Contacts of the helix formed by residues 282 - 310 (chain D) in PDB entry 5BJ3
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 282 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG* 3.3 45.8 + - - +
278D ALA 5.1 0.4 - - - -
279D LEU 3.6 18.3 + - - +
280D THR* 3.0 10.3 + - - +
281D ASN* 1.3 75.2 - - - +
283D GLU* 1.3 56.3 + - - +
285D SER* 4.5 4.9 - - - -
286D ARG* 2.8 49.4 + - - +
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Residues in contact with GLU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ASN* 3.2 9.5 + - - +
282D GLN* 1.3 80.7 - - - +
284D ALA* 1.3 62.9 + - - +
286D ARG* 3.6 20.7 + - - +
287D ALA* 3.2 22.3 + - - +
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Residues in contact with ALA 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D HIS* 3.6 30.2 + - + -
281D ASN* 3.2 28.6 - - - +
283D GLU* 1.3 80.1 - - - +
285D SER* 1.3 61.6 + - - +
287D ALA* 3.5 8.0 + - - +
288D PHE* 3.3 17.7 + - - +
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Residues in contact with SER 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D HIS* 2.9 26.7 - - - -
236D PHE* 3.9 19.0 - - - -
278D ALA* 2.7 30.4 + - - +
281D ASN 3.1 10.3 + - - -
282D GLN* 4.1 4.7 - - - -
284D ALA* 1.3 72.3 - - - +
286D ARG* 1.3 67.6 + - - +
288D PHE* 3.1 6.9 + - - +
289D VAL* 2.9 28.4 + - - +
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Residues in contact with ARG 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D GLN* 2.8 34.8 + - - +
283D GLU* 3.6 27.0 + - - +
285D SER* 1.3 75.1 - - - +
287D ALA* 1.3 59.1 + - - +
289D VAL* 3.2 7.9 + - - +
290D GLU* 2.8 55.9 + - - +
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Residues in contact with ALA 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D GLU 3.2 10.5 + - - +
284D ALA* 3.6 12.1 - - - +
286D ARG* 1.3 80.8 - - - +
288D PHE* 1.3 61.3 + - - +
290D GLU* 3.6 6.3 + - - +
291D MET* 3.1 24.4 + - - +
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Residues in contact with PHE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO* 5.9 0.9 - - + -
43D PHE* 3.9 24.2 - + + -
44D ASP 3.8 14.1 - - - -
46D PRO* 4.0 30.7 - - + -
234D LYS 5.6 0.4 - - - -
235D ALA 3.5 24.0 - - - -
236D PHE* 3.8 20.9 - + + -
237D ALA* 3.9 13.5 - - + -
284D ALA 3.3 10.2 + - - +
285D SER* 3.1 9.5 + - - +
287D ALA* 1.3 75.2 - - - +
289D VAL* 1.3 68.8 + - - +
291D MET* 3.2 32.4 + - + +
292D ALA* 3.0 32.6 + - + +
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Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D HIS* 3.8 36.3 - - + +
209D LEU* 5.8 2.0 - - + +
235D ALA 4.1 11.9 - - - +
236D PHE* 3.9 24.0 - - + -
285D SER 2.9 18.1 + - - +
286D ARG* 3.2 10.3 + - - +
288D PHE* 1.3 78.5 - - - +
290D GLU* 1.3 58.7 + - - +
292D ALA* 3.9 3.7 - - - +
293D ARG* 2.9 54.6 + - - +
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Residues in contact with GLU 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ARG* 2.8 50.3 + - + +
287D ALA* 4.0 6.3 - - - +
289D VAL* 1.3 79.3 - - - +
291D MET* 1.3 63.7 - - - +
293D ARG* 2.8 45.2 + - - +
294D GLU* 3.1 26.2 + - - +
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Residues in contact with MET 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 3.7 31.6 - - + -
287D ALA 3.1 18.4 + - - +
288D PHE* 3.2 38.6 + - + +
290D GLU* 1.3 77.6 - - - +
292D ALA* 1.3 68.1 + - - +
294D GLU* 3.5 6.6 + - - +
295D ALA* 3.1 22.1 + - + +
298D ARG* 5.5 0.5 + - - -
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Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 4.0 26.0 - - + -
209D LEU* 6.0 2.9 - - + -
235D ALA 5.7 0.9 - - - +
288D PHE* 3.0 29.4 + - + +
289D VAL* 3.9 4.5 - - - +
291D MET* 1.3 76.4 - - + +
293D ARG* 1.3 59.2 - - - +
295D ALA* 3.0 3.6 + - - +
296D TYR* 2.8 52.1 + - + +
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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
----------------------------------------------------------
208D HIS* 3.6 22.9 + - - +
209D LEU* 5.3 3.1 - - + +
210D LEU* 3.4 27.2 + - - +
211D TYR* 3.5 16.0 - - + -
289D VAL* 2.9 34.1 + - - +
290D GLU* 2.8 44.2 + - - +
292D ALA* 1.3 75.0 - - - +
294D GLU* 1.3 57.7 + - - +
296D TYR* 3.4 9.0 + - - -
297D ARG* 2.9 41.7 + - - +
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Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D GLU 3.1 18.3 + - - +
291D MET* 3.8 6.5 - - - +
293D ARG* 1.3 75.3 - - - +
295D ALA* 1.3 65.2 + - - +
297D ARG* 3.5 13.7 + - + +
298D ARG* 2.8 61.5 + - + +
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 3.8 24.9 - - + -
291D MET* 3.1 14.4 + - + +
292D ALA 3.0 9.0 + - - +
294D GLU* 1.3 76.6 - - - +
296D TYR* 1.3 62.1 + - - +
298D ARG* 3.4 18.7 + - - +
299D ARG* 3.2 36.7 + - - +
368D GLU* 5.1 0.3 - - - +
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Residues in contact with TYR 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO* 3.4 31.4 - - + +
42D ASP* 4.0 2.7 - - - -
43D PHE* 3.6 19.6 - + - -
209D LEU* 3.7 29.8 - - + -
211D TYR* 2.9 27.6 - - + +
234D LYS 5.6 0.9 - - - -
292D ALA* 2.8 32.7 + - + +
293D ARG* 3.7 5.4 - - - +
295D ALA* 1.3 74.8 - - - +
297D ARG* 1.3 58.4 + - - +
299D ARG* 3.2 33.8 + - - +
300D ARG* 2.9 25.6 + - - +
321D PHE* 4.1 18.6 - + + -
364D TYR* 3.4 19.1 - - + -
365D ALA* 4.5 4.9 - - - -
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Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU 4.4 0.2 + - - -
211D TYR* 2.8 56.3 + - + +
212D GLU* 4.0 7.3 + - - -
293D ARG* 2.9 37.6 + - - +
294D GLU* 3.7 13.7 - - - +
296D TYR* 1.3 76.5 - - - +
298D ARG* 1.3 63.1 + - - +
300D ARG* 3.2 17.4 + - - +
301D ASP* 3.1 40.6 + - - +
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Residues in contact with ARG 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D MET 5.5 0.4 + - - -
294D GLU* 2.8 57.4 + - + +
295D ALA* 3.6 19.9 - - - +
296D TYR 3.3 0.2 - - - -
297D ARG* 1.3 80.3 - - + +
299D ARG* 1.3 58.2 + - - +
301D ASP* 3.4 7.5 + - - +
302D LEU* 3.0 28.9 + - - +
368D GLU* 3.6 22.2 - - - +
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Residues in contact with ARG 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ASP* 2.8 41.4 + - - -
43D PHE* 4.2 12.3 - - - -
295D ALA* 3.2 24.1 + - - +
296D TYR* 3.2 28.9 + - - +
298D ARG* 1.3 74.7 - - - +
300D ARG* 1.3 60.3 + - - +
302D LEU* 3.6 5.3 - - - +
303D LEU* 2.9 30.5 + - - +
364D TYR* 3.2 25.0 + - + +
366D THR 2.9 23.1 + - - +
367D SER* 4.5 6.3 - - - +
368D GLU* 4.2 17.6 - - + +
371D LEU* 3.6 24.3 - - + +
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Residues in contact with ARG 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D TYR* 3.5 20.0 - - + +
212D GLU* 2.6 34.8 + - - -
296D TYR 2.9 13.8 + - - +
297D ARG* 3.5 22.6 + - - +
299D ARG* 1.3 76.3 - - - +
301D ASP* 1.3 82.0 + - - +
303D LEU* 3.2 3.7 + - - +
304D LEU* 2.9 50.1 + - + +
316D ARG* 3.2 24.1 - - - +
317D PRO* 3.0 33.5 + - + -
323D VAL* 5.2 0.4 - - + -
364D TYR* 3.6 34.1 - - + +
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Residues in contact with ASP 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ARG* 3.1 27.0 + - - +
298D ARG* 3.8 6.3 - - - +
300D ARG* 1.3 104.7 + - - +
302D LEU* 1.3 62.9 + - - +
304D LEU* 3.4 6.3 + - - +
305D GLU* 3.0 42.5 + - + +
316D ARG* 5.0 2.8 + - - -
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D ARG 3.0 16.8 + - - +
299D ARG 3.6 4.3 - - - +
301D ASP* 1.3 76.8 - - - +
303D LEU* 1.3 64.3 + - - +
305D GLU* 3.4 10.3 + - - +
306D GLY* 3.2 18.0 + - - -
368D GLU* 3.8 41.1 - - + +
371D LEU* 4.0 20.0 - - + -
372D ARG* 3.8 30.3 - - + +
375D LEU* 3.9 21.8 - - + +
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Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 5.6 5.4 - - + -
299D ARG 2.9 17.7 + - - +
300D ARG* 3.6 4.3 - - - +
302D LEU* 1.3 81.8 - - - +
304D LEU* 1.3 63.7 + - + +
306D GLY* 3.2 4.0 + - - -
307D LEU* 3.0 45.1 + - + +
323D VAL* 4.1 26.7 - - + -
362D LEU* 4.4 24.2 - - + -
363D SER 5.5 0.2 - - - -
364D TYR* 4.1 18.2 - - + +
371D LEU* 4.2 22.2 - - + +
374D ALA* 6.3 1.3 - - + -
375D LEU* 4.1 18.3 - - + +
378D PHE* 5.2 2.5 - - + -
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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 ARG* 2.9 41.7 + - + +
301D ASP* 3.9 6.3 - - - +
303D LEU* 1.3 72.8 - - + +
305D GLU* 1.3 62.6 + - + +
307D LEU* 3.3 13.0 + - + +
308D THR* 3.0 29.5 + - - +
314D ALA* 4.6 11.2 - - + +
316D ARG* 3.5 41.3 - - + +
317D PRO* 4.0 8.3 - - + -
323D VAL* 4.2 27.8 - - + -
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Residues in contact with GLU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ASP* 3.0 35.7 + - - +
302D LEU* 3.7 8.0 + - - +
304D LEU* 1.3 76.7 - - + +
306D GLY* 1.3 58.4 + - - +
308D THR* 3.3 6.9 + - - -
309D ALA* 2.9 30.4 + - - +
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Residues in contact with GLY 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D LEU 3.2 4.8 + - - -
303D LEU 3.2 6.5 + - - -
305D GLU* 1.3 80.1 - - - +
307D LEU* 1.3 60.4 + - - +
309D ALA* 3.4 7.4 + - - +
310D LEU* 3.1 28.1 + - - +
375D LEU* 3.8 26.9 - - - -
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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
----------------------------------------------------------
303D LEU* 3.0 30.0 + - + +
304D LEU* 3.3 13.4 + - + +
306D GLY* 1.3 74.1 - - - +
308D THR* 1.3 61.9 + - - +
310D LEU* 3.0 6.8 + - - +
311D GLY 2.9 4.9 + - - -
312D LEU* 2.9 42.9 + - + +
314D ALA* 4.1 24.2 - - + -
323D VAL* 4.4 8.1 - - + -
325D MET* 3.9 16.2 - - + -
362D LEU* 4.2 12.8 - - + -
375D LEU* 4.0 7.2 - - + -
378D PHE* 3.8 34.5 - - + -
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Residues in contact with THR 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 3.0 19.0 + - - +
305D GLU* 3.6 6.7 - - - -
307D LEU* 1.3 76.1 - - - +
309D ALA* 1.3 59.9 + - - +
311D GLY* 2.9 20.9 + - - +
312D LEU 4.2 5.9 + - - +
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Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D GLU 2.9 17.0 + - - +
306D GLY* 3.5 9.4 - - - +
307D LEU 3.2 0.2 - - - -
308D THR* 1.3 78.6 - - - +
310D LEU* 1.3 63.7 + - + +
311D GLY 3.3 0.4 + - - -
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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
----------------------------------------------------------
306D GLY 3.1 13.8 + - - +
307D LEU 3.0 8.5 + - - +
309D ALA* 1.3 80.6 - - + +
311D GLY* 1.3 61.5 + - - +
312D LEU* 3.6 16.3 + - + -
375D LEU* 3.8 19.1 - - + +
378D PHE* 3.6 32.3 - - + -
379D ALA* 3.8 26.9 - - + +
382D LEU* 4.0 19.8 - - + +
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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