Contacts of the helix formed by residues 329 - 359 (chain B) in PDB entry 2JIF
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 PHE 329 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN 3.5 25.4 - - - -
322B PHE* 3.7 13.0 - + + -
324B LYS* 3.6 34.8 - - + +
325B ARG 3.9 9.9 - - - -
326B LEU* 3.2 33.7 + - + +
327B PHE 4.0 0.4 - - - +
328B ASP* 1.3 75.6 - - - +
330B GLN* 1.3 61.7 - - - +
331B GLY 3.3 0.7 - - - -
332B LEU* 3.1 7.4 + - + +
333B GLN* 2.9 23.7 + - - +
330C GLN* 3.4 17.0 - - - +
1433D FAD 3.3 60.1 - + + +
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASN* 3.3 17.3 + - - +
1433A FAD 2.9 38.9 + - - -
328B ASP 3.4 5.3 + - - +
329B PHE* 1.3 71.6 - - - +
331B GLY* 1.3 57.6 + - - +
333B GLN* 3.1 13.8 + - - +
334B HIS* 2.8 50.2 + - + +
329C PHE* 3.4 16.0 - - - +
330C GLN* 3.4 13.6 + - + +
331C GLY* 2.9 26.6 + - - +
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Residues in contact with GLY 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLN* 1.3 76.6 - - - +
332B LEU* 1.3 62.2 + - - +
334B HIS* 3.4 4.7 + - - +
335B GLN* 3.2 33.9 + - - +
330C GLN* 3.0 19.2 + - - +
331C GLY* 4.1 10.1 - - - +
334C HIS* 3.6 21.5 - - - -
418D ASN* 4.5 0.4 - - - -
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE* 3.6 31.6 - - + -
326B LEU* 3.8 29.6 - - + +
327B PHE* 4.5 2.9 - - + -
329B PHE* 3.1 13.2 + - + +
331B GLY* 1.3 73.7 - - - +
333B GLN* 1.3 64.7 + - - +
335B GLN* 3.2 8.4 + - - +
336B VAL* 2.9 32.7 + - + +
388B TRP* 4.1 21.8 - - + +
330C GLN* 4.2 0.6 + - - -
418D ASN* 4.0 14.7 - - - +
1433D FAD 3.5 43.1 - - - +
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASN* 4.1 18.0 - - - +
425A ALA* 3.6 29.2 - - + +
426A LYS* 5.9 1.5 - - - +
327B PHE* 2.9 39.1 + - + +
328B ASP* 3.8 23.0 + - - +
329B PHE 2.9 9.0 + - - +
330B GLN* 3.1 18.1 + - - +
332B LEU* 1.3 75.6 - - - +
334B HIS* 1.3 61.1 + - + +
336B VAL* 3.3 9.0 + - - +
337B ALA* 2.8 31.2 + - - +
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Residues in contact with HIS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ASN* 3.5 41.2 + - + -
421A LEU* 3.5 35.3 - - + +
422A ASN* 2.7 29.9 + - - -
330B GLN* 2.8 42.0 + - + +
331B GLY* 3.7 5.8 - - - +
332B LEU 3.2 0.2 - - - -
333B GLN* 1.3 74.3 - - + +
335B GLN* 1.3 61.3 + - + +
337B ALA* 3.4 1.4 + - - +
338B HIS* 2.9 30.9 + - - +
331C GLY* 3.6 15.3 - - - -
335C GLN* 4.7 3.2 + - - -
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Residues in contact with GLN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLY 3.2 19.0 + - - +
332B LEU* 3.5 8.7 - - - +
334B HIS* 1.3 77.1 - - + +
336B VAL* 1.3 56.6 + - - +
338B HIS* 3.4 6.3 + - - +
339B VAL* 3.0 34.0 + - - +
384B LYS* 4.0 25.3 + - - +
387B GLU* 4.8 3.1 - - - +
388B TRP* 3.1 32.6 + - + +
334C HIS* 4.6 4.6 + - - -
418D ASN* 2.9 33.0 + - - +
421D LEU* 5.9 1.8 - - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ALA* 5.8 1.1 - - - -
428A ILE* 4.1 16.8 - - + -
309B PHE* 3.8 21.6 - - + -
313B ILE* 3.9 9.4 - - + -
316B ILE* 3.8 14.4 - - + -
327B PHE* 4.4 9.9 - - + -
332B LEU* 2.9 36.5 + - + +
333B GLN* 3.3 11.0 + - - +
335B GLN* 1.3 76.2 - - - +
337B ALA* 1.3 58.4 + - - +
339B VAL* 3.8 1.9 - - - +
340B ALA* 2.9 27.0 + - - +
388B TRP* 3.6 23.3 - - + -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 3.4 40.6 - - + +
424A ILE* 3.6 22.9 - - + +
425A ALA* 4.2 4.3 - - + +
428A ILE* 5.5 0.4 - - - -
333B GLN 2.8 18.6 + - - +
334B HIS 3.9 1.3 - - - +
336B VAL* 1.3 71.2 - - - +
338B HIS* 1.3 59.3 + - - +
340B ALA* 3.4 3.9 + - - +
341B THR* 2.8 34.1 + - - -
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Residues in contact with HIS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 2.9 34.9 + + - +
373A TYR* 6.3 3.1 - + - -
421A LEU* 4.1 6.4 - - + +
334B HIS 2.9 18.4 + - - +
335B GLN* 3.6 7.2 - - - +
337B ALA* 1.3 77.1 - - - +
339B VAL* 1.3 66.4 + - + +
341B THR* 3.1 16.7 + - - -
342B GLN* 3.1 49.9 + - + +
380B GLN* 4.9 2.7 + - - -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PHE* 3.7 16.6 - - + -
335B GLN* 3.0 20.8 + - - +
336B VAL 3.8 3.4 - - - +
338B HIS* 1.3 79.4 - - + +
340B ALA* 1.3 57.6 + - - +
342B GLN* 3.2 18.1 + - - +
343B LEU* 2.9 28.9 + - + +
380B GLN* 5.0 1.8 - - + +
381B THR* 3.5 42.2 - - + +
384B LYS* 4.3 17.0 - - + -
388B TRP* 3.8 19.1 - - + -
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A MET* 3.5 23.1 - - + +
424A ILE* 4.5 0.4 - - + -
428A ILE* 3.9 24.7 - - + -
309B PHE* 4.0 11.2 - - + -
336B VAL 2.9 20.7 + - - +
337B ALA* 3.6 9.4 - - - +
338B HIS 3.3 0.2 - - - -
339B VAL* 1.3 72.4 - - - +
341B THR* 1.3 56.6 + - - +
343B LEU* 3.4 9.8 + - - +
344B GLU* 3.0 23.4 + - - +
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Residues in contact with THR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 4.3 3.8 - - + +
369A MET* 3.6 49.5 - - + +
372A TYR* 4.3 12.0 - - + -
373A TYR* 3.9 25.1 - - + -
424A ILE* 3.8 9.2 - - - +
337B ALA 2.8 19.0 + - - -
338B HIS* 3.1 10.9 + - - -
340B ALA* 1.3 77.2 - - - +
342B GLN* 1.3 57.1 + - - +
344B GLU* 3.3 3.6 + - - +
345B ALA* 2.9 27.6 + - - +
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A TYR* 5.2 4.5 - - + -
338B HIS* 3.1 44.5 + - + +
339B VAL* 3.5 20.3 - - - +
341B THR* 1.3 74.3 - - - +
343B LEU* 1.3 58.9 + - - +
345B ALA 3.3 0.5 + - - -
346B ALA* 2.8 30.3 + - - +
373B TYR* 3.4 24.0 - - - +
377B ILE* 3.9 26.1 - - + +
380B GLN* 3.4 27.3 + - - +
381B THR* 5.2 1.7 + - - +
1438B CL 3.7 20.2 - - + +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 3.8 11.5 - - + +
305B ALA* 3.6 31.9 - - + -
306B GLN* 3.9 28.7 - - - +
309B PHE* 3.6 47.8 - - + -
339B VAL* 2.9 17.8 + - + +
340B ALA* 3.6 9.4 - - - +
342B GLN* 1.3 75.7 - - - +
344B GLU* 1.3 57.0 + - - +
346B ALA* 3.4 2.8 + - - +
347B ARG* 3.0 31.9 + - - +
377B ILE* 3.8 13.7 - - + -
381B THR* 4.1 6.5 - - + +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.4 21.8 - - + -
352A ASN* 4.1 18.9 + - - -
356A LEU* 5.5 0.2 - - - +
365A LYS* 4.8 8.8 + - - -
366A GLU* 4.1 17.2 - - + +
369A MET* 3.7 24.1 - - - +
340B ALA 3.0 13.4 + - - +
341B THR 3.4 8.7 - - - +
343B LEU* 1.3 73.6 - - - +
345B ALA* 1.3 64.4 + - - +
347B ARG* 3.4 17.9 + - - +
348B LEU* 3.1 33.5 + - + +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA* 3.9 20.7 - - + +
349A LEU* 4.0 19.7 - - + +
373A TYR* 5.0 3.1 - - + -
341B THR 2.9 16.7 + - - +
342B GLN 3.7 4.0 - - - +
344B GLU* 1.3 75.4 - - - +
346B ALA* 1.3 57.7 + - - +
348B LEU* 3.4 4.3 + - - +
349B LEU* 2.9 34.3 + - - +
373B TYR* 3.8 20.9 - - + +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 4.3 8.7 - - + -
342B GLN 2.8 18.2 + - - +
343B LEU 3.7 4.3 - - - +
345B ALA* 1.3 73.6 - - - +
347B ARG* 1.3 62.1 + - - +
349B LEU* 3.5 4.0 + - - +
350B THR* 2.8 31.2 + - - -
370B ALA 5.9 0.2 - - - -
373B TYR* 3.7 17.0 - - + -
374B ALA* 4.1 15.4 - - + +
377B ILE* 3.8 20.9 - - + -
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Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLU* 2.9 27.9 + - - -
130B LYS* 4.8 2.4 - - - +
302B LEU* 3.6 22.8 - - - +
306B GLN* 3.0 44.8 + - - +
343B LEU* 3.0 22.0 + - - +
344B GLU* 3.7 16.8 + - - +
346B ALA* 1.3 75.4 - - - +
348B LEU* 1.3 62.5 + - + +
350B THR* 3.2 1.6 + - - -
351B TYR* 2.9 63.9 + - + -
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.3 8.5 - - + +
348A LEU* 3.5 44.0 - - + +
349A LEU* 3.7 27.4 - - + +
352A ASN* 3.7 35.0 - - + +
344B GLU* 3.1 23.6 + - + +
345B ALA* 3.9 3.8 - - - +
347B ARG* 1.3 80.7 - - + +
349B LEU* 1.3 63.0 + - - +
351B TYR* 4.3 7.6 - - + +
352B ASN* 3.0 27.9 + - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A THR* 4.4 4.7 - - + +
344A GLU* 3.6 31.4 - - + -
345A ALA* 4.1 19.7 - - + +
348A LEU* 3.8 13.2 - - + -
345B ALA 2.9 22.6 + - - +
346B ALA* 3.8 3.6 - - - +
348B LEU* 1.3 76.3 - - - +
350B THR* 1.3 63.1 + - - +
352B ASN* 4.0 1.0 - - - +
353B ALA* 3.1 25.1 + - - +
366B GLU* 4.6 4.8 - - + +
369B MET* 4.3 16.2 - - + +
370B ALA* 3.9 14.9 - - - +
373B TYR* 3.6 41.3 - - + -
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Residues in contact with THR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 3.9 16.6 - - + -
295B ILE* 3.9 14.2 - - + +
298B ALA* 3.5 21.4 + - + +
299B ALA* 3.7 29.4 - - - +
302B LEU* 4.3 9.4 - - + +
346B ALA 2.8 22.5 + - - -
347B ARG 3.2 3.3 + - - -
349B LEU* 1.3 77.1 - - - +
351B TYR* 1.3 65.0 + - + +
353B ALA* 3.4 3.3 + - - +
354B ALA* 3.1 20.6 + - - +
370B ALA* 3.9 9.3 - - - +
374B ALA* 4.4 2.9 - - - +
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Residues in contact with TYR 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 3.5 28.7 - + - -
65B LYS* 5.2 5.0 + - - -
119B LEU* 4.4 15.8 - - + +
122B VAL* 4.4 10.1 - - + -
123B LEU* 3.6 19.2 - - + +
126B GLU* 2.6 35.8 + - - -
302B LEU* 4.2 7.4 - - + -
347B ARG* 2.9 49.5 + - + +
348B LEU* 4.3 8.1 - - + +
350B THR* 1.3 78.6 - - - +
352B ASN* 1.3 58.4 + - - +
354B ALA* 3.3 7.0 + - - +
355B ARG* 2.9 43.9 + - - +
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Residues in contact with ASN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO* 3.3 11.4 - - - +
54A LEU* 3.1 28.4 + - + +
55A GLN* 2.5 33.6 + - - +
344A GLU* 4.4 5.3 + - - -
348A LEU* 3.8 21.8 - - + +
348B LEU 3.0 19.9 + - - +
349B LEU 4.0 2.2 - - - +
351B TYR* 1.3 75.0 - - - +
353B ALA* 1.3 61.6 + - - +
355B ARG* 3.3 6.4 + - - +
356B LEU* 2.9 45.3 + - - +
366B GLU* 5.2 1.4 - - - +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.8 22.7 - - + +
349B LEU 3.1 18.8 + - - +
350B THR 3.6 5.4 - - - +
352B ASN* 1.3 75.1 - - - +
354B ALA* 1.3 57.9 + - - +
356B LEU* 3.4 5.8 + - - +
357B LEU* 3.0 28.1 + - - +
363B PHE* 4.0 3.9 - - - +
366B GLU* 3.9 36.9 - - + +
367B ALA* 4.0 2.2 - - + +
370B ALA* 4.5 3.1 - - + -
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 3.9 29.3 - - + -
119B LEU* 3.6 26.5 - - + -
122B VAL* 4.0 8.1 - - + -
295B ILE* 4.1 1.3 - - + +
350B THR 3.1 10.9 + - - +
351B TYR* 3.4 9.0 - - - +
352B ASN 3.2 0.2 - - - -
353B ALA* 1.3 80.0 - - - +
355B ARG* 1.3 57.1 + - - +
357B LEU* 3.4 4.0 + - - +
358B GLU* 3.0 33.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 3.7 37.7 + - - +
53A PRO* 4.1 19.6 - - + +
56B THR* 3.1 33.9 + - - +
57B PHE* 3.6 22.8 - - - +
61B GLU* 5.1 3.2 + - - -
119B LEU* 3.7 22.2 - - + +
351B TYR* 2.9 29.6 + - - +
352B ASN* 3.8 6.1 - - - +
354B ALA* 1.3 72.6 - - - +
356B LEU* 1.3 56.9 + - - +
358B GLU* 3.2 14.3 + - - +
359B ALA* 2.8 36.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO* 3.9 19.7 - - + -
55A GLN* 3.7 15.9 - - + +
352B ASN* 2.9 35.6 + - - +
353B ALA 3.6 4.7 - - - +
355B ARG* 1.3 71.8 - - - +
357B LEU* 1.3 63.9 + - - +
359B ALA* 3.4 1.4 + - - +
360B GLY 3.3 3.1 + - - -
361B LYS* 2.9 53.1 + - + +
362B PRO 3.8 11.7 - - - +
363B PHE* 4.0 3.4 - - + -
366B GLU* 3.6 42.6 - - + +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 3.9 33.9 - - + -
292B GLU* 3.8 36.3 - - + +
295B ILE* 4.1 3.1 - - + -
353B ALA 3.0 13.2 + - - +
354B ALA* 3.5 9.0 - - - +
356B LEU* 1.3 75.6 - - - +
358B GLU* 1.3 68.7 + - + +
360B GLY* 3.1 15.1 + - - -
361B LYS 4.5 0.4 - - - -
363B PHE* 3.9 43.8 - - + +
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 4.7 3.2 - - - +
117B SER* 3.3 13.2 - - - -
118B PHE* 3.2 23.6 + - + +
119B LEU* 2.9 39.6 + - - +
354B ALA 3.0 21.0 + - - +
355B ARG* 3.2 17.1 + - - +
357B LEU* 1.3 79.3 - - + +
359B ALA* 1.3 60.3 + - - +
360B GLY* 3.1 1.3 + - - -
----------------------------------------------------------
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO* 4.7 13.0 - - + -
355B ARG 2.8 21.3 + - - +
356B LEU* 3.9 1.6 - - - +
357B LEU 3.3 0.2 - - - -
358B GLU* 1.3 72.4 - - - +
360B GLY* 1.3 61.2 + - - +
361B LYS* 3.7 22.6 - - + +
----------------------------------------------------------
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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