Contacts of the helix formed by residues 266 - 299 (chain A) in PDB entry 3D4S
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 LEU 266 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.6 8.1 - - + +
230A LEU* 6.2 0.7 - - + -
264A PHE 3.7 0.2 - - - -
265A CYS* 1.3 79.8 - - - +
267A LYS* 1.3 69.0 + - + +
268A GLU* 3.3 22.0 - - - +
269A HIS* 3.2 36.7 + - + +
270A LYS* 3.2 13.3 + - - +
1005A GLU* 3.3 42.4 - - + +
1008A ARG* 3.8 30.1 - - - +
1009A ILE* 3.4 27.1 - - + +
1161A TYR 4.9 0.2 + - - -
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A CYS 3.8 1.2 + - - -
266A LEU* 1.3 78.5 - - + +
268A GLU* 1.3 74.1 + - + +
270A LYS* 3.4 13.4 + - - +
271A ALA* 3.2 19.6 + - - +
330A PRO* 3.7 33.1 - - + +
331A ASP* 3.7 23.2 + - - -
1008A ARG* 6.4 1.8 - - - +
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.5 51.1 - - + -
266A LEU* 3.3 25.1 - - - +
267A LYS* 1.3 87.8 + - + +
269A HIS* 1.3 57.4 + - + +
271A ALA* 3.4 10.1 - - - +
272A LEU* 3.0 31.2 + - - +
1060A LYS* 5.5 4.7 + - - -
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 2.6 34.0 + + - -
226A ALA* 3.3 49.3 - - + +
230A LEU* 4.3 13.9 - - + +
264A PHE* 3.4 39.9 + - + -
266A LEU* 3.2 33.7 + - + +
268A GLU* 1.3 74.0 - - - +
270A LYS* 1.3 60.9 + - - +
271A ALA 3.2 0.4 - - - -
272A LEU* 3.3 9.6 + - - +
273A LYS 2.9 22.0 + - - -
1005A GLU* 3.6 8.6 + - - -
1161A TYR 5.3 1.5 + - - -
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Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 2.9 33.6 + - + +
265A CYS* 3.6 19.7 - - - +
266A LEU 3.2 10.3 + - - +
267A LYS* 3.7 10.1 - - - +
268A GLU 3.3 0.2 - - - -
269A HIS* 1.3 75.6 - - - +
271A ALA* 1.3 54.0 + - - +
273A LYS* 3.4 7.9 + - - +
274A THR* 2.8 38.2 + - - +
328A ARG* 4.0 13.7 + - - +
330A PRO* 6.3 4.7 - - + -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS 3.2 13.7 + - - +
268A GLU* 3.4 14.4 - - - +
270A LYS* 1.3 76.5 - - - +
272A LEU* 1.3 62.4 + - - +
274A THR* 3.5 8.3 + - - -
275A LEU* 3.3 29.4 + - + +
329A SER* 5.9 7.4 - - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 3.7 31.4 - - + +
135A ILE* 4.2 19.3 - - + -
141A TYR* 4.2 18.2 - - + -
219A TYR* 2.7 36.1 + - + +
222A VAL* 3.9 23.8 - - + -
223A PHE* 4.1 9.6 - - + -
226A ALA* 4.3 12.3 - - + -
264A PHE* 5.7 1.1 - - + -
268A GLU 3.0 19.0 + - - +
269A HIS* 3.6 11.4 - - - +
270A LYS 3.3 0.4 - - - -
271A ALA* 1.3 75.0 - - - +
273A LYS* 1.3 58.7 + - - +
275A LEU* 3.3 3.0 + - + -
276A GLY 3.0 16.1 + - - -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 4.0 12.2 - - + -
264A PHE* 3.6 45.2 - - + +
269A HIS 2.9 18.1 + - - +
270A LYS* 3.6 6.7 - - - +
271A ALA 3.4 0.2 - - - -
272A LEU* 1.3 72.5 - - - +
274A THR* 1.3 60.9 + - - +
276A GLY* 3.1 2.4 + - - -
277A ILE* 2.9 42.2 + - + +
328A ARG* 3.5 28.0 - - - +
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS 2.8 22.7 + - - -
271A ALA* 3.6 8.9 - - - -
272A LEU 3.3 0.2 - - - -
273A LYS* 1.3 76.1 - - - +
275A LEU* 1.3 62.9 + - + +
277A ILE* 3.1 6.0 + - - +
278A ILE* 3.0 22.6 + - + +
325A ILE* 3.6 31.6 - - + +
326A TYR* 4.4 17.3 - - + -
328A ARG* 3.1 30.3 + - + +
329A SER* 4.5 10.8 + - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 3.8 32.5 - - + -
72A ILE* 4.0 21.3 - - + -
124A LEU* 5.4 0.2 - - - +
127A ILE* 4.1 17.7 - - + -
131A ARG* 3.9 24.0 - - + -
219A TYR* 3.4 24.5 - - + +
271A ALA* 3.3 17.1 + - + +
272A LEU* 3.6 3.1 - - + +
273A LYS 3.3 0.2 - - - -
274A THR* 1.3 79.3 - - + +
276A GLY* 1.3 61.1 + - - +
278A ILE* 3.4 13.8 + - + +
279A MET* 3.2 29.0 + - + +
326A TYR* 5.3 2.2 - - + +
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 3.7 23.0 - - - -
223A PHE* 3.9 11.4 - - - -
272A LEU 3.0 10.8 + - - -
273A LYS 3.1 6.0 + - - -
275A LEU* 1.3 75.5 - - - +
277A ILE* 1.3 58.4 + - - +
279A MET* 3.5 3.7 + - - +
280A GLY* 2.8 26.7 + - - -
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LYS* 2.9 27.2 + - + +
274A THR 3.1 7.6 + - - +
276A GLY* 1.3 75.0 - - - +
278A ILE* 1.3 57.0 + - - +
280A GLY* 4.4 1.1 - - - +
281A THR* 2.7 48.4 + - - +
325A ILE* 3.7 22.0 - - + -
328A ARG* 3.8 41.1 - - - +
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.8 26.0 - - + -
124A LEU* 3.8 11.2 - - + -
274A THR 3.0 18.6 + - - +
275A LEU* 3.6 15.7 - - + +
277A ILE* 1.3 76.2 - - - +
279A MET* 1.3 61.1 + - - +
281A THR* 4.0 1.9 - - - -
282A PHE* 3.2 22.9 + - - +
318A ASN* 5.3 0.5 - - - +
322A ASN* 3.2 33.7 - - - +
325A ILE* 3.5 35.0 - - + -
326A TYR* 3.7 29.8 - - + +
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Residues in contact with MET 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.4 42.4 - - + +
127A ILE* 3.8 17.0 - - + -
128A ALA* 3.6 16.4 - - + +
215A MET* 3.7 34.4 - - + +
219A TYR* 3.6 40.8 - - + -
275A LEU 3.2 17.9 + - - +
276A GLY* 3.7 3.4 - - - +
278A ILE* 1.3 75.4 - - - +
280A GLY* 1.3 59.6 + - - +
282A PHE* 3.4 4.2 + - - +
283A THR* 2.9 32.0 + - - -
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY 2.8 21.5 + - - -
277A ILE* 3.8 1.3 - - - -
279A MET* 1.3 71.3 - - - +
281A THR* 1.3 56.9 + - - +
283A THR* 3.3 7.7 + - - -
284A LEU* 3.0 38.0 + - - +
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Residues in contact with THR 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 2.7 30.7 + - - +
278A ILE 4.0 3.1 - - - -
280A GLY* 1.3 73.0 - - - +
282A PHE* 1.3 61.0 + - - +
284A LEU* 3.3 8.4 + - - +
285A CYS* 2.9 41.3 + - - -
318A ASN* 3.3 17.7 - - - +
321A PHE* 4.3 22.4 - - + -
322A ASN* 5.8 0.7 - - - -
325A ILE* 3.7 15.7 - - + +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 5.6 2.0 - - + -
79A ASP* 6.0 0.4 - - - -
117A VAL* 3.8 25.6 - - + -
120A SER* 3.6 22.0 - - - -
121A ILE* 3.6 38.4 - - + -
124A LEU* 3.7 17.0 - - + -
208A PHE* 3.7 17.7 - + - -
212A LEU* 5.6 0.2 - - + -
215A MET* 5.5 0.4 - - + -
278A ILE 3.2 12.6 + - - +
279A MET 3.5 9.2 - - - +
281A THR* 1.3 78.1 - - - +
283A THR* 1.3 59.6 + - - +
286A TRP* 2.9 51.3 + + - +
318A ASN* 3.2 27.1 + - - +
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Residues in contact with THR 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PHE* 5.3 1.3 - - - -
212A LEU* 3.5 30.7 - - + +
215A MET* 3.7 7.1 - - - +
216A VAL* 4.6 9.2 - - + +
279A MET 2.9 15.6 + - - -
280A GLY* 3.5 11.2 - - - -
281A THR 3.2 0.2 - - - -
282A PHE* 1.3 78.3 - - - +
284A LEU* 1.3 61.2 + - + +
287A LEU* 2.8 59.0 + - + +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY 3.0 25.0 + - - +
281A THR* 3.9 7.2 - - - +
283A THR* 1.3 79.3 - - + +
285A CYS* 1.3 59.6 + - - +
287A LEU* 5.2 0.7 - - - -
288A PRO* 3.4 22.0 - - - +
314A ILE* 4.9 3.8 - - - +
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR* 2.9 33.3 + - - +
282A PHE 4.1 0.7 - - - +
284A LEU* 1.3 81.4 - - - +
286A TRP* 1.3 59.6 + - + +
288A PRO* 4.1 5.2 - - - +
289A PHE* 5.0 0.5 + - - +
311A LEU 4.0 6.2 - - - +
314A ILE* 3.4 37.2 - - - +
315A GLY* 3.5 17.9 + - - -
317A VAL* 5.3 0.2 - - - -
318A ASN* 3.7 30.7 - - + -
321A PHE* 4.4 11.2 - - - -
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Residues in contact with TRP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 4.1 11.2 - - + -
117A VAL* 3.4 25.8 - - + +
208A PHE* 3.7 19.1 - - + -
282A PHE* 2.9 57.1 + + - +
285A CYS* 1.3 77.5 - - - +
287A LEU* 1.3 64.0 + - - +
288A PRO* 3.4 3.1 - - - -
289A PHE* 3.2 34.8 + + + +
290A PHE* 3.2 34.5 + + + -
312A ASN* 3.3 28.5 - - - -
315A GLY* 3.4 36.4 + - - -
316A TYR 4.0 0.7 - - - -
318A ASN* 4.0 7.5 - - - +
319A SER* 6.0 0.2 - - - -
401A TIM 3.1 23.3 - - - -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PHE* 3.9 13.6 - - + -
209A TYR* 4.1 11.9 - - + -
212A LEU* 3.9 23.6 - - + -
283A THR* 2.8 44.4 + - + +
284A LEU* 5.2 0.9 - - + -
286A TRP* 1.3 72.2 - - - +
288A PRO* 1.4 59.7 - - + +
290A PHE 3.3 1.0 + - - -
291A ILE* 2.8 60.6 + - + +
----------------------------------------------------------
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Residues in contact with PRO 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 3.4 25.1 - - - +
285A CYS 4.1 5.4 - - - +
286A TRP 3.5 4.0 - - - -
287A LEU* 1.4 92.7 - - + +
289A PHE* 1.3 60.0 + - - +
291A ILE* 3.6 9.4 + - + +
292A VAL* 3.1 31.4 + - + +
311A LEU* 4.0 24.5 - - + +
314A ILE* 6.1 3.1 - - + -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A CYS 5.0 0.2 - - - +
286A TRP* 3.2 31.4 + + + +
288A PRO* 1.3 79.7 - - - +
290A PHE* 1.3 65.3 + + - +
292A VAL* 3.4 5.0 + - + +
293A ASN* 2.9 27.1 + - + +
308A TYR* 3.6 49.7 - + - -
311A LEU* 3.7 25.6 + - + +
312A ASN* 3.6 35.2 - - + -
401A TIM 3.9 52.9 - - + -
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Residues in contact with PHE 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 4.0 5.6 - - + -
204A SER* 4.0 22.4 - - - -
208A PHE* 3.4 64.4 - + + -
209A TYR* 3.1 15.5 + - + +
286A TRP* 3.2 43.8 + + - +
287A LEU 4.0 0.7 - - - +
289A PHE* 1.3 80.4 - + - +
291A ILE* 1.3 65.6 + - - +
293A ASN* 3.3 6.1 - - - +
294A ILE* 3.2 23.0 + - - +
401A TIM 3.5 58.8 - + - -
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 3.2 13.9 + - + +
287A LEU* 2.8 50.7 + - + +
288A PRO* 3.9 8.1 - - + +
290A PHE* 1.3 72.6 - - - +
292A VAL* 1.3 60.6 + - + +
294A ILE* 3.4 3.6 + - - +
295A VAL* 3.1 42.8 + - + +
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PRO* 3.1 20.9 + - + +
289A PHE* 3.7 3.8 - - + +
291A ILE* 1.3 77.0 - - + +
293A ASN* 1.3 58.9 + - - +
295A VAL* 3.8 8.0 - - + +
296A HIS* 3.1 27.5 + - - +
303A ILE* 3.6 41.5 - - + +
307A VAL* 5.2 4.3 - - + -
308A TYR* 4.5 15.3 - - + -
311A LEU* 3.5 24.0 - - + -
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Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 3.5 13.7 + - - +
204A SER* 2.8 28.1 + - - -
289A PHE* 2.9 16.0 + - + +
290A PHE* 3.2 15.1 + - + +
292A VAL* 1.3 79.0 - - - +
294A ILE* 1.3 60.3 + - - +
296A HIS* 3.6 9.2 + - - +
297A VAL* 3.3 19.1 + - - +
308A TYR* 3.6 28.6 + - + -
401A TIM 2.9 32.5 + - - +
----------------------------------------------------------
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA 4.7 4.7 - - - +
201A ILE* 5.1 19.1 - - + +
204A SER* 4.4 16.6 - - - +
205A ILE* 4.9 10.3 - - + -
209A TYR* 3.4 36.3 - - + +
290A PHE 3.2 12.2 + - - +
291A ILE* 4.1 3.6 - - - +
293A ASN* 1.3 73.9 - - - +
295A VAL* 1.3 65.7 + - + +
297A VAL* 3.1 17.5 + - - +
298A ILE* 3.3 24.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE* 3.1 34.3 + - + +
292A VAL* 3.9 7.9 - - + +
293A ASN 3.4 0.2 - - - -
294A ILE* 1.3 77.2 - - + +
296A HIS* 1.3 57.1 + - - +
298A ILE* 3.5 7.4 + - - +
299A GLN* 3.0 29.3 + - + +
302A LEU* 3.7 32.5 - - + -
303A ILE* 4.5 11.9 - - + -
----------------------------------------------------------
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Residues in contact with HIS 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL 3.1 17.8 + - - +
293A ASN* 3.8 8.2 + - - +
294A ILE 3.2 0.6 - - - -
295A VAL* 1.3 74.2 - - - +
297A VAL* 1.3 62.6 + - - +
299A GLN 3.5 5.4 - - - -
300A ASP* 3.2 51.2 + - + +
303A ILE* 3.5 43.0 + - + +
308A TYR* 5.8 3.9 - + + -
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN* 3.6 58.4 + - + +
200A ALA* 3.5 27.6 - - + -
201A ILE* 3.8 24.0 - - + -
293A ASN 3.3 18.2 - - - +
294A ILE* 3.1 11.6 + - - +
296A HIS* 1.3 79.8 - - + +
298A ILE* 1.3 66.5 + - + +
300A ASP* 4.9 2.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 5.2 11.7 - - + -
294A ILE* 3.3 25.3 + - + +
295A VAL* 3.5 8.5 + - - +
297A VAL* 1.3 82.2 - - + +
299A GLN* 1.3 77.4 + - + +
300A ASP 4.2 0.7 + - - -
----------------------------------------------------------
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 3.0 17.0 + - + +
296A HIS* 3.5 8.2 - - - +
298A ILE* 1.3 95.0 - - + +
300A ASP* 1.3 56.5 + - - +
301A ASN* 3.2 21.3 + - - +
302A LEU* 3.9 33.2 + - + +
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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