +
309D ILE* 3.6 20.7 - - + +
310D LEU* 3.1 30.5 + - - +
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Residues in contact with ASN 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D LEU* 6.1 0.6 - - - +
254D TYR* 5.2 5.1 + - - -
258D ILE* 4.0 31.4 - - - +
261D MET* 3.3 28.1 - - - +
303D PHE* 2.8 40.8 + - + +
304D LEU* 4.6 4.0 - - + +
306D ALA* 1.3 72.8 - - - +
308D ILE* 1.3 56.3 + - + +
310D LEU* 3.5 5.0 + - - +
311D ALA* 2.7 34.7 + - - +
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Residues in contact with ILE 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 3.3 25.0 + - + +
305D LEU* 2.8 11.9 + - - +
307D ASN* 1.3 78.1 - - + +
309D ILE* 1.3 64.9 + - + +
311D ALA* 3.8 8.4 - - + +
312D PHE* 3.2 24.0 + - + +
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Residues in contact with ILE 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LEU* 2.7 26.5 + - + +
306D ALA* 3.6 29.4 - - + +
308D ILE* 1.3 76.3 - - + +
310D LEU* 1.3 58.5 + - + +
312D PHE* 3.6 8.7 + - + +
313D LEU* 3.0 45.9 + - + +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D TYR* 4.7 6.7 - - + +
257D ALA* 3.8 27.4 - - + -
258D ILE* 4.0 23.6 - - + +
261D MET* 4.4 14.6 - - + -
306D ALA 3.1 17.4 + - - +
307D ASN* 3.7 5.6 - - - +
309D ILE* 1.3 77.1 - - + +
311D ALA* 1.3 68.1 + - - +
313D LEU* 2.9 33.9 + - + +
314D PHE* 2.9 37.8 + - + +
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Residues in contact with ALA 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D TYR* 4.3 20.5 - - - +
307D ASN 2.7 22.1 + - - +
308D ILE* 3.8 13.0 - - + +
310D LEU* 1.3 72.8 - - - +
312D PHE* 1.3 64.0 + - - +
314D PHE 3.3 0.7 + - - -
315D PHE* 3.2 30.6 + - + +
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Residues in contact with PHE 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ILE* 3.2 15.6 + - + +
309D ILE* 3.7 8.3 - - + +
310D LEU 3.1 0.6 - - - -
311D ALA* 1.3 77.8 - - - +
313D LEU* 1.3 65.7 + - + +
314D PHE 2.8 12.1 + - - -
315D PHE* 2.9 27.1 + - - +
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D ILE* 3.0 34.3 + - + +
310D LEU* 2.9 33.5 + - + +
312D PHE* 1.3 80.6 - - + +
314D PHE* 1.3 63.4 + - + -
404D HXA 5.1 16.9 - - + +
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Residues in contact with PHE 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ARG* 3.6 32.5 - - + -
118D ARG* 3.7 22.6 + - + +
252D MET* 3.4 34.5 - - + -
253D THR 3.7 11.7 - - - -
254D TYR* 3.7 20.0 - + + -
257D ALA* 4.1 20.0 - - + -
310D LEU* 2.9 29.1 + - + +
312D PHE 2.8 1.8 + - - -
313D LEU* 1.3 79.7 - - + +
315D PHE* 1.3 82.9 + - + +
404D HXA 4.8 8.7 - - + +
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Residues in contact with PHE 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ARG* 3.8 47.1 - - + +
121D PHE* 4.2 37.0 - + + -
254D TYR* 4.1 24.2 - + - -
311D ALA* 3.3 20.4 - - - +
312D PHE* 2.9 23.6 + - - +
313D LEU 3.7 0.2 - - - -
314D PHE* 1.3 109.6 - - + +
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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