Contacts of the helix formed by residues 293 - 317 (chain E) in PDB entry 2GPV
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 293 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 1.3 77.2 - - - +
294E LEU* 1.3 66.5 + - - +
295E ALA* 4.2 3.1 - - - -
296E ASP* 2.9 33.4 + - - +
297E GLN* 3.1 10.4 + - - +
383E GLU* 3.2 25.4 + - - +
384E ASP* 5.5 3.0 - - - +
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Residues in contact with LEU 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR 5.2 2.7 - - - +
258A PRO* 3.5 27.8 - - + -
451A LEU* 4.3 7.2 - - + -
454A LEU* 3.9 37.0 - - + +
455A GLU* 4.1 31.0 - - + +
292E LEU 3.8 1.6 + - - -
293E SER* 1.3 72.2 - - - +
295E ALA* 1.3 63.7 + - - +
297E GLN* 3.1 18.0 + - - +
298E MET* 3.0 29.2 + - - +
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Residues in contact with ALA 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 3.8 17.6 - - + +
259A ASP 3.9 19.5 - - - +
293E SER* 3.1 1.4 + - - -
294E LEU* 1.3 77.3 - - - +
296E ASP* 1.3 55.0 + - - +
298E MET* 3.8 9.2 - - - +
299E SER* 2.7 37.9 + - - +
381E HIS 5.7 0.7 - - - +
383E GLU* 3.8 34.3 - - + +
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Residues in contact with ASP 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 4.1 18.6 - - + +
293E SER* 2.9 21.1 + - - +
295E ALA* 1.3 79.5 - - - +
297E GLN* 1.3 58.9 + - - +
299E SER* 3.5 4.8 - - - -
300E LEU* 3.1 34.9 + - - +
381E HIS 4.4 1.0 - - - +
382E ILE* 3.6 13.0 - - - -
383E GLU* 2.7 31.4 + - - +
384E ASP* 3.0 31.2 + - - +
388E VAL* 3.7 10.7 - - + +
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Residues in contact with GLN 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 3.6 32.4 - - + +
284E LYS* 5.1 1.9 - - - +
289E PHE* 3.5 51.4 + - + +
290E SER* 3.8 13.8 + - - +
292E LEU* 2.9 28.2 + - + +
293E SER 3.1 13.4 + - - +
294E LEU* 3.6 18.7 - - - +
296E ASP* 1.3 73.4 - - - +
298E MET* 1.3 66.0 + - - +
300E LEU* 3.5 0.7 + - - +
301E LEU* 3.2 28.8 + - - +
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Residues in contact with MET 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 4.6 11.2 - - + +
260A SER* 4.0 15.9 - - - +
447A HIS* 3.1 39.0 - - + +
450A PHE* 3.9 27.3 - - + -
451A LEU* 3.9 34.3 - - - +
454A LEU* 4.0 10.3 - - + +
294E LEU* 3.0 18.9 + - + +
295E ALA* 3.8 11.9 - - - +
297E GLN* 1.3 73.0 - - - +
299E SER* 1.3 57.1 + - - +
301E LEU* 3.3 3.6 + - - +
302E GLN* 2.7 44.0 + - + +
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Residues in contact with SER 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E ALA* 2.7 22.5 + - - +
296E ASP* 3.5 9.4 - - - -
297E GLN 3.2 0.2 - - - -
298E MET* 1.3 77.5 - - - +
300E LEU* 1.3 58.5 + - - +
302E GLN* 3.2 12.9 + - - +
303E SER* 2.9 33.3 + - - -
379E SER* 4.0 19.3 + - - -
381E HIS* 3.4 20.9 + - - +
382E ILE* 4.6 4.3 - - - -
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Residues in contact with LEU 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E PHE* 4.0 19.3 - - + -
292E LEU* 4.0 18.4 - - + -
296E ASP 3.1 20.3 + - - +
297E GLN 4.0 3.6 - - - +
298E MET 3.3 0.2 - - - -
299E SER* 1.3 76.9 - - - +
301E LEU* 1.3 57.9 + - - +
303E SER* 3.4 3.0 + - - -
304E ALA* 2.9 31.2 + - - +
374E LEU* 3.6 21.1 - - + +
375E ALA* 4.6 10.1 - - - +
377E SER* 3.2 21.4 + - - +
378E ASP 5.4 1.6 - - - +
379E SER* 5.1 1.1 - - - -
382E ILE* 4.0 22.9 - - + -
388E VAL* 4.2 22.4 - - + -
391E LEU* 4.7 3.6 - - + -
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Residues in contact with LEU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PHE* 4.3 16.2 - - + -
454A LEU* 3.8 26.0 - - + -
279E ILE* 4.7 18.4 - - + -
280E ILE* 4.3 21.3 - - + -
283E ALA* 4.1 9.4 - - + -
289E PHE* 4.0 13.2 - - + -
297E GLN 3.2 17.8 + - - +
298E MET* 3.8 3.4 - - - +
300E LEU* 1.3 74.0 - - - +
302E GLN* 1.3 67.1 + - - +
303E SER 3.0 1.6 - - - -
304E ALA* 2.9 0.8 + - - +
305E TRP* 2.9 32.3 + - + +
308E ILE* 4.9 4.7 - - + -
374E LEU* 3.7 27.8 - - + -
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Residues in contact with GLN 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER* 5.9 1.8 - - - -
261A ASP* 3.8 24.5 + - - +
262A ILE* 4.4 2.4 - - - +
443A LYS* 5.2 10.2 - - + +
446A MET* 6.3 0.7 - - + -
447A HIS* 3.7 29.4 + - - +
450A PHE* 3.4 27.5 - - + -
298E MET* 2.7 26.0 + - - +
299E SER* 3.5 12.2 + - - +
301E LEU* 1.3 71.7 - - - +
303E SER* 1.3 58.5 + - - +
305E TRP* 3.1 23.1 + - - +
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Residues in contact with SER 303 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E SER 2.9 18.7 + - - -
300E LEU 3.5 5.6 - - - -
301E LEU 3.0 0.2 - - - -
302E GLN* 1.3 79.0 - - - +
304E ALA* 1.3 59.2 + - - +
305E TRP* 3.6 1.1 + - - -
306E MET* 5.1 1.4 + - - +
307E GLU* 5.0 7.4 - - - +
377E SER* 3.6 28.2 - - - +
378E ASP 4.8 0.3 + - - -
379E SER* 3.2 24.4 + - - -
425E ARG* 6.1 0.2 - - - -
428E SER* 5.4 1.7 + - - -
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Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E LEU 2.9 21.1 + - - +
301E LEU 2.9 0.4 + - - -
303E SER* 1.3 73.8 - - - +
305E TRP* 1.3 67.1 + - - +
306E MET 3.2 2.5 - - - -
307E GLU* 2.9 24.2 + - + +
308E ILE* 3.1 16.4 + - + +
373E ALA 3.7 21.1 - - - +
374E LEU* 3.6 22.7 - - + -
377E SER* 4.0 4.3 - - - -
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Residues in contact with TRP 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LYS* 6.3 0.8 - - - +
446A MET* 3.4 36.1 - - + +
450A PHE* 4.7 12.1 - + + -
276E LEU* 3.8 26.6 - - + +
279E ILE* 4.9 4.6 - - + +
301E LEU* 2.9 17.5 + - + +
302E GLN* 3.1 31.9 + - - +
303E SER 3.6 1.5 - - - -
304E ALA* 1.3 76.8 - - - +
306E MET* 1.3 99.6 + - + +
308E ILE* 3.4 9.0 + - - +
309E LEU* 3.1 52.4 + - + +
432E VAL* 4.7 10.2 - - + +
435E PHE* 5.2 6.3 - + - -
436E TYR* 4.1 9.4 + - - -
504E OHT 3.9 26.7 - + - -
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Residues in contact with MET 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E SER 5.1 0.6 + - - +
304E ALA 3.2 1.0 - - - -
305E TRP* 1.3 109.9 - - + +
307E GLU* 1.3 58.4 + - - +
309E LEU* 3.2 6.9 + - - +
310E ILE* 2.9 45.4 + - + +
428E SER* 3.0 32.1 + - - +
431E ALA* 4.0 13.2 - - + +
432E VAL* 3.4 37.5 - - + +
435E PHE* 5.2 2.7 - - + -
504E OHT 4.0 30.5 - - + -
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Residues in contact with GLU 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E SER 5.0 5.0 - - - +
304E ALA* 2.9 17.3 + - - +
306E MET* 1.3 76.2 - - - +
308E ILE* 1.3 56.7 + - - +
311E LEU* 2.9 33.2 + - - +
373E ALA* 4.0 27.1 - - + +
377E SER* 5.6 1.5 - - - -
421E LEU* 5.2 2.1 - - - +
424E LEU* 3.7 26.6 - - + +
425E ARG* 2.8 54.8 + - - +
428E SER* 3.2 26.5 + - - +
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Residues in contact with ILE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E ILE* 3.6 38.3 - - + +
282E TRP* 4.0 23.3 - - + -
301E LEU* 4.9 2.0 - - + -
304E ALA* 3.1 30.4 + - + +
305E TRP* 3.8 9.0 - - - +
307E GLU* 1.3 72.8 - - - +
309E LEU* 1.3 63.6 + - - +
311E LEU* 4.1 5.3 - - - +
312E GLY* 3.2 17.0 + - - -
370E LYS* 3.8 37.7 - - + +
373E ALA* 4.9 4.3 - - + -
374E LEU* 4.0 19.1 - - + +
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Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ALA* 4.0 10.8 - - + +
275E GLU* 3.7 33.9 - - + +
276E LEU* 4.1 8.5 - - + -
279E ILE* 3.5 23.8 - - + -
305E TRP* 3.1 47.9 + - + +
306E MET* 3.2 9.8 + - - +
308E ILE* 1.3 74.8 - - - +
310E ILE* 1.3 64.7 + - - +
312E GLY* 3.0 12.1 + - - -
313E VAL 3.2 9.9 + - - -
316E ARG* 4.7 0.2 + - - -
504E OHT 3.6 43.3 + - + +
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Residues in contact with ILE 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E MET* 2.9 30.9 + - + +
307E GLU 4.1 1.6 - - - +
309E LEU* 1.3 71.6 - - - +
311E LEU* 1.3 60.9 + - - +
313E VAL* 2.9 11.3 - - + +
314E VAL* 2.8 39.6 + - + +
349E ILE* 4.0 29.6 - - + -
352E LEU* 4.1 13.9 - - + -
424E LEU* 4.2 4.7 - - + -
427E THR* 3.8 14.4 - - + +
428E SER* 3.7 32.3 - - - +
431E ALA* 4.0 10.1 - - + -
504E OHT 4.5 10.3 - - + -
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Residues in contact with LEU 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E GLU 2.9 19.3 + - - +
308E ILE* 4.1 4.0 - - - +
310E ILE* 1.3 76.5 - - - +
312E GLY* 1.3 57.0 + - - +
314E VAL* 3.3 8.9 + - + +
315E TYR* 2.9 29.5 + - + +
352E LEU* 6.1 0.2 - - + -
356E TYR* 3.9 34.5 - - + +
361E LEU* 5.5 2.7 - - + -
366E PHE* 4.1 17.3 - - + +
369E LEU* 4.2 10.5 - - + +
370E LYS* 3.3 45.1 - - + +
373E ALA* 5.1 2.0 - - + -
421E LEU* 5.9 0.4 - - + -
424E LEU* 4.1 25.2 - - + +
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Residues in contact with GLY 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E GLU* 5.7 0.4 - - - -
308E ILE 3.2 9.4 + - - -
309E LEU 3.0 9.7 + - - -
311E LEU* 1.3 77.7 - - - +
313E VAL* 1.3 62.5 + - - +
315E TYR* 3.2 4.3 + - - +
316E ARG* 3.1 42.5 + - - +
366E PHE* 4.2 15.3 - - - -
370E LYS* 5.6 2.5 - - - -
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Residues in contact with VAL 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E LEU 3.2 5.3 + - - +
310E ILE* 2.9 34.8 - - + +
312E GLY* 1.3 73.8 - - - +
314E VAL* 1.3 57.6 + - - +
316E ARG* 3.4 19.7 + - - +
317E SER* 2.4 43.8 + - - +
324E LEU* 4.1 12.3 - - + -
325E VAL 3.6 18.6 - - - +
326E TYR* 3.6 35.9 - - + -
349E ILE* 4.2 13.7 - - + -
504E OHT 4.2 3.1 - - + +
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Residues in contact with VAL 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E ILE* 2.8 25.8 + - + +
311E LEU* 3.4 9.2 - - + +
313E VAL* 1.3 71.9 - - - +
315E TYR* 1.3 63.5 + - - +
317E SER* 3.2 15.2 + - - -
318E LEU* 3.5 10.1 + - + +
349E ILE* 3.8 20.2 - - + +
352E LEU* 3.7 31.6 - - + -
353E VAL* 3.9 24.6 - - + +
356E TYR* 3.4 37.0 - - + -
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Residues in contact with TYR 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E LEU* 2.9 8.5 + - + +
312E GLY 3.7 2.7 - - - +
314E VAL* 1.3 78.3 - - - +
316E ARG* 1.3 71.2 + - + +
317E SER 3.2 0.5 + - - -
318E LEU* 3.3 47.4 + - + +
361E LEU* 4.5 11.3 + - + -
363E LYS* 3.4 50.8 + - - +
366E PHE* 3.4 64.8 - + + -
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Residues in contact with ARG 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E LYS* 5.9 9.4 - - - +
275E GLU* 3.8 17.5 + - - -
312E GLY* 3.1 30.2 + - - +
313E VAL* 3.4 15.5 - - - +
315E TYR* 1.3 81.6 - - + +
317E SER* 1.3 59.4 + - - +
318E LEU 3.4 0.6 + - - -
319E SER* 4.8 1.7 + - - -
320E PHE* 3.7 10.6 - - - -
325E VAL* 3.1 49.0 + - + +
326E TYR 3.1 24.0 + - - -
327E ALA* 4.9 3.8 - - - +
328E ASP* 5.8 1.6 - - - +
504E OHT 3.2 24.4 + - - -
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Residues in contact with SER 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E VAL* 2.4 27.9 + - - +
314E VAL 3.4 7.2 - - - -
315E TYR 3.1 0.6 - - - -
316E ARG* 1.3 77.3 - - - +
318E LEU* 1.3 61.6 + - - +
319E SER 3.4 2.2 - - - -
320E PHE* 3.1 24.8 + - - +
323E GLU 3.6 16.9 - - - +
324E LEU* 3.5 5.7 - - - +
325E VAL* 3.1 27.1 + - - -
353E VAL* 3.9 20.2 - - - +
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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