Contacts of the helix formed by residues 281 - 308 (chain B) in PDB entry 5TIN
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 LYS 281 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.3 37.2 - - + +
143B LYS 3.2 6.7 - - - -
145B PHE* 4.2 10.1 - - + +
271B ARG* 3.9 22.2 - - - +
274B LEU* 3.8 30.1 - - + -
275B PRO 5.4 0.6 + - - -
277B VAL* 3.6 27.5 + - + +
279B TYR* 3.7 14.2 + - + +
280B VAL* 1.3 81.8 - - - +
282B ALA* 1.3 65.4 + - - +
283B ILE* 3.3 6.7 - - + +
284B ASP* 3.0 40.5 + - - +
285B ILE* 3.2 11.1 + - - +
345B TYR* 4.9 0.9 - - - -
222C TYR* 6.1 0.2 - - - -
225C ILE* 5.4 2.0 - - - +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LYS 2.9 7.7 + - - +
144B ASN 3.7 13.0 - - - +
145B PHE 3.3 11.5 + - - +
147B MET* 4.0 5.6 - - + -
281B LYS* 1.3 74.3 - - - +
283B ILE* 1.3 62.0 + - - +
285B ILE* 3.3 3.5 + - - +
286B TRP 3.3 12.8 + - - -
341B TYR* 2.8 25.9 + - - +
345B TYR* 3.4 42.8 - - + -
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.0 34.5 + - + +
146B PRO* 4.1 7.1 - - + +
227B MET* 4.0 25.8 - - + -
228B TYR* 3.6 36.1 - - + +
270B SER* 3.9 30.5 - - - +
281B LYS* 4.3 10.8 - - + -
282B ALA* 1.3 74.6 - - - +
284B ASP* 1.3 71.3 + - - +
286B TRP* 3.5 2.7 + - + +
287B MET* 3.0 38.1 + - + +
341B TYR* 3.9 3.3 + - - -
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER* 4.4 0.9 + - - -
271B ARG* 3.0 37.2 + - - +
279B TYR 4.0 0.7 - - - +
280B VAL* 3.9 13.3 - - + -
281B LYS* 3.0 50.9 + - - +
283B ILE* 1.3 80.3 - - - +
285B ILE* 1.3 60.8 - - - +
287B MET* 3.4 6.0 + - - +
288B ALA* 2.9 32.5 + - - +
225C ILE* 4.5 12.8 - - + +
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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
----------------------------------------------------------
280B VAL* 3.5 21.1 - - + -
281B LYS 3.2 13.1 + - - +
282B ALA 3.3 7.1 + - - +
284B ASP* 1.3 76.8 - - - +
286B TRP* 1.3 58.6 + - - +
288B ALA* 3.3 5.5 + - + +
289B VAL* 3.0 40.9 + - + +
337B PHE* 4.7 4.9 - - + -
341B TYR* 4.3 16.8 - - + -
345B TYR* 4.0 16.8 - - + +
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Residues in contact with TRP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 3.4 42.5 - + + -
231B SER* 2.8 24.1 + - - -
232B LEU* 4.8 9.9 - - + -
282B ALA 3.3 2.0 + - - -
283B ILE* 3.6 7.9 - - + +
284B ASP 3.2 0.2 - - - -
285B ILE* 1.3 80.7 - - - +
287B MET* 1.3 74.8 + - + +
289B VAL* 3.4 2.3 + - - +
290B CYS* 2.9 46.8 + - - +
334B PHE* 4.3 8.5 - + - -
337B PHE* 3.7 30.3 - + - -
338B ASN* 3.7 33.7 - - - -
341B TYR* 3.7 39.0 - + + +
342B TRP* 4.1 14.6 - + - -
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B MET* 3.7 44.2 - - + +
231B SER* 4.1 0.9 - - - -
263B MET* 3.4 27.8 - - + +
266B GLN* 4.0 24.9 - - + +
267B SER* 4.0 23.4 - - - +
270B SER* 4.0 17.0 - - - +
271B ARG* 5.8 0.2 - - - +
283B ILE* 3.0 25.7 + - + +
284B ASP* 3.9 5.2 - - - +
286B TRP* 1.3 91.7 - - + +
288B ALA* 1.3 58.6 + - - +
290B CYS* 3.7 2.5 - - - +
291B LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASP 2.9 18.6 + - - +
285B ILE* 3.6 6.7 - - + +
287B MET* 1.3 77.6 - - - +
289B VAL* 1.3 59.2 + - + +
291B LEU* 3.2 10.5 + - - +
292B LEU* 2.9 31.1 + - - +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 3.0 26.6 + - + +
286B TRP 3.9 0.2 - - - +
288B ALA* 1.3 74.1 - - + +
290B CYS* 1.3 66.2 + - - +
292B LEU* 3.1 14.0 + - + +
293B PHE* 2.9 42.7 + - + -
334B PHE* 5.1 0.2 - - + -
337B PHE* 3.5 52.9 - - + -
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Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B SER* 4.3 7.6 - - - -
235B VAL* 3.8 24.4 - - + +
263B MET* 3.7 22.7 - - + -
286B TRP* 2.9 54.0 + - - +
287B MET 3.7 0.7 - - - +
289B VAL* 1.3 77.5 - - - +
291B LEU* 1.3 61.2 + - - +
293B PHE* 3.4 4.8 + - - +
294B VAL* 3.1 27.2 + - - +
334B PHE* 4.1 11.9 - - - -
337B PHE* 5.5 0.4 - - - -
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 3.8 25.6 - - + +
263B MET* 3.7 29.3 - - + +
264B THR* 4.1 18.6 - - + -
267B SER* 5.6 5.6 - - - -
287B MET 2.9 19.6 + - - +
288B ALA* 3.4 9.2 - - - +
290B CYS* 1.3 77.4 - - - +
292B LEU* 1.3 58.0 + - - +
294B VAL* 3.4 1.4 + - - -
295B PHE* 2.9 34.0 + - + +
230C PRO* 6.1 1.1 - - + -
233C LEU* 3.4 32.1 - - + -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA 2.9 14.6 + - - +
289B VAL* 3.1 18.8 + - + +
291B LEU* 1.3 76.3 - - - +
293B PHE* 1.3 54.9 + - + +
295B PHE* 3.3 7.3 + - + +
296B SER* 2.8 48.6 + - - +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 4.5 12.6 - - + -
238B SER* 4.6 2.2 + - - -
239B TRP* 4.8 5.3 + - - +
289B VAL* 2.9 44.7 + - + +
290B CYS* 3.7 6.7 - - - +
291B LEU 3.4 0.2 - - - -
292B LEU* 1.3 78.5 - - + +
294B VAL* 1.3 58.3 + - - +
296B SER* 3.5 5.2 + - - -
297B ALA* 3.1 23.2 + - - +
330B PHE* 3.5 40.4 - + - -
333B ALA* 3.7 17.3 - - + -
334B PHE* 3.5 53.4 - + + -
337B PHE* 4.7 5.2 - - + -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 3.9 18.4 - - + +
235B VAL* 3.9 13.2 - - + -
238B SER* 3.7 26.7 - - - +
256B GLY* 5.1 0.9 - - - -
259B THR* 3.3 17.0 + - - +
260B VAL* 3.2 44.8 - - + +
263B MET* 4.6 5.6 - - + -
290B CYS 3.1 17.5 + - - +
291B LEU* 3.9 3.8 - - - +
293B PHE* 1.3 76.8 - - - +
295B PHE* 1.3 65.3 - - - +
297B ALA* 3.5 4.7 + - - +
298B LEU* 3.5 14.6 + - - +
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Residues in contact with PHE 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 3.8 26.5 - - + -
291B LEU* 2.9 22.6 + - + +
292B LEU* 3.7 9.2 - - + +
294B VAL* 1.3 75.1 - - - +
296B SER* 1.3 59.2 + - - +
298B LEU* 3.2 8.4 + - + +
299B LEU* 3.0 53.7 + - + +
233C LEU* 3.8 35.2 - - + -
236C ILE* 3.8 31.4 - - + -
237C LEU* 4.0 24.5 - - + -
240C VAL* 5.0 3.8 - - + -
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Residues in contact with SER 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 2.8 35.3 + - - +
293B PHE* 3.6 9.0 - - - -
294B VAL 3.3 0.2 - - - -
295B PHE* 1.3 77.2 - - - +
297B ALA* 1.3 51.9 + - - +
299B LEU* 3.3 13.4 + - - +
300B GLU* 2.8 33.8 + - - +
330B PHE* 3.7 17.7 - - - -
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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
----------------------------------------------------------
238B SER* 4.0 26.2 - - - +
241B SER* 5.2 5.3 + - - -
242B PHE* 3.8 22.4 - - + -
256B GLY* 6.3 1.1 - - - -
293B PHE 3.1 14.0 + - - +
294B VAL 3.7 9.9 - - - +
295B PHE 3.2 0.4 - - - -
296B SER* 1.3 75.9 - - - +
298B LEU* 1.3 62.4 + - - +
300B GLU* 3.3 9.1 - - - +
301B TYR* 3.2 18.4 + - - +
330B PHE* 3.6 10.7 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG 4.7 2.5 - - - +
253B VAL* 4.4 28.0 - - + +
256B GLY* 4.0 37.8 - - - +
257B ILE 4.4 1.1 - - - +
260B VAL* 4.6 4.9 - - + -
294B VAL 3.5 6.6 + - - +
295B PHE* 3.2 15.3 + - + +
297B ALA* 1.3 76.2 - - - +
299B LEU* 1.3 65.8 + - + +
301B TYR* 3.0 9.8 + - + -
302B ALA* 3.0 20.0 + - + +
237C LEU* 3.5 34.1 - - + -
240C VAL* 4.5 22.4 - - + -
244C ILE* 6.2 1.8 - - + -
255C LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PHE* 3.0 39.6 + - + +
296B SER* 3.6 13.9 - - - +
298B LEU* 1.3 72.7 - - + +
300B GLU* 1.3 66.6 + - - +
302B ALA* 3.2 10.1 + - + +
303B ALA* 3.0 22.9 + - - +
236C ILE* 6.1 1.6 - - + -
240C VAL* 4.1 25.8 - - + -
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 3.6 18.8 - - + -
252B ARG* 3.9 4.9 + - - -
296B SER 2.8 17.8 + - - +
297B ALA* 3.3 13.6 - - - +
299B LEU* 1.3 72.5 - - - +
301B TYR* 1.3 64.0 + - - +
303B ALA* 3.3 9.9 + - - +
304B VAL* 3.0 24.9 + - - +
322B ILE* 3.5 20.7 - - + +
323B ASP* 2.8 28.3 - - - +
326B SER* 3.0 31.5 + - - +
330B PHE* 4.4 7.6 - - + -
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Residues in contact with TYR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 4.9 1.3 - - - +
246B MET* 2.9 25.5 + - - -
249B ALA* 3.1 27.6 - - + +
252B ARG* 3.0 55.9 - - + +
253B VAL* 3.9 31.0 - - + -
297B ALA 3.2 6.7 + - - +
298B LEU* 3.0 13.3 + - + +
300B GLU* 1.3 79.7 + - - +
302B ALA* 1.3 61.8 + - - +
304B VAL* 4.0 18.4 - - + -
305B ASN* 2.8 59.6 + - + +
244C ILE* 4.6 4.5 - - + -
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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 LEU* 3.0 13.8 + - + +
299B LEU* 3.2 17.7 + - + +
301B TYR* 1.3 75.7 - - - +
303B ALA* 1.3 57.8 + - - +
305B ASN* 3.8 1.9 - - - +
306B PHE* 2.9 31.3 + - - +
240C VAL* 4.8 16.8 - - + -
243C TRP* 4.4 14.6 - - + +
244C ILE* 4.2 21.5 - - + -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU 3.0 12.0 + - - +
300B GLU* 3.4 12.1 - - - +
301B TYR 3.1 0.2 - - - -
302B ALA* 1.3 73.4 - - - +
304B VAL* 1.3 59.7 + - - +
306B PHE* 4.4 4.5 - - - -
307B VAL* 2.8 41.9 + - + +
322B ILE* 4.6 16.4 - - + -
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET* 3.8 30.5 - - + -
300B GLU* 3.0 20.9 + - - +
301B TYR* 3.1 19.3 + - + +
303B ALA* 1.3 75.3 - - - +
305B ASN* 1.3 55.0 + - - +
307B VAL* 4.3 5.8 - - - -
308B SER* 2.7 35.2 + - - +
319B ALA* 3.7 20.5 - - + +
322B ILE* 3.7 24.0 - - + -
323B ASP* 3.7 24.2 - - - +
----------------------------------------------------------
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET 4.8 2.9 + - - -
249B ALA* 4.1 11.3 - - - +
301B TYR* 2.8 53.3 + - + +
302B ALA 3.8 3.8 - - - +
304B VAL* 1.3 75.1 - - - +
306B PHE* 1.3 61.4 + - - +
308B SER* 3.5 13.0 + - - -
309B ARG* 3.6 14.0 + - - +
243C TRP 4.0 1.4 - - - +
244C ILE* 3.7 15.5 - - + +
245C ASN* 3.1 40.5 + - - +
----------------------------------------------------------
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 2.9 19.8 + - - +
303B ALA* 3.7 4.9 - - - +
305B ASN* 1.3 74.1 - - - +
307B VAL* 1.3 75.6 + - + +
308B SER 3.2 2.0 + - - -
309B ARG* 3.0 73.9 + - - -
243C TRP* 3.7 49.4 - + + +
327C ARG* 3.9 21.8 - - - -
----------------------------------------------------------
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA* 2.8 30.3 + - + +
304B VAL 3.8 0.2 - - - +
306B PHE* 1.3 83.0 - - + +
308B SER* 1.3 60.2 + - - +
309B ARG* 3.7 1.4 + - - +
310B ALA 5.0 0.9 + - - -
315B PHE* 3.4 35.6 - - + +
318B ARG* 4.5 5.4 - - + -
319B ALA* 3.6 35.7 - - + +
322B ILE* 4.2 15.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET* 4.3 10.2 + - - +
304B VAL* 2.7 22.3 + - - +
305B ASN* 3.5 8.8 + - - -
306B PHE 3.2 0.4 - - - -
307B VAL* 1.3 78.7 - - - +
309B ARG* 1.3 65.1 + - - +
310B ALA 3.4 12.2 + - - +
311B GLY* 4.2 1.2 + - - -
315B PHE 4.2 6.7 - - - -
316B ILE* 4.1 23.0 - - - +
319B ALA* 3.8 17.0 - - - -
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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