Contacts of the helix formed by residues 251 - 285 (chain B) in PDB entry 4LOU
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 THR 251 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ALA* 4.0 6.3 - - + -
248B PRO* 3.0 40.5 - - + +
249B LEU 2.9 0.2 - - - -
250B ASN* 1.3 79.7 - - - +
252B LEU* 1.3 64.3 + - - +
253B TRP* 3.3 6.1 - - - +
254B LEU* 3.2 22.5 + - - +
255B TYR* 3.7 24.1 - - + +
382B TYR* 3.6 19.3 + - - +
384B LEU* 3.4 27.8 - - + +
389B PHE* 5.6 0.2 - - + -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ILE* 4.3 15.3 - - + -
247B ALA* 4.3 9.6 - - + +
248B PRO 3.9 11.0 - - - +
249B LEU* 3.4 29.2 + - + +
251B THR* 1.3 77.8 - - - +
253B TRP* 1.3 57.5 + - - +
255B TYR* 2.8 33.5 + - + +
256B LEU* 3.3 7.3 + - - +
423B LEU* 4.0 20.9 - - + -
424B PRO* 4.2 27.4 - - + -
427B ILE* 4.0 27.9 - - + +
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Residues in contact with TRP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU 4.9 0.8 + - - -
250B ASN 3.3 28.0 + - - -
251B THR 4.1 2.7 - - - -
252B LEU* 1.3 76.9 - - - +
254B LEU* 1.3 87.5 + - + +
256B LEU* 3.2 20.3 + - + +
257B ILE* 3.3 32.2 + - + +
379B PHE* 3.9 25.4 - + - -
382B TYR* 3.4 23.3 + + - -
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 3.2 12.8 + - - +
252B LEU 3.0 1.0 + - - -
253B TRP* 1.3 120.9 - - + +
255B TYR* 1.3 62.9 + - - +
257B ILE* 3.2 10.2 + - + +
258B LEU 3.1 18.7 + - - -
371B PHE* 3.6 19.2 - - + -
375B ALA* 4.1 6.1 - - + -
379B PHE* 4.0 24.9 - - + -
382B TYR* 4.1 8.3 - - + -
384B LEU* 3.9 28.0 - - + -
389B PHE* 3.8 20.4 - - + -
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 4.2 7.2 - - + +
251B THR* 3.7 34.6 - - + +
252B LEU* 2.8 16.2 + - + +
254B LEU* 1.3 73.9 - - - +
256B LEU* 1.3 61.9 + - - +
257B ILE 3.3 0.2 - - - -
258B LEU* 4.0 4.5 - - + -
259B GLY 3.4 9.9 + - - -
384B LEU* 5.3 0.9 - - - +
388B THR* 2.7 37.3 + - - -
389B PHE* 3.3 35.4 - + - -
392B ALA* 3.6 24.0 - - + -
424B PRO* 3.3 40.8 - - + +
427B ILE* 3.4 12.1 - - + -
428B THR* 3.1 29.2 + - - +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU 3.3 4.4 + - - +
253B TRP* 3.2 19.6 + - + +
254B LEU 3.2 0.8 - - - -
255B TYR* 1.3 73.9 - - - +
257B ILE* 1.3 67.7 + - + +
259B GLY* 3.6 1.9 + - - -
260B ILE* 3.2 34.5 + - + +
427B ILE* 3.4 17.0 - - + +
431B GLY* 4.3 19.7 - - - -
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Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B TRP* 3.3 36.9 + - + +
254B LEU* 3.2 12.2 + - + +
256B LEU* 1.3 78.8 - - + +
258B LEU* 1.3 66.5 + - - +
260B ILE* 2.9 25.0 + - + +
261B ILE* 3.0 20.8 + - + +
371B PHE* 3.6 24.5 - - + -
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU 3.1 15.3 + - - +
255B TYR* 4.1 7.0 - - + +
256B LEU 3.4 0.2 - - - -
257B ILE* 1.3 78.3 - - - +
259B GLY* 1.3 63.9 + - - +
261B ILE* 3.0 12.6 + - + +
262B PHE* 3.0 38.7 + - + -
367B LEU* 4.7 6.1 - - + +
368B GLY* 4.3 9.4 - - - -
371B PHE* 3.5 39.7 - - + -
389B PHE* 3.9 34.5 - - + +
392B ALA* 4.6 1.3 - - + -
393B GLY* 3.9 17.9 - - - +
428B THR* 4.3 10.5 - - + +
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Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B TYR 3.4 8.3 + - - -
256B LEU 3.9 3.1 - - - -
257B ILE 3.3 0.6 - - - -
258B LEU* 1.3 77.9 - - - +
260B ILE* 1.3 56.0 + - - +
262B PHE* 3.6 2.5 + - - -
263B GLY 2.8 22.0 + - - -
428B THR* 3.3 35.0 - - - +
431B GLY 3.1 17.1 - - - +
432B ALA* 3.1 6.0 - - - -
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Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LEU* 3.2 36.0 + - + +
257B ILE* 2.9 19.1 + - + +
259B GLY* 1.3 75.2 - - - +
261B ILE* 1.3 68.4 + - + +
263B GLY* 3.0 9.2 + - - -
264B ILE* 3.1 24.5 + - + +
431B GLY* 4.0 5.2 - - - +
435B LEU* 4.1 30.6 - - + +
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 3.0 16.9 + - + +
258B LEU* 3.0 12.9 + - + +
260B ILE* 1.3 77.6 - - + +
262B PHE* 1.3 63.7 + - - +
263B GLY 3.1 0.5 + - - -
264B ILE* 3.1 16.8 + - + +
265B PHE* 3.1 24.1 + - + +
367B LEU* 4.2 24.9 - - + -
371B PHE* 4.2 30.3 - - + -
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Residues in contact with PHE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LEU* 3.0 31.8 + - + +
259B GLY 3.7 8.5 - - - +
261B ILE* 1.3 77.7 - - - +
263B GLY* 1.3 56.9 + - - +
264B ILE 3.4 0.2 - - - -
265B PHE* 3.9 7.4 - + - -
266B GLY* 3.0 21.3 + - - -
337B PHE* 6.4 0.2 - + - -
363B LEU 5.2 0.4 - - - -
364B GLY* 3.4 17.5 - - - -
367B LEU* 3.5 33.7 - - + -
368B GLY 4.6 0.2 - - - -
393B GLY* 3.0 33.7 - - - -
396B ALA* 3.4 16.4 - - + -
397B LEU* 3.3 50.7 - - + -
400B ALA* 3.1 14.5 - - - +
432B ALA* 4.1 6.7 - - + -
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B GLY 2.8 16.7 + - - -
260B ILE 3.0 5.7 + - - -
262B PHE* 1.3 73.8 - - - +
264B ILE* 1.3 59.6 + - - +
267B PRO* 3.3 16.6 - - - +
400B ALA* 4.4 1.3 - - - -
432B ALA* 3.4 24.7 - - - -
435B LEU* 3.5 13.7 - - - +
436B ALA* 3.2 16.3 + - - -
439B THR* 3.7 0.9 + - - -
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ILE* 3.1 21.4 + - + +
261B ILE* 3.1 18.6 + - + +
263B GLY* 1.3 77.2 - - - +
265B PHE* 1.3 67.6 + - + +
267B PRO* 4.2 4.2 - - - +
268B ILE* 3.4 27.4 + - + +
435B LEU* 4.6 17.7 - - + -
439B THR* 4.5 16.0 + - + -
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Residues in contact with PHE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ILE* 3.1 19.0 + - + +
262B PHE* 4.2 6.3 - + - +
264B ILE* 1.3 82.0 - - + +
266B GLY* 1.3 68.5 + - - +
268B ILE* 3.0 17.4 + - + +
269B PHE* 2.9 53.6 + + + -
272B TRP* 4.8 16.6 - + - -
337B PHE* 3.8 35.0 - + - -
341B VAL* 4.6 8.3 - - + -
363B LEU* 5.9 0.4 - - + -
367B LEU* 5.2 9.4 - - + -
397B LEU* 4.1 26.7 - - + -
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B PHE 3.0 10.7 + - - -
265B PHE* 1.3 77.4 - - - +
267B PRO* 1.3 62.6 - - - +
269B PHE* 3.2 1.9 + - - +
270B ASN* 2.9 23.4 + - - +
397B LEU* 4.2 6.5 - - - -
400B ALA* 3.6 17.3 - - - -
401B SER* 3.0 28.2 + - - -
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Residues in contact with PRO 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLY 3.3 15.9 - - - +
264B ILE 4.2 4.0 - - - +
265B PHE 3.8 1.1 - - - -
266B GLY* 1.3 84.2 - - - +
268B ILE* 1.3 60.7 + - + +
269B PHE 3.2 1.6 - - - -
270B ASN* 3.0 11.6 + - + +
271B LYS* 2.8 38.8 + - - +
400B ALA 4.7 1.8 - - - +
436B ALA* 3.8 16.6 - - + -
439B THR* 3.7 24.5 - - - +
441B GLY* 3.6 33.9 - - - +
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Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.4 22.2 - - + +
265B PHE* 3.0 18.7 + - + +
267B PRO* 1.3 77.1 - - + +
269B PHE* 1.3 61.2 + - - +
271B LYS* 3.8 14.6 + - - +
272B TRP* 3.2 57.6 + - + +
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Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B PHE* 2.9 40.8 + + + +
266B GLY 3.4 8.7 - - - +
268B ILE* 1.3 77.3 - - - +
270B ASN* 1.3 62.0 - - - +
272B TRP* 3.4 10.9 + + - +
273B VAL* 3.0 34.1 + - + +
341B VAL* 4.3 18.8 - - + -
344B THR* 3.9 24.9 - - + -
345B LEU* 3.9 25.1 - - + -
356B ILE* 3.9 21.1 - - + -
360B MET* 4.4 12.8 - - + -
363B LEU* 4.3 15.9 - - + -
397B LEU* 4.5 5.2 - - + -
401B SER* 3.9 16.2 - - - +
444B LEU* 5.8 1.1 - - + -
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Residues in contact with ASN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLY 2.9 13.2 + - - +
267B PRO* 3.0 14.1 + - + +
269B PHE* 1.3 76.6 - - - +
271B LYS* 1.3 66.6 + - - +
273B VAL* 3.1 16.7 - - - +
274B LEU* 3.2 18.2 + - + +
400B ALA 4.9 0.4 + - - -
401B SER* 2.8 35.2 + - - +
441B GLY* 5.9 0.2 - - - -
442B LYS* 2.7 34.5 + - - +
444B LEU* 3.5 29.8 - - + +
447B ALA* 5.9 0.8 - - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B PRO* 2.8 24.6 + - - +
268B ILE* 4.0 17.0 - - - +
270B ASN* 1.3 71.2 - - - +
272B TRP* 1.3 59.4 + - + +
274B LEU* 3.0 8.2 + - - +
275B GLY* 2.5 36.5 + - - -
439B THR 6.0 0.4 + - - -
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Residues in contact with TRP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B PHE* 4.8 12.3 - + - -
268B ILE* 3.2 37.5 + - + +
269B PHE* 3.4 13.9 + + - +
270B ASN 3.4 0.2 - - - -
271B LYS* 1.3 84.1 - - + +
273B VAL* 1.3 57.1 + - - +
275B GLY* 4.3 2.2 - - - +
276B MET* 2.8 39.7 + - + +
341B VAL* 4.2 18.2 - - + -
345B LEU* 3.9 29.4 - - + -
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B PHE* 3.0 27.8 + - + +
270B ASN* 3.1 24.2 - - - +
272B TRP* 1.3 72.8 - - - +
274B LEU* 1.3 64.4 + - + +
277B GLN* 3.0 26.6 + - + +
345B LEU* 3.5 19.4 - - + +
348B PHE* 3.7 37.2 - - + -
349B SER* 3.1 11.3 + - - +
356B ILE* 5.3 1.8 - - + -
444B LEU* 4.0 23.1 - - + -
448B ILE* 5.2 0.2 - - + -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ASN* 3.2 16.1 + - + +
271B LYS* 3.0 9.7 + - - +
273B VAL* 1.3 76.4 - - + +
275B GLY* 1.3 63.8 + - - +
277B GLN* 3.2 25.6 - - - +
278B ASP* 3.4 7.4 + - - +
444B LEU* 4.1 10.1 - - + -
447B ALA* 4.1 23.3 - - + +
448B ILE* 4.0 24.5 - - + -
451B ARG* 3.2 46.9 + - + +
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LYS 2.5 20.3 + - - -
272B TRP* 3.2 2.0 + - - -
274B LEU* 1.3 73.8 - - - +
276B MET* 1.3 58.6 + - - +
278B ASP* 3.1 14.3 - - - +
279B LEU* 3.1 22.8 + - - +
282B ARG* 5.0 0.5 + - - -
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Residues in contact with MET 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B TRP* 2.8 23.2 + - + +
275B GLY* 1.3 69.0 - - - -
277B GLN* 1.3 66.3 + - - +
278B ASP 3.1 1.8 - - - -
279B LEU* 3.7 26.9 - - + +
280B LEU* 3.0 43.5 + - + +
345B LEU* 4.9 17.9 - - + -
346B LEU* 4.3 20.4 - - + -
349B SER* 3.8 12.3 - - - +
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B VAL* 3.0 19.7 + - + +
274B LEU* 3.2 22.1 - - - +
276B MET* 1.3 77.6 - - - +
278B ASP* 1.3 60.6 + - - +
280B LEU* 4.2 2.8 - - - +
281B HIS* 3.4 18.2 + - - +
348B PHE* 4.7 11.7 + - - -
349B SER* 3.5 32.1 + - - +
448B ILE* 4.1 27.4 - - - +
451B ARG* 3.0 23.4 + - - +
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LEU 3.4 9.5 - - - +
275B GLY* 3.1 12.7 - - - +
276B MET 3.1 0.2 - - - -
277B GLN* 1.3 75.3 - - - +
279B LEU* 1.3 60.4 + - - +
281B HIS* 2.8 29.5 + - - +
282B ARG* 3.3 29.9 + - - +
451B ARG* 3.2 33.3 + - - -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLY 3.1 10.6 + - - +
276B MET* 3.3 28.4 + - + +
278B ASP* 1.3 79.8 - - - +
280B LEU* 1.3 73.7 + - + +
282B ARG* 3.3 35.5 + - - +
283B VAL* 3.6 12.9 + - + +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B MET* 3.0 32.3 + - + +
277B GLN 4.2 3.6 - - - +
279B LEU* 1.3 82.8 - - + +
281B HIS* 1.3 61.1 + - - +
282B ARG 3.2 0.4 - - - -
283B VAL* 2.9 33.8 + - + +
284B HIS* 3.4 14.4 - - - +
294B MET* 3.8 24.2 - - + -
298B ILE* 4.5 7.9 - - + -
346B LEU* 4.0 19.1 - - + +
349B SER* 4.2 1.6 - - - +
350B SER* 3.5 43.1 - - - +
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Residues in contact with HIS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLN 3.4 12.2 + - - +
278B ASP* 2.8 15.4 + - - +
280B LEU* 1.3 79.2 - - - +
282B ARG* 1.3 58.3 + - + +
284B HIS* 3.7 17.8 + + + -
285B GLY* 3.0 36.0 + - - -
286B GLY* 4.1 19.7 - - - -
291B TRP* 4.6 10.8 - + - -
455B LYS* 4.8 17.7 + - - -
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLY 5.0 0.6 + - - -
278B ASP* 3.3 22.8 + - - +
279B LEU* 3.3 45.4 - - + +
281B HIS* 1.3 77.3 - - + +
283B VAL* 1.3 66.2 + - + +
284B HIS 3.2 1.0 + - - -
285B GLY* 3.7 7.0 + - - -
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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 LEU* 3.7 19.5 - - + +
280B LEU* 2.9 26.0 + - + +
282B ARG* 1.3 78.6 - - + +
284B HIS* 1.3 55.8 + - + +
290B LYS* 4.4 10.3 - - + +
294B MET* 3.8 26.0 - - + -
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Residues in contact with HIS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 3.4 13.1 + - - +
281B HIS* 3.7 27.8 + - - -
283B VAL* 1.3 78.9 - - + +
285B GLY* 1.3 54.0 + - - +
286B GLY 2.7 35.4 + - - -
287B ASN* 2.9 22.7 + - - +
290B LYS* 3.5 21.1 + - + +
291B TRP* 3.2 79.7 + + - +
294B MET* 3.4 31.3 - - + +
350B SER 4.7 1.0 + - - -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B HIS* 3.0 30.4 + - - -
282B ARG* 3.7 7.4 + - - -
284B HIS* 1.3 74.0 - - - +
286B GLY* 1.3 56.4 + - - +
287B ASN* 3.4 1.3 - - - -
290B LYS* 5.9 1.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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