Contacts of the helix formed by residues 431 - 455 (chain C) in PDB entry 5YD6
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 PRO 431 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ASP 3.9 0.2 - - - -
430C LEU* 1.4 87.1 - - + +
432C LYS* 1.3 55.7 + - - +
433C ALA* 3.2 2.5 - - + +
434C ASP* 2.9 33.8 + - - +
435C GLN* 2.8 31.9 + - - +
519C LYS* 4.5 16.8 - - + -
520C GLU* 3.8 33.9 - - + +
523C ARG* 4.0 5.2 - - - +
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Residues in contact with LYS 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 4.1 17.4 - - - +
422C GLU* 5.7 0.8 + - - -
430C LEU 3.5 2.0 + - - -
431C PRO* 1.3 71.1 - - - +
433C ALA* 1.3 56.9 + - - +
435C GLN* 3.5 21.3 + - - +
436C ASP* 2.7 70.3 + - - +
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Residues in contact with ALA 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C PRO* 3.2 1.4 - - + +
432C LYS* 1.3 78.4 - - - +
434C ASP* 1.3 58.5 + - - +
436C ASP* 3.5 7.5 + - - +
437C LEU* 3.0 28.6 + - - +
519C LYS* 3.9 35.0 - - + +
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Residues in contact with ASP 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 4.6 5.6 - - + -
431C PRO* 2.9 25.7 + - + +
433C ALA* 1.3 76.2 - - - +
435C GLN* 1.3 59.3 + - - +
437C LEU* 3.7 3.0 - - - +
438C LEU* 2.8 41.0 + - + +
517C GLY 4.2 1.7 - - - +
518C LEU* 3.4 24.4 - - + +
519C LYS* 2.6 34.4 + - - +
520C GLU* 2.9 30.5 + - - +
524C VAL* 4.8 2.4 - - + +
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Residues in contact with GLN 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C GLU* 4.4 16.2 + - - +
427C PHE* 3.3 57.5 - - + +
428C ALA* 3.0 20.0 - - - +
430C LEU* 3.0 21.7 - - + +
431C PRO 2.8 15.1 + - - +
432C LYS* 3.6 24.5 - - + +
434C ASP* 1.3 71.5 - - - +
436C ASP* 1.3 62.1 + - - +
438C LEU* 4.8 0.4 - - - +
439C PHE* 3.0 31.0 + - - +
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Residues in contact with ASP 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 4.7 7.4 + - - -
432C LYS* 2.7 55.3 + - - +
433C ALA* 3.8 6.5 - - - +
435C GLN* 1.3 75.7 - - - +
437C LEU* 1.3 58.3 + - - +
439C PHE* 3.5 5.5 + - - +
440C GLU* 3.0 50.4 + - - +
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C ALA 3.0 17.7 + - - +
434C ASP* 3.3 5.1 + - - +
436C ASP* 1.3 73.4 - - - +
438C LEU* 1.3 59.2 + - - +
440C GLU* 4.3 3.3 - - + +
441C SER* 2.7 48.1 + - - +
515C ARG* 4.2 14.6 - - + -
516C HIS 3.4 26.0 - - - +
517C GLY* 3.7 24.5 - - - +
518C LEU* 3.8 9.2 - - + +
594C ASP* 5.2 10.1 - - + +
595C THR* 5.8 3.6 - - - +
601C 8SU 5.9 0.7 - - - +
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Residues in contact with LEU 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C PHE* 3.7 26.5 - - + -
430C LEU* 3.7 22.0 - - + -
434C ASP 2.8 25.1 + - - +
435C GLN 3.9 2.9 - - - +
437C LEU* 1.3 72.3 - - - +
439C PHE* 1.3 64.9 + - - +
441C SER* 4.0 3.1 - - - -
442C ALA* 3.3 16.1 + - - +
511C MET* 3.4 36.8 - - + +
512C VAL* 5.1 4.9 - - + -
513C THR 3.4 21.3 - - - +
515C ARG* 4.1 11.6 + - + -
518C LEU* 4.1 12.8 - - + -
524C VAL* 4.2 16.8 - - + -
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Residues in contact with PHE 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C MET* 3.6 28.7 - - + -
417C ILE* 4.0 18.2 - - + -
418C ARG* 3.6 57.0 - - + -
421C ALA* 5.2 2.2 - - + -
427C PHE* 4.9 4.0 - - + -
435C GLN 3.0 19.6 + - - +
436C ASP* 3.9 5.4 - - - +
438C LEU* 1.3 77.3 - - - +
440C GLU* 1.3 77.4 + - + +
442C ALA* 3.2 2.6 + - - +
443C PHE* 2.8 46.8 + + + -
511C MET* 3.9 16.6 - - - +
591C LEU* 4.0 20.6 - - + -
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Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ASP* 3.0 35.4 + - - +
437C LEU* 4.3 3.6 - - + +
439C PHE* 1.3 86.2 - - + +
441C SER* 1.3 59.8 + - - +
442C ALA 3.4 0.3 + - - -
443C PHE* 3.5 0.5 + - - +
590C LYS* 5.0 5.0 - - - -
591C LEU* 3.5 42.5 - - + +
594C ASP* 2.6 40.3 - - + +
595C THR* 3.7 13.8 + - - +
601C 8SU 2.8 30.7 + - - +
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Residues in contact with SER 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C LEU* 2.7 36.3 + - - +
438C LEU 4.0 1.8 - - - -
440C GLU* 1.3 78.5 - - - +
442C ALA* 1.3 55.8 + - - +
443C PHE 3.5 0.2 - - - -
445C GLU* 4.3 2.1 - - - +
515C ARG* 3.3 42.4 + - - +
595C THR* 4.0 11.5 + - - +
601C 8SU 3.4 39.1 + - - +
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Residues in contact with ALA 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C LEU 3.3 14.8 + - - +
439C PHE 3.2 2.3 + - - +
441C SER* 1.3 76.9 - - - +
443C PHE* 1.3 67.1 + - - +
444C LEU 3.4 2.5 - - - -
445C GLU* 3.1 10.5 + - + +
446C LEU* 2.8 37.0 + - + +
510C ALA 3.5 25.1 - - - +
511C MET* 3.8 9.0 - - + -
515C ARG* 3.8 7.4 - - - +
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Residues in contact with PHE 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 3.3 33.2 - - + -
413C SER* 4.1 1.8 - - - -
414C MET* 3.4 28.0 - - + -
417C ILE* 3.7 27.8 - - + -
439C PHE* 2.8 32.8 + + + +
440C GLU 3.9 3.1 - - - +
441C SER 3.5 2.0 - - - -
442C ALA* 1.3 74.9 - - - +
444C LEU* 1.3 72.2 + - + +
446C LEU* 3.0 6.2 + - - +
447C PHE* 2.7 42.1 + - + -
591C LEU* 4.1 17.9 - - + -
601C 8SU 3.4 40.2 - - + +
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Residues in contact with LEU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 3.8 29.4 - - + -
442C ALA 3.4 0.2 - - - -
443C PHE* 1.3 81.3 - - + +
445C GLU* 1.3 56.7 + - - +
447C PHE* 3.6 3.8 - - + +
448C VAL* 2.9 35.3 + - - +
482C TRP* 3.9 18.4 - - + -
566C CYS* 3.7 20.6 - - - +
569C GLY* 3.8 11.0 - - - -
570C LEU* 3.7 29.6 - - - +
573C ILE* 4.4 9.2 - - + -
601C 8SU 3.1 41.8 + - + -
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Residues in contact with GLU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C SER 4.3 3.1 - - - +
442C ALA* 3.1 13.3 + - + +
444C LEU* 1.3 78.3 - - - +
446C LEU* 1.3 57.1 + - - +
448C VAL* 3.4 0.8 + - - -
449C LEU* 2.9 30.8 + - - +
510C ALA* 4.8 11.3 - - + +
515C ARG* 3.9 12.9 + - - -
559C LEU* 4.0 6.1 - - - +
562C LEU* 3.3 34.2 - - + +
563C ARG* 2.8 56.6 + - - +
566C CYS* 3.6 21.7 - - + -
601C 8SU 4.2 7.6 - - - +
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ILE* 4.1 17.9 - - + -
420C TRP* 3.8 17.9 - - + -
442C ALA* 2.8 43.7 + - + +
443C PHE 3.6 3.4 - - - +
445C GLU* 1.3 69.9 - - - +
447C PHE* 1.3 67.1 + - - +
449C LEU* 4.1 9.0 - - + -
450C ARG* 3.0 43.9 + - - +
507C ALA* 3.4 41.5 - - + +
510C ALA* 3.8 15.7 - - + -
511C MET* 3.9 11.0 - - + -
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Residues in contact with PHE 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C LEU* 3.7 22.4 - - + -
410C LEU* 3.7 30.3 - - + -
413C SER* 3.6 20.9 - - - -
417C ILE* 3.9 7.9 - - + +
443C PHE* 2.7 31.3 + + + +
444C LEU* 3.6 11.2 - - + +
446C LEU* 1.3 72.8 - - - +
448C VAL* 1.3 71.5 + - + +
450C ARG* 4.2 2.0 - - - +
451C LEU* 3.2 39.7 + - + +
454C ARG* 5.3 3.1 + - - -
464C PHE* 3.8 33.0 - + - -
465C CYS 6.3 0.4 - - - -
479C PHE* 4.1 16.2 - + - -
482C TRP* 4.7 6.1 - + - -
486C ILE* 5.3 0.4 - - + -
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Residues in contact with VAL 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C LEU 2.9 20.3 + - - +
445C GLU* 3.8 2.7 - - - +
447C PHE* 1.3 78.0 - - + +
449C LEU* 1.3 62.5 + - - +
451C LEU* 3.4 7.6 + - - +
452C ALA* 2.9 28.1 + - - +
482C TRP* 3.3 38.4 - - + +
486C ILE* 4.1 17.4 - - + +
489C PHE* 4.5 4.7 - - + -
562C LEU* 3.7 13.2 - - + +
565C LEU* 3.3 35.7 - - + +
566C CYS* 5.6 1.1 - - - -
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C GLU 2.9 20.9 + - - +
446C LEU* 3.9 10.3 - - + +
448C VAL* 1.3 74.5 - - - +
450C ARG* 1.3 56.0 + - - +
452C ALA* 3.2 7.3 + - - +
453C TYR* 3.1 27.7 + - - +
489C PHE* 4.0 23.6 - - + -
493C LEU* 4.0 12.7 - - + +
503C PHE* 3.6 20.0 - - + -
506C ILE* 4.4 14.8 - - + +
507C ALA* 3.7 37.5 - - + +
510C ALA* 4.4 1.3 - - + -
558C LYS* 6.0 1.3 - - + -
562C LEU* 3.8 23.3 - - + -
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Residues in contact with ARG 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C HIS* 4.5 4.7 - - + -
375C SER* 2.9 44.6 + - - -
376C ASN* 3.4 22.1 + - - +
416C ILE* 3.3 19.8 - - - +
417C ILE* 3.6 23.3 - - - +
420C TRP* 4.1 18.4 - - - +
446C LEU* 3.0 42.2 + - + +
447C PHE* 4.4 2.0 - - - +
449C LEU* 1.3 74.2 - - - +
451C LEU* 1.3 64.8 + - - +
453C TYR* 3.4 2.3 + - - +
454C ARG* 3.3 47.1 + - - +
465C CYS* 4.6 4.4 - - - +
503C PHE* 4.2 22.0 - - + -
507C ALA* 5.2 2.7 - - + -
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C PHE* 3.2 36.6 + - + +
448C VAL* 3.4 4.7 - - - +
450C ARG* 1.3 75.2 - - - +
452C ALA* 1.3 60.5 + - - +
454C ARG* 3.4 12.5 + - - +
455C SER* 2.6 45.0 + - - +
462C LEU* 3.9 16.8 - - + -
463C ILE 3.4 24.9 - - - +
464C PHE* 3.8 35.4 - - + -
479C PHE* 4.9 2.9 - - + -
483C ILE* 5.7 0.4 - - + -
486C ILE* 3.9 28.7 - - + -
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Residues in contact with ALA 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C VAL* 2.9 19.1 + - + +
449C LEU 3.2 6.0 + - - +
451C LEU* 1.3 77.9 - - - +
453C TYR* 1.3 58.1 + - - +
455C SER* 4.0 1.7 + - - -
462C LEU* 6.1 0.4 - - - -
486C ILE* 4.7 4.9 - - + +
489C PHE* 3.7 30.1 - - + -
490C SER* 2.5 42.5 + - - +
493C LEU* 4.1 4.5 - - + -
494C GLN* 3.1 12.6 - - - +
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Residues in contact with TYR 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ARG* 5.0 3.8 + - - -
372C HIS* 4.2 18.4 - + - -
449C LEU 3.1 6.9 + - - +
450C ARG 3.9 4.3 - - - +
451C LEU 3.3 0.2 - - - -
452C ALA* 1.3 78.0 - - - +
454C ARG* 1.3 63.1 + - + +
455C SER 4.3 0.2 - - - +
493C LEU* 4.1 15.3 - - + -
494C GLN* 3.7 20.5 - - + +
498C ILE* 2.7 36.0 + - + -
499C ASP* 3.3 16.5 - - - -
500C ILE* 3.5 12.1 + - + +
503C PHE* 3.5 65.1 - + + -
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Residues in contact with ARG 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ASN* 2.8 38.8 + - - -
377C PRO* 3.6 17.9 - - - -
379C MET* 3.6 33.4 - - + +
447C PHE* 5.3 2.4 + - - -
450C ARG* 3.3 36.1 + - - +
451C LEU* 3.7 19.7 - - - +
453C TYR* 1.3 81.6 - - + +
455C SER* 1.3 64.2 + - - +
463C ILE* 3.0 43.5 + - + +
464C PHE* 3.3 4.9 + - - +
465C CYS* 3.1 38.0 - - - +
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Residues in contact with SER 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C LEU* 2.6 26.1 + - - +
452C ALA* 4.0 0.6 + - - -
453C TYR 3.5 0.7 - - - +
454C ARG* 1.3 80.5 - - - +
456C ASN* 1.3 56.4 + - - +
457C PRO* 3.6 1.8 - - - -
461C LYS 3.0 18.6 - - - -
462C LEU* 3.3 12.0 - - - +
463C ILE* 2.9 27.5 + - - -
490C SER* 4.3 11.0 - - - -
494C GLN* 2.7 29.5 + - - +
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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