Contacts of the helix formed by residues 276 - 307 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 5.9 6.7 - - + -
187B LEU* 6.5 0.9 - - + -
190B ALA* 5.9 1.6 - - + -
274B ASN 4.5 1.6 - - - +
275B LEU* 1.3 92.8 - - + +
277B HIS* 1.3 67.9 + - - +
278B GLY* 4.5 2.0 - - - +
279B VAL* 3.2 42.0 - - + +
280B CYS* 3.2 11.5 + - - -
343B LEU* 5.3 0.7 - - + -
1385B NAD 6.5 0.9 - - - -
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Residues in contact with HIS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 5.1 6.2 + - - +
160B LYS* 6.3 0.4 - - - -
194B ASP* 3.2 19.4 + - - -
263B HIS* 3.5 8.7 - + - -
266B ALA* 5.0 2.9 + - - +
267B HIS* 3.5 34.8 - + - -
270B GLY* 6.1 1.3 - - - -
275B LEU 3.4 4.7 + - - -
276B PRO* 1.3 73.3 - - - +
278B GLY* 1.3 64.3 + - - +
280B CYS* 3.4 11.9 + - - +
281B ASN* 3.2 25.5 + - - +
501B FE2 2.2 31.5 - - - -
1385B NAD 3.2 65.3 + + - -
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ALA* 3.6 30.4 - - - +
191B THR* 4.7 1.8 - - - -
194B ASP* 4.1 15.2 + - - +
276B PRO* 3.3 2.6 - - - +
277B HIS* 1.3 82.6 - - - +
279B VAL* 1.3 61.0 + - - +
281B ASN* 3.6 2.4 + - - +
282B ALA* 3.1 22.2 + - - +
1385B NAD 4.6 8.1 + - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY 5.3 1.6 - - - +
190B ALA* 3.8 20.6 - - + +
276B PRO* 3.2 46.1 - - + +
278B GLY* 1.3 72.2 - - - +
280B CYS* 1.3 65.6 + - - +
282B ALA* 3.2 7.2 + - - +
283B VAL* 3.0 28.3 + - - +
336B ILE* 5.3 4.5 - - + -
337B PRO* 4.9 15.9 - - + -
343B LEU* 3.9 22.7 - - + -
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Residues in contact with CYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 3.8 23.6 - - + +
269B LEU* 3.7 25.1 - - + +
270B GLY* 4.1 6.1 - - - -
275B LEU* 3.4 33.7 - - - -
276B PRO 3.2 21.6 + - - +
277B HIS* 3.7 5.6 - - - +
278B GLY 3.4 0.2 - - - -
279B VAL* 1.3 82.2 - - - +
281B ASN* 1.3 61.9 + - - +
283B VAL* 3.2 22.2 - - - +
284B LEU* 3.2 14.6 + - - +
343B LEU* 5.1 2.2 - - - -
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 4.1 7.0 - - - +
197B THR* 3.9 15.9 - - + +
262B VAL* 3.2 30.0 + - + +
263B HIS* 3.0 38.3 + - - +
266B ALA* 3.4 11.3 - - - +
277B HIS* 3.2 39.8 + - - +
278B GLY 4.0 2.9 - - - +
279B VAL 3.3 0.2 - - - -
280B CYS* 1.3 77.4 - - - +
282B ALA* 1.3 59.6 + - - +
284B LEU 3.2 0.2 + - - -
285B LEU* 2.8 36.4 + - - +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ALA* 5.0 0.4 - - - +
193B MET* 3.6 38.6 + - + +
197B THR* 4.5 1.5 + - - -
278B GLY 3.1 16.8 + - - +
279B VAL* 3.2 13.4 + - - +
281B ASN* 1.3 77.7 - - - +
283B VAL* 1.3 62.1 + - - +
285B LEU* 3.9 3.5 - - - +
286B PRO* 3.7 14.2 - - - +
331B ALA* 5.0 3.6 - - - +
336B ILE* 3.9 26.1 - - + +
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL 3.0 12.7 + - - +
280B CYS* 3.2 16.4 - - - +
282B ALA* 1.3 76.2 - - - +
284B LEU* 1.3 65.2 + - - +
286B PRO* 3.7 8.9 - - - +
287B HIS* 3.4 19.8 + - - -
336B ILE* 3.5 12.6 - - + -
337B PRO* 3.1 40.6 - - + +
338B ALA 5.4 1.2 - - - +
339B ASN* 4.6 8.5 - - - +
340B LEU* 3.6 28.5 - - + -
343B LEU* 3.8 10.5 - - + -
382B ALA* 5.2 0.6 - - - +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL* 3.9 11.2 - - + +
265B MET* 3.7 22.4 - - + -
266B ALA* 3.6 32.3 - - - +
269B LEU* 3.9 9.4 - - + -
280B CYS 3.2 14.3 + - - +
281B ASN 3.2 2.4 + - - +
283B VAL* 1.3 81.5 - - - +
285B LEU* 1.3 67.4 + - - +
287B HIS* 3.0 19.4 + - + +
288B VAL* 3.1 20.5 + - + +
340B LEU* 3.7 37.9 - - + -
378B LEU* 6.1 0.9 - - + -
379B PHE* 4.5 4.9 - - + -
382B ALA* 3.9 12.3 - - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B MET* 4.1 13.9 - - + -
196B LEU* 4.4 11.0 - - + -
197B THR* 3.6 42.6 - - + +
200B PHE* 4.3 11.4 - - + -
201B GLU* 5.5 0.2 - - + -
262B VAL* 3.9 13.2 - - + +
281B ASN 2.8 21.4 + - - +
282B ALA 3.9 2.9 - - - +
284B LEU* 1.3 70.8 - - - +
286B PRO* 1.3 65.7 - - + +
288B VAL* 3.0 3.8 + - - +
289B LEU* 2.8 58.1 + - + +
327B VAL* 3.7 20.4 - - + -
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Residues in contact with PRO 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA 3.7 8.1 - - - +
283B VAL* 3.7 15.5 - - - +
285B LEU* 1.3 97.1 - - + +
287B HIS* 1.3 68.6 + - + +
289B LEU* 3.7 11.0 - - + +
290B ALA* 3.2 23.4 + - - +
324B ILE* 3.7 14.9 - - + +
327B VAL* 4.2 11.0 - - + -
328B ARG* 3.7 39.6 + - + +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL 3.4 25.3 + - - -
284B LEU* 3.0 7.6 + - + +
286B PRO* 1.3 80.0 - - + +
288B VAL* 1.3 65.5 + - + +
290B ALA* 3.6 6.4 + - - +
291B TYR* 3.2 19.8 + - - +
328B ARG* 5.9 6.3 + - - +
338B ALA 5.1 7.5 + - - -
339B ASN* 5.9 0.6 - - - +
378B LEU* 3.8 20.0 - - + +
381B SER* 3.6 27.2 + - - +
382B ALA* 3.5 31.7 + - + +
----------------------------------------------------------
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TYR* 3.9 17.9 - - + -
262B VAL* 3.4 42.2 - - + -
265B MET* 4.1 21.1 - - - -
284B LEU* 3.1 17.8 + - + +
285B LEU 3.0 2.5 + - - +
287B HIS* 1.3 75.8 - - - +
289B LEU* 1.3 68.7 + - + +
291B TYR* 3.0 6.8 + - + +
292B ASN* 2.8 41.1 + - - +
366B ASN* 4.5 0.2 - - - +
378B LEU* 4.2 10.1 - - + -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 3.8 46.7 - - + -
201B GLU* 6.2 1.6 - - + -
204B SER* 5.2 2.7 - - - +
262B VAL* 5.4 3.1 - - + -
285B LEU* 2.8 45.6 + - + +
286B PRO* 3.7 7.0 - - + +
288B VAL* 1.3 77.2 - - - +
290B ALA* 1.3 51.2 + - - +
292B ASN* 3.2 9.3 + - + +
293B ALA* 2.7 35.9 + - - +
300B LEU* 3.5 17.4 - - + +
324B ILE* 3.6 25.6 - - + -
327B VAL* 4.1 12.6 - - + -
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO 3.2 14.6 + - - +
287B HIS* 3.8 6.5 - - - +
289B LEU* 1.3 78.2 - - - +
291B TYR* 1.3 64.5 + - - +
293B ALA* 3.4 15.1 + - - +
294B SER* 4.2 2.3 + - - -
321B GLU* 5.2 3.6 - - - +
324B ILE* 3.5 16.3 - - + +
328B ARG* 4.7 11.2 - - - +
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Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TYR* 3.9 26.6 - + - -
287B HIS 3.2 12.6 + - - +
288B VAL* 3.0 12.9 + - + +
290B ALA* 1.3 80.8 - - - +
292B ASN* 1.3 79.7 + - - +
293B ALA 3.5 0.2 + - - -
294B SER* 3.7 4.3 + - - -
368B ARG* 2.8 75.1 + - + +
370B GLY* 3.3 22.5 + - - -
374B GLU* 2.9 33.8 + - + +
375B VAL* 5.8 0.4 - - + -
378B LEU* 3.9 27.4 - - + -
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Residues in contact with ASN 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 5.2 1.6 + - - -
204B SER* 5.2 5.4 - - - +
262B VAL* 5.8 0.2 - - - +
288B VAL* 2.8 28.1 + - - +
289B LEU* 3.8 8.9 - - + +
291B TYR* 1.3 83.3 - - - +
293B ALA* 1.3 65.8 + - - +
294B SER 3.0 3.8 - - - -
295B VAL* 2.9 15.6 + - - +
296B VAL* 3.0 26.8 + - + +
300B LEU* 5.3 1.3 - - + -
366B ASN* 2.8 44.3 + - - -
367B PRO* 3.7 12.8 - - + +
368B ARG* 3.6 9.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU 2.7 21.4 + - - +
290B ALA* 3.4 14.8 - - - +
291B TYR 3.3 1.0 - - - -
292B ASN* 1.3 72.0 - - - +
294B SER* 1.3 57.3 + - - +
295B VAL 3.2 0.2 - - - -
297B ALA* 3.0 33.3 + - + +
300B LEU* 3.7 19.0 - - + +
320B ALA* 4.7 10.1 - - + -
324B ILE* 4.3 7.0 - - + -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 4.2 2.3 + - - -
291B TYR 3.7 7.6 + - - -
292B ASN 2.9 1.2 + - - -
293B ALA* 1.3 78.3 - - - +
295B VAL* 1.3 71.7 + - - +
297B ALA* 5.5 0.4 - - - -
368B ARG* 3.6 22.6 + - - -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASN 2.9 5.6 + - - +
294B SER* 1.3 92.4 + - - +
296B VAL* 1.3 71.0 + - + +
297B ALA 3.7 1.7 + - - -
367B PRO* 3.8 20.4 - - + +
368B ARG* 3.8 28.0 - - + -
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B SER* 4.2 17.9 - - - +
292B ASN* 3.0 29.8 + - + +
293B ALA 4.0 0.2 - - - -
295B VAL* 1.3 86.0 - - + +
297B ALA* 1.3 64.2 + - - +
298B GLY 3.1 3.4 - - - +
299B ARG* 3.1 24.9 + - + +
300B LEU* 2.9 32.8 + - + +
367B PRO* 3.6 29.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA* 3.0 23.2 + - + +
294B SER 5.5 0.2 - - - -
295B VAL 3.7 1.8 + - - -
296B VAL* 1.3 75.0 - - - +
298B GLY* 1.3 57.9 + - - +
300B LEU* 3.2 4.5 + - - +
301B LYS* 3.0 26.5 + - - +
316B ASP* 3.8 26.0 - - + +
317B LYS* 4.3 6.5 - - - +
320B ALA* 3.6 19.4 - - + +
----------------------------------------------------------
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL 3.1 1.0 - - - -
297B ALA* 1.3 80.8 - - - +
299B ARG* 1.3 61.2 + - - +
301B LYS* 3.2 5.9 + - - +
302B ASP* 3.2 24.1 + - - +
316B ASP* 3.4 29.8 + - - +
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR* 2.6 60.2 + - + +
204B SER* 4.6 4.8 - - - +
205B SER 5.4 1.2 + - - -
208B ALA* 3.8 10.9 - - - +
213B ASP* 2.4 43.0 + - - -
296B VAL* 3.1 28.0 + - + +
298B GLY* 1.3 73.7 - - - +
300B LEU* 1.3 67.0 + - - +
302B ASP* 3.1 28.2 + - - +
303B VAL* 3.2 7.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 3.9 24.7 - - + -
204B SER* 3.8 22.4 - - - +
289B LEU* 3.5 39.0 - - + +
292B ASN* 5.3 1.1 - - + -
293B ALA* 3.7 24.2 - - + +
296B VAL* 2.9 21.4 + - + +
297B ALA 3.2 8.0 + - - +
299B ARG* 1.3 79.7 - - - +
301B LYS* 1.3 60.6 + - - +
303B VAL* 3.4 6.7 + - + +
304B GLY 3.2 14.9 + - - -
320B ALA* 4.0 11.7 - - + +
323B THR* 3.3 15.3 + - - +
324B ILE* 4.4 10.1 - - + -
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA 3.0 13.3 + - - +
298B GLY 3.5 9.6 - - - +
299B ARG 3.1 0.2 - - - -
300B LEU* 1.3 75.9 - - - +
302B ASP* 1.3 66.1 + - - +
304B GLY* 3.1 1.9 + - - -
305B VAL* 3.0 26.4 + - + +
311B ILE* 3.1 37.1 - - + +
312B ALA* 2.9 23.1 + - - +
314B LEU 2.6 25.2 + - - +
315B GLY 4.4 1.8 - - - +
316B ASP* 3.5 26.0 + - - +
319B GLY* 4.0 5.2 - - - -
320B ALA* 4.3 7.6 - - - +
323B THR* 4.0 8.1 - - - -
----------------------------------------------------------
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR* 2.8 36.0 + - + +
217B LEU* 4.5 7.7 - - + +
298B GLY 3.2 11.3 + - - +
299B ARG* 3.1 19.3 + - - +
301B LYS* 1.3 80.1 - - - +
303B VAL* 1.3 61.0 + - - +
305B VAL* 3.3 8.9 + - - +
306B ALA* 3.0 21.7 + - - +
----------------------------------------------------------
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA* 5.6 0.9 - - + +
200B PHE* 3.3 54.3 - - + +
203B TYR* 3.7 26.7 - - + -
217B LEU* 4.2 10.8 - - + -
220B ALA* 3.8 24.9 - - + -
299B ARG 3.5 13.9 - - - +
300B LEU* 3.6 4.5 - - + +
301B LYS 3.2 0.4 - - - -
302B ASP* 1.3 73.2 - - - +
304B GLY* 1.3 68.3 + - - +
306B ALA* 3.0 4.5 + - - +
307B MET* 2.8 27.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU 3.2 5.3 + - - -
301B LYS 3.1 5.5 + - - -
303B VAL* 1.3 78.9 - - - +
305B VAL* 1.3 60.5 + - - +
307B MET* 3.0 6.1 + - - -
309B LEU* 3.0 47.4 + - - +
311B ILE* 3.9 1.8 - - - -
323B THR* 3.4 25.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LYS* 3.0 22.2 + - + +
302B ASP* 3.6 10.3 - - - +
304B GLY* 1.3 73.1 - - - +
306B ALA* 1.3 61.4 + - - +
308B GLY* 2.9 20.1 + - - -
309B LEU 4.3 8.9 - - - +
311B ILE* 3.9 16.4 - - + -
312B ALA* 4.3 24.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 3.6 39.7 - - + +
220B ALA* 4.8 1.3 - - + -
221B SER* 3.0 31.4 + - - +
225B LYS* 5.0 2.4 - - - -
302B ASP 3.0 12.4 + - - +
303B VAL* 3.0 11.7 + - - +
305B VAL* 1.3 77.0 - - - +
307B MET* 1.3 57.4 + - - +
308B GLY* 3.1 4.3 + - - -
----------------------------------------------------------
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Residues in contact with MET 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 4.3 24.7 - - + -
200B PHE* 4.0 27.8 - - - -
220B ALA* 3.7 22.4 - - + +
221B SER* 4.4 1.3 - - - +
224B ALA* 3.6 33.4 - - + +
225B LYS* 5.6 4.4 - - - +
303B VAL* 2.8 19.1 + - - +
304B GLY* 3.0 13.2 + - - +
306B ALA* 1.3 74.7 - - - +
308B GLY* 1.3 60.7 + - - +
309B LEU* 3.3 18.3 + - + +
323B THR* 4.7 4.0 - - - -
326B ALA* 5.1 8.7 - - + +
327B VAL* 4.7 9.9 - - + +
330B LEU* 4.6 11.7 - - + -
----------------------------------------------------------
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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