Contacts of the helix formed by residues 399 - 423 (chain A) in PDB entry 5Y41
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 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A ASP* 1.3 78.2 - - - +
400A THR* 1.3 64.1 + - - +
401A GLN* 3.7 20.2 - - + +
402A HIS* 3.3 35.9 + - - +
403A ILE* 3.4 14.4 + - - +
477A ARG* 3.0 21.3 + - - +
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Residues in contact with THR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASP 3.4 1.4 + - - -
399A ASP* 1.3 71.9 + - - +
401A GLN* 1.3 62.6 + - - +
403A ILE* 3.4 1.8 + - - -
404A GLN* 2.9 30.5 + - - +
581A LEU* 3.8 28.9 - - + +
582A VAL* 3.5 26.1 - - + +
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Residues in contact with GLN 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASP* 4.0 18.2 - - + +
400A THR* 1.3 80.7 + - - +
402A HIS* 1.3 61.3 + - + +
404A GLN* 3.3 5.7 + - - +
405A GLN* 3.0 54.2 + - - +
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Residues in contact with HIS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASP* 3.3 34.1 + - + +
401A GLN* 1.3 77.9 - - + +
403A ILE* 1.3 60.4 + - - +
405A GLN* 3.5 15.5 + - - +
406A PHE* 3.0 27.5 + - - +
474A GLN* 3.8 24.8 + - + +
477A ARG* 3.6 54.9 + - + -
478A GLY* 3.7 12.5 - - - +
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Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASP* 4.6 5.2 - - - +
399A ASP 3.4 13.4 + - - +
400A THR 3.4 7.1 + - - +
401A GLN 3.3 0.8 - - - -
402A HIS* 1.3 72.3 - - - +
404A GLN* 1.3 67.0 - - - +
406A PHE* 3.1 10.5 + - - +
407A TYR* 2.9 52.8 + - + +
477A ARG 4.5 11.9 - - - +
478A GLY* 4.6 1.6 - - - -
576A LEU* 3.9 25.1 - - + -
579A GLU* 3.7 23.1 - - - +
581A LEU* 4.1 23.8 - - + -
582A VAL* 3.9 14.6 - - + +
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Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A THR 2.9 17.1 + - - +
401A GLN* 3.3 7.8 + - - +
403A ILE* 1.3 76.3 - - - +
405A GLN* 1.3 58.2 + - + +
407A TYR* 3.1 17.3 + - - +
408A ASP* 2.8 62.8 + - - +
582A VAL* 3.5 21.8 - - + +
583A PRO 5.4 0.2 - - - +
585A PRO* 5.6 5.9 - - - +
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Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 3.9 27.3 + - - +
401A GLN* 3.0 40.8 + - - +
402A HIS* 3.8 16.2 - - - +
404A GLN* 1.3 75.1 - - + +
406A PHE* 1.3 55.7 + - - +
408A ASP* 3.2 13.9 + - - +
409A LEU* 2.8 45.9 + - + +
470A LEU* 5.8 3.9 - - + +
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Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A HIS 3.0 15.3 + - - +
403A ILE 3.2 9.4 - - - +
405A GLN* 1.3 76.4 - - - +
407A TYR* 1.3 76.1 + + - +
409A LEU* 3.3 4.4 + - - +
410A LEU* 3.1 50.9 + - + +
478A GLY* 3.6 16.2 - - - +
479A PHE* 3.6 46.0 - + + -
482A TRP* 3.6 28.9 - + - -
572A ARG* 3.9 13.7 - - + -
573A ILE* 4.3 10.8 - - + -
576A LEU* 3.6 30.5 - - + -
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Residues in contact with TYR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ILE* 2.9 31.9 + - + +
404A GLN* 3.5 20.2 - - - +
406A PHE* 1.3 98.5 - + - +
408A ASP* 1.3 55.2 + - - +
410A LEU* 3.1 11.4 + - + +
411A THR* 2.8 39.2 + - + +
573A ILE* 5.2 5.6 + - + -
576A LEU* 3.5 23.2 - - + +
577A LYS 4.6 0.2 + - - -
582A VAL* 2.7 31.5 + - + -
583A PRO 3.3 12.1 - - - -
584A PRO* 3.5 27.1 - - + +
585A PRO* 3.6 29.2 - - + -
588A ILE* 4.9 6.7 - - + -
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 2.8 49.9 + - - +
405A GLN* 3.2 16.7 + - - +
407A TYR* 1.3 70.6 - - - +
409A LEU* 1.3 59.4 + - + +
411A THR* 3.3 8.7 + - - -
412A GLY* 2.8 29.6 + - - -
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ARG* 5.6 5.4 - - - +
405A GLN* 2.8 30.0 + - + +
406A PHE* 3.7 4.5 - - - +
408A ASP* 1.3 74.5 - - + +
410A LEU* 1.3 62.8 + - - +
412A GLY* 5.2 0.4 - - - -
413A SER* 3.1 25.8 + - - -
447A PHE* 4.1 5.3 - - + -
464A PHE* 3.7 62.1 - - + -
465A CYS* 5.1 2.0 - - - -
466A ASN* 4.5 15.7 - - - +
468A VAL* 5.4 3.6 - - + -
470A LEU* 4.4 12.1 - - + -
479A PHE* 4.0 18.6 - - + -
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A PHE* 3.1 46.3 + - + +
407A TYR* 3.1 9.8 + - + +
409A LEU* 1.3 77.0 - - - +
411A THR* 1.3 58.3 + - - +
413A SER* 3.3 3.0 + - - -
414A MET* 3.0 25.3 + - - +
443A PHE* 3.5 16.4 - - + -
444A LEU* 4.1 20.9 - - + -
447A PHE* 3.9 34.1 - - + -
482A TRP* 4.4 7.0 - - + -
573A ILE* 4.1 21.1 - - + -
588A ILE* 4.2 21.5 - - + -
601A RPG 5.5 0.4 - - + -
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Residues in contact with THR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A TYR 2.8 21.8 + - - +
408A ASP* 3.3 14.6 + - - -
410A LEU* 1.3 68.6 - - - +
412A GLY* 1.3 67.5 + - - +
414A MET* 3.3 22.7 + - - +
415A GLU* 3.5 8.3 + - - +
585A PRO* 4.0 12.8 - - + -
587A ILE* 4.0 19.3 - - + -
588A ILE* 3.7 26.5 - - + -
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Residues in contact with GLY 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ASP 2.8 21.6 + - - -
409A LEU* 4.2 0.7 - - - -
411A THR* 1.3 72.5 + - - +
413A SER* 1.3 60.2 + - - +
415A GLU* 3.4 15.1 + - - +
416A ILE* 3.4 19.6 + - - +
465A CYS* 4.2 7.6 - - - -
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A LEU 3.1 21.2 + - - -
410A LEU 3.7 2.9 - - - -
411A THR 3.3 0.2 - - - -
412A GLY* 1.3 74.0 - - - +
414A MET* 1.3 58.7 + - - +
416A ILE* 3.3 1.0 + - - +
417A ILE* 2.8 48.2 + - - +
443A PHE* 3.6 2.9 - - - -
447A PHE* 3.2 29.0 - - - -
465A CYS* 3.7 21.1 - - - -
604A CL 3.4 4.8 - - - +
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Residues in contact with MET 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A LEU 3.0 12.1 + - - +
411A THR* 3.3 11.4 + - - +
413A SER* 1.3 74.7 + - - +
415A GLU* 1.3 62.1 + - - +
417A ILE* 4.8 0.2 - - - -
418A ARG* 3.0 54.9 + - - +
439A PHE* 3.5 13.4 - - + -
443A PHE* 3.4 36.7 - - + -
587A ILE* 4.0 23.8 - - + -
588A ILE* 4.0 20.6 - - - -
591A LEU* 3.8 32.1 - - + -
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A THR 3.5 6.6 + - - +
412A GLY* 3.4 10.2 + - - +
413A SER 3.3 0.4 - - - -
414A MET* 1.3 83.4 - - - +
416A ILE* 1.3 60.6 + - + +
418A ARG* 3.4 26.2 + - - +
419A GLY* 3.0 23.7 + - - -
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A SER* 3.1 36.8 - - - +
412A GLY* 3.4 14.0 + - - +
413A SER 3.3 3.9 + - - +
415A GLU* 1.3 78.4 - - + +
417A ILE* 1.3 58.0 + - + +
419A GLY* 3.2 3.6 + - - -
420A TRP* 2.9 25.8 + - - +
423A LYS* 5.3 0.3 + - - -
450A ARG* 3.6 8.3 - - - +
465A CYS* 3.4 41.3 - - + +
466A ASN* 4.8 5.8 - - + +
380B THR* 5.3 8.7 - - + -
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A SER* 2.8 37.6 + - - +
414A MET 4.1 2.7 - - - +
416A ILE* 1.3 73.4 - - - +
418A ARG* 1.3 60.8 + - - +
420A TRP* 3.3 24.1 + - + +
421A ALA* 2.9 27.4 + - - +
439A PHE* 3.9 17.9 - - + -
443A PHE* 4.0 12.3 - - + -
446A LEU* 4.0 18.6 - - + -
447A PHE* 3.6 25.4 - - - +
450A ARG* 3.6 19.3 - - - +
511A MET* 6.0 0.4 - - - -
604A CL 3.6 12.6 - - + -
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Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A MET* 3.0 34.2 + - - +
415A GLU* 3.5 27.5 + - - +
416A ILE 3.3 0.2 - - - -
417A ILE* 1.3 75.0 - - - +
419A GLY* 1.3 62.3 + - - +
421A ALA* 3.3 4.9 + - + +
422A GLU* 3.1 43.0 + - + +
432A LYS* 4.9 8.6 - - - +
436A ASP* 4.3 14.8 + - - -
439A PHE* 3.3 50.3 - - + +
440A GLU* 5.4 4.4 + - - -
587A ILE* 5.9 2.2 - - - +
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Residues in contact with GLY 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A GLU 3.0 14.0 + - - -
416A ILE* 3.2 4.2 + - - -
418A ARG* 1.3 73.9 - - - +
420A TRP* 1.3 63.6 + - - +
422A GLU* 3.4 11.5 + - - +
423A LYS* 3.2 40.8 + - - +
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Residues in contact with TRP 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU 4.9 1.6 + - - -
371A ALA* 3.4 35.9 - - + +
372A HIS* 3.8 9.2 + - - +
375A SER* 3.4 25.1 - - - +
416A ILE 2.9 9.1 + - - +
417A ILE* 3.3 22.9 + - + +
419A GLY* 1.3 76.7 - - - +
421A ALA* 1.3 68.7 + - + +
423A LYS* 3.0 25.2 + - - +
424A ILE* 3.5 29.5 + - + +
446A LEU* 3.6 21.3 - - + -
450A ARG* 3.8 15.3 - - - +
504A SER 4.9 2.6 + - - -
507A ALA* 3.3 32.1 - - + +
508A ALA* 3.5 23.3 - - + -
511A MET* 3.7 28.5 - - + -
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ILE 2.9 19.8 + - - +
418A ARG* 3.3 9.2 + - + +
420A TRP* 1.3 79.5 - - + +
422A GLU* 1.3 58.4 + - - +
424A ILE* 3.0 23.0 + - - +
427A PHE* 3.3 33.8 - - + +
439A PHE* 4.8 5.2 - - + -
511A MET* 3.6 29.2 - - + -
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ARG* 3.1 38.0 + - + +
419A GLY* 3.8 9.8 - - - +
420A TRP 3.3 0.2 - - - -
421A ALA* 1.3 74.5 - - - +
423A LYS* 1.3 60.8 + - + +
424A ILE 3.7 4.6 + - - +
427A PHE* 4.3 17.0 - - + -
428A ALA* 4.6 18.8 - - + +
432A LYS* 4.6 12.5 + - - -
435A GLN* 4.7 9.5 + - - +
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Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ALA* 4.2 5.9 - - - +
370A ARG 5.4 0.4 - - - -
371A ALA* 3.7 32.6 - - + +
374A ASP* 3.7 35.1 + - + +
375A SER* 4.4 4.4 - - - -
416A ILE 5.3 0.2 + - - -
419A GLY* 3.2 30.0 + - - +
420A TRP 3.0 13.8 + - - +
422A GLU* 1.3 77.1 - - + +
424A ILE* 1.3 62.2 + - - +
425A PRO* 3.5 9.0 - - - +
379B MET* 6.1 2.7 - - - -
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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) + - + + + + + -
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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