Contacts of the helix formed by residues 217 - 258 (chain A) in PDB entry 5C5B
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 ASN 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLU* 4.0 13.5 - - + +
213A MET* 3.0 36.1 + - + +
216A GLU* 1.3 89.1 - - - +
218A LEU* 1.3 66.5 + - - +
219A ASN 3.2 2.1 + - - -
220A GLU* 3.5 11.9 + - - +
221A GLN* 3.4 19.9 + - - +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 3.6 14.6 - - + +
95A GLU* 3.8 18.7 + - + +
96A LEU* 3.4 44.4 - - + +
99A CYS* 4.8 5.8 - - - -
213A MET 3.9 0.8 + - - -
214A GLY* 3.0 21.3 + - - +
217A ASN* 1.3 75.6 - - - +
219A ASN* 1.3 58.4 + - - +
220A GLU 3.5 0.2 + - - -
221A GLN* 3.5 4.4 + - + +
222A LEU* 3.0 54.9 + - + +
207B GLN* 4.8 1.6 - - + +
211B PHE* 3.5 36.3 - - + -
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLY 3.1 6.9 + - - +
215A SER* 2.9 27.9 + - - +
216A GLU* 5.0 0.2 - - - -
217A ASN 3.2 0.6 - - - -
218A LEU* 1.3 75.1 - - - +
220A GLU* 1.3 60.2 + - - +
222A LEU* 3.5 8.3 + - - +
223A GLU* 2.9 31.8 + - - +
208B ILE* 3.6 32.9 - - - +
211B PHE* 5.1 6.0 - - + +
212B LYS* 3.9 25.9 + - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER 4.9 0.4 + - - -
216A GLU* 4.7 10.2 + - - +
217A ASN* 3.5 11.2 + - - +
218A LEU 3.4 0.6 - - - -
219A ASN* 1.3 78.5 - - - +
221A GLN* 1.3 60.9 + - + +
223A GLU* 3.1 9.7 + - - +
224A GLU* 3.0 37.0 + - - +
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Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 3.1 36.9 + - - +
92A VAL* 3.9 10.9 - - + +
95A GLU* 2.4 49.8 + - - +
217A ASN* 3.4 15.3 + - - +
218A LEU* 3.5 5.5 + - + +
219A ASN 3.4 0.2 - - - -
220A GLU* 1.3 75.1 - - + +
222A LEU* 1.3 60.3 + - - +
224A GLU* 4.1 11.5 - - - +
225A PHE* 2.9 32.6 + - - +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 4.3 24.5 - - + +
218A LEU* 3.0 45.8 + - + +
219A ASN* 3.7 2.5 - - - +
220A GLU 3.2 0.2 - - - -
221A GLN* 1.3 77.4 - - - +
223A GLU* 1.3 56.3 + - - +
225A PHE* 3.7 5.7 - - + +
226A LEU* 2.9 34.3 + - - +
203B PHE* 5.1 8.1 - - + -
204B ALA* 4.2 24.7 - - + +
207B GLN* 3.8 23.6 - - + -
208B ILE* 3.6 31.4 - - + +
211B PHE* 5.4 0.9 - - + -
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Residues in contact with GLU 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASN* 2.9 19.0 + - - +
220A GLU* 3.2 10.8 - - - +
222A LEU* 1.3 76.2 - - - +
224A GLU* 1.3 60.2 + - + +
226A LEU* 3.2 11.1 + - - +
227A ALA* 2.9 26.9 + - - +
208B ILE* 4.8 3.5 - - + +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 3.0 25.1 + - - +
221A GLN* 4.1 9.7 - - - +
223A GLU* 1.3 76.1 - - + +
225A PHE* 1.3 62.4 + - - +
227A ALA* 3.1 8.3 + - - +
228A ASN* 3.0 34.6 + - - +
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Residues in contact with PHE 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR 3.8 1.6 - - - -
88A GLN* 3.9 28.7 - - + +
89A PHE* 3.4 48.0 - + + -
92A VAL* 4.4 13.0 - - + -
221A GLN 2.9 19.6 + - - +
222A LEU* 3.7 5.8 - - + +
224A GLU* 1.3 76.7 - - - +
226A LEU* 1.3 66.1 + - - +
228A ASN* 3.2 3.3 + - - +
229A ILE* 2.9 53.4 + - + +
200B MET* 3.4 43.5 - - + -
201B ILE* 5.0 0.7 - - - -
204B ALA* 4.1 15.9 - - + -
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Residues in contact with LEU 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU 2.9 22.1 + - - +
223A GLU* 3.4 8.1 - - - +
225A PHE* 1.3 77.8 - - + +
227A ALA* 1.3 64.0 + - - +
229A ILE* 4.7 1.8 - - - +
230A GLY* 2.9 23.0 + - - -
201B ILE* 3.7 35.6 - - + +
204B ALA* 3.6 29.4 - - + -
205B HIS* 3.6 31.6 - - + +
208B ILE* 3.9 17.9 - - + -
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Residues in contact with ALA 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU 2.9 13.1 + - - +
224A GLU* 3.1 14.3 + - - +
226A LEU* 1.3 78.8 - - - +
228A ASN* 1.3 66.7 + - - +
230A GLY* 3.9 0.9 - - - -
231A THR* 3.2 25.2 + - - +
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Residues in contact with ASN 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 6.3 0.7 - - + -
88A GLN* 3.6 31.8 + - - +
224A GLU* 3.0 19.5 + - - +
225A PHE* 3.8 4.7 - - - +
227A ALA* 1.3 78.2 - - - +
229A ILE* 1.3 64.6 + - + +
231A THR* 2.6 28.9 + - - -
232A SER* 3.0 11.5 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 3.6 38.4 - - + -
88A GLN* 4.2 5.4 - - - +
225A PHE* 2.9 45.4 + - + +
226A LEU 4.2 2.0 - - - +
228A ASN* 1.3 75.5 - - + +
230A GLY* 1.3 57.3 + - - +
232A SER* 3.3 0.9 + - - -
233A VAL* 2.9 39.1 + - + +
197B MET* 3.6 24.0 - - + +
200B MET* 3.6 13.7 - - + -
201B ILE* 3.6 28.3 - - + -
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Residues in contact with GLY 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU 2.9 17.2 + - - -
227A ALA 3.5 1.8 + - - -
229A ILE* 1.3 77.5 - - - +
231A THR* 1.3 61.9 + - - +
233A VAL* 3.3 2.9 + - - +
234A GLN* 3.0 24.0 + - - +
201B ILE* 4.4 12.7 - - - +
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Residues in contact with THR 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ALA 3.2 17.9 - - - +
228A ASN* 2.6 20.5 + - - -
230A GLY* 1.3 74.3 - - - +
232A SER* 1.3 71.2 + - - +
234A GLN* 3.1 7.6 + - - +
235A ASN* 3.0 34.7 + - - +
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Residues in contact with SER 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 4.3 16.8 - - - +
85A THR* 4.4 5.4 - - - +
228A ASN* 3.0 14.1 + - - +
229A ILE 3.7 2.5 - - - -
230A GLY 3.3 0.2 - - - -
231A THR* 1.3 83.5 + - - +
233A VAL* 1.3 58.6 + - - +
235A ASN* 3.1 12.6 + - - +
236A VAL* 3.0 33.3 + - - +
197B MET* 3.4 27.9 - - - +
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Residues in contact with VAL 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 2.9 22.5 + - + +
230A GLY 3.6 4.9 - - - +
232A SER* 1.3 72.2 - - - +
234A GLN* 1.3 66.8 + - - +
236A VAL* 3.1 8.8 - - + +
237A ARG* 2.9 24.9 + - + +
194B MET* 4.0 17.9 - - + +
197B MET* 3.5 34.5 - - + -
198B GLU* 5.0 3.1 - - + +
201B ILE* 3.9 22.0 - - + -
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Residues in contact with GLN 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY 3.0 13.3 + - - +
231A THR* 3.1 13.0 + - - +
233A VAL* 1.3 78.4 - - - +
235A ASN* 1.3 64.9 + - - +
237A ARG* 3.3 6.2 + - - +
238A ARG* 3.0 25.2 + - - +
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Residues in contact with ASN 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A THR* 3.0 22.4 + - - +
232A SER* 3.1 10.5 + - - +
234A GLN* 1.3 78.1 - - - +
236A VAL* 1.3 65.5 + - + +
238A ARG* 3.2 7.0 + - - +
239A GLU* 3.0 27.0 + - - +
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Residues in contact with VAL 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 5.5 7.2 - - + -
232A SER 3.0 17.5 + - - +
233A VAL* 3.1 21.5 - - - +
235A ASN* 1.3 74.7 - - + +
237A ARG* 1.3 61.1 + - - +
239A GLU* 4.1 7.9 - - - +
240A MET* 2.9 28.7 + - - +
190B TYR* 4.4 7.8 - - + +
193B GLN* 3.8 40.8 - - + +
194B MET* 3.5 23.1 - - + -
197B MET* 4.7 10.3 - - - -
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Residues in contact with ARG 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 2.9 21.2 + - + +
234A GLN* 3.4 7.9 - - - +
236A VAL* 1.3 76.4 - - - +
238A ARG* 1.3 62.4 + - - +
240A MET* 3.1 5.4 + - - +
241A ASP* 2.7 37.0 + - - +
194B MET* 3.6 24.9 - - + -
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Residues in contact with ARG 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLN 3.0 13.8 + - - +
235A ASN* 3.6 9.0 - - - +
237A ARG* 1.3 75.8 - - - +
239A GLU* 1.3 63.8 + - - +
240A MET 3.2 0.2 + - - -
241A ASP* 3.2 4.9 + - - +
242A SER* 2.9 24.2 + - - -
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Residues in contact with GLU 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASN* 3.0 17.3 + - - +
236A VAL* 4.1 7.5 - - - +
238A ARG* 1.3 78.1 - - - +
240A MET* 1.3 57.1 + - - +
242A SER* 3.3 8.6 - - - -
243A ASP* 3.0 34.3 + - - +
190B TYR* 3.2 34.3 + - + +
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Residues in contact with MET 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL 2.9 19.6 + - - +
237A ARG 3.6 3.6 - - - +
239A GLU* 1.3 77.3 - - - +
241A ASP* 1.3 66.8 + - - +
244A ILE* 3.0 47.5 + - + +
187B ALA* 4.7 1.8 - - + +
190B TYR* 3.6 39.7 - - + -
191B ARG* 3.6 45.8 - - + +
194B MET* 4.3 22.9 - - + -
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Residues in contact with ASP 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ARG* 2.7 31.2 + - - +
238A ARG* 4.1 4.5 + - - +
240A MET* 1.3 84.8 - - - +
242A SER* 1.3 60.3 + - - +
244A ILE* 4.3 5.8 - - - +
245A GLU* 2.9 29.7 + - - +
194B MET* 5.9 0.2 - - - +
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Residues in contact with SER 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ARG 2.9 13.5 + - - -
239A GLU* 3.3 14.2 - - - +
241A ASP* 1.3 76.9 - - - +
243A ASP* 1.3 71.3 + - - +
245A GLU* 3.0 25.2 + - - +
246A THR* 3.1 12.6 + - - +
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Residues in contact with ASP 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLU* 3.0 19.0 + - - +
242A SER* 1.3 90.0 + - - +
244A ILE* 1.3 61.7 + - - +
246A THR* 4.5 9.7 - - - +
247A MET* 3.0 47.5 + - + +
190B TYR* 3.2 31.1 + - + -
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Residues in contact with ILE 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A MET* 3.0 42.5 + - + +
241A ASP* 4.3 5.2 - - - +
243A ASP* 1.3 75.2 - - - +
245A GLU* 1.3 66.3 + - - +
247A MET* 3.9 15.9 - - + +
248A GLN* 3.0 27.4 + - + +
183B CYS* 4.8 9.6 - - - -
187B ALA* 3.5 31.9 - - + -
190B TYR* 6.1 1.3 - - + -
191B ARG* 5.6 7.0 - - - +
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Residues in contact with GLU 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ASP 2.9 22.4 + - - +
242A SER* 3.0 13.0 + - - +
244A ILE* 1.3 80.6 - - - +
246A THR* 1.3 58.7 + - - +
248A GLN* 3.6 12.5 + - - +
249A GLN* 4.1 8.5 + - - +
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Residues in contact with THR 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A SER* 3.1 12.0 + - - +
243A ASP* 4.5 11.2 - - - +
245A GLU* 1.3 75.7 - - - +
247A MET* 1.3 58.5 + - + +
248A GLN 3.2 1.6 - - - -
249A GLN* 4.8 2.0 - - - +
250A THR* 2.1 48.5 + - - +
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Residues in contact with MET 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP* 3.0 39.7 + - + +
244A ILE* 3.9 24.9 - - + +
246A THR* 1.3 79.4 - - + +
248A GLN* 1.3 64.2 + - - +
250A THR* 3.7 6.4 - - - +
251A ILE* 2.9 30.8 + - - +
9B LEU* 3.9 13.2 - - + +
183B CYS* 3.8 26.7 - - - +
186B ASN* 3.6 44.0 - - + +
187B ALA* 4.2 3.1 - - - +
190B TYR* 5.7 3.1 - - + -
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Residues in contact with GLN 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ILE* 3.0 21.3 + - + +
245A GLU* 3.7 7.4 - - - +
246A THR 3.2 0.6 - - - -
247A MET* 1.3 77.1 - - - +
249A GLN* 1.3 66.6 + - + +
251A ILE* 3.0 28.1 - - - +
252A GLU* 3.0 6.2 + - - +
183B CYS* 4.9 3.3 - - - -
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Residues in contact with GLN 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A GLU 4.1 8.1 + - - +
246A THR* 3.9 3.8 + - - +
248A GLN* 1.3 83.4 + - + +
250A THR* 1.3 60.3 + - - +
252A GLU* 3.2 26.6 - - + +
253A ASP* 2.9 40.2 + - - +
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Residues in contact with THR 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A THR* 2.1 40.8 + - - +
247A MET* 3.7 8.5 - - - -
249A GLN* 1.3 76.5 - - - +
251A ILE* 1.3 58.4 + - - +
253A ASP* 3.5 5.7 + - - +
254A LEU* 2.9 49.5 + - + +
9B LEU* 4.4 11.7 - - + -
10B GLU* 5.9 2.2 - - + +
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Residues in contact with ILE 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A MET 2.9 17.2 + - - +
248A GLN* 3.0 15.9 - - - +
250A THR* 1.3 76.8 - - - +
252A GLU* 1.3 55.1 + - - +
254A LEU* 3.2 6.8 + - - +
255A GLU* 2.9 59.5 + - + +
9B LEU* 3.6 15.3 - - + -
179B LEU* 3.7 24.2 - - + +
180B GLN* 3.8 20.4 - - - +
183B CYS* 3.6 33.7 - - + -
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Residues in contact with GLU 252 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A GLN 3.0 9.5 + - - +
249A GLN* 3.2 40.9 - - + +
251A ILE* 1.3 78.8 - - - +
253A ASP* 1.3 60.1 + - - +
255A GLU* 3.4 9.5 + - - +
256A VAL* 2.9 33.6 + - + +
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Residues in contact with ASP 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A GLN* 2.9 21.6 + - - +
250A THR* 4.1 5.0 - - - +
252A GLU* 1.3 78.4 - - - +
254A LEU* 1.3 61.5 + - + +
256A VAL* 3.3 10.0 + - - +
257A ALA* 2.9 32.2 + - - +
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Residues in contact with LEU 254 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A THR* 2.9 29.9 + - + +
251A ILE 3.6 4.0 - - - +
253A ASP* 1.3 77.3 - - - +
255A GLU* 1.3 57.6 + - - +
257A ALA* 4.9 3.8 - - + -
258A SER* 2.3 44.7 + - - +
9B LEU* 3.4 44.9 - - + +
10B GLU* 3.6 23.3 - - + +
175B HIS* 4.7 6.1 - - + +
179B LEU* 4.0 15.3 - - + -
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Residues in contact with GLU 255 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 2.9 41.1 + - - +
252A GLU* 3.7 7.8 - - - +
254A LEU* 1.3 75.3 - - - +
256A VAL* 1.3 64.8 + - + +
257A ALA 3.6 0.2 + - - -
258A SER* 3.9 7.5 + - - -
259A ASP* 4.1 12.8 + - - +
262A TYR* 4.7 6.7 + - - -
176B LEU* 3.5 35.3 - - + +
179B LEU* 3.8 13.2 - - + +
180B GLN* 4.1 10.0 + - - -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A GLU* 2.9 23.7 + - + +
253A ASP* 3.5 11.0 - - + +
254A LEU 3.3 0.2 - - - -
255A GLU* 1.3 79.9 - - + +
257A ALA* 1.3 63.9 + - + +
259A ASP* 3.9 13.0 + - - +
260A PRO* 4.6 2.1 - - - +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ASP 2.9 16.9 + - - +
254A LEU* 4.4 5.4 - - + +
256A VAL* 1.3 77.3 - - + +
258A SER* 1.3 59.1 + - - +
259A ASP 3.2 5.2 - - - -
260A PRO* 3.2 20.3 - - - +
261A LEU* 3.2 11.5 - - - +
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 2.3 32.0 + - - +
255A GLU 3.9 0.9 + - - -
256A VAL 3.4 0.8 - - - -
257A ALA* 1.3 76.1 - - - +
259A ASP* 1.3 58.2 + - - +
260A PRO* 3.4 1.3 - - - -
261A LEU* 3.1 27.5 + - - +
262A TYR* 3.2 38.2 + - - -
13B LEU* 4.1 11.6 - - - +
175B HIS* 3.1 19.4 - - - -
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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
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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