Contacts of the helix formed by residues 276 - 307 (chain D) in PDB entry 3OX4
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 PRO 276 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D PRO* 5.9 8.1 - - + -
71D ASN* 5.7 0.2 - - - +
190D ALA* 5.9 2.0 - - + -
274D ASN 4.5 1.8 - - - +
275D LEU* 1.3 95.7 - - + +
277D HIS* 1.3 66.1 + - - +
278D GLY* 4.7 2.7 - - - +
279D VAL* 3.2 28.3 - - + +
280D CYS* 3.1 19.3 - - - -
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Residues in contact with HIS 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ASN* 5.3 3.2 + - - +
160D LYS* 5.5 1.6 - - - -
194D ASP* 3.1 27.9 + - - -
263D HIS* 3.5 12.8 - + - -
266D ALA* 5.1 4.9 + - - +
267D HIS* 3.6 24.2 - + - -
270D GLY* 6.1 1.3 - - - -
275D LEU 3.4 4.5 + - - -
276D PRO* 1.3 72.8 - - - +
278D GLY* 1.3 67.2 + - - +
280D CYS* 3.2 5.3 + - - +
281D ASN* 3.2 38.3 + - - +
501D FE2 2.3 24.2 - - - -
1385D NAD 3.3 63.2 + + - +
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Residues in contact with GLY 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ALA* 3.4 33.1 - - - +
191D THR* 4.9 1.6 - - - -
194D ASP* 4.0 14.0 + - - +
276D PRO* 3.4 2.6 - - - +
277D HIS* 1.3 81.1 - - - +
279D VAL* 1.3 56.5 + - - +
281D ASN* 3.3 3.1 + - - +
282D ALA* 2.9 26.0 + - - +
1385D NAD 5.0 7.0 + - - -
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Residues in contact with VAL 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D GLY 5.4 1.3 - - - +
190D ALA* 3.7 20.6 - - + +
275D LEU* 5.3 0.2 - - + -
276D PRO* 3.2 36.7 - - + +
278D GLY* 1.3 68.1 - - - +
280D CYS* 1.3 66.4 + - - +
282D ALA* 3.0 7.5 + - - +
283D VAL* 2.8 36.6 + - - +
336D ILE* 4.7 5.4 - - + -
337D PRO* 4.2 22.2 - - + -
343D LEU* 4.1 23.1 - - + -
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Residues in contact with CYS 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ALA* 3.9 22.4 - - + +
269D LEU* 3.9 24.5 - - + +
270D GLY* 4.4 3.8 - - - -
275D LEU* 3.6 32.5 - - - -
276D PRO 3.1 20.9 - - - +
277D HIS* 3.2 9.3 + - - +
279D VAL* 1.3 84.3 - - - +
281D ASN* 1.3 64.3 + - - +
283D VAL* 3.4 2.6 + - - +
284D LEU* 3.1 26.5 + - - +
343D LEU* 4.2 9.6 - - - -
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Residues in contact with ASN 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D ASP* 3.7 7.0 - - - +
197D THR* 3.8 15.5 - - - +
262D VAL* 3.3 20.4 + - - +
263D HIS* 3.1 37.9 + - - -
266D ALA* 3.3 15.7 - - - +
277D HIS* 3.2 42.8 + - - +
278D GLY 3.7 6.7 - - - +
280D CYS* 1.3 79.7 - - - +
282D ALA* 1.3 55.0 + - - +
284D LEU 3.2 0.7 + - - -
285D LEU* 2.8 36.9 + - - +
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D MET* 3.7 38.9 - - + +
197D THR* 4.5 1.5 + - - -
278D GLY 2.9 14.9 + - - +
279D VAL* 3.0 12.8 + - - +
281D ASN* 1.3 77.4 - - - +
283D VAL* 1.3 62.5 + - - +
285D LEU* 3.7 3.5 - - - +
286D PRO* 3.5 17.0 - - - +
331D ALA* 5.3 2.8 - - - +
336D ILE* 3.7 26.0 - - + +
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Residues in contact with VAL 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D VAL 2.8 24.6 + - - +
280D CYS 3.9 3.4 - - - +
282D ALA* 1.3 73.0 - - - +
284D LEU* 1.3 61.9 + - + +
286D PRO* 3.6 6.2 - - - +
287D HIS* 3.5 17.9 + - + -
336D ILE* 4.0 9.2 - - + -
337D PRO* 3.4 23.6 - - + +
338D ALA 4.3 4.9 - - - +
339D ASN* 3.6 34.1 - - - +
340D LEU* 3.9 14.6 - - + +
343D LEU* 3.7 22.9 - - + -
382D ALA* 4.5 3.8 - - + +
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D VAL* 4.0 13.7 - - + +
265D MET* 3.5 43.1 - - + -
266D ALA* 3.8 12.1 - - + +
269D LEU* 4.1 14.8 - - + -
280D CYS 3.1 13.4 + - - +
281D ASN 3.9 2.2 - - - +
283D VAL* 1.3 78.9 - - - +
285D LEU* 1.3 66.8 + - - +
286D PRO 3.4 0.2 - - - -
287D HIS* 3.1 8.5 + - + +
288D VAL* 3.1 22.5 + - + +
340D LEU* 3.8 22.7 - - + -
378D LEU 5.5 0.7 - - - +
379D PHE* 4.3 5.6 - - + -
382D ALA* 3.7 28.3 - - + -
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Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D MET* 4.1 13.9 - - + -
196D LEU* 4.4 4.5 - - + -
197D THR* 3.8 26.2 - - + +
200D PHE* 4.3 25.8 - - + -
201D GLU* 5.7 0.2 - - + -
262D VAL* 4.0 18.1 - - + +
281D ASN 2.8 20.1 + - - +
282D ALA 3.7 4.0 - - - +
284D LEU* 1.3 73.3 - - - +
286D PRO* 1.3 64.6 - - + +
288D VAL* 3.2 1.6 + - - +
289D LEU* 2.8 59.0 + - + +
327D VAL* 3.6 23.8 - - + -
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Residues in contact with PRO 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ALA 3.5 12.3 - - - +
283D VAL 3.6 7.6 - - - +
284D LEU 3.6 2.9 - - - -
285D LEU* 1.3 95.6 - - + +
287D HIS* 1.3 62.2 + - + +
289D LEU* 3.7 6.3 - - + +
290D ALA* 2.9 29.1 + - - +
324D ILE* 3.8 18.3 - - + +
327D VAL* 3.8 19.5 - - + -
328D ARG* 3.9 35.3 + - + +
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Residues in contact with HIS 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D VAL* 3.5 26.3 + - - +
284D LEU* 3.1 8.5 + - + +
286D PRO* 1.3 81.5 - - + +
288D VAL* 1.3 60.5 + - + +
290D ALA* 3.3 7.7 + - - +
291D TYR* 3.0 26.2 + - - +
328D ARG* 6.1 2.5 - - - -
338D ALA 5.4 5.3 + - - -
339D ASN* 6.2 0.2 - - - +
378D LEU* 3.7 14.7 - - + +
381D SER* 3.2 41.5 + - - +
382D ALA* 3.7 23.4 + - + -
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU* 4.7 0.2 - - - +
261D TYR* 3.8 17.5 - - + -
262D VAL* 3.4 43.3 - - + +
265D MET* 4.0 22.2 - - - -
284D LEU* 3.1 17.6 + - + +
285D LEU 3.8 1.1 - - - +
287D HIS* 1.3 73.9 - - + +
289D LEU* 1.3 62.2 + - + +
291D TYR* 3.1 10.0 + - + +
292D ASN* 2.8 48.0 + - - +
366D ASN* 4.4 0.2 - - - +
378D LEU* 4.5 6.3 - - + -
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Residues in contact with LEU 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D PHE* 3.8 47.1 - - + -
201D GLU* 6.3 0.7 - - + -
204D SER* 5.2 2.2 - - - +
262D VAL* 5.5 3.4 - - + -
285D LEU* 2.8 48.6 + - + +
286D PRO* 3.7 7.0 - - + +
288D VAL* 1.3 77.1 - - + +
290D ALA* 1.3 57.7 + - - +
292D ASN* 3.7 6.5 - - + +
293D ALA* 2.8 32.2 + - - +
300D LEU* 3.6 19.1 - - + +
323D THR* 5.5 0.2 - - + -
324D ILE* 3.7 22.9 - - + -
327D VAL* 4.1 12.1 - - + -
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Residues in contact with ALA 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D PRO 2.9 18.8 + - - +
287D HIS* 3.4 8.5 - - - +
288D VAL 3.2 0.2 - - - -
289D LEU* 1.3 75.9 - - - +
291D TYR* 1.3 61.6 + - - +
293D ALA* 3.3 15.7 - - - +
294D SER* 4.2 2.4 + - - -
321D GLU* 5.5 3.8 - - - +
324D ILE* 3.6 17.0 - - + +
328D ARG* 5.1 7.4 - - - +
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Residues in contact with TYR 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D TYR* 3.8 24.4 - + - -
287D HIS 3.0 14.3 + - - +
288D VAL* 3.3 8.7 - - + +
290D ALA* 1.3 78.3 - - - +
292D ASN* 1.3 83.0 + - - +
293D ALA 3.3 0.5 + - - -
294D SER* 3.2 19.1 + - - -
368D ARG* 3.3 52.4 + - + +
370D GLY* 3.3 16.8 + - - -
374D GLU* 2.7 37.9 + - + +
378D LEU* 3.6 35.0 - - + -
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Residues in contact with ASN 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU* 5.3 1.8 + - - -
204D SER* 5.0 5.0 - - - +
288D VAL* 2.8 30.2 + - - +
289D LEU* 4.1 8.4 - - + +
291D TYR* 1.3 81.0 - - - +
293D ALA* 1.3 52.3 + - - +
294D SER* 3.0 7.0 - - - -
295D VAL* 2.7 27.4 + - - +
296D VAL* 3.0 20.1 + - + +
300D LEU* 5.5 0.9 - - + -
366D ASN* 2.8 40.6 + - - -
367D PRO* 3.4 26.2 - - + +
368D ARG* 3.7 9.4 - - - +
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Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D LEU 2.8 18.4 + - - +
290D ALA* 3.3 15.0 - - - +
291D TYR 3.2 0.4 - - - -
292D ASN* 1.3 76.9 - - - +
294D SER* 1.3 56.2 + - - +
295D VAL 2.9 5.6 + - - -
297D ALA* 3.2 28.1 + - + +
300D LEU* 3.8 20.4 - - + +
320D ALA* 4.6 7.4 - - + -
321D GLU* 4.4 16.4 - - - +
324D ILE* 4.5 2.5 - - + -
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Residues in contact with SER 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ALA 4.2 2.3 + - - -
291D TYR 3.2 7.4 + - - -
292D ASN 2.9 1.0 + - - -
293D ALA* 1.3 77.7 - - - +
295D VAL* 1.3 64.6 + - - +
368D ARG* 2.7 40.0 + - - -
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Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ASN 2.7 8.2 + - - +
293D ALA 2.9 0.2 - - - -
294D SER* 1.3 95.9 - - - +
296D VAL* 1.3 67.9 + - + +
297D ALA 3.6 2.6 + - - -
367D PRO* 3.9 18.8 - - + +
368D ARG* 4.2 22.2 - - + -
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Residues in contact with VAL 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D SER* 4.1 18.2 - - - +
292D ASN* 3.0 30.0 + - + +
295D VAL* 1.3 84.9 - - + +
297D ALA* 1.3 65.5 + - - +
298D GLY 3.1 2.7 - - - -
299D ARG* 3.0 30.4 + - + +
300D LEU* 2.9 27.8 + - + +
367D PRO* 3.5 30.1 - - + -
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ALA* 3.2 22.7 + - + +
295D VAL 3.6 2.0 + - - -
296D VAL* 1.3 75.6 - - - +
298D GLY* 1.3 63.5 + - - +
300D LEU* 3.2 5.4 + - - +
301D LYS* 3.0 18.5 + - - +
316D ASP* 3.8 22.0 - - + +
317D LYS* 4.3 4.9 - - - +
320D ALA* 3.6 27.0 - - + +
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Residues in contact with GLY 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D VAL* 3.1 1.4 - - - +
297D ALA* 1.3 79.5 - - - +
299D ARG* 1.3 61.2 + - - +
301D LYS* 3.1 14.4 + - - +
302D ASP* 3.2 17.3 + - - +
316D ASP* 3.5 30.6 + - - +
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Residues in contact with ARG 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D TYR* 2.7 57.1 + - + +
204D SER* 4.7 4.7 - - - +
205D SER 5.6 0.6 + - - -
208D ALA* 4.4 6.5 - - - +
213D ASP* 2.9 40.0 + - - -
296D VAL* 3.0 33.2 + - + +
298D GLY* 1.3 72.8 - - - +
300D LEU* 1.3 67.8 + - - +
302D ASP* 2.9 29.4 + - - +
303D VAL* 3.2 5.7 + - - +
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Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D PHE* 3.9 16.4 - - + -
203D TYR* 6.4 0.2 - - + -
204D SER* 4.0 16.6 - - - +
289D LEU* 3.6 52.5 - - + +
292D ASN* 6.0 0.9 - - + -
293D ALA* 3.8 24.5 - - + +
296D VAL* 2.9 20.5 + - + +
297D ALA 3.5 7.2 - - - +
299D ARG* 1.3 75.4 - - - +
301D LYS* 1.3 62.5 + - - +
303D VAL* 3.2 9.7 + - + +
304D GLY 3.1 17.0 + - - -
320D ALA* 4.0 15.9 - - + +
323D THR* 3.3 12.0 + - + +
324D ILE* 4.5 8.1 - - + -
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Residues in contact with LYS 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ALA 3.0 12.2 + - - +
298D GLY 3.4 10.1 - - - +
299D ARG 3.1 0.2 - - - -
300D LEU* 1.3 76.2 - - - +
302D ASP* 1.3 60.7 + - - +
304D GLY* 3.1 1.9 + - - -
305D VAL* 2.8 37.3 + - + +
311D ILE* 3.5 24.6 - - + +
312D ALA* 3.0 25.0 + - - +
314D LEU 2.8 25.7 + - - +
315D GLY* 3.9 6.5 - - - +
316D ASP* 4.1 15.2 + - - +
319D GLY* 3.5 29.6 - - - -
320D ALA* 4.2 1.0 - - - +
323D THR* 4.0 7.4 - - - -
----------------------------------------------------------
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Residues in contact with ASP 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D TYR* 3.2 28.6 + - + +
217D LEU* 4.2 9.1 - - + +
298D GLY 3.4 7.9 - - - +
299D ARG* 2.9 26.5 + - - +
301D LYS* 1.3 80.7 - - - +
303D VAL* 1.3 58.4 + - - +
305D VAL* 3.4 9.2 + - - +
306D ALA* 3.0 26.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ALA* 5.5 1.1 - - + +
200D PHE* 3.3 48.5 - - + +
203D TYR* 3.6 26.5 - - + -
204D SER* 6.2 0.2 - - - +
217D LEU* 4.0 12.6 - - + -
220D ALA* 3.8 22.4 - - + -
299D ARG 3.2 12.7 + - - +
300D LEU* 3.5 8.7 - - + +
301D LYS 3.1 0.2 - - - -
302D ASP* 1.3 75.6 - - - +
304D GLY* 1.3 53.5 + - - +
306D ALA* 3.0 3.5 + - - +
307D MET* 2.7 41.0 + - + +
----------------------------------------------------------
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Residues in contact with GLY 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D LEU 3.1 10.3 + - - -
301D LYS 3.1 1.7 + - - -
303D VAL* 1.3 77.5 - - - +
305D VAL* 1.3 60.8 + - - +
307D MET* 3.0 15.4 + - - +
308D GLY 3.2 0.3 + - - -
309D LEU* 3.0 25.1 + - - +
311D ILE* 3.9 9.6 - - - -
323D THR* 3.3 29.3 + - - +
----------------------------------------------------------
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D LYS* 2.8 25.9 + - + +
302D ASP* 3.5 11.7 - - - +
303D VAL 3.2 0.2 - - - -
304D GLY* 1.3 77.0 - - - +
306D ALA* 1.3 57.7 + - - +
308D GLY* 2.8 21.8 + - - -
309D LEU 3.9 10.1 + - - +
311D ILE* 4.0 16.1 - - + +
312D ALA* 4.2 27.1 - - + +
----------------------------------------------------------
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Residues in contact with ALA 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D LEU* 3.6 39.3 - - + +
220D ALA* 4.7 1.1 - - + -
221D SER* 3.1 31.0 + - - +
225D LYS* 5.5 1.6 - - - -
302D ASP 3.0 15.0 + - - +
303D VAL* 3.4 9.4 - - - +
305D VAL* 1.3 77.3 - - - +
307D MET* 1.3 57.7 + - - +
308D GLY* 3.1 4.7 + - - -
----------------------------------------------------------
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Residues in contact with MET 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D LEU* 4.3 24.5 - - + -
200D PHE* 4.0 28.7 - - - -
220D ALA* 3.9 19.3 - - + +
221D SER* 4.4 1.3 - - - +
224D ALA* 3.4 36.2 - - + +
225D LYS* 5.6 3.3 - - - +
303D VAL* 2.7 20.8 + - - +
304D GLY* 3.0 10.0 + - - +
306D ALA* 1.3 71.3 - - - +
308D GLY* 1.3 60.1 + - - +
309D LEU* 3.5 14.9 + - + +
323D THR* 4.5 10.5 - - - +
326D ALA* 5.1 11.2 - - + -
327D VAL* 4.9 8.3 - - + +
330D LEU* 4.4 12.3 - - + -
----------------------------------------------------------
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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