Contacts of the helix formed by residues 240 - 278 (chain B) in PDB entry 5W0P
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 SER 240 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLN* 4.2 15.9 + - - +
238B GLN 3.4 1.1 - - - -
239B GLU* 1.3 77.5 - - - +
241B ALA* 1.3 59.7 + - - +
242B THR* 2.8 27.0 + - - +
243B THR* 2.7 39.9 + - - +
244B GLN* 3.5 12.5 + - - +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN 5.3 0.7 - - - -
239B GLU 3.3 7.5 + - - +
240B SER* 1.3 71.1 + - - +
242B THR* 1.3 67.2 + - + +
244B GLN* 3.3 18.3 + - - +
245B LYS* 3.5 15.2 + - - +
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Residues in contact with THR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B SER* 2.8 21.8 + - - -
241B ALA* 1.3 80.7 - - + +
243B THR* 1.3 62.1 + - - +
244B GLN 3.5 0.3 + - - -
245B LYS* 3.8 14.3 - - - +
246B ALA* 3.6 19.9 + - - +
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Residues in contact with THR 243 (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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230B VAL* 5.4 1.9 - - - +
233B ALA 5.8 0.9 - - - -
234B ALA* 4.2 12.4 - - - +
237B GLN* 3.5 26.3 + - + +
240B SER* 2.7 38.3 + - - +
242B THR* 1.3 80.3 + - - +
244B GLN* 1.3 63.3 + - - +
246B ALA* 3.9 7.3 + - - +
247B GLU* 3.5 18.7 + - - +
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Residues in contact with GLN 244 (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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234B ALA* 2.8 37.2 + - - +
237B GLN 3.2 13.9 + - - -
238B GLN* 3.6 24.4 + - + +
240B SER 3.5 12.1 - - - +
241B ALA* 3.3 12.3 + - + +
242B THR 3.3 1.0 - - - -
243B THR* 1.3 78.2 + - - +
245B LYS* 1.3 63.1 + - - +
246B ALA 3.2 0.2 - - - -
247B GLU* 3.4 20.9 + - - +
248B LYS* 3.3 17.5 + - - +
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Residues in contact with LYS 245 (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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241B ALA 3.5 10.1 + - - +
242B THR* 3.8 17.3 - - - +
244B GLN* 1.3 75.2 - - - +
246B ALA* 1.3 63.3 + - - +
248B LYS* 3.3 15.2 - - + +
249B GLU* 3.0 31.9 + - + +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B VAL* 5.4 1.6 - - + -
242B THR 3.6 13.8 + - - +
243B THR* 3.9 8.1 - - - +
244B GLN 3.2 0.2 - - - -
245B LYS* 1.3 79.9 - - + +
247B GLU* 1.3 54.4 + - - +
249B GLU* 3.0 8.5 + - - +
250B VAL* 2.7 43.9 + - + +
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Residues in contact with GLU 247 (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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227B VAL* 5.7 3.0 - - + +
230B VAL* 3.8 31.7 - - + +
231B LYS* 4.1 34.4 + - + +
234B ALA* 3.5 21.3 - - + +
243B THR 3.5 9.5 + - - +
244B GLN* 3.4 19.0 + - - +
246B ALA* 1.3 77.6 - - - +
248B LYS* 1.3 55.9 + - - +
250B VAL* 3.8 2.4 - - + +
251B THR* 2.7 46.0 + - - +
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Residues in contact with LYS 248 (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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-147A ARG* 6.0 2.2 - - - +
244B GLN 3.3 7.7 + - - +
245B LYS* 3.3 20.0 - - + +
246B ALA 3.1 0.2 - - - -
247B GLU* 1.3 79.9 - - - +
249B GLU* 1.3 58.4 + - + +
251B THR* 3.6 3.4 + - - -
252B ARG* 3.1 37.2 + - - +
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Residues in contact with GLU 249 (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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245B LYS* 3.0 18.2 + - + +
246B ALA* 3.0 11.0 + - - +
248B LYS* 1.3 75.3 - - + +
250B VAL* 1.3 65.8 + - + +
252B ARG* 3.8 30.9 + - - +
253B MET* 3.2 36.4 + - + +
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Residues in contact with VAL 250 (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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226B LEU* 5.1 10.5 - - + -
227B VAL* 3.9 27.6 - - + -
230B VAL* 4.9 20.0 - - + -
246B ALA* 2.7 28.4 + - + +
247B GLU* 3.8 8.3 - - - +
249B GLU* 1.3 71.6 - - + +
251B THR* 1.3 62.7 + - - +
253B MET* 3.2 4.5 + - - +
254B VAL* 2.9 39.6 + - + +
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Residues in contact with THR 251 (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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227B VAL* 4.1 24.0 - - + +
247B GLU* 2.7 32.1 + - - +
248B LYS* 4.1 3.6 - - - -
250B VAL* 1.3 78.1 - - - +
252B ARG* 1.3 61.8 + - - +
254B VAL* 4.1 4.6 - - - +
255B ILE* 3.3 40.4 + - + +
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Residues in contact with ARG 252 (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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248B LYS* 3.1 25.9 + - + +
249B GLU* 3.8 32.5 + - - +
250B VAL 3.2 0.2 - - - -
251B THR* 1.3 80.5 - - - +
253B MET* 1.3 70.9 + - - +
255B ILE* 3.6 7.1 + - - +
256B ILE* 3.2 39.4 + - + +
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Residues in contact with MET 253 (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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249B GLU* 3.2 26.0 + - - +
250B VAL* 3.2 4.5 + - - +
252B ARG* 1.3 86.7 - - + +
254B VAL* 1.3 60.8 + - + +
256B ILE* 3.2 26.2 + - + +
257B TYR* 2.8 73.5 + - + +
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Residues in contact with VAL 254 (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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223B TYR* 3.9 41.1 - - + +
224B GLY* 5.1 1.3 - - - +
226B LEU* 5.2 4.0 - - + -
227B VAL* 3.8 24.0 - - + -
250B VAL* 2.9 28.0 + - + +
251B THR* 4.1 3.6 - - - +
252B ARG 3.4 0.2 - - - -
253B MET* 1.3 72.9 - - + +
255B ILE* 1.3 63.0 + - + +
257B TYR* 3.1 16.6 + - + +
258B VAL* 2.9 37.1 + - + +
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Residues in contact with ILE 255 (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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251B THR* 3.3 34.4 + - + +
252B ARG* 3.8 7.2 - - - +
254B VAL* 1.3 79.3 - - + +
256B ILE* 1.3 59.4 + - + +
258B VAL* 3.4 8.6 + - + +
259B ILE* 3.0 45.7 + - + +
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Residues in contact with ILE 256 (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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252B ARG* 3.2 35.2 + - + +
253B MET* 3.2 32.3 + - + +
255B ILE* 1.3 76.6 - - + +
257B TYR* 1.3 64.4 + - + +
259B ILE* 3.8 10.1 - - + +
260B ALA* 2.8 34.2 + - + +
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Residues in contact with TYR 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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131B LEU* 6.4 0.9 - - + -
135B ARG* 3.2 32.7 + - - -
219B ILE* 5.4 4.1 - - + +
223B TYR* 4.2 36.1 - + + -
253B MET* 2.8 57.0 + - + +
254B VAL* 3.1 18.6 + - + +
256B ILE* 1.3 79.5 - - + +
258B VAL* 1.3 61.9 + - - +
260B ALA* 4.0 5.8 - - + +
261B PHE* 3.1 24.1 + - - +
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Residues in contact with VAL 258 (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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219B ILE* 6.1 1.3 - - + -
220B PHE* 3.6 39.0 - - + -
223B TYR* 6.0 3.1 - - + -
254B VAL* 2.9 29.0 + - + +
255B ILE* 3.5 11.2 - - + +
257B TYR* 1.3 74.8 - - + +
259B ILE* 1.3 62.7 + - + +
261B PHE* 3.2 3.6 + - - +
262B LEU* 2.8 50.7 + - + +
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Residues in contact with ILE 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 ILE* 3.0 38.7 + - + +
256B ILE* 3.9 8.7 - - + +
258B VAL* 1.3 78.6 - - + +
260B ALA* 1.3 55.3 + - - +
262B LEU* 3.7 8.9 - - + -
263B ILE* 2.8 56.5 + - + +
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Residues in contact with ALA 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 ILE* 2.8 28.2 + - + +
257B TYR* 4.0 7.6 - - + +
259B ILE* 1.3 73.7 - - - +
261B PHE* 1.3 61.5 + - - +
263B ILE* 4.2 5.6 - - - +
264B CYS* 3.3 23.9 + - - +
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Residues in contact with PHE 261 (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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125B LEU* 3.6 17.0 - - + -
128B LEU* 5.4 12.6 - - + -
212B PHE* 4.5 12.3 - + - -
215B PRO* 4.2 5.4 - - + -
216B MET* 3.6 47.8 - - + -
219B ILE* 3.9 22.9 - - + -
220B PHE* 4.1 20.2 - + + -
257B TYR 3.1 19.9 + - - +
258B VAL* 3.2 5.1 + - - +
260B ALA* 1.3 75.0 - - - +
262B LEU* 1.3 67.7 + - + +
264B CYS* 3.4 3.8 + - - +
265B TRP* 3.1 52.2 + + + +
266B VAL* 4.5 0.8 + - + -
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Residues in contact with LEU 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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212B PHE* 6.2 0.7 - - + -
216B MET* 5.3 3.1 - - + -
220B PHE* 3.9 23.3 - - + -
258B VAL* 2.8 38.2 + - + +
259B ILE* 3.2 9.6 + - + +
261B PHE* 1.3 79.8 - - + +
263B ILE* 1.3 66.6 + - + +
266B VAL* 3.1 50.8 + - + +
267B PRO* 3.7 0.2 - - - +
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Residues in contact with ILE 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 ILE* 2.8 44.9 + - + +
260B ALA* 4.2 5.8 - - - +
262B LEU* 1.3 72.6 - - + +
264B CYS* 1.3 60.9 + - - +
267B PRO* 3.2 21.6 - - - +
294B PHE* 3.3 35.3 - - + +
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Residues in contact with CYS 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 ALA 3.3 17.7 + - - +
261B PHE* 3.7 4.7 - - - +
262B LEU 3.1 0.6 - - - -
263B ILE* 1.3 82.6 - - - +
265B TRP* 1.3 92.6 + - + +
267B PRO* 3.9 5.6 - - - +
268B TYR* 4.6 5.2 - - - -
294B PHE* 4.3 11.6 - - - +
295B ALA* 4.1 36.3 + - - +
298B ALA* 4.9 10.5 - - - -
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Residues in contact with TRP 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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121B GLY* 3.7 31.9 - - - -
122B GLU* 4.3 17.0 - - + -
125B LEU* 3.6 30.7 - - + +
128B LEU* 6.2 1.8 - - - +
207B MET* 5.3 10.5 - - + -
211B HIS 5.5 2.5 - - - -
212B PHE* 3.4 32.0 - + + -
261B PHE* 3.1 40.2 + + + +
264B CYS* 1.3 101.9 - - + +
266B VAL* 1.3 63.9 + - - +
267B PRO* 3.5 2.0 - - - -
268B TYR* 3.6 25.6 + + + +
269B ALA 3.2 14.9 + - - -
295B ALA* 5.5 7.2 - - + -
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Residues in contact with VAL 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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212B PHE* 4.4 13.2 - - + -
261B PHE* 6.3 0.7 - - + -
262B LEU* 3.1 48.6 + - + +
265B TRP* 1.3 76.1 - - - +
267B PRO* 1.4 58.6 - - + +
269B ALA* 3.0 7.3 + - + -
270B SER* 2.6 43.1 + - - -
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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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262B LEU 3.7 0.7 - - - +
263B ILE* 3.2 27.8 - - - +
264B CYS 3.9 3.1 - - - +
265B TRP 3.6 2.9 - - - -
266B VAL* 1.4 93.9 - - + +
268B TYR* 1.3 56.6 + - - +
270B SER* 3.7 4.7 - - - -
271B VAL* 2.9 36.5 + - + +
290B ILE* 5.7 2.0 - - + -
291B PRO* 3.6 28.3 - - + +
294B PHE* 3.6 23.8 - - + -
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Residues in contact with TYR 268 (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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181B GLU* 3.8 16.3 + - - -
189B ILE* 5.9 6.1 - - + -
191B TYR* 3.8 39.7 - + - -
207B MET* 6.4 3.1 - - + -
264B CYS 4.6 6.1 - - - -
265B TRP* 3.6 25.0 + + + +
266B VAL 3.3 0.6 - - - -
267B PRO* 1.3 78.2 - - - +
269B ALA* 1.3 58.4 + - - +
271B VAL* 4.7 1.3 - - - -
272B ALA* 2.9 38.1 + - + +
291B PRO* 3.2 33.0 - - + -
292B ALA* 3.6 18.7 - - - +
295B ALA* 3.5 23.8 - - + +
296B LYS* 5.4 2.4 - - - +
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Residues in contact with ALA 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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208B PHE* 4.2 16.9 - - + -
212B PHE* 3.5 44.2 - - + -
265B TRP 3.2 6.2 + - - +
266B VAL* 3.0 9.7 + - + +
268B TYR* 1.3 79.1 - - - +
270B SER* 1.3 58.5 + - - +
272B ALA* 5.2 1.1 - - - -
273B PHE* 3.1 28.1 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 2.6 28.2 + - - +
267B PRO* 3.7 7.0 - - - -
269B ALA* 1.3 74.2 - - - +
271B VAL* 1.3 62.0 + - - +
273B PHE* 3.8 3.2 - - - +
274B TYR* 3.0 31.7 + - - +
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 4.0 14.4 - - + +
267B PRO* 2.9 24.4 + - + +
268B TYR* 4.2 2.0 - - - +
270B SER* 1.3 73.9 - - - +
272B ALA* 1.3 60.8 + - - +
274B TYR* 3.1 6.9 + - - +
275B ILE* 2.9 53.4 + - + +
287B PHE* 3.8 29.8 - - + +
288B MET* 5.2 1.8 - - - -
290B ILE* 5.9 1.3 - - + -
291B PRO* 3.8 30.5 - - + -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 3.8 42.0 - - + +
204B VAL* 4.7 16.4 - - + +
268B TYR* 2.9 20.5 + - + +
269B ALA* 5.1 1.1 - - - +
271B VAL* 1.3 77.6 - - - +
273B PHE* 1.3 56.4 + - - +
275B ILE* 3.7 4.4 + - - +
276B PHE* 3.2 25.6 + - - +
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Residues in contact with PHE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 6.1 1.1 - - - -
208B PHE* 4.7 26.4 - + + -
269B ALA 3.1 23.0 + - - +
270B SER* 3.8 3.6 - - - +
271B VAL 3.2 0.4 - - - -
272B ALA* 1.3 77.8 - - - +
274B TYR* 1.3 67.6 + + - +
276B PHE* 3.3 12.7 + + + +
277B THR* 2.8 46.0 + - + -
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Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-153B ARG* 5.6 3.6 + - - -
-101B LYS* 4.2 15.8 - - - +
270B SER* 3.0 20.4 + - - +
271B VAL* 3.5 6.5 - - - +
273B PHE* 1.3 80.8 - + + +
275B ILE* 1.3 52.8 + - - +
277B THR* 3.3 1.5 + - - -
278B HIS* 2.7 85.1 + + + +
281B SER* 5.9 0.9 - - - -
283B PHE* 3.8 24.0 - + - -
287B PHE* 4.6 13.2 - + + -
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 4.3 14.8 - - + +
192B TYR* 3.5 56.3 - - + +
271B VAL* 2.9 39.5 + - + +
272B ALA* 4.0 4.7 - - - +
274B TYR* 1.3 78.3 - - - +
276B PHE* 1.3 57.5 + - - +
279B GLN* 2.8 35.8 + - + +
283B PHE* 3.9 28.7 - - + -
287B PHE* 4.0 16.2 - - + -
288B MET* 5.0 0.7 - - + -
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Residues in contact with PHE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR 5.6 2.4 + - - +
194B LEU* 4.2 27.1 - - + +
201B GLU* 3.8 46.7 - - + -
204B VAL* 5.0 17.7 - - + -
205B ILE* 4.8 13.0 - - + -
272B ALA 3.2 19.5 + - - +
273B PHE* 3.6 13.5 - + + +
274B TYR 3.3 0.4 - - - -
275B ILE* 1.3 77.6 - - - +
277B THR* 1.3 61.5 + - - +
279B GLN* 2.9 20.1 - - - +
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 2.8 39.5 + - + -
274B TYR* 3.7 3.6 - - - -
276B PHE* 1.3 82.2 - - - +
278B HIS* 1.3 76.4 + - + +
279B GLN* 2.9 13.3 + - - +
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Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-153B ARG* 5.5 3.8 + - - -
-101B LYS* 3.9 21.1 + - - -
274B TYR* 2.7 78.6 + + + +
275B ILE 3.6 2.5 - - - -
277B THR* 1.3 89.8 + - + +
279B GLN* 1.3 53.7 + - - +
280B GLY 3.0 3.8 - - - -
281B SER* 2.7 40.5 + - - +
283B PHE* 3.6 7.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il