Contacts of the helix formed by residues 329 - 359 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN* 3.4 16.8 - - - +
1433B FAD 3.2 61.9 - + + +
321D GLN 3.5 24.9 - - - -
322D PHE* 3.8 13.2 - + + -
324D LYS* 3.6 28.0 - - + +
325D ARG 3.8 10.3 - - - -
326D LEU* 3.1 31.1 + - + +
327D PHE 3.8 1.3 - - - +
328D ASP* 1.3 76.7 - - - +
330D GLN* 1.3 60.2 + - - +
331D GLY 3.3 0.7 - - - -
332D LEU* 3.1 7.0 + - + +
333D GLN* 2.9 24.3 + - - +
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Residues in contact with GLN 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A PHE* 3.4 10.0 - - - +
330A GLN* 3.4 20.2 + - + +
331A GLY* 2.9 26.8 + - - +
422C ASN* 3.4 17.8 + - - +
1433C FAD 3.0 36.9 + - - -
324D LYS* 5.4 0.4 - - - +
328D ASP 3.5 5.3 + - - +
329D PHE* 1.3 68.5 - - - +
331D GLY* 1.3 61.2 + - - +
333D GLN* 3.4 12.9 + - - +
334D HIS* 2.8 51.5 + - + +
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Residues in contact with GLY 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN* 2.9 19.4 + - - +
331A GLY* 4.1 9.4 - - - +
334A HIS* 3.7 20.9 - - - -
418B ASN* 4.4 0.9 - - - -
330D GLN* 1.3 76.7 - - - +
332D LEU* 1.3 62.0 + - - +
334D HIS* 3.4 4.6 + - - +
335D GLN* 3.2 32.4 + - - +
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN* 4.2 0.8 + - - -
418B ASN* 4.0 13.4 - - - +
1433B FAD 3.5 40.6 - - - +
316D ILE* 3.6 31.0 - - + -
326D LEU* 3.8 28.5 - - + +
327D PHE* 4.4 3.8 - - - -
329D PHE* 3.1 12.4 + - + +
331D GLY* 1.3 77.0 - - - +
333D GLN* 1.3 58.2 + - - +
335D GLN* 3.0 10.1 + - - +
336D VAL* 2.9 37.9 + - + +
388D TRP* 4.0 23.8 - - + +
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Residues in contact with GLN 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ASN* 4.1 18.9 - - - +
425C ALA* 3.6 29.6 - - + +
426C LYS* 6.1 0.3 - - - +
327D PHE* 3.0 39.8 + - + +
328D ASP* 3.8 21.6 + - - +
329D PHE 2.9 7.8 + - - +
330D GLN* 3.2 16.2 + - - +
332D LEU* 1.3 78.0 - - - +
334D HIS* 1.3 62.5 + - + +
336D VAL* 3.3 8.5 + - - +
337D ALA* 2.9 30.1 + - - +
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Residues in contact with HIS 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLY* 3.7 15.0 - - - -
335A GLN* 4.7 2.8 + - - -
418C ASN* 3.5 42.7 + - + -
421C LEU* 3.7 31.5 - - + +
422C ASN* 2.8 29.5 + - - -
330D GLN* 2.8 44.7 + - + +
331D GLY* 3.7 5.4 - - - +
333D GLN* 1.3 74.9 - - + +
335D GLN* 1.3 59.8 + - + +
337D ALA* 3.8 1.2 - - - +
338D HIS* 2.9 31.8 + - - +
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Residues in contact with GLN 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A HIS* 4.8 3.6 + - - -
418B ASN* 3.0 31.9 + - - +
421B LEU* 6.0 1.2 - - - +
331D GLY 3.2 16.9 + - - +
332D LEU* 3.0 9.6 + - - +
334D HIS* 1.3 76.5 - - + +
336D VAL* 1.3 57.4 + - - +
338D HIS* 3.4 6.0 + - - +
339D VAL* 3.0 34.3 + - - +
384D LYS* 4.1 28.4 + - + +
387D GLU* 4.7 2.6 - - - +
388D TRP* 3.0 33.6 + - + +
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Residues in contact with VAL 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ALA* 5.7 0.4 - - + -
428C ILE* 3.9 24.7 - - + -
309D PHE* 3.8 4.4 - - + -
313D ILE* 3.8 20.4 - - + -
316D ILE* 3.7 27.1 - - + -
327D PHE* 4.3 9.9 - - + -
332D LEU* 2.9 24.6 + - + +
333D GLN* 3.6 10.5 - - - +
335D GLN* 1.3 76.8 - - - +
337D ALA* 1.3 55.9 + - - +
339D VAL* 3.4 2.8 + - - +
340D ALA* 2.9 28.1 + - - +
388D TRP* 3.7 23.3 - - + -
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU* 3.4 41.7 - - + +
424C ILE* 3.6 21.9 - - + +
425C ALA* 4.1 4.0 - - - +
428C ILE* 4.0 3.6 - - - -
333D GLN 2.9 16.0 + - - +
334D HIS 3.9 1.3 - - - +
336D VAL* 1.3 74.7 - - - +
338D HIS* 1.3 62.1 + - - +
340D ALA* 3.4 2.4 + - - +
341D THR* 2.9 29.7 + - - -
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Residues in contact with HIS 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C TYR* 2.7 34.4 + + - +
373C TYR* 6.3 2.7 - + - -
421C LEU* 3.9 9.8 - - + +
334D HIS 2.9 18.4 + - - +
335D GLN* 3.8 6.1 - - - +
337D ALA* 1.3 75.2 - - - +
339D VAL* 1.3 66.4 + - + +
341D THR* 3.2 8.9 + - - -
342D GLN* 3.1 58.9 + - + +
380D GLN* 4.9 2.5 + - - -
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D PHE* 3.7 24.5 - - + -
335D GLN* 3.0 20.5 + - + +
336D VAL 3.7 3.1 - - - +
338D HIS* 1.3 77.1 - - + +
340D ALA* 1.3 59.6 + - - +
342D GLN* 3.2 18.7 + - - +
343D LEU* 2.9 28.5 + - + +
380D GLN* 5.0 1.3 - - + +
381D THR* 3.5 34.3 - - + +
384D LYS* 4.3 17.0 - - + -
388D TRP* 3.8 19.3 - - + -
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Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C MET* 3.7 15.8 - - + +
428C ILE* 3.4 34.3 - - + -
309D PHE* 3.9 14.8 - - + -
336D VAL 2.9 14.2 + - - +
337D ALA 3.6 4.3 - - - +
338D HIS 3.3 0.2 - - - -
339D VAL* 1.3 73.6 - - - +
341D THR* 1.3 58.1 + - - +
343D LEU* 3.3 8.4 + - - +
344D GLU* 2.9 29.1 + - - +
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Residues in contact with THR 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C LEU* 4.5 3.9 - - + +
369C MET* 3.5 48.9 - - + +
372C TYR* 4.2 14.7 - - + -
373C TYR* 4.0 25.4 - - + -
424C ILE* 3.7 10.2 - - - +
337D ALA 2.9 15.6 + - - -
338D HIS 3.2 8.5 + - - -
340D ALA* 1.3 76.8 - - - +
342D GLN* 1.3 58.1 + - - +
344D GLU* 3.2 3.6 + - - +
345D ALA* 2.9 27.6 + - - +
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Residues in contact with GLN 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C TYR* 5.2 4.0 - - + -
338D HIS* 3.1 43.3 + - + +
339D VAL* 3.2 19.5 + - - +
341D THR* 1.3 74.0 - - - +
343D LEU* 1.3 59.5 + - - +
345D ALA* 3.4 0.7 + - - -
346D ALA* 2.8 30.8 + - - +
373D TYR* 3.4 24.7 - - - +
377D ILE* 3.9 25.0 - - + +
380D GLN* 3.2 30.5 + - - +
381D THR* 5.1 2.2 + - - +
1441D CL 3.8 20.3 - - + +
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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
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302D LEU* 3.6 12.7 - - + +
305D ALA* 3.5 36.1 - - + -
306D GLN* 3.9 25.1 - - - +
309D PHE* 3.7 46.2 - - + -
339D VAL* 2.9 18.4 + - + +
340D ALA* 3.5 9.2 - - - +
342D GLN* 1.3 75.0 - - - +
344D GLU* 1.3 57.5 + - - +
346D ALA* 3.4 0.8 + - - -
347D ARG* 2.9 33.2 + - - +
377D ILE* 3.7 14.4 - - + -
381D THR* 4.0 6.3 - - - +
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C LEU* 3.5 21.1 - - + -
352C ASN* 4.3 12.5 + - - -
365C LYS* 4.6 9.5 + - - -
366C GLU* 3.8 23.7 - - + +
369C MET* 3.7 23.3 - - - +
340D ALA 2.9 13.5 + - - +
341D THR 3.4 8.5 - - - +
343D LEU* 1.3 74.0 - - - +
345D ALA* 1.3 64.5 + - - +
347D ARG* 3.3 18.2 + - - +
348D LEU* 3.0 35.5 + - + +
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Residues in contact with ALA 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C ALA* 3.8 21.7 - - + +
349C LEU* 4.1 20.3 - - + +
373C TYR* 4.8 2.5 - - + -
341D THR 2.9 16.2 + - - +
342D GLN* 3.7 4.5 - - - +
344D GLU* 1.3 76.8 - - - +
346D ALA* 1.3 56.5 + - - +
348D LEU* 3.3 4.1 + - - +
349D LEU* 2.9 34.3 + - - +
373D TYR* 3.8 21.5 - - + +
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D LEU* 4.1 10.5 - - + -
342D GLN 2.8 20.6 + - - +
343D LEU 3.7 4.7 - - - +
344D GLU 3.3 0.2 - - - -
345D ALA* 1.3 72.4 - - - +
347D ARG* 1.3 60.4 + - - +
349D LEU* 3.8 3.7 - - - +
350D THR* 2.8 31.1 + - - -
370D ALA 5.5 0.4 - - - +
373D TYR* 3.7 19.9 - - + -
374D ALA* 4.1 15.2 - - + +
377D ILE* 4.0 17.3 - - + -
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Residues in contact with ARG 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLN* 5.7 5.4 - - - -
126D GLU* 3.0 28.9 + - - -
130D LYS* 5.0 1.4 - - - +
302D LEU* 3.6 25.7 - - + +
306D GLN* 2.9 43.4 + - - +
343D LEU* 2.9 22.2 + - - +
344D GLU* 3.6 19.0 + - - +
345D ALA 3.3 0.2 - - - -
346D ALA* 1.3 77.2 - - - +
348D LEU* 1.3 61.8 + - + +
350D THR* 3.3 0.7 + - - -
351D TYR* 3.0 64.0 + - + -
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LEU* 3.6 44.4 - - + +
349C LEU* 3.8 26.5 - - + +
352C ASN* 4.0 24.2 - - + +
54D LEU* 3.5 33.7 - - + +
55D GLN* 5.3 2.9 - - + +
344D GLU* 3.0 23.0 + - + +
345D ALA* 3.8 3.8 - - - +
347D ARG* 1.3 81.2 - - + +
349D LEU* 1.3 57.2 + - - +
351D TYR* 5.6 0.9 - - + -
352D ASN* 2.9 33.6 + - - +
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C THR* 4.3 6.3 - - + +
344C GLU* 3.4 37.5 - - + -
345C ALA* 4.0 16.6 - - + +
348C LEU* 3.7 13.0 - - + -
345D ALA 2.9 18.8 + - - +
346D ALA* 3.8 4.5 - - - +
348D LEU* 1.3 77.1 - - - +
350D THR* 1.3 61.2 + - - +
352D ASN* 4.0 0.7 - - - +
353D ALA* 3.1 25.3 + - - +
366D GLU* 4.6 4.0 - - + +
369D MET* 4.3 15.3 - - + +
370D ALA* 3.7 14.4 - - + +
373D TYR* 3.7 40.2 - - + -
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Residues in contact with THR 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D VAL* 3.9 20.2 - - + -
295D ILE* 3.7 14.7 - - + +
298D ALA* 3.4 20.5 + - + +
299D ALA* 3.8 24.5 - - - +
302D LEU* 4.4 7.6 - - + +
346D ALA 2.8 22.4 + - - -
347D ARG 3.7 3.6 - - - -
349D LEU* 1.3 73.5 - - - +
351D TYR* 1.3 69.8 + - + +
353D ALA* 3.4 4.5 + - - +
354D ALA* 3.2 21.1 + - - +
370D ALA* 3.9 9.5 - - - +
374D ALA* 4.5 3.1 - - - +
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Residues in contact with TYR 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LEU* 3.5 39.0 - - + +
55D GLN* 4.6 5.6 - - + -
57D PHE* 3.7 21.4 - + - -
65D LYS* 5.1 4.7 + - - -
119D LEU* 4.2 10.7 - - + +
122D VAL* 4.2 16.6 - - + -
123D LEU* 3.4 19.8 - - + +
126D GLU* 2.5 36.1 + - - -
302D LEU* 4.2 7.2 - - + -
347D ARG* 3.0 50.1 + - + +
348D LEU* 5.6 0.4 - - + -
350D THR* 1.3 78.9 - - - +
352D ASN* 1.3 58.6 + - - +
354D ALA* 3.3 7.6 + - - +
355D ARG* 2.9 32.7 + - - +
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Residues in contact with ASN 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLU* 4.2 5.9 + - - -
347C ARG* 4.0 13.3 - - - +
348C LEU* 3.9 28.2 - - + +
54D LEU* 3.9 22.6 - - + +
348D LEU 2.9 19.8 + - - +
349D LEU 4.0 2.0 - - - +
351D TYR* 1.3 74.3 - - - +
353D ALA* 1.3 58.7 + - - +
355D ARG* 3.2 4.9 + - - +
356D LEU* 2.9 52.4 + - - +
366D GLU* 4.9 2.0 - - - +
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Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D ILE* 3.8 27.2 - - + +
349D LEU 3.1 18.9 + - - +
350D THR 3.6 4.9 - - - +
351D TYR 3.4 0.2 - - - -
352D ASN* 1.3 75.1 - - - +
354D ALA* 1.3 56.0 + - - +
356D LEU* 3.3 5.3 + - - +
357D LEU* 3.0 28.2 + - - +
363D PHE* 4.0 3.9 - - - +
366D GLU* 3.9 34.9 - - + +
367D ALA* 4.0 1.8 - - - +
370D ALA* 4.6 2.0 - - + -
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Residues in contact with ALA 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D PHE* 3.7 31.4 - - + -
119D LEU* 4.0 18.4 - - + -
122D VAL* 3.9 13.9 - - + -
295D ILE* 4.1 1.7 - - + +
350D THR 3.2 11.5 + - - +
351D TYR 3.5 8.3 - - - +
352D ASN 3.2 0.2 - - - -
353D ALA* 1.3 77.5 - - - +
355D ARG* 1.3 57.5 + - - +
357D LEU* 3.4 4.4 + - - +
358D GLU* 3.0 34.0 + - - +
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Residues in contact with ARG 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO 4.4 1.7 + - - -
54D LEU* 2.8 57.3 + - + +
56D THR 3.1 24.8 + - - -
57D PHE* 3.9 2.4 - - - -
61D GLU* 5.0 3.2 + - - -
119D LEU* 3.6 30.1 - - + +
351D TYR* 2.9 16.9 + - - +
352D ASN* 3.8 6.7 - - - +
354D ALA* 1.3 73.7 - - - +
356D LEU* 1.3 62.4 + - - +
358D GLU* 3.3 18.3 + - - +
359D ALA* 2.9 31.1 + - - +
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Residues in contact with LEU 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ARG* 6.1 0.2 - - - +
352D ASN* 2.9 39.1 + - - +
353D ALA 3.6 4.0 - - - +
355D ARG* 1.3 73.4 - - - +
357D LEU* 1.3 65.6 + - - +
359D ALA* 3.2 7.3 + - - -
361D LYS* 3.0 50.3 + - + +
362D PRO* 3.8 13.9 - - + +
363D PHE* 3.9 3.1 - - + -
366D GLU* 3.4 46.4 - - + +
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Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D PHE* 3.8 44.2 - - + -
292D GLU* 3.7 37.7 - - + +
295D ILE* 4.1 3.4 - - + -
353D ALA 3.0 13.8 + - - +
354D ALA* 3.5 8.7 - - - +
355D ARG 3.3 0.2 - - - -
356D LEU* 1.3 74.3 - - - +
358D GLU* 1.3 66.6 + - + +
360D GLY* 3.1 14.7 + - - -
361D LYS 4.7 0.2 - - - -
363D PHE* 3.9 35.8 - - + +
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Residues in contact with GLU 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLU* 4.7 2.8 - - - +
117D SER* 3.2 21.6 - - - -
118D PHE* 3.2 16.5 + - + +
119D LEU* 2.9 38.9 + - - +
354D ALA 3.0 18.3 + - - +
355D ARG* 3.3 22.6 + - - +
357D LEU* 1.3 78.5 - - + +
359D ALA* 1.3 60.6 + - - +
360D GLY 3.2 1.4 + - - -
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Residues in contact with ALA 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ARG 2.9 16.8 + - - +
356D LEU* 3.2 6.6 + - + +
358D GLU* 1.3 74.1 - - - +
360D GLY* 1.3 60.3 + - - +
361D LYS* 3.4 27.1 + - + +
----------------------------------------------------------
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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