Contacts of the helix formed by residues 284 - 315 (chain E) in PDB entry 5J0Z
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 GLN 284 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E LEU* 3.2 24.7 + - + +
282E GLU* 4.6 4.7 - - + +
283E SER* 1.3 79.8 - - - +
285E PRO* 1.4 52.4 - - - +
286E ALA* 2.6 21.8 + - - +
287E ARG* 2.6 78.7 + - + +
288E ALA* 3.1 10.2 + - - -
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Residues in contact with PRO 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E LEU 4.6 2.5 - - - +
280E LYS* 4.7 25.8 - - + +
283E SER* 3.3 14.1 - - - -
284E GLN* 1.4 86.6 - - - +
286E ALA* 1.3 60.8 + - - +
288E ALA* 3.9 11.1 - - + +
289E ALA* 3.1 26.5 + - - +
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Residues in contact with ALA 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E GLN* 2.6 7.7 + - - +
285E PRO* 1.3 75.1 - - - +
287E ARG* 1.3 51.4 + - - +
289E ALA 3.5 1.4 - - - -
290E SER* 2.8 39.6 + - - +
293E ARG* 4.8 3.8 + - - +
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Residues in contact with ARG 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E LEU* 3.9 14.8 - - + +
284E GLN* 2.6 56.2 + - + +
286E ALA* 1.3 73.4 - - - +
288E ALA* 1.3 66.3 + - - +
290E SER* 3.3 9.4 + - - -
291E ILE* 3.3 28.0 + - + +
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Residues in contact with ALA 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E GLN* 3.7 23.2 - - + +
279E LEU* 3.5 33.6 - - + +
280E LYS* 4.4 6.5 - - + +
284E GLN 3.1 7.4 + - - +
285E PRO* 3.9 13.0 - - + +
287E ARG* 1.3 79.7 - - - +
289E ALA* 1.3 59.2 + - + +
291E ILE* 3.2 7.6 + - - +
292E THR* 3.1 26.1 + - - -
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Residues in contact with ALA 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E THR* 5.3 12.6 - - + -
276E GLN* 5.4 2.5 - - + +
285E PRO 3.1 16.0 + - - +
286E ALA 3.5 3.1 - - - -
288E ALA* 1.3 76.0 - - + +
290E SER* 1.3 60.1 + - - +
292E THR* 4.1 14.6 - - - +
293E ARG* 3.0 38.7 + - + +
296E ARG* 6.4 0.4 - - - +
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Residues in contact with SER 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E ALA 2.8 24.9 + - - -
287E ARG* 3.4 12.1 - - - -
288E ALA 3.2 0.4 - - - -
289E ALA* 1.3 75.6 - - - +
291E ILE* 1.3 56.2 + - - +
293E ARG* 3.1 18.6 + - - +
294E ALA* 2.8 34.9 + - - +
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Residues in contact with ILE 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E GLU* 4.0 25.8 - - + +
275E VAL* 3.8 30.7 - - + -
276E GLN 5.6 0.7 - - - +
279E LEU* 3.9 13.0 - - + -
287E ARG* 3.4 21.8 - - + +
288E ALA 3.2 6.5 + - - +
290E SER* 1.3 78.5 - - - +
292E THR* 1.3 65.4 + - - +
294E ALA* 2.8 20.1 + - - +
295E SER* 2.8 17.6 + - - +
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Residues in contact with THR 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ALA 4.3 0.2 - - - +
216E PHE* 2.7 39.5 - - - +
218E SER 4.2 0.4 - - - +
219E THR* 5.6 1.1 - - + -
272E GLU* 2.6 27.0 + - - +
276E GLN* 3.0 43.4 + - - +
288E ALA 3.1 7.9 + - - -
289E ALA* 4.2 8.1 - - + -
291E ILE* 1.3 78.2 - - - +
293E ARG* 1.3 61.3 + - - +
295E SER* 3.5 5.1 - - - -
296E ARG* 3.4 23.6 + - - +
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Residues in contact with ARG 293 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 5.8 0.2 - - - -
286E ALA* 4.8 4.0 + - - +
289E ALA* 3.0 36.3 + - + +
290E SER* 3.1 14.7 + - - +
292E THR* 1.3 75.6 - - - +
294E ALA* 1.3 68.9 + - - +
296E ARG* 3.2 53.7 - - - +
297E ILE* 4.1 6.4 + - - +
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Residues in contact with ALA 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E SER 2.8 13.7 + - - +
291E ILE* 2.8 13.7 + - - +
293E ARG* 1.3 73.8 - - - +
295E SER* 1.3 67.8 + - - +
297E ILE* 2.7 18.5 + - - +
298E ALA* 3.0 14.1 + - + +
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Residues in contact with SER 295 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E PHE* 3.7 28.4 - - - -
272E GLU* 3.5 18.4 - - - +
291E ILE* 2.8 18.7 + - - +
292E THR 3.5 9.4 - - - -
294E ALA* 1.3 72.1 - - - +
296E ARG* 1.3 55.7 + - - +
297E ILE 2.7 12.1 + - - -
298E ALA* 3.0 21.1 + - - +
299E PHE* 3.1 27.8 + - - +
300E PRO* 3.8 0.3 - - - +
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Residues in contact with ARG 296 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.8 27.1 + - - -
216E PHE* 3.1 33.0 + - + -
217E TRP* 3.4 72.4 - - + +
219E THR* 6.0 3.4 - - - +
289E ALA* 6.4 0.6 - - - +
292E THR* 3.4 16.0 + - - +
293E ARG* 3.2 45.1 - - - +
294E ALA 2.9 0.6 + - - -
295E SER* 1.3 75.9 - - - +
297E ILE* 1.3 68.4 + - + +
300E PRO* 3.6 16.5 - - - +
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Residues in contact with ILE 297 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E TRP* 6.4 0.2 - - + -
293E ARG 4.4 6.1 - - - +
294E ALA 2.7 10.3 + - - +
295E SER 2.7 2.6 + - - -
296E ARG* 1.3 87.1 - - + +
298E ALA* 1.3 65.8 + - - +
299E PHE 3.1 3.0 + - - -
300E PRO* 3.3 5.6 - - - +
301E VAL* 3.0 40.7 + - + +
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Residues in contact with ALA 298 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E ALA* 3.0 10.6 + - + +
295E SER* 3.8 17.7 - - - +
297E ILE* 1.3 77.3 - - - +
299E PHE* 1.3 60.7 + - + +
301E VAL* 3.7 4.4 - - - +
302E VAL* 2.8 46.9 + - + +
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Residues in contact with PHE 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E TRP* 3.5 27.6 - + + -
216E PHE* 3.4 37.5 - + + -
265E PHE* 4.0 18.0 - + - -
268E VAL* 3.4 30.1 - - + -
269E ALA* 3.7 26.0 - - + -
272E GLU* 4.5 5.6 - - + -
295E SER* 3.1 30.7 + - - +
297E ILE 3.1 0.2 + - - -
298E ALA* 1.3 81.9 - - + +
300E PRO* 1.3 74.9 - - + +
301E VAL 3.1 0.3 + - - -
302E VAL* 3.8 2.8 - - - -
303E PHE* 2.9 24.9 + - - +
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Residues in contact with PRO 300 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E TRP* 3.9 31.6 - - + -
216E PHE* 5.6 1.1 - - + -
217E TRP* 6.3 0.2 - - + -
295E SER 3.8 1.1 - - - +
296E ARG* 3.6 22.9 - - - +
297E ILE* 3.3 8.7 - - - +
299E PHE* 1.3 95.6 - - + +
301E VAL* 1.3 56.1 + - + +
303E PHE* 3.7 2.1 - - - +
304E LEU* 3.1 28.9 + - - +
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Residues in contact with VAL 301 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E ILE* 3.0 39.8 + - + +
298E ALA* 3.7 4.3 - - - +
300E PRO* 1.3 73.6 - - + +
302E VAL* 1.3 75.7 + - + +
303E PHE 3.0 1.1 - - - -
304E LEU* 2.8 18.9 + - - +
305E LEU* 2.9 32.0 + - + +
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Residues in contact with VAL 302 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E PHE* 3.9 19.1 - - + -
298E ALA* 2.8 32.8 + - + +
299E PHE* 4.0 2.7 - - - +
301E VAL* 1.3 80.1 - - + +
303E PHE* 1.3 54.6 + - - +
305E LEU* 3.7 12.3 - - + +
306E ALA* 2.9 31.9 + - + +
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Residues in contact with PHE 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E LEU* 3.6 28.0 - - + -
209E LEU* 3.6 23.6 - - + -
210E PHE* 4.8 5.2 - + - -
213E TRP* 4.0 16.6 - + + -
258E ILE* 5.8 1.6 - - + -
261E MET* 3.3 28.7 - - + -
262E ILE* 4.2 14.8 - - + -
265E PHE* 3.3 28.8 - + + -
299E PHE 2.9 17.5 + - - +
300E PRO 3.7 4.7 - - - +
301E VAL 2.9 0.6 + - - -
302E VAL* 1.3 74.5 - - - +
304E LEU* 1.3 62.7 + - + +
306E ALA* 3.2 0.8 + - - -
307E ASN* 2.8 52.5 + - - +
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Residues in contact with LEU 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E PRO 3.1 12.9 + - - +
301E VAL* 2.8 10.1 + - - +
303E PHE* 1.3 75.3 - - + +
305E LEU* 1.3 68.0 + - - +
307E ASN* 4.6 5.5 - - + +
308E ILE* 3.3 37.2 + - + +
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Residues in contact with LEU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301E VAL* 2.9 33.2 + - + +
302E VAL* 3.7 14.1 - - + +
304E LEU* 1.3 77.1 - - + +
306E ALA* 1.3 53.6 + - + +
308E ILE* 2.8 13.7 + - - +
309E ILE* 2.7 45.9 + - + +
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Residues in contact with ALA 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E MET* 4.0 20.0 - - - +
265E PHE* 5.0 2.2 - - + -
302E VAL* 2.9 23.6 + - + +
303E PHE* 4.1 2.0 - - - +
305E LEU* 1.3 79.1 - - + +
307E ASN* 1.3 58.7 + - - +
309E ILE* 3.6 20.7 - - + +
310E LEU* 3.1 30.5 + - - +
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Residues in contact with ASN 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E LEU* 6.1 0.6 - - - +
254E TYR* 5.1 5.4 + - - -
258E ILE* 4.0 31.5 - - - +
261E MET* 3.2 28.3 - - - +
303E PHE* 2.8 40.2 + - + +
304E LEU* 4.6 6.7 - - + +
306E ALA* 1.3 72.8 - - - +
308E ILE* 1.3 55.5 + - + +
310E LEU* 3.7 4.4 - - - +
311E ALA* 2.7 34.9 + - - +
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Residues in contact with ILE 308 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E LEU* 3.3 30.8 + - + +
305E LEU* 2.8 12.8 + - - +
307E ASN* 1.3 77.0 - - + +
309E ILE* 1.3 64.9 + - + +
311E ALA* 3.8 9.3 - - + +
312E PHE* 3.2 24.3 + - + +
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Residues in contact with ILE 309 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E LEU* 2.7 26.8 + - + +
306E ALA* 3.6 30.3 - - + +
308E ILE* 1.3 74.5 - - + +
310E LEU* 1.3 58.5 + - + +
312E PHE* 3.7 8.4 - - + +
313E LEU* 3.0 45.9 + - + +
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Residues in contact with LEU 310 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E TYR* 4.7 5.6 - - + +
257E ALA* 3.8 26.9 - - + -
258E ILE* 4.0 23.3 - - + +
261E MET* 4.4 15.0 - - + -
306E ALA 3.1 16.2 + - - +
307E ASN* 3.7 5.8 - - - +
309E ILE* 1.3 78.2 - - + +
311E ALA* 1.3 68.0 + - - +
313E LEU* 2.9 33.9 + - + +
314E PHE* 2.9 37.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E TYR* 4.3 20.7 - - - +
307E ASN 2.7 23.0 + - - +
308E ILE* 3.8 12.6 - - + +
310E LEU* 1.3 71.1 - - - +
312E PHE* 1.3 65.4 + - - +
314E PHE 3.2 0.3 + - - -
315E PHE* 3.2 30.7 + - + +
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Residues in contact with PHE 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E ILE* 3.2 15.0 + - + +
309E ILE* 3.7 7.4 - - + +
310E LEU 3.1 0.6 - - - -
311E ALA* 1.3 76.4 - - - +
313E LEU* 1.3 67.4 + - + +
314E PHE 2.8 12.0 + - - -
315E PHE* 2.9 27.6 + - - +
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Residues in contact with LEU 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ILE* 3.0 36.4 + - + +
310E LEU* 2.9 32.5 + - + +
312E PHE* 1.3 80.7 - - + +
314E PHE* 1.3 63.0 + - + -
315E PHE 3.7 0.2 - - - -
404E HXA 5.3 5.7 - - - +
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Residues in contact with PHE 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ARG* 3.6 26.0 - - + -
118E ARG* 3.4 24.3 + - - +
252E MET* 3.4 33.4 - - + -
253E THR 3.7 11.9 - - - -
254E TYR* 3.7 29.6 - + + -
257E ALA* 4.1 16.6 - - + -
310E LEU* 2.9 30.7 + - + +
312E PHE 2.8 1.6 + - - -
313E LEU* 1.3 77.5 - - + +
315E PHE* 1.3 83.6 + - + +
404E HXA 5.1 4.6 - - - +
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Residues in contact with PHE 315 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ARG* 3.9 46.0 - - + +
121E PHE* 4.2 37.2 - + + -
254E TYR* 4.1 24.7 - + - -
311E ALA* 3.2 21.1 + - + +
312E PHE* 2.9 23.7 + - - +
313E LEU 3.7 0.2 - - - -
314E PHE* 1.3 109.5 - - + +
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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