Contacts of the helix formed by residues 223 - 257 (chain A) in PDB entry 6KJV
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 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 5.7 6.0 - - - +
219A SER 3.5 7.8 + - - -
220A TYR* 2.9 30.3 + - - -
221A GLN 4.2 0.7 - - - +
222A ASP* 1.3 83.0 - - - +
224A LEU* 1.3 61.5 + - - +
225A ALA* 4.1 8.1 - - - +
226A CYS* 3.5 18.5 + - - +
227A ARG* 3.3 18.3 + - - +
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Residues in contact with LEU 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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223A SER* 1.3 71.0 - - - +
225A ALA* 1.3 66.0 + - - +
226A CYS 3.2 2.2 - - - -
227A ARG* 3.1 18.0 + - + +
228A LEU* 3.0 48.4 + - + +
289A TYR* 4.3 28.7 - - + +
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Residues in contact with ALA 225 (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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196A PHE* 5.7 6.3 - - + -
220A TYR* 4.7 7.0 - - + -
223A SER* 3.5 8.8 + - - +
224A LEU* 1.3 79.2 - - - +
226A CYS* 1.3 55.9 + - - +
228A LEU* 3.2 11.5 + - - +
229A VAL* 2.9 38.4 + - + +
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Residues in contact with CYS 226 (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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197A LYS* 5.8 5.4 - - - -
220A TYR* 3.3 56.8 - - + +
223A SER* 3.5 5.7 + - - +
224A LEU 3.2 0.6 - - - -
225A ALA* 1.3 79.8 - - - +
227A ARG* 1.3 56.1 + - - +
229A VAL* 3.3 2.6 + - - +
230A PHE* 2.9 28.5 + - - +
296A CYS* 2.0 48.2 - - - -
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Residues in contact with ARG 227 (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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221A GLN 3.5 12.0 + - - -
222A ASP* 3.5 22.0 + - - +
223A SER 3.3 17.3 + - - +
224A LEU* 3.1 21.5 + - + +
226A CYS* 1.3 74.7 - - - +
228A LEU* 1.3 58.9 + - + +
230A PHE* 3.4 5.1 + - - +
231A LEU* 2.9 28.8 + - - +
289A TYR* 5.3 3.4 - - - -
293A ASP* 2.8 41.2 + - - -
294A GLU* 4.0 1.0 - - - +
295A GLY 3.8 10.9 - - - +
296A CYS* 2.9 39.2 - - - +
297A TRP* 3.6 42.4 - - + +
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Residues in contact with LEU 228 (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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224A LEU* 3.0 39.2 + - + +
225A ALA* 3.6 11.7 - - - +
226A CYS 3.2 0.2 - - - -
227A ARG* 1.3 76.4 - - + +
229A VAL* 1.3 61.5 + - + +
231A LEU* 3.2 16.6 + - + +
232A LEU* 2.9 30.0 + - - +
297A TRP* 6.1 2.2 - - + -
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Residues in contact with VAL 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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193A CYS* 4.0 33.2 - - + +
196A PHE* 3.6 36.6 - - + -
197A LYS* 4.6 8.1 - - + +
220A TYR* 4.2 12.3 - - - +
225A ALA* 2.9 22.7 + - + +
226A CYS 3.3 3.8 + - - +
228A LEU* 1.3 76.0 - - + +
230A PHE* 1.3 57.0 + - - +
232A LEU* 3.4 8.0 + - + +
233A MET* 2.9 27.1 + - + +
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Residues in contact with PHE 230 (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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226A CYS* 2.9 18.1 + - - +
227A ARG* 3.7 5.2 - - - +
229A VAL* 1.3 74.7 - - - +
231A LEU* 1.3 58.7 + - - +
233A MET* 3.3 12.6 + - + +
234A GLN* 2.9 42.5 + - + +
284A TRP* 3.3 39.3 - + - -
296A CYS* 3.3 27.8 - - + +
297A TRP* 4.0 17.5 - + + -
298A THR* 5.7 2.5 - - - -
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Residues in contact with LEU 231 (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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227A ARG 2.9 17.6 + - - +
228A LEU* 3.2 18.8 + - + +
230A PHE* 1.3 77.6 - - - +
232A LEU* 1.3 56.5 + - - +
234A GLN* 3.3 5.5 + - - +
235A TYR* 3.0 27.7 + - - +
281A VAL* 3.6 30.1 - - + +
282A VAL* 5.6 8.5 - - + -
284A TRP* 3.5 29.8 - - + -
285A GLY* 4.2 12.3 - - - -
297A TRP* 4.4 8.7 - - + -
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Residues in contact with LEU 232 (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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189A LEU* 5.3 12.3 - - + -
193A CYS* 3.8 19.7 - - - -
228A LEU 2.9 16.7 + - - +
229A VAL* 3.7 7.6 - - + +
231A LEU* 1.3 75.0 - - - +
233A MET* 1.3 57.2 + - - +
235A TYR* 3.2 21.6 + - + +
236A CYS* 2.9 33.9 + - - -
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Residues in contact with MET 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 4.9 5.2 - - - +
152A TYR* 4.4 3.8 - - - +
190A ARG* 3.6 41.3 - - + +
193A CYS* 3.8 23.7 - - + -
194A VAL* 4.1 25.1 - - + -
197A LYS* 6.5 0.4 - - - -
229A VAL* 2.9 17.2 + - + +
230A PHE* 3.6 14.8 - - + +
232A LEU* 1.3 73.7 - - - +
234A GLN* 1.3 63.8 + - - +
236A CYS* 3.1 6.4 + - - +
237A VAL* 2.9 29.4 + - + +
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Residues in contact with GLN 234 (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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230A PHE* 2.9 33.2 + - + +
231A LEU* 3.5 11.0 - - - +
233A MET* 1.3 76.2 - - - +
235A TYR* 1.3 64.3 + - - +
237A VAL* 3.2 19.7 + - - +
238A ALA* 3.1 22.9 + - - +
281A VAL* 4.4 5.3 - - + +
284A TRP* 4.3 18.8 - - + -
309A ILE* 3.6 41.6 - - + +
310A ARG* 4.7 12.7 + - - +
313A ILE* 4.7 6.1 - - - +
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Residues in contact with TYR 235 (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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189A LEU* 5.8 3.1 - - + -
231A LEU 3.0 13.5 + - - +
232A LEU* 3.4 24.7 - - + +
234A GLN* 1.3 76.2 - - - +
236A CYS* 1.3 62.1 + - - +
238A ALA* 3.3 3.6 + - - +
239A ALA* 2.9 27.2 + - - +
274A TRP* 2.4 69.7 + + - +
277A PRO* 3.8 14.6 - - + -
278A LEU* 3.7 38.2 - - + +
281A VAL* 4.2 16.7 - - + +
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Residues in contact with CYS 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A SER* 4.1 6.9 - - - +
189A LEU* 3.4 44.6 - - - -
190A ARG* 3.7 24.0 - - + +
193A CYS* 4.5 3.8 - - - -
232A LEU* 2.9 24.3 + - - -
233A MET 3.1 8.0 + - - +
235A TYR* 1.3 80.3 - - - +
237A VAL* 1.3 57.4 + - - +
239A ALA* 3.2 8.3 + - - +
240A ASN* 2.9 36.0 + - - +
274A TRP* 5.8 1.1 - - - -
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Residues in contact with VAL 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ARG* 4.1 31.6 - - - +
233A MET* 2.9 29.0 + - + +
234A GLN* 3.2 20.6 + - - +
236A CYS* 1.3 74.3 - - - +
238A ALA* 1.3 66.1 + - - +
240A ASN* 3.1 15.5 + - - +
241A TYR* 3.0 44.1 + - + -
310A ARG* 5.0 4.5 - - - +
313A ILE* 4.4 9.0 - - + -
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Residues in contact with ALA 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLN* 3.1 12.6 + - - +
235A TYR 3.8 4.0 - - - +
237A VAL* 1.3 76.6 - - - +
239A ALA* 1.3 57.8 + - - +
241A TYR* 3.3 5.8 + - - +
242A TYR* 3.0 36.4 + - + +
277A PRO* 3.6 24.2 - - + -
280A PHE* 3.6 28.5 - - + -
281A VAL* 4.3 3.8 - - + -
309A ILE* 5.9 0.4 - - + -
313A ILE* 4.8 8.5 - - + +
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Residues in contact with ALA 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A SER* 3.9 8.3 - - - -
235A TYR* 2.9 16.5 + - + +
236A CYS* 3.4 10.8 - - - +
237A VAL 3.1 0.2 - - - -
238A ALA* 1.3 73.7 - - - +
240A ASN* 1.3 66.3 + - - +
243A TRP* 2.9 31.2 + - + +
273A GLY 3.6 20.4 - - - +
274A TRP* 3.9 27.6 - - + -
277A PRO* 3.9 2.8 - - + +
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Residues in contact with ASN 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 3.9 7.6 - - - +
186A SER* 2.7 42.7 + - - -
187A PHE* 3.6 24.7 + - + -
190A ARG* 3.2 42.9 - - - +
236A CYS 2.9 18.3 + - - +
237A VAL* 3.3 9.7 - - - +
239A ALA* 1.3 75.4 - - - +
241A TYR* 1.3 69.1 + - + +
243A TRP 3.9 0.3 - - - -
244A LEU* 2.9 24.8 + - - +
360A LEU* 5.2 6.5 - - + +
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Residues in contact with TYR 241 (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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190A ARG* 5.5 5.2 + - - -
237A VAL* 3.0 46.5 + - + -
238A ALA* 3.9 5.6 - - - +
239A ALA 3.2 0.2 - - - -
240A ASN* 1.3 86.5 - - + +
242A TYR* 1.3 61.5 + - + +
244A LEU* 3.3 12.0 + - + +
245A LEU* 2.9 23.9 + - - +
310A ARG* 5.9 0.9 - - - -
313A ILE* 4.1 24.7 - - + -
316A ALA* 4.5 14.8 - - + +
317A CYS* 3.8 26.5 - - - -
320A ASN* 3.8 6.0 + - - +
360A LEU* 3.2 39.2 + - + -
361A CYS* 3.9 5.8 - - - -
364A GLU* 4.9 9.6 + - + +
394A GLN* 5.0 7.4 + - - -
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Residues in contact with TYR 242 (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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238A ALA* 3.0 27.7 + - + +
241A TYR* 1.3 78.1 - - + +
243A TRP* 1.3 60.7 + - - +
245A LEU* 3.1 19.8 + - + +
246A VAL* 3.0 30.7 + - - +
272A ILE* 3.6 39.2 - - + +
273A GLY* 3.9 8.3 - - - +
276A VAL* 3.9 20.3 - - + +
277A PRO* 4.2 8.5 - - + -
280A PHE* 3.8 23.9 - + - -
312A PRO* 3.3 29.7 + - - +
313A ILE* 5.1 2.5 - - + -
315A PHE* 4.2 13.9 - + - -
316A ALA* 3.9 21.9 - - + +
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Residues in contact with TRP 243 (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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179A ILE* 4.2 21.6 - - + +
182A ASN* 3.3 37.9 - - + -
183A LEU* 3.8 24.4 - - + +
186A SER* 4.9 0.9 - - - +
239A ALA* 2.9 27.1 + - + +
242A TYR* 1.3 73.9 - - - +
244A LEU* 1.3 59.9 + - - +
246A VAL* 3.2 34.1 - - + +
247A GLU* 2.9 28.6 + - - +
266A PHE* 5.4 2.2 - + - -
269A TYR* 4.0 8.7 - - + -
270A VAL* 3.6 33.2 - - + -
273A GLY* 3.3 26.1 - - - -
274A TRP* 3.1 53.3 - + - +
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Residues in contact with LEU 244 (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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183A LEU* 3.9 11.1 - - + +
240A ASN 2.9 18.9 + - - +
241A TYR* 3.4 9.6 - - + +
243A TRP* 1.3 75.0 - - - +
245A LEU* 1.3 64.3 + - - +
247A GLU* 3.2 17.3 + - + +
248A GLY* 3.0 18.7 + - - -
320A ASN* 3.7 20.1 - - - +
353A THR* 5.1 2.8 - - + +
356A LEU* 4.3 26.0 - - + +
357A ILE* 4.4 24.5 - - + +
360A LEU* 4.0 36.3 - - + -
361A CYS* 4.8 7.4 - - - -
402A TYR* 5.1 0.9 - - - +
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Residues in contact with LEU 245 (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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241A TYR 2.9 14.4 + - - +
242A TYR* 3.1 36.1 + - + +
244A LEU* 1.3 76.4 - - - +
246A VAL* 1.3 58.0 + - + +
248A GLY* 3.2 3.1 + - - -
249A VAL* 2.9 44.8 + - + +
272A ILE* 4.7 11.2 - - + -
315A PHE* 5.5 5.6 - - + -
316A ALA* 4.8 4.5 - - + +
319A VAL* 3.6 33.9 - - + -
320A ASN* 3.4 21.1 - - - +
323A ILE* 5.0 6.1 - - + -
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Residues in contact with VAL 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ILE* 4.1 8.0 - - + +
242A TYR 3.0 13.9 + - - +
243A TRP* 3.2 42.0 - - + +
245A LEU* 1.3 73.8 - - + +
247A GLU* 1.3 63.7 + - - +
249A VAL* 3.8 8.2 - - + +
250A TYR* 2.9 31.9 + - - +
269A TYR* 3.9 32.9 - - + +
272A ILE* 3.7 32.8 - - + -
273A GLY 4.4 1.1 - - - +
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Residues in contact with GLU 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG 4.9 0.2 - - - +
179A ILE* 3.3 22.1 - - - +
180A HIS* 3.1 38.7 + - - -
183A LEU* 4.3 7.4 - - + +
243A TRP 2.9 15.2 + - - +
244A LEU* 3.3 18.4 - - + +
246A VAL* 1.3 78.5 - - - +
248A GLY* 1.3 55.7 + - - +
250A TYR* 3.7 11.9 - - - +
251A LEU* 3.0 28.1 + - - +
349A LEU* 4.4 7.6 - - - +
353A THR* 4.0 8.9 + - + +
402A TYR* 3.1 34.3 + - + +
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Residues in contact with GLY 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LEU 3.0 13.4 + - - -
245A LEU 3.2 3.6 + - - -
247A GLU* 1.3 74.9 - - - +
249A VAL* 1.3 58.8 + - - +
251A LEU* 3.2 8.6 + - - +
252A TYR* 2.9 28.1 + - - +
320A ASN* 5.0 4.0 - - - -
323A ILE* 3.8 23.0 - - - +
353A THR* 4.5 12.0 - - - +
357A ILE* 5.2 2.9 - - - -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU* 2.9 39.1 + - + +
246A VAL* 3.8 8.7 - - + +
248A GLY* 1.3 74.6 - - - +
250A TYR* 1.3 63.1 + - - +
252A TYR* 3.2 8.8 + - + +
253A THR* 3.0 30.8 + - + +
269A TYR* 4.4 20.2 - - + +
272A ILE* 6.3 2.9 - - + -
323A ILE* 5.3 10.3 - - + -
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Residues in contact with TYR 250 (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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175A THR* 3.3 26.5 + - - -
176A ARG* 3.6 30.4 - - + +
179A ILE* 3.7 26.5 - - + -
246A VAL 2.9 18.3 + - - +
247A GLU* 3.7 11.7 - - - +
249A VAL* 1.3 76.8 - - - +
251A LEU* 1.3 58.5 + - - +
253A THR* 3.0 11.2 + - - -
254A LEU* 2.9 56.0 + - + +
269A TYR* 4.1 19.7 + + + +
349A LEU* 4.1 20.6 - - + -
1156A THR* 6.0 2.3 - - - +
1158A ASP* 4.7 3.1 + - - -
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Residues in contact with LEU 251 (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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247A GLU 3.0 15.7 + - - +
248A GLY* 3.2 9.6 + - - +
250A TYR* 1.3 80.7 - - - +
252A TYR* 1.3 63.0 + - - +
254A LEU* 3.2 10.6 + - + +
255A LEU* 3.0 35.6 + - + +
323A ILE* 6.0 0.2 - - + -
327A VAL* 4.0 24.2 - - + -
346A ALA 4.0 10.5 - - - +
349A LEU* 4.0 18.6 - - + -
350A ALA* 3.8 39.5 - - + +
353A THR* 4.0 22.2 - - + +
354A LEU* 5.2 4.0 - - + -
357A ILE* 6.2 0.4 - - + -
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Residues in contact with TYR 252 (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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248A GLY 2.9 13.3 + - - +
249A VAL* 3.2 11.9 + - + +
251A LEU* 1.3 76.3 - - - +
253A THR* 1.3 74.3 + - + +
255A LEU* 3.0 13.7 + - + +
256A ALA* 3.0 28.5 + - + +
323A ILE* 4.8 14.6 - - + -
326A ARG* 3.4 36.8 - - + +
327A VAL* 4.5 16.8 - - + +
330A ILE* 4.9 11.5 - - + +
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Residues in contact with THR 253 (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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249A VAL* 3.0 21.8 + - + +
250A TYR* 3.0 21.0 + - - -
252A TYR* 1.3 85.6 - - + +
254A LEU* 1.3 59.8 + - - +
256A ALA* 3.1 17.9 + - + +
257A PHE* 3.1 17.2 + - - +
269A TYR* 4.2 9.2 + - - +
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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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176A ARG* 5.3 2.0 - - - -
250A TYR* 2.9 44.1 + - + +
251A LEU* 3.2 8.3 + - + +
253A THR* 1.3 78.6 + - - +
255A LEU* 1.3 60.5 + - + +
256A ALA 3.5 0.2 + - - -
257A PHE* 3.7 15.4 + - - +
345A ILE* 4.7 18.4 - - + -
346A ALA* 4.5 24.1 - - + +
349A LEU* 3.8 28.5 - - + -
1156A THR* 6.5 0.4 - - - -
1157A TRP* 3.8 33.6 + - + +
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Residues in contact with LEU 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.0 27.0 + - + +
252A TYR* 3.0 8.9 + - + +
254A LEU* 1.3 76.5 - - - +
256A ALA* 1.3 61.0 + - - +
257A PHE 3.4 4.4 + - - +
327A VAL* 3.9 34.5 - - + -
330A ILE* 4.0 24.4 - - + +
331A VAL* 4.2 18.8 - - + -
334A LYS* 4.3 23.3 + - + +
340A MET* 3.7 29.4 - - + -
346A ALA* 3.8 20.0 - - + +
1001A ASN* 5.7 1.0 + - - -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.0 24.2 + - + +
253A THR* 3.1 12.9 + - + +
255A LEU* 1.3 77.7 - - - +
257A PHE* 1.3 60.9 + - - +
1001A ASN* 4.0 8.3 + - - -
1004A GLU* 4.1 12.5 - - - +
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Residues in contact with PHE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR 3.1 13.6 + - - +
254A LEU* 3.7 13.0 + - - +
255A LEU 3.4 4.4 - - - +
256A ALA* 1.3 77.4 - - - +
334A LYS* 5.7 1.9 + - - -
1001A ASN* 1.3 84.2 + - - +
1004A GLU* 3.7 20.6 - - + -
1005A MET* 3.7 22.2 - - + -
1008A ILE* 4.9 7.4 - - + -
1157A TRP* 3.5 55.9 + + + -
1160A TYR* 3.9 31.4 - + + -
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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
------------------------------------------------------------
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