Contacts of the helix formed by residues 394 - 424 (chain B) in PDB entry 5U3Y
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 TYR 394 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA 4.1 1.2 + - - -
393B GLN* 1.3 88.4 + - + +
395B LEU* 1.3 58.7 + - - +
396B PHE 3.4 2.2 - - - -
397B PRO* 3.3 21.3 - - + +
398B LYS* 3.0 40.9 + - + +
504B PEG 3.7 31.2 + - - -
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.9 46.4 - - + +
343B LEU* 4.2 8.3 - - + -
385B LEU* 3.8 29.6 - - + -
389B HIS* 3.9 26.7 - - + +
392B ALA* 4.1 24.4 + - + -
393B GLN 3.1 4.1 + - - +
394B TYR* 1.3 77.7 - - - +
396B PHE* 1.3 57.6 + - - +
398B LYS* 3.2 7.5 + - + +
399B LEU* 2.9 38.2 + - + +
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Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.5 44.0 - - + -
381B LEU* 4.2 15.7 - - + -
382B GLU* 3.4 49.6 - - + +
385B LEU* 4.0 21.3 - - + +
395B LEU* 1.3 78.0 - - - +
397B PRO* 1.3 73.9 - - + +
399B LEU* 3.0 15.2 + - + +
400B LEU* 3.0 40.2 + - + +
504B PEG 6.0 4.3 - - - -
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Residues in contact with PRO 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TYR* 3.3 40.2 - - + +
396B PHE* 1.3 101.2 - - + +
398B LYS* 1.3 58.7 + - - -
400B LEU* 3.2 15.2 + - + +
401B GLN* 3.0 22.7 + - - +
504B PEG 4.5 27.8 - - - +
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Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.0 29.4 - - + +
393B GLN* 3.2 22.0 + - - +
394B TYR* 3.0 33.8 + - + +
395B LEU* 3.2 10.8 - - + +
396B PHE 3.1 0.2 - - - -
397B PRO* 1.3 77.3 - - - +
399B LEU* 1.3 57.1 + - - +
401B GLN* 3.2 9.6 + - - +
402B LYS* 3.1 32.0 + - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PHE* 4.2 6.5 - - + -
341B LEU* 3.6 25.4 - - + -
343B LEU* 3.7 38.6 - - + -
351B PHE* 3.5 27.1 - - + -
381B LEU* 4.5 11.7 - - + -
385B LEU* 3.7 31.2 - - + -
395B LEU* 2.9 18.2 + - + +
396B PHE* 3.0 7.2 + - + +
398B LYS* 1.3 72.8 - - - +
400B LEU* 1.3 67.1 + - + +
402B LYS* 3.1 5.5 + - - +
403B MET* 3.0 27.0 + - + +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.9 33.4 - - + -
396B PHE* 3.0 46.4 + - + +
397B PRO* 3.2 13.9 + - + +
399B LEU* 1.3 77.1 - - + +
401B GLN* 1.3 62.0 + - - +
403B MET* 3.3 19.9 + - + +
404B ALA* 3.2 18.7 + - - +
504B PEG 4.9 11.7 - - - +
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PRO 3.0 12.5 + - - +
398B LYS* 3.2 10.7 + - - +
400B LEU* 1.3 75.4 - - - +
402B LYS* 1.3 60.8 + - + +
404B ALA* 3.1 16.8 + - - +
405B ASP* 2.8 59.5 + - - +
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 4.2 13.2 - - + -
337B LYS* 3.9 32.1 + - - +
338B PHE* 4.0 37.4 - - + +
341B LEU* 3.9 29.2 - - + -
351B PHE* 4.2 2.9 - - + -
398B LYS* 3.1 15.7 + - - +
399B LEU* 3.1 9.6 + - - +
401B GLN* 1.3 76.5 - - + +
403B MET* 1.3 56.9 + - - +
405B ASP* 3.1 20.4 + - - +
406B LEU* 2.7 35.5 + - - +
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Residues in contact with MET 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 4.7 2.8 - - - +
351B PHE* 3.6 35.0 - - + +
354B ALA* 3.6 32.1 - - + +
355B ILE* 4.5 12.6 - - + -
374B GLN* 5.8 5.2 - - - -
378B LEU* 3.9 16.2 - - + -
381B LEU* 4.4 7.2 - - + -
399B LEU* 3.0 16.0 + - + +
400B LEU* 3.4 26.9 - - + +
402B LYS* 1.3 76.9 - - - +
404B ALA* 1.3 61.8 + - - +
406B LEU* 3.4 11.0 + - - +
407B ARG* 3.2 29.4 + - - +
502B PGO 5.5 1.8 - - + -
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU 3.2 8.2 + - - +
401B GLN* 3.1 24.0 + - - +
403B MET* 1.3 75.3 - - - +
405B ASP* 1.3 67.3 + - - +
407B ARG* 3.1 13.4 + - - +
408B GLN* 3.3 12.0 + - - +
502B PGO 4.0 34.9 + - + +
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Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 3.9 18.5 - - + -
401B GLN* 2.8 46.1 + - - +
402B LYS* 3.1 30.1 + - - +
404B ALA* 1.3 74.0 - - - +
406B LEU* 1.3 57.3 + - - +
408B GLN* 3.1 8.8 + - - +
409B LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 3.6 31.4 - - + +
291B PHE* 4.0 12.1 - - + -
292B ALA* 3.8 19.5 - - + +
334B PHE* 3.4 34.8 - - + -
351B PHE* 4.0 11.0 - - + -
355B ILE* 3.8 28.3 - - + -
402B LYS 2.7 22.4 + - - +
403B MET* 3.7 7.2 - - - +
404B ALA 3.2 0.4 - - - -
405B ASP* 1.3 73.1 - - - +
407B ARG* 1.3 58.5 + - - +
409B LEU* 3.3 8.4 + - + +
410B VAL* 3.0 34.7 + - - +
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Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 3.2 26.2 + - - +
358B CYS* 3.0 26.0 - - - -
360B ASP* 2.7 38.7 + - - +
361B ARG* 4.3 9.0 - - - +
374B GLN* 4.8 4.8 - - - +
403B MET* 3.2 16.2 + - - +
404B ALA 3.1 7.9 + - - +
406B LEU* 1.3 77.2 - - - +
408B GLN* 1.3 60.4 + - - +
410B VAL* 3.5 1.8 + - - +
411B THR* 2.9 30.0 + - - +
502B PGO 3.7 47.1 + - - +
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Residues in contact with GLN 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ALA 3.3 7.4 + - - +
405B ASP* 3.1 11.1 + - - +
407B ARG* 1.3 77.0 - - - +
409B LEU* 1.3 65.2 + - - +
411B THR* 3.2 13.7 + - - +
412B GLU* 2.9 66.0 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 4.0 33.9 - - + -
330B PRO* 3.9 36.6 - - + +
331B LYS* 4.4 15.4 + - + +
334B PHE* 4.0 31.0 - - + -
405B ASP 2.9 15.9 + - - +
406B LEU* 3.3 10.1 + - + +
408B GLN* 1.3 77.5 - - - +
410B VAL* 1.3 56.4 + - - +
412B GLU* 3.7 13.2 + - + +
413B HIS* 3.0 25.5 + - - +
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR 5.7 3.4 - - - +
287B HIS* 3.9 17.5 - - + +
288B GLU* 3.6 38.1 - - + +
291B PHE* 3.7 22.0 - - + -
406B LEU* 3.0 21.3 + - + +
407B ARG* 4.1 2.9 - - - +
409B LEU* 1.3 75.4 - - + +
411B THR* 1.3 61.1 - - - +
413B HIS* 3.5 8.0 - - + +
414B ALA* 2.8 33.0 + - + +
437B TYR* 6.1 1.6 - - + -
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Residues in contact with THR 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ARG* 2.9 19.8 + - - +
408B GLN* 3.2 18.9 + - - +
410B VAL* 1.3 77.4 - - - +
412B GLU* 1.3 62.4 + - + +
414B ALA* 3.3 6.2 + - - +
415B GLN* 3.0 42.4 + - + +
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Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B PRO* 5.4 5.0 - - - +
408B GLN* 2.9 47.1 + - - +
409B LEU* 4.0 15.3 - - + +
411B THR* 1.3 75.3 - - + +
413B HIS* 1.3 62.9 + - - +
415B GLN* 3.2 16.5 + - - +
416B MET* 3.0 35.3 + - + +
----------------------------------------------------------
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Residues in contact with HIS 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B HIS* 4.3 4.0 - + + -
291B PHE* 4.0 23.2 - + + -
327B ILE* 3.4 27.7 - - + +
331B LYS* 3.0 25.9 + - - +
409B LEU 3.0 20.2 + - - +
410B VAL* 3.2 8.9 + - + +
412B GLU* 1.3 76.1 - - - +
414B ALA* 1.3 57.8 + - - +
416B MET* 3.2 13.7 + - - +
417B MET* 3.0 29.3 + - + +
437B TYR* 2.9 18.0 + + - -
501B 7U7 2.5 45.8 + - + -
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Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B VAL* 2.8 22.8 + - + +
411B THR* 3.7 6.7 - - - +
412B GLU 3.3 0.2 - - - -
413B HIS* 1.3 73.1 - - - +
415B GLN* 1.3 62.6 + - - +
417B MET* 3.3 2.9 + - - +
418B GLN* 3.0 23.0 + - - +
437B TYR* 3.9 31.2 - - + -
----------------------------------------------------------
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B THR* 3.0 34.5 + - + +
412B GLU* 3.2 17.1 + - - +
414B ALA* 1.3 77.0 - - + +
416B MET* 1.3 62.6 + - + +
418B GLN* 3.2 14.2 + - - +
419B ARG* 3.1 20.1 + - - +
----------------------------------------------------------
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PRO* 5.4 6.4 - - + +
326B ASP* 3.6 31.4 - - - +
327B ILE* 3.7 23.3 - - + -
330B PRO* 4.6 9.4 - - + -
331B LYS* 3.7 26.0 - - - +
412B GLU* 3.0 30.3 + - + +
413B HIS* 3.6 9.2 - - - +
415B GLN* 1.3 76.9 - - + +
417B MET* 1.3 58.0 + - - +
419B ARG* 3.1 10.1 + - - +
420B ILE* 3.0 31.6 + - + +
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Residues in contact with MET 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PHE* 3.8 20.9 - - + -
327B ILE* 3.4 22.2 - - + -
413B HIS* 3.0 32.6 + - - +
414B ALA* 3.6 9.0 - - - +
415B GLN 3.2 0.2 - - - -
416B MET* 1.3 77.3 - - - +
418B GLN* 1.3 56.2 + - - +
420B ILE* 3.2 6.9 + - + +
421B LYS* 2.9 27.5 + - - +
429B LEU* 3.7 28.9 - - + +
437B TYR* 3.9 25.6 - - + -
501B 7U7 3.6 31.0 - - + +
----------------------------------------------------------
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Residues in contact with GLN 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ALA 3.0 13.5 + - - +
415B GLN* 3.2 15.1 + - - +
417B MET* 1.3 75.5 - - - +
419B ARG* 1.3 62.2 + - - +
421B LYS* 3.3 11.9 + - + +
422B LYS* 3.1 56.5 + - + +
439B ASP 6.1 2.7 - - - -
----------------------------------------------------------
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PRO* 5.1 13.5 - - + -
415B GLN 3.1 11.9 + - - +
416B MET* 3.1 13.9 + - - +
418B GLN* 1.3 76.1 - - - +
420B ILE* 1.3 53.8 + - + +
422B LYS* 3.1 5.3 + - - -
423B THR* 2.7 60.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PHE* 4.0 41.7 - - + -
323B PRO* 3.6 30.3 - - + +
324B PHE* 4.1 15.3 - - + -
327B ILE* 4.1 16.4 - - + -
416B MET* 3.0 18.1 + - + +
417B MET* 3.6 9.6 - - + +
419B ARG* 1.3 75.0 - - - +
421B LYS* 1.3 60.0 + - - +
423B THR* 4.0 5.2 - - - -
424B GLU* 2.8 47.6 + - + +
427B THR* 4.6 6.7 - - + -
----------------------------------------------------------
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B MET 2.9 12.7 + - - +
418B GLN* 3.5 15.0 - - + +
420B ILE* 1.3 80.1 - - - +
422B LYS* 1.3 90.7 + - - +
424B GLU 4.6 5.2 + - - +
425B THR* 4.9 5.2 - - - -
429B LEU* 6.0 7.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLN* 3.2 44.7 - - + +
419B ARG* 3.1 6.9 + - - +
421B LYS* 1.3 105.6 - - + +
423B THR* 1.3 66.4 + - + +
425B THR* 5.2 3.5 + - - -
----------------------------------------------------------
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Residues in contact with THR 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PRO* 5.0 3.1 - - - +
419B ARG* 2.7 53.7 + - - +
420B ILE* 4.0 0.3 - - - -
422B LYS* 1.3 86.5 - - + +
424B GLU* 1.3 78.4 + - - +
425B THR* 3.4 8.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ARG* 2.9 44.0 + - - -
323B PRO* 3.6 16.5 - - + +
324B PHE* 4.0 11.8 - - + -
420B ILE* 2.8 36.1 + - + +
421B LYS* 4.9 0.9 - - - +
423B THR* 1.3 91.4 + - - +
425B THR* 1.3 64.0 + - - +
426B GLU* 3.1 3.1 - - - -
427B THR* 2.9 33.1 + - - +
----------------------------------------------------------
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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