Contacts of the helix formed by residues 326 - 356 (chain D) in PDB entry 1EGE
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 THR 326 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ASP* 3.8 20.4 + - - -
256D ARG* 5.3 5.4 + - - +
324D ARG* 2.8 47.7 + - - +
325D ASN* 1.3 81.2 + - - +
327D TYR* 1.3 76.1 + - + +
329D ALA* 3.7 6.0 - - - +
330D SER* 3.2 24.9 + - - -
385D ILE* 4.2 10.9 - - - +
388D ARG* 4.2 3.5 + - - -
389D GLU* 3.6 23.0 + - + +
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Residues in contact with TYR 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.2 29.3 - - + +
306A GLU* 3.2 29.4 + - + +
324D ARG 4.2 1.1 + - - +
325D ASN 2.7 5.4 + - - -
326D THR* 1.3 84.0 - - + +
328D TYR* 1.3 79.9 + + + +
330D SER* 3.1 11.2 + - - -
331D ILE* 3.2 37.9 + - + +
385D ILE* 6.1 0.2 - - - -
386D VAL* 3.8 25.7 - - + +
389D GLU* 3.5 30.5 - - + -
390D HIS* 3.9 10.0 + - + -
393D LYS* 3.7 26.7 + - + -
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Residues in contact with TYR 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLU* 3.4 37.9 + - + -
310A MET* 4.6 9.0 - - + -
311D SER 4.1 3.3 - - - +
314D ARG* 2.9 52.9 + - + -
315D ALA* 3.9 21.0 - - + +
318D GLU* 3.7 25.6 - - + -
325D ASN* 2.8 10.2 + - - +
327D TYR* 1.3 92.2 - + + +
329D ALA* 1.3 56.3 + - - +
331D ILE* 2.9 14.6 + - + +
332D ALA* 2.8 31.9 + - - +
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Residues in contact with ALA 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ASP* 4.7 4.3 - - - +
256D ARG* 4.3 17.2 - - + +
257D PRO* 4.2 16.4 - - + -
315D ALA* 3.8 11.3 - - - +
325D ASN* 2.7 38.6 + - - +
326D THR* 3.7 8.3 - - - +
328D TYR* 1.3 72.2 - - - +
330D SER* 1.3 57.5 + - - +
332D ALA* 4.0 1.8 - - - +
333D LYS* 3.1 29.7 + - - +
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Residues in contact with SER 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ARG* 4.1 7.2 + - - +
326D THR 3.2 15.8 + - - -
327D TYR 3.1 3.0 + - - -
329D ALA* 1.3 75.0 - - - +
331D ILE* 1.3 64.8 + - - +
333D LYS* 4.1 3.0 - - - +
334D ALA* 3.4 21.5 + - - +
382D GLN* 3.4 29.7 + - - +
385D ILE* 3.6 19.0 - - - +
386D VAL* 3.4 28.4 - - - +
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 4.0 31.3 - - + +
306A GLU* 3.6 22.7 - - + -
307A LEU* 3.9 27.8 - - + -
310A MET* 5.3 3.1 - - + -
311D SER* 4.7 2.2 - - - +
327D TYR* 3.2 44.3 + - + +
328D TYR* 2.9 14.6 + - + +
330D SER* 1.3 75.9 - - - +
332D ALA* 1.3 68.3 + - - +
334D ALA* 3.2 3.5 + - - +
335D PHE* 2.9 22.7 + - - +
386D VAL* 4.3 15.7 - - + -
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D PRO* 5.1 2.5 - - + -
260D ALA* 3.8 7.6 - - + -
311D SER* 3.0 44.8 + - - +
312D TYR* 3.6 15.0 - - + -
315D ALA* 4.8 3.8 - - + -
328D TYR 2.8 14.6 + - - +
329D ALA* 4.0 4.0 - - - +
331D ILE* 1.3 72.8 - - - +
333D LYS* 1.3 58.1 + - - +
336D ALA* 2.8 36.6 + - - +
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Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ARG* 4.3 16.2 - - + +
259D VAL* 4.3 22.0 - - + +
260D ALA* 4.0 10.8 - - - +
329D ALA 3.1 17.3 + - - +
330D SER* 4.1 5.2 - - - +
332D ALA* 1.3 78.8 - - - +
334D ALA* 1.3 57.0 + - - +
336D ALA* 4.3 0.3 - - - +
337D GLY* 3.0 22.9 + - - -
372D TYR* 3.1 27.9 + - - +
374D ILE 4.9 0.8 - - - +
375D TYR 2.9 25.3 + - - -
376D GLU* 3.4 7.0 + - - +
377D GLY 2.8 22.6 + - - -
379D SER 6.1 0.2 - - - +
382D GLN* 3.1 31.9 - - + +
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Residues in contact with ALA 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 4.0 18.2 - - + -
330D SER 3.4 16.2 + - - +
331D ILE 3.2 3.6 + - - +
333D LYS* 1.3 77.7 - - - +
335D PHE* 1.3 67.3 + - - +
337D GLY* 3.7 0.4 - - - -
338D ASP* 2.9 32.2 + - - +
379D SER* 5.6 2.2 - - - +
382D GLN* 4.2 13.7 - - + -
383D ARG* 3.7 24.7 - - - +
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Residues in contact with PHE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 4.5 10.4 - - - -
304A LYS* 4.5 13.5 - - - -
307A LEU* 3.6 29.4 - - + -
335A PHE* 5.3 4.0 - + - -
304D LYS* 3.3 30.1 - - + -
307D LEU* 3.4 28.0 - - + -
308D ALA* 3.3 32.5 - - + -
311D SER* 4.4 5.6 - - - +
331D ILE 2.9 16.5 + - - +
332D ALA 3.8 1.8 - - - +
334D ALA* 1.3 75.5 - - - +
336D ALA* 1.3 63.7 + - - +
338D ASP* 2.9 7.4 + - + +
339D ILE* 2.9 45.2 + - + +
383D ARG* 5.7 0.2 - - - +
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Residues in contact with ALA 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D ALA* 3.6 35.2 - - + +
263D ALA* 3.9 6.6 - - + +
264D VAL* 4.5 2.9 - - + +
308D ALA* 4.2 15.5 - - + +
311D SER* 5.0 1.3 - - - +
332D ALA 2.8 20.7 + - - +
335D PHE* 1.3 73.2 - - - +
337D GLY* 1.3 56.8 + - - +
339D ILE* 3.5 11.3 - - - +
340D ALA* 2.8 35.5 + - - +
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Residues in contact with GLY 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ALA* 4.3 1.1 - - - +
333D LYS 3.0 21.0 + - - -
334D ALA 3.7 1.6 - - - -
335D PHE 3.2 0.2 - - - -
336D ALA* 1.3 77.3 - - - +
338D ASP* 1.3 61.2 + - - +
340D ALA* 3.8 1.4 - - - +
341D ASN* 2.8 30.1 + - - -
372D TYR* 3.8 28.6 - - - +
373D GLN* 3.5 5.6 - - - +
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Residues in contact with ASP 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D ALA* 2.9 20.2 + - - +
335D PHE* 2.9 8.2 + - + +
337D GLY* 1.3 74.6 - - - +
339D ILE* 1.3 56.6 + - + +
340D ALA 3.0 3.4 - - - -
341D ASN* 2.7 28.8 + - - +
342D GLN* 3.1 25.0 + - - +
373D GLN* 4.0 13.0 - - - +
379D SER* 3.7 20.0 + - - -
383D ARG* 2.8 27.3 + - - -
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Residues in contact with ILE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 4.8 3.6 - - - -
267D ALA* 3.6 24.5 - - + -
304D LYS* 3.8 36.1 - - + +
305D VAL* 4.1 1.3 - - - +
308D ALA* 3.7 25.1 - - + -
335D PHE* 2.9 54.2 + - + +
336D ALA* 3.5 10.3 - - - +
338D ASP* 1.3 73.2 - - + +
340D ALA* 1.3 64.7 + - - +
342D GLN* 3.8 13.9 - - - +
343D LEU* 3.0 29.4 + - + +
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Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ALA* 3.7 27.6 - - + +
266D LEU* 4.1 5.5 - - + +
267D ALA* 4.3 8.9 - - - +
336D ALA 2.8 20.0 + - - +
337D GLY* 3.8 7.6 - - - +
339D ILE* 1.3 82.1 - - - +
341D ASN* 1.3 64.0 + - - +
343D LEU* 4.0 1.9 - - - +
344D ALA* 3.2 22.5 + - - +
369D ALA* 4.0 14.8 - - + +
372D TYR* 4.9 3.6 - - + -
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Residues in contact with ASN 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C THR* 4.8 2.1 + - - -
366C MET* 4.8 4.5 - - - +
337D GLY 2.8 23.4 + - - +
338D ASP 2.7 15.7 + - - +
340D ALA* 1.3 76.1 - - - +
342D GLN* 1.3 59.4 + - + +
344D ALA* 3.7 2.5 + - - +
345D THR* 3.2 26.2 + - - -
366D MET* 5.1 1.2 - - - +
369D ALA* 3.0 28.6 + - - +
370D LYS* 3.2 26.7 + - - +
373D GLN* 3.3 32.7 + - - +
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Residues in contact with GLN 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LYS* 3.4 34.4 - - + +
338D ASP* 3.1 33.2 + - - +
339D ILE* 3.8 11.5 + - - +
340D ALA 3.4 0.2 - - - -
341D ASN* 1.3 73.4 - - + +
343D LEU* 1.3 62.2 + - + +
345D THR* 3.3 4.4 + - - -
346D ASP* 2.8 42.0 + - - +
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D ALA* 3.3 39.3 - - + +
270D ALA* 3.9 4.1 - - + +
271D LEU* 3.8 17.7 - - + +
301D MET* 3.7 57.9 - - + +
304D LYS* 3.9 21.5 - - + -
305D VAL* 4.4 3.4 - - + -
339D ILE* 3.0 28.8 + - + +
340D ALA 4.0 2.7 - - - +
342D GLN* 1.3 77.2 - - + +
344D ALA* 1.3 56.1 + - - +
346D ASP* 3.8 1.1 - - - +
347D ALA* 2.8 32.1 + - - +
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Residues in contact with ALA 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D LEU* 4.2 6.5 - - + -
270D ALA* 4.0 11.6 - - - +
340D ALA 3.2 17.7 + - - +
341D ASN 3.9 4.7 - - - +
343D LEU* 1.3 74.9 - - - +
345D THR* 1.3 66.0 + - - +
347D ALA* 2.9 15.1 + - - +
348D VAL* 2.9 18.5 + - - +
362D VAL* 4.8 0.5 - - - +
365D LEU* 3.8 12.6 - - + +
366D MET* 3.6 28.7 - - + +
369D ALA* 4.3 3.8 - - + -
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Residues in contact with THR 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ASN* 5.4 3.1 - - + +
370C LYS* 3.3 36.3 - - + +
373C GLN* 4.6 5.8 - - - +
341D ASN 3.2 15.6 + - - -
342D GLN* 3.3 4.8 + - - -
344D ALA* 1.3 76.2 - - - +
346D ASP* 1.3 60.1 + - - +
348D VAL* 3.0 11.2 + - - +
349D GLN* 2.7 28.8 + - + +
366D MET* 3.5 22.5 - - + +
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Residues in contact with ASP 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D MET* 3.6 25.0 - - + +
301D MET* 3.9 24.5 - - + +
304D LYS* 6.1 1.2 - - - -
342D GLN* 2.8 31.1 + - - +
343D LEU* 3.9 3.5 - - - +
345D THR* 1.3 74.3 - - - +
347D ALA* 1.3 56.4 + - - +
349D GLN* 3.1 9.6 - - - +
350D ILE* 2.8 36.1 + - - +
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Residues in contact with ALA 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ALA* 3.7 25.1 - - + +
274D ALA* 3.9 15.5 - - + -
301D MET* 4.6 0.6 - - - -
343D LEU 2.8 15.0 + - - +
344D ALA* 3.1 12.6 - - - +
346D ASP* 1.3 74.1 - - - +
348D VAL* 1.3 61.7 + - - +
350D ILE* 3.2 2.2 + - - +
351D LEU* 3.0 30.1 + - - +
362D VAL* 3.6 21.8 - - + -
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Residues in contact with VAL 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C MET* 5.3 2.9 - - + -
370C LYS* 3.9 21.3 - - + -
374C ILE* 4.7 3.4 - - + +
344D ALA 2.9 21.7 + - - +
345D THR* 3.4 6.7 - - - +
347D ALA* 1.3 76.5 - - - +
349D GLN* 1.3 61.5 + - - +
351D LEU 3.5 0.7 + - - -
352D GLY* 3.2 23.6 + - - +
355D GLY* 3.6 27.3 - - - +
356D PHE* 4.1 9.4 - - + +
362D VAL* 3.4 35.0 - - + +
363D GLU* 5.0 1.8 - - - -
366D MET* 3.8 20.4 - - + -
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Residues in contact with GLN 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LYS* 2.8 27.8 + - - +
373C GLN* 2.8 35.4 + - - +
374C ILE* 3.2 14.1 - - - +
378C THR* 4.2 5.5 - - - +
379C SER* 4.5 3.3 + - - -
380C GLN* 3.3 25.2 + - - +
399C FAD 2.8 26.3 + - - +
297D MET* 4.0 17.0 - - + -
345D THR* 2.7 13.1 + - + +
346D ASP* 3.1 17.0 - - - +
347D ALA 3.1 0.2 - - - -
348D VAL* 1.3 77.4 - - - +
350D ILE* 1.3 61.4 + - - +
352D GLY* 3.3 8.5 + - - -
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Residues in contact with ILE 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C FAD 3.6 18.0 - - - +
274D ALA* 4.2 13.2 - - + +
277D TYR* 3.7 12.2 - - + -
278D ALA* 4.1 24.7 - - + -
288D LEU* 4.0 8.6 - - + +
294D ILE* 4.4 15.0 - - + -
297D MET* 3.8 30.7 - - + -
298D LEU* 4.1 12.1 - - + -
301D MET* 3.3 35.2 - - + -
346D ASP 2.8 19.0 + - - +
347D ALA* 3.2 4.7 + - - +
349D GLN* 1.3 70.7 - - - +
351D LEU* 1.3 64.1 + - + +
352D GLY 3.4 0.3 + - - -
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Residues in contact with LEU 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C FAD 4.8 3.2 + - - -
273D GLU* 4.3 4.9 - - + +
274D ALA* 4.1 15.9 - - - +
277D TYR* 3.4 55.3 + - + -
347D ALA 3.0 25.0 + - - +
348D VAL 3.9 0.2 - - - +
350D ILE* 1.3 78.0 - - - +
352D GLY* 1.3 62.9 + - - +
353D GLY 3.8 0.9 + - - -
354D ASN* 4.0 8.2 + - + +
355D GLY* 3.6 16.3 + - - +
360D TYR* 3.9 29.4 - - + -
361D PRO* 4.8 6.3 - - + -
362D VAL* 3.4 32.8 - - + -
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Residues in contact with GLY 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ILE* 3.6 19.6 - - - +
399C FAD 3.9 17.7 - - - -
348D VAL* 3.2 9.4 + - - +
349D GLN 3.3 10.2 + - - -
350D ILE 3.2 4.4 - - - -
351D LEU* 1.3 76.2 - - - +
353D GLY* 1.3 58.9 + - - +
355D GLY* 2.7 25.6 + - - -
356D PHE* 3.4 3.8 + - - +
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Residues in contact with GLY 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C TRP* 4.3 14.1 - - - -
374C ILE* 3.6 5.9 - - - +
399C FAD 2.8 50.1 + - - +
351D LEU 3.8 0.4 + - - -
352D GLY* 1.3 68.4 - - - -
354D ASN* 1.3 53.3 + - - +
356D PHE* 2.8 29.8 + - - +
357D ASN* 3.1 8.1 + - - +
----------------------------------------------------------
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Residues in contact with ASN 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C PRO 5.3 2.2 + - - -
165C MET* 6.0 0.5 - - - +
166C TRP* 3.5 21.3 + - - +
399C FAD 4.7 0.6 + - - -
277D TYR* 3.4 26.4 + - + +
281D ARG* 4.4 9.1 - - - +
351D LEU* 4.0 8.4 + - + +
352D GLY 3.2 0.6 - - - -
353D GLY* 1.3 74.2 - - - +
355D GLY* 1.3 60.9 + - - +
356D PHE 3.3 0.2 - - - -
357D ASN* 3.1 14.0 + - - -
360D TYR* 3.0 68.6 + - + +
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Residues in contact with GLY 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D VAL* 3.6 20.8 - - - +
351D LEU* 3.6 22.1 - - - +
352D GLY 2.7 14.0 + - - -
354D ASN* 1.3 80.6 - - - +
356D PHE* 1.3 57.8 + - - -
357D ASN 3.4 5.7 + - - +
362D VAL* 3.6 19.2 - - - +
363D GLU* 3.7 9.9 - - - +
----------------------------------------------------------
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Residues in contact with PHE 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ASN* 3.1 24.3 - - + +
215C MET* 2.9 42.4 + - + +
216C GLY* 3.5 44.4 - - - -
217C GLN* 5.1 1.8 - - + -
367C ARG 3.6 10.5 - - - -
368C ASP 4.4 1.1 - - - -
370C LYS* 3.5 19.7 - - + -
371C ILE* 3.3 56.1 - - + -
374C ILE* 5.2 4.9 - - + -
399C FAD 4.3 17.9 - - + -
348D VAL* 4.1 7.0 - - + +
352D GLY 3.4 4.8 + - - +
353D GLY* 2.8 10.0 + - - +
355D GLY* 1.3 74.1 - - - +
357D ASN* 1.3 61.2 + - - +
363D GLU* 4.9 0.2 - - - -
----------------------------------------------------------
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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