Contacts of the helix formed by residues 392 - 417 (chain A) in PDB entry 5UQ9
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 ASP 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ALA* 2.9 22.1 - - - +
382A ARG* 2.7 37.9 + - - -
386A LEU* 4.1 16.8 - - + -
388A ASN 4.2 0.2 + - - -
389A LEU 3.4 14.0 + - - +
390A LEU 3.1 2.4 - - - -
391A LEU* 1.3 79.1 - - - +
393A ASP* 1.3 76.4 + - - +
394A PHE 3.9 3.6 + - - -
395A PHE* 3.5 13.5 - - + -
396A LYS* 2.8 32.5 + - - +
79H GLN* 5.3 1.6 - - - +
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ARG* 5.9 0.2 - - - +
391A LEU 4.1 1.2 + - - +
392A ASP* 1.3 83.6 + - - +
394A PHE* 1.3 62.3 + - - +
396A LYS* 3.5 28.6 + - - +
397A SER* 3.0 29.3 + - - -
303B LYS* 5.1 4.9 + - - -
79H GLN* 5.0 19.2 - - - +
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Residues in contact with PHE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 6.0 3.1 - - + -
328A TYR* 3.4 25.8 - - - -
372A PHE* 5.4 0.2 - + - -
375A LYS* 3.6 52.7 - - + -
382A ARG* 3.9 21.5 - - - +
392A ASP* 3.4 5.9 + - - +
393A ASP* 1.3 78.6 - - - +
395A PHE* 1.3 79.5 + + + +
397A SER* 4.2 2.8 - - - -
398A ALA* 3.2 25.1 + - + +
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 4.0 28.9 - - + +
372A PHE* 3.4 33.2 - + - -
375A LYS* 3.9 6.5 - - + -
376A ILE* 3.5 31.2 - - + -
379A ALA* 3.5 25.6 - - + -
389A LEU* 3.5 39.7 - - + +
390A LEU* 4.8 2.2 - - - -
392A ASP* 3.4 15.8 + - + +
393A ASP 3.2 0.2 - - - -
394A PHE* 1.3 92.5 - + - +
396A LYS* 1.3 60.6 + - - +
397A SER 3.2 1.8 - - - -
398A ALA* 3.9 3.2 - - - +
399A VAL* 3.0 35.7 + - - +
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Residues in contact with LYS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.4 17.3 + - - +
392A ASP 2.8 24.9 + - - +
393A ASP* 3.5 32.2 + - - +
395A PHE* 1.3 74.6 - - - +
397A SER* 1.3 69.7 + - - +
399A VAL* 3.8 4.4 + - - +
400A GLU* 3.1 24.8 + - - +
430A TYR* 5.4 1.6 + - - -
303B LYS* 3.8 39.9 + - - +
304B LEU* 3.9 16.7 - - + +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASP 3.0 20.0 + - - -
394A PHE* 4.2 2.9 - - - -
396A LYS* 1.3 86.6 - - - +
398A ALA* 1.3 59.5 + - - +
400A GLU* 3.3 7.7 + - - +
401A ASN* 2.9 47.0 + - - -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TYR* 3.6 32.3 - - + +
332A ILE* 3.7 12.3 - - + -
394A PHE* 3.2 23.2 + - + +
395A PHE* 3.4 1.1 + - - +
397A SER* 1.3 76.6 - - - +
399A VAL* 1.3 57.8 + - - +
401A ASN* 3.4 8.0 + - - +
402A CYS* 3.0 35.9 + - - -
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ALA* 4.9 6.0 - - + +
332A ILE* 3.9 28.3 - - + -
333A ILE* 4.2 12.1 - - + -
390A LEU* 4.3 7.2 - - + -
395A PHE 3.0 21.6 + - - +
396A LYS* 4.0 5.6 - - - +
398A ALA* 1.3 74.6 - - - +
400A GLU* 1.3 58.4 + - - +
402A CYS* 3.2 4.8 + - - +
403A GLN* 2.8 31.1 + - + +
406A TRP* 4.5 13.0 - - + -
430A TYR* 3.6 42.2 - - + +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LYS 3.1 19.2 + - - +
397A SER* 3.3 9.6 + - - +
399A VAL* 1.3 78.5 - - - +
401A ASN* 1.3 64.2 + - - +
402A CYS 3.5 0.3 + - - -
403A GLN* 3.6 27.8 + - - +
404A ASP* 4.8 1.4 + - - +
430A TYR* 5.0 2.6 + - - -
305B LYS* 3.6 30.1 + - - +
308B GLN* 3.9 26.8 + - - +
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Residues in contact with ASN 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 3.5 20.5 + - - +
397A SER* 2.9 36.0 + - - +
398A ALA* 3.9 8.0 - - - +
400A GLU* 1.3 80.8 - - - +
402A CYS* 1.3 62.6 + - - +
404A ASP* 5.1 2.3 + - - +
405A SER* 5.5 1.6 + - - -
114G ARG* 6.2 1.8 - - - -
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Residues in contact with CYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ARG* 5.8 1.3 - - - -
325A LYS* 3.5 48.3 - - + +
328A TYR* 3.8 24.2 - - - -
329A ALA* 3.8 11.9 - - + -
398A ALA* 3.0 24.4 + - - +
399A VAL 3.2 1.3 + - - +
401A ASN* 1.3 79.5 - - - +
403A GLN* 1.3 58.6 + - - +
404A ASP 3.4 2.7 - - - -
405A SER* 3.5 2.7 + - - +
406A TRP* 2.8 30.9 + - - +
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Residues in contact with GLN 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A VAL* 2.8 17.2 + - + +
400A GLU* 3.6 29.5 + - - +
401A ASN 3.5 2.0 - - - -
402A CYS* 1.3 77.4 - - - +
404A ASP* 1.3 63.6 + - - +
406A TRP* 3.2 13.3 + - + +
407A ARG* 2.6 72.4 + - + +
430A TYR* 3.7 12.5 + - + -
305B LYS 3.5 6.9 + - - +
306B GLY* 2.8 36.7 + - - -
307B PRO* 3.9 3.2 - - + +
308B GLN* 4.9 1.8 - - - +
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Residues in contact with ASP 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLU 4.8 2.4 + - - +
401A ASN 5.1 1.9 + - - +
402A CYS 3.4 0.2 - - - -
403A GLN* 1.3 79.3 - - - +
405A SER* 1.3 57.2 + - - +
407A ARG* 3.4 7.2 + - - +
408A ARG* 3.0 51.3 + - - +
309B LYS* 3.5 24.6 + - - +
118G ALA* 4.2 10.7 - - - +
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Residues in contact with SER 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP* 2.6 49.7 + - - +
325A LYS* 3.5 30.9 + - - +
401A ASN 5.5 1.6 + - - -
402A CYS* 3.5 2.9 + - - -
403A GLN 3.4 0.2 - - - -
404A ASP* 1.3 76.4 - - - +
406A TRP* 1.3 65.6 + - - +
408A ARG* 3.2 13.8 + - - +
409A ALA* 3.1 18.5 + - - +
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Residues in contact with TRP 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA* 3.5 29.1 - - + +
329A ALA* 3.5 23.1 - - + -
330A SER* 3.2 28.7 + - - -
333A ILE* 3.7 23.8 - - + -
399A VAL* 4.5 8.7 - - + -
402A CYS 2.8 19.9 + - - +
403A GLN* 3.2 15.0 + - + +
405A SER* 1.3 77.7 - - - +
407A ARG* 1.3 61.7 + - + +
409A ALA* 3.5 1.6 + - - +
410A VAL* 3.1 37.4 + - + +
423A PHE* 3.7 11.9 + - + +
426A ALA* 3.4 21.5 - - + -
427A LEU* 3.3 43.6 - - + +
430A TYR* 4.3 12.1 - + + -
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Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLN* 2.6 51.8 + - - +
404A ASP* 4.0 6.3 - - - +
406A TRP* 1.3 72.9 - - - +
408A ARG* 1.3 61.1 + - - +
410A VAL* 3.9 0.6 - - - +
411A SER* 2.8 36.6 + - - +
427A LEU* 4.0 20.8 - - + +
430A TYR* 4.6 1.4 - - - -
431A ASP* 2.7 40.0 + - - -
434A ARG* 4.3 0.2 - - - +
307B PRO* 3.5 31.1 - - - +
414B VAL* 2.6 48.5 + - + +
415B GLN* 4.3 12.3 - - + +
417B GLY* 3.5 5.0 - - - -
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Residues in contact with ARG 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PHE* 4.0 6.9 - - + -
322A ASP* 2.9 44.0 + - - +
404A ASP* 3.0 52.0 + - - +
405A SER* 3.2 19.8 + - - +
406A TRP 3.3 0.2 - - - -
407A ARG* 1.3 76.2 - - - +
409A ALA* 1.3 59.1 + - - +
411A SER* 4.1 4.4 - - - -
412A THR* 2.8 36.7 + - - +
415B GLN* 6.1 1.6 - - - +
118G ALA* 5.9 1.4 - - - +
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Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.7 7.5 - - + +
319A PHE* 3.8 24.5 - - + -
322A ASP* 4.0 18.4 - - + +
323A ILE* 4.4 6.5 - - + +
326A ALA* 4.3 9.6 - - + -
405A SER 3.1 18.3 + - - +
406A TRP 4.0 2.9 - - - +
408A ARG* 1.3 75.5 - - - +
410A VAL* 1.3 59.7 + - + +
412A THR* 3.9 0.5 - - - -
413A GLY* 2.9 26.9 + - - -
420A MET* 4.1 5.9 - - - +
423A PHE* 6.3 0.2 - - + -
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA* 5.4 1.1 - - + -
406A TRP* 3.1 37.3 + - + +
407A ARG 3.9 3.1 - - - +
409A ALA* 1.3 77.9 - - + +
411A SER* 1.3 56.8 + - - +
414A VAL* 3.0 33.9 + - + +
420A MET* 3.3 8.6 - - + +
423A PHE* 4.4 22.4 - - + +
424A THR* 4.0 22.9 - - + -
427A LEU* 4.1 9.9 - - + -
414B VAL* 3.8 31.2 - - + -
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Residues in contact with SER 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG 2.8 24.6 + - - -
408A ARG* 4.1 4.3 - - - -
410A VAL* 1.3 78.0 - - - +
412A THR* 1.3 61.1 + - - +
414A VAL* 3.3 6.8 + - - +
415A GLN* 3.1 28.0 + - - +
411B SER* 3.4 24.7 + - - +
414B VAL* 3.6 8.9 - - - +
415B GLN* 3.4 27.2 - - - +
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 4.2 10.3 - - + -
310A PHE* 4.0 22.3 - - + -
312A PHE* 4.4 10.9 - - + -
319A PHE* 3.6 31.4 - - + -
408A ARG* 2.8 26.6 + - - +
409A ALA 3.9 0.2 - - - -
411A SER* 1.3 77.4 - - - +
413A GLY* 1.3 57.1 + - - +
415A GLN* 3.3 8.0 + - - +
416A ALA* 2.9 25.8 + - - +
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.0 13.6 - - - +
208A VAL* 5.1 0.2 - - - -
409A ALA 2.9 17.5 + - - -
412A THR* 1.3 76.5 - - - +
414A VAL* 1.3 61.1 + - - +
416A ALA* 3.2 5.7 + - - -
417A GLY 3.0 4.0 + - - -
418A ILE* 3.0 28.7 + - - +
420A MET* 3.8 21.8 - - - -
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A VAL* 3.0 28.6 + - + +
411A SER* 3.6 6.5 - - - +
413A GLY* 1.3 75.2 - - - +
415A GLN* 1.3 61.1 + - - +
417A GLY 3.3 1.2 + - - -
418A ILE 5.3 1.6 - - - +
420A MET* 4.3 9.2 - - + -
424A THR* 4.9 6.3 - - + -
407B ARG* 2.8 58.5 + - + +
410B VAL* 3.7 24.5 - - + -
411B SER* 4.5 4.3 - - - +
414B VAL* 5.7 0.2 - - + -
424B THR* 5.1 0.4 - - + -
427B LEU* 3.6 25.6 - - + -
431B ASP* 5.4 1.1 - - - -
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Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PRO* 3.7 18.0 - - - +
310A PHE* 4.0 25.8 - - + +
411A SER 3.1 15.8 + - - +
412A THR* 3.3 8.3 + - - +
414A VAL* 1.3 75.7 - - - +
416A ALA* 1.3 60.9 + - - +
417A GLY 3.6 0.3 + - - -
404B ASP 5.8 0.2 + - - -
407B ARG* 3.7 36.0 + - - +
408B ARG* 4.4 7.1 - - - +
411B SER* 3.9 13.9 + - - +
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP 5.7 0.4 - - - +
208A VAL* 3.9 9.4 - - + -
307A PRO* 3.5 13.4 - - - +
310A PHE* 3.4 32.3 - - + +
412A THR 2.9 16.9 + - - +
413A GLY 3.7 0.9 - - - +
414A VAL 3.2 0.6 - - - -
415A GLN* 1.3 77.4 - - - +
417A GLY* 1.3 60.5 + - - +
418A ILE* 3.7 25.6 - - + +
434B ARG* 4.3 2.3 + - - -
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Residues in contact with GLY 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PRO* 3.6 3.1 - - - +
413A GLY 3.0 3.6 + - - -
414A VAL 3.3 4.8 + - - -
415A GLN 3.3 0.8 + - - -
416A ALA* 1.3 79.4 - - - +
418A ILE* 1.3 61.9 + - - +
407B ARG* 3.6 21.3 - - - -
431B ASP* 3.6 8.0 - - - +
434B ARG* 2.8 30.7 + - - -
435B HIS* 3.3 15.1 - - - -
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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