Contacts of the helix formed by residues 267 - 303 (chain B) in PDB entry 3M0A
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 GLU 267 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 4.3 14.0 - - + +
268B LEU* 1.3 58.6 + - + +
269B LEU 2.8 17.2 + - - -
270B GLN* 2.9 19.7 + - - +
271B ARG* 3.1 48.5 + - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 3.5 40.4 - - + +
269A LEU* 3.4 34.9 - - + +
272A CYS* 3.7 31.6 - - + -
267B GLU* 1.3 77.9 - - - +
269B LEU* 1.3 56.4 + - - +
270B GLN 3.5 0.2 - - - -
271B ARG* 4.3 5.6 - - - +
272B CYS* 2.9 31.6 + - + +
268C LEU* 3.9 12.7 - - + +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU 2.8 5.9 + - - -
268B LEU* 1.3 77.8 - - - +
270B GLN* 1.3 55.5 + - - +
272B CYS* 3.8 5.1 - - - +
273B GLU* 3.2 21.3 + - - +
267C GLU* 5.5 3.1 - - - +
268C LEU* 4.1 28.9 - - + +
271C ARG* 4.4 15.7 + - - +
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Residues in contact with GLN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU 2.9 10.7 + - - +
269B LEU* 1.3 74.4 - - - +
271B ARG* 1.3 61.1 + - - +
272B CYS 3.0 1.6 - - - -
273B GLU* 3.0 7.2 + - - +
274B SER* 2.9 31.2 + - - -
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 4.4 22.1 + - - +
272A CYS* 3.2 23.1 - - - +
273A GLU* 4.4 12.3 + - - +
276A GLU* 3.3 35.1 + - + +
267B GLU* 3.1 55.4 + - - +
268B LEU* 4.0 6.5 - - - +
270B GLN* 1.3 75.4 - - - +
272B CYS* 1.3 60.6 + - - +
274B SER* 3.6 7.8 - - - -
275B LEU* 3.4 23.3 + - + +
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Residues in contact with CYS 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A CYS* 4.7 9.4 - - - -
268B LEU* 2.9 23.5 + - + +
269B LEU 3.9 5.2 - - - +
270B GLN 3.0 0.4 - - - -
271B ARG* 1.3 78.0 - - - +
273B GLU* 1.3 63.9 + - - +
275B LEU* 3.2 17.1 + - - +
276B GLU* 3.3 13.6 + - - +
268C LEU* 3.4 30.3 - - + -
271C ARG* 4.6 15.7 - - - -
272C CYS* 5.0 9.0 - - - -
275C LEU* 4.3 12.9 - - - +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU 3.2 16.9 + - - +
270B GLN* 3.0 9.8 + - - +
272B CYS* 1.3 72.5 - - - +
274B SER* 1.3 59.9 + - - +
276B GLU* 3.2 9.5 + - - +
277B LYS* 3.0 26.9 + - - +
271C ARG* 4.4 16.6 - - - +
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLN 2.9 16.3 + - - -
271B ARG* 3.6 9.6 - - - -
273B GLU* 1.3 75.5 - - - +
275B LEU* 1.3 64.8 + - - +
276B GLU 3.1 0.9 + - - -
277B LYS* 3.2 7.4 + - - +
278B LYS* 3.1 26.5 + - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A CYS* 3.8 28.7 - - - +
275A LEU* 3.6 37.9 - - + -
276A GLU* 3.5 32.3 - - + +
279A THR* 4.1 19.3 - - + +
271B ARG 3.4 8.7 + - - +
272B CYS* 3.2 12.9 + - + +
274B SER* 1.3 77.4 - - - +
276B GLU* 1.3 56.8 + - - +
278B LYS* 4.6 1.7 - - - +
279B THR* 2.8 35.7 + - - +
275C LEU* 3.4 16.0 - - + +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B CYS* 3.3 9.6 + - - +
273B GLU* 3.2 11.0 + - - +
274B SER 3.1 1.2 - - - -
275B LEU* 1.3 73.7 - - - +
277B LYS* 1.3 69.9 + - - +
279B THR* 3.3 1.4 + - - +
280B ALA* 3.0 24.0 + - - +
271C ARG* 3.3 64.2 + - - +
275C LEU* 3.7 23.5 - - + +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLU 3.0 16.4 + - - +
274B SER* 3.8 9.0 - - - +
276B GLU* 1.3 72.5 - - - +
278B LYS* 1.3 63.9 - - - +
280B ALA* 3.1 15.8 + - - +
281B THR* 3.3 11.9 + - - +
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 4.4 20.2 - - + -
274B SER* 3.1 15.4 + - - +
275B LEU* 4.6 1.8 - - - +
277B LYS* 1.3 70.7 - - - +
279B THR* 1.3 54.4 + - - +
280B ALA 2.7 5.5 + - - -
281B THR* 2.7 43.2 + - - +
282B PHE* 3.3 10.9 + - + -
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 4.1 11.4 + - - +
275B LEU* 2.8 24.2 + - - +
276B GLU 3.3 2.7 + - - +
278B LYS* 1.3 76.9 - - - +
280B ALA* 1.3 61.0 + - - +
282B PHE* 3.4 27.0 - - + +
283B GLU* 3.9 1.2 + - - +
275C LEU* 4.1 22.8 - - + +
278C LYS* 4.5 11.4 - - + -
279C THR* 3.8 21.2 + - - +
282C PHE* 3.8 17.9 - - + -
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU 3.0 12.4 + - - +
277B LYS* 3.2 13.9 - - - +
278B LYS 2.7 1.4 + - - -
279B THR* 1.3 77.2 - - - +
281B THR* 1.3 63.2 + - + +
282B PHE 3.1 1.5 + - - -
283B GLU* 3.5 16.0 + - - +
284B ASN* 4.4 2.1 + - - +
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Residues in contact with THR 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LYS 3.4 15.7 - - - +
278B LYS* 2.7 25.7 + - - +
280B ALA* 1.3 73.9 - - + +
282B PHE* 1.3 72.9 + - - -
284B ASN* 3.1 16.6 + - - +
285B ILE* 3.1 24.4 + - - +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 3.6 50.5 - - + -
282A PHE* 3.4 37.2 - + + -
283A GLU* 4.2 15.3 - - + -
278B LYS* 3.7 11.2 - - + -
279B THR* 3.4 24.7 - - + +
280B ALA 3.1 1.0 - - - -
281B THR* 1.3 93.8 + - - +
283B GLU* 1.3 64.4 + - - +
285B ILE* 3.1 15.6 + - + +
286B VAL* 2.9 27.9 + - - +
279C THR* 4.9 6.1 - - + -
282C PHE* 3.7 23.3 - + + -
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B THR 3.9 1.4 + - - +
280B ALA* 3.5 12.3 + - - +
281B THR 3.3 0.8 - - - -
282B PHE* 1.3 76.9 - - - +
284B ASN* 1.3 57.3 + - - +
286B VAL* 3.4 3.3 + - - +
287B CYS* 3.1 30.7 + - - -
282C PHE* 3.9 25.3 - - + -
25D MET 5.6 5.4 - - - +
26D LEU* 4.5 12.0 - - + +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA 4.4 1.5 + - - +
281B THR* 3.1 11.0 + - - +
283B GLU* 1.3 76.5 - - - +
285B ILE* 1.3 67.8 + - - +
287B CYS* 3.0 20.7 + - - +
288B VAL* 3.0 31.3 + - - +
291B ARG* 5.0 5.7 + - - -
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 5.5 2.5 - - + -
283A GLU* 6.5 1.1 - - + -
286A VAL* 4.1 33.2 - - + -
281B THR* 3.1 27.2 + - - +
282B PHE* 3.5 18.4 - - + +
284B ASN* 1.3 78.0 - - + +
286B VAL* 1.3 64.2 + - + +
288B VAL* 3.8 5.8 + - - +
289B LEU* 3.2 23.1 + - + +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.7 18.6 - - + -
286A VAL* 5.3 0.4 - - + -
282B PHE 2.9 18.2 + - - +
283B GLU 3.9 3.8 - - - +
285B ILE* 1.3 78.8 - - + +
287B CYS* 1.3 65.1 + - - +
289B LEU* 3.9 5.0 - - - +
290B ASN* 3.1 22.2 + - + +
282C PHE* 4.3 16.2 - - + -
285C ILE* 3.8 40.2 - - + -
286C VAL* 3.7 27.1 - - + -
289C LEU* 4.9 1.7 - - + +
26D LEU* 5.0 5.8 - - + -
30D LEU* 5.2 4.5 - - + -
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Residues in contact with CYS 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU* 3.1 19.2 + - - +
284B ASN* 3.0 16.0 + - - +
286B VAL* 1.3 76.4 - - - +
288B VAL* 1.3 62.7 + - - +
290B ASN* 3.2 9.0 + - - +
291B ARG* 3.1 51.7 + - - +
26D LEU* 4.1 25.6 - - - -
30D LEU* 4.5 8.3 - - - -
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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
----------------------------------------------------------
284B ASN* 3.0 31.1 + - - +
285B ILE* 3.9 6.5 - - - +
287B CYS* 1.3 73.4 - - - +
289B LEU* 1.3 67.5 + - - +
290B ASN 3.0 0.9 + - - -
291B ARG* 3.0 23.5 + - - +
292B GLU* 2.9 51.4 + - + +
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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
----------------------------------------------------------
286A VAL* 3.7 25.1 - - + -
289A LEU* 3.0 38.4 - - + -
290A ASN* 3.8 26.0 - - + +
293A VAL* 4.1 4.7 - - + -
285B ILE 3.2 15.1 + - - +
286B VAL* 3.9 5.2 - - - +
287B CYS 3.4 0.2 - - - -
288B VAL* 1.3 78.7 - - - +
290B ASN* 1.3 51.9 + - - +
292B GLU* 3.8 9.2 - - - +
293B VAL* 2.7 55.2 + - + +
286C VAL* 4.3 18.2 - - + -
289C LEU* 4.6 5.4 - - + -
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Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 3.1 12.6 + - + +
287B CYS* 3.2 12.3 + - - +
289B LEU* 1.3 80.7 - - - +
291B ARG* 1.4 57.5 + - - +
293B VAL* 3.2 1.2 + - - +
294B GLU* 2.7 33.0 + - - +
289C LEU* 4.1 13.7 - - + -
29D GLU* 5.3 3.8 + - - -
30D LEU* 3.8 31.2 - - + +
33D MET* 3.7 10.6 - - - +
48D ARG* 2.7 43.6 + - - +
52D ARG* 6.0 0.2 - - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASN* 5.0 5.1 + - - -
287B CYS* 3.1 35.2 + - + +
288B VAL* 3.0 30.8 + - - +
290B ASN* 1.4 82.7 - - - +
292B GLU* 1.3 56.3 + - + +
294B GLU* 2.8 11.2 + - - +
295B ARG* 2.5 38.8 + - - +
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASN* 4.7 10.6 + - - +
293A VAL* 4.3 15.6 - - + +
288B VAL* 2.9 42.3 + - + +
289B LEU* 3.7 15.3 - - + +
291B ARG* 1.3 74.3 - - + +
293B VAL* 1.3 59.2 + - - +
295B ARG* 3.6 6.9 - - - +
296B VAL* 2.8 37.8 + - + +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.8 0.4 - - + -
293A VAL* 3.8 5.2 - - + -
289B LEU* 2.7 47.6 + - + +
290B ASN 3.5 4.3 - - - +
292B GLU* 1.3 77.2 - - - +
294B GLU* 1.3 61.4 + - - +
296B VAL* 3.3 5.7 + - + +
297B ALA* 3.0 20.8 + - + +
289C LEU* 4.1 18.2 - - + +
292C GLU* 3.7 34.3 - - + +
293C VAL* 3.5 35.2 - - + +
296C VAL* 5.3 0.8 - - + +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ASN* 2.7 20.9 + - - +
291B ARG* 2.8 15.7 + - - +
293B VAL* 1.3 68.2 - - - +
295B ARG* 1.3 65.1 + - - +
297B ALA* 2.9 15.6 + - + +
298B MET* 3.0 31.6 + - + +
292C GLU* 5.1 0.2 - - - +
48D ARG* 3.6 31.8 + - - +
52D ARG* 2.8 46.3 + - - -
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG 2.5 25.1 + - - +
292B GLU* 3.6 8.5 - - - +
294B GLU* 1.3 71.0 - - - +
296B VAL* 1.3 68.3 + - + +
297B ALA 3.1 0.5 + - - -
298B MET* 3.1 8.5 + - - +
299B THR* 3.1 25.4 + - - +
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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
----------------------------------------------------------
293A VAL* 3.8 21.3 - - + -
296A VAL* 3.6 30.3 - - + -
297A ALA* 4.0 23.8 - - + +
300A ALA* 4.8 7.9 - - + -
292B GLU 2.8 19.2 + - - +
293B VAL* 3.9 5.4 - - - +
295B ARG* 1.3 80.3 - - + +
297B ALA* 1.3 61.4 + - - +
299B THR* 3.4 6.3 + - - -
300B ALA* 3.0 22.3 + - - +
293C VAL* 6.4 1.1 - - + -
296C VAL* 4.4 4.9 - - + -
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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 VAL 3.0 14.1 + - - +
294B GLU* 2.9 7.5 + - + +
296B VAL* 1.3 79.1 - - - +
298B MET* 1.3 62.2 - - + +
300B ALA* 3.9 2.0 - - - +
301B GLU* 3.3 22.3 + - - +
292C GLU* 4.1 16.2 - - - +
296C VAL* 3.5 32.0 - - + +
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Residues in contact with MET 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 3.0 31.5 + - + +
295B ARG* 3.1 9.6 + - - +
297B ALA* 1.3 80.5 - - + +
299B THR* 1.3 58.3 + - - +
301B GLU* 3.2 4.4 + - - +
302B ALA* 2.9 31.4 + - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 3.5 27.4 - - + -
301A GLU* 5.0 1.1 - - - +
304A SER* 4.5 11.7 + - - +
295B ARG* 3.1 14.3 + - - +
296B VAL* 3.5 12.8 - - + -
298B MET* 1.3 75.4 - - - +
300B ALA* 1.3 57.3 + - - +
302B ALA* 3.5 5.6 + - - +
303B CYS* 2.8 31.2 + - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 5.8 0.2 - - + -
300A ALA* 5.0 7.4 - - + -
296B VAL* 3.0 14.4 + - + +
297B ALA 4.0 2.7 - - - +
299B THR* 1.3 81.4 - - - +
301B GLU* 1.3 57.9 + - - +
303B CYS* 3.8 7.2 - - - +
304B SER* 3.3 26.2 + - - -
296C VAL* 3.6 24.5 - - + +
299C THR* 3.5 20.1 - - + +
300C ALA* 5.0 8.7 - - + +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA 3.3 14.8 + - - +
298B MET* 3.2 5.8 + - - +
300B ALA* 1.3 75.9 - - - +
302B ALA* 1.3 66.3 + - - +
304B SER* 3.6 12.7 + - - +
305B ARG* 3.5 48.3 + - - +
299C THR* 5.1 5.1 + - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B MET 2.9 16.9 + - - +
299B THR* 3.8 5.8 - - - +
301B GLU* 1.3 75.5 - - - +
303B CYS* 1.3 54.0 + - - +
305B ARG* 2.8 30.9 + - - +
306B GLN* 3.2 15.2 + - + +
----------------------------------------------------------
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Residues in contact with CYS 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 3.4 9.4 - - - -
303A CYS* 3.0 40.4 - - - +
304A SER* 3.1 33.1 + - - +
299B THR* 2.8 20.5 + - + +
300B ALA* 3.8 10.1 - - - +
302B ALA* 1.3 74.9 - - - +
304B SER* 1.3 55.6 + - - +
305B ARG 3.3 1.1 - - - -
306B GLN* 3.6 21.8 + - - +
307B HIS* 3.8 4.9 + - - +
300C ALA* 6.6 0.4 - - - -
303C CYS* 3.7 12.1 - - - -
----------------------------------------------------------
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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