Contacts of the helix formed by residues 369 - 396 (chain B) in PDB entry 6V3O
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 GLU 369 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 3.7 21.1 + - - -
330B LEU 5.3 0.2 - - - +
331B SER* 3.7 24.6 - - - +
332B MET 3.9 2.7 - - - +
366B PRO* 3.4 29.9 + - - +
367B PRO 3.1 3.5 - - - -
368B ASN* 1.3 97.1 + - - +
370B PRO* 1.3 68.0 - - - +
371B TYR 3.4 1.8 - - - -
372B ARG* 3.1 47.8 + - + +
373B VAL* 3.3 14.8 + - - +
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Residues in contact with PRO 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B MET 3.3 17.7 - - - +
333B TRP* 3.8 10.8 - - - +
335B CYS* 3.6 24.7 - - + -
339B LEU* 3.3 24.0 - - + -
343B ALA* 4.0 12.3 - - + -
367B PRO 4.7 6.5 - - - +
368B ASN 3.5 7.0 - - - +
369B GLU* 1.3 85.1 - - - +
371B TYR* 1.3 67.9 + - + +
373B VAL* 3.2 13.9 + - + +
374B ILE* 3.2 24.1 + - - +
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Residues in contact with TYR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.9 35.2 - - + +
332B MET* 3.9 35.4 - - + -
334B ARG 3.0 28.0 + - - -
335B CYS* 3.7 8.4 - - + -
339B LEU* 3.7 17.0 - - + -
369B GLU 3.4 0.2 - - - -
370B PRO* 1.3 77.4 - - + +
372B ARG* 1.3 58.5 + - - +
374B ILE* 3.5 1.3 + - - +
375B LEU* 3.0 36.6 + - + +
419B CYS* 3.9 27.4 - - + -
422B SER* 2.6 29.3 + - - -
423B LEU* 3.5 33.2 + - + +
426B CYS* 4.7 0.5 - - - -
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Residues in contact with ARG 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 5.3 0.2 - - - +
185A SER* 3.0 10.5 + - - -
1002A SO4 2.5 34.2 + - - -
327B MET* 2.7 48.7 + - + +
328B PHE* 2.9 35.0 + - - +
330B LEU 3.6 13.2 + - - +
331B SER* 3.9 12.3 - - - +
366B PRO* 6.3 2.9 - - + -
369B GLU* 3.1 44.6 + - + +
371B TYR* 1.3 78.7 - - - +
373B VAL* 1.3 60.4 + - + +
376B GLY* 2.9 25.3 + - - -
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Residues in contact with VAL 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ALA* 3.7 37.5 - - + +
346B LEU* 4.2 11.5 - - + +
347B HIS* 3.8 20.0 - - + +
366B PRO* 3.7 22.9 - - + +
367B PRO* 4.9 0.9 - - + +
369B GLU 3.5 12.6 - - - +
370B PRO* 3.2 12.9 + - + +
372B ARG* 1.3 76.5 - - + +
374B ILE* 1.3 68.9 + - - +
376B GLY* 3.6 1.5 + - - +
377B HIS* 3.3 19.9 + - - +
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.5 39.7 - - + +
342B ARG* 4.2 20.4 - - + +
343B ALA* 4.7 4.7 - - - -
346B LEU* 4.8 5.2 - - + -
370B PRO 3.2 12.4 + - - +
371B TYR 3.9 3.8 - - - +
373B VAL* 1.3 83.3 - - + +
375B LEU* 1.3 64.7 + - + +
377B HIS* 3.1 9.2 + - - +
378B VAL* 3.1 24.3 + - + +
415B PRO* 4.0 25.4 - - + +
418B LEU* 3.7 20.2 - - + -
419B CYS* 4.0 17.0 - - - -
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 3.5 20.8 - - + +
326B LEU* 3.7 36.1 - - + +
327B MET* 3.5 32.1 - - + +
330B LEU* 5.0 6.7 - - + -
371B TYR* 3.0 28.1 + - + +
374B ILE* 1.3 77.0 - - + +
376B GLY* 1.3 58.5 + - - +
378B VAL* 3.3 8.8 + - + +
379B ARG* 3.0 23.2 + - - +
416B LEU* 3.9 28.3 - - + -
419B CYS* 4.7 16.6 - - + -
436B LEU* 5.9 0.7 - - + -
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Residues in contact with GLY 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B MET* 3.9 17.9 - - - -
372B ARG 2.9 18.5 + - - -
373B VAL* 3.6 2.0 + - - -
374B ILE 3.2 0.4 - - - -
375B LEU* 1.3 76.5 - - - +
377B HIS* 1.3 60.7 + - - +
379B ARG* 3.4 12.0 + - - +
380B ASP* 3.0 32.6 + - - +
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Residues in contact with HIS 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.5 34.2 - - + +
373B VAL 3.3 5.9 + - - +
374B ILE* 3.1 10.6 + - - +
376B GLY* 1.3 74.6 - - - +
378B VAL* 1.3 68.8 + - + +
380B ASP* 3.2 10.0 + - + +
381B LYS* 3.0 50.0 + - + +
406B PHE* 6.1 0.2 - + - -
415B PRO* 6.1 3.4 - - + -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 3.5 25.6 - - + -
374B ILE* 3.1 17.2 + - + +
375B LEU* 3.3 15.2 + - + +
377B HIS* 1.3 78.1 - - + +
379B ARG* 1.3 58.4 + - - +
381B LYS 3.3 1.2 + - - -
382B LEU* 2.9 28.7 + - + +
406B PHE* 3.6 19.2 - - + -
412B PHE* 3.6 23.1 - - + +
415B PRO* 3.8 31.4 - - + -
416B LEU* 4.8 4.3 - - + -
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ILE* 4.2 12.3 - - + +
323B ILE* 4.3 10.5 - - + +
324B GLU* 3.3 37.3 + - + +
327B MET* 4.3 21.7 - - - +
375B LEU 3.0 14.0 + - - +
376B GLY* 3.6 16.5 + - - +
377B HIS 3.2 0.4 - - - -
378B VAL* 1.3 76.6 - - - +
380B ASP* 1.3 75.4 + - - +
382B LEU* 3.2 12.8 + - - +
383B TYR* 2.9 45.3 + - + -
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Residues in contact with ASP 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLY 3.0 18.6 + - - +
377B HIS* 3.2 11.0 + - + +
379B ARG* 1.3 96.4 + - - +
381B LYS* 1.3 61.2 + - + +
383B TYR* 3.2 12.3 + - - +
384B ASN* 3.0 35.3 + - - +
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B HIS* 3.0 47.4 + - + +
380B ASP* 1.3 75.8 - - + +
382B LEU* 1.3 52.3 + - - +
384B ASN* 3.6 4.8 + - - +
385B THR* 2.6 35.0 + - - -
403B GLU* 4.0 14.1 + - - -
404B SER* 3.8 13.7 - - - +
405B SER* 3.6 21.4 + - - -
406B PHE* 3.4 34.9 - - + -
411B GLU* 2.9 28.7 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA* 4.0 15.4 - - + +
319B TYR* 3.7 37.2 - - + -
320B ILE* 3.6 15.5 - - + +
323B ILE* 3.6 31.6 - - + -
378B VAL 2.9 14.4 + - - +
379B ARG* 3.4 10.8 - - - +
380B ASP 3.1 0.2 - - - -
381B LYS* 1.3 76.1 - - - +
383B TYR* 1.3 65.1 + - - +
385B THR* 3.1 8.3 + - + +
386B ARG* 2.9 23.6 + - - +
406B PHE* 4.0 19.7 - - + -
412B PHE* 4.3 11.0 - - + -
448B LEU* 5.1 7.2 - - + -
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Residues in contact with TYR 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR 5.2 9.4 - - - -
359A ILE* 4.1 19.3 - - + +
320B ILE* 3.7 31.4 - - + +
324B GLU* 4.1 7.0 + - - -
379B ARG* 2.9 50.3 + - + -
380B ASP* 3.2 12.5 + - - +
382B LEU* 1.3 76.2 - - - +
384B ASN* 1.3 58.1 + - - +
386B ARG* 3.2 14.0 + - - +
387B GLU* 2.9 45.1 + - + +
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Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ASP* 3.0 20.3 + - - +
381B LYS* 3.7 6.3 - - - +
383B TYR* 1.3 77.2 - - - +
385B THR* 1.3 57.3 + - - +
387B GLU* 3.3 5.8 + - - +
388B ARG* 2.8 32.9 + - - +
400B ILE* 3.9 17.9 - - + +
404B SER* 3.0 46.5 + - - +
405B SER* 4.2 2.2 - - - -
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Residues in contact with THR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 5.6 10.1 - - + +
316B ALA* 5.0 8.1 - - + -
381B LYS 2.6 22.5 + - - -
382B LEU* 3.1 14.9 + - + -
384B ASN* 1.3 76.2 - - - +
386B ARG* 1.3 62.2 + - - +
388B ARG* 3.6 4.6 + - - +
389B ALA* 3.3 20.8 + - - +
405B SER* 3.2 8.6 - - - -
406B PHE* 2.9 43.0 + - + +
448B LEU* 5.6 7.4 - - + -
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS 2.8 25.9 + - - -
357A TYR* 4.5 3.0 - - - +
358A TYR 2.9 28.2 + - - -
359A ILE* 3.7 6.3 + - - +
362A TRP* 4.8 4.9 - - - +
312B ARG 5.3 0.4 - - - -
313B MET* 3.9 37.3 - - + +
316B ALA* 3.7 17.0 - - + -
317B ASN* 3.2 37.9 + - - +
320B ILE* 5.2 4.0 - - + -
382B LEU 2.9 11.3 + - - +
383B TYR* 3.8 16.9 - - - +
385B THR* 1.3 76.3 - - - +
387B GLU* 1.3 89.0 + - - +
389B ALA* 3.1 7.4 + - - +
390B ARG* 2.9 33.7 + - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS 4.4 1.9 - - - +
357A TYR* 5.3 3.0 - - - -
383B TYR* 2.9 29.4 + - + +
384B ASN* 3.9 2.7 - - - +
386B ARG* 1.3 116.4 + - - +
388B ARG* 1.3 63.4 + - - +
390B ARG* 2.5 40.3 + - - +
391B HIS* 2.9 29.9 + - + +
400B ILE* 3.7 21.1 - - + -
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASN 2.8 18.6 + - - +
385B THR* 3.8 5.8 - - - +
387B GLU* 1.3 77.5 - - - +
389B ALA* 1.3 61.2 + - - +
391B HIS* 3.3 1.9 + - - +
392B LEU* 3.0 52.7 + - + +
398B SER* 2.8 45.9 + - - +
400B ILE* 2.9 31.1 + - + +
401B SER* 4.6 1.3 - - - +
402B ALA* 4.4 21.1 - - - +
405B SER* 3.9 20.2 + - - -
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 4.0 30.8 - - + +
312B ARG* 4.5 12.3 - - + -
313B MET* 3.7 18.6 - - + +
385B THR 3.3 10.3 + - - +
386B ARG* 3.1 9.7 + - - +
388B ARG* 1.3 79.4 - - - +
390B ARG* 1.3 62.9 + - - +
392B LEU* 3.4 4.4 + - - +
393B LEU* 2.9 25.7 + - - +
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Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.9 46.8 + - - +
362A TRP* 4.0 28.0 - - + -
313B MET* 3.8 26.8 - - + -
386B ARG* 2.9 17.2 + - - +
387B GLU* 2.5 37.9 + - - +
389B ALA* 1.3 77.4 - - - +
391B HIS* 1.3 83.1 + - - +
393B LEU* 3.3 6.1 + - + +
394B ALA* 3.0 28.8 + - + +
----------------------------------------------------------
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Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLU* 2.9 23.4 + - - +
390B ARG* 1.3 104.2 + - - +
392B LEU* 1.3 59.2 + - - +
394B ALA* 3.1 4.6 + - + -
395B SER* 2.7 39.9 + - - +
397B VAL 3.5 6.5 - - - +
398B SER* 3.6 19.8 - - - -
400B ILE* 4.6 16.5 - - + +
399D GLU* 2.5 32.4 + - - -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ARG* 2.7 30.7 + - - +
309B LEU* 3.9 25.8 - - + -
388B ARG* 3.0 51.5 + - + +
389B ALA* 3.8 4.5 - - - +
391B HIS* 1.3 75.5 - - - +
393B LEU* 1.3 55.2 + - - +
396B GLY 3.1 18.5 + - - +
397B VAL* 3.8 12.1 + - - +
398B SER* 3.9 26.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TRP* 4.5 12.1 - - + -
305B ARG* 3.5 14.6 + - - +
306B ASP* 3.5 50.2 - - + +
309B LEU* 3.7 13.9 - - + +
310B LEU* 3.9 26.2 - - + -
313B MET* 4.4 13.0 - - - -
389B ALA 2.9 18.1 + - - +
390B ARG* 3.5 6.3 - - + +
391B HIS 3.1 0.2 - - - -
392B LEU* 1.3 78.5 - - - +
394B ALA* 1.3 62.0 + - + +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ARG* 3.0 23.2 + - + +
391B HIS* 4.0 3.8 - - + +
393B LEU* 1.3 78.6 - - + +
395B SER* 1.3 61.6 + - - +
396B GLY 3.8 0.2 - - - -
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Residues in contact with SER 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B HIS* 2.7 16.6 + - - +
394B ALA* 1.3 76.8 - - - +
396B GLY* 1.3 56.1 + - - +
397B VAL* 2.4 52.1 + - - +
399D GLU* 5.2 2.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ARG* 3.8 14.2 + - - +
392B LEU* 3.1 31.9 + - - +
393B LEU 4.6 0.8 + - - -
394B ALA 3.8 0.6 - - - -
395B SER* 1.3 75.5 - - - +
397B VAL* 1.3 57.3 + - - +
----------------------------------------------------------
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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