Contacts of the helix formed by residues 496 - 527 (chain D) in PDB entry 2I0J
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 THR 496 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D GLY 5.0 2.7 - - - +
495D LEU* 1.3 78.5 - - - +
497D LEU* 1.3 59.2 + - - +
498D GLN* 3.5 8.4 + - - +
499D GLN* 2.8 46.9 + - + +
500D GLN* 2.8 27.4 + - - +
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Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C LEU* 3.7 39.9 - - + -
487D ILE* 5.9 0.7 - - + -
496D THR* 1.3 73.4 - - - +
498D GLN* 1.3 64.2 + - - +
500D GLN* 3.0 34.0 + - + +
501D HIS* 3.1 20.6 + - + +
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Residues in contact with GLN 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ASP* 3.0 38.9 + - - +
496D THR* 3.4 6.6 + - - +
497D LEU* 1.3 78.8 - - - +
499D GLN* 1.3 63.8 + - + +
501D HIS* 2.9 32.8 - - + +
502D GLN* 2.9 24.2 + - - +
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Residues in contact with GLN 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D GLY 4.4 1.2 - - - +
495D LEU* 3.2 30.6 - - + +
496D THR* 2.8 53.7 + - + +
498D GLN* 1.3 80.1 - - + +
500D GLN* 1.3 62.1 + - - +
502D GLN* 3.9 13.9 - - - +
503D ARG* 3.2 25.8 + - - +
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Residues in contact with GLN 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D ILE* 3.1 36.0 - - + +
490D MET* 3.2 48.2 - - + +
491D ALA* 3.3 28.2 - - - +
495D LEU* 3.1 24.9 + - + -
496D THR 2.8 17.9 + - - +
497D LEU* 3.0 28.8 + - + +
499D GLN* 1.3 79.2 - - - +
501D HIS* 1.3 61.7 + - - +
504D LEU* 3.3 10.6 + - - +
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Residues in contact with HIS 501 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C THR* 3.4 15.5 - - + +
484C ASP* 3.0 27.2 + - + -
487C ILE* 3.1 45.1 - - + +
501C HIS* 5.0 10.1 - - + -
504C LEU* 3.9 16.1 - - + +
487D ILE* 4.6 3.1 - - + -
497D LEU* 3.1 9.8 + - + +
498D GLN* 2.9 41.3 + - + -
500D GLN* 1.3 75.9 - - - +
502D GLN* 1.3 71.2 + - + +
504D LEU* 3.4 7.8 - - - +
505D ALA* 3.1 21.1 + - - +
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Residues in contact with GLN 502 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C ASP* 3.4 44.4 + - - +
483C THR* 4.1 6.5 - - - -
484C ASP* 3.2 31.1 - - - +
498D GLN* 2.9 36.0 + - - +
499D GLN* 3.9 13.4 - - - +
500D GLN 3.3 0.2 - - - -
501D HIS* 1.3 81.0 - - + +
503D ARG* 1.3 61.4 + - - +
504D LEU 3.1 1.3 - - - -
505D ALA* 3.3 3.8 + - - +
506D GLN* 2.9 36.1 + - - +
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Residues in contact with ARG 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D MET* 3.0 49.2 + - - +
439D ASN 3.5 10.3 + - - -
440D LEU* 3.6 7.9 - - - +
441D GLN* 5.2 1.2 - - - +
444D GLU* 2.8 36.8 + - - -
490D MET* 3.4 20.4 - - + -
495D LEU* 3.9 21.5 - - + +
499D GLN 3.2 15.6 + - - +
502D GLN* 1.3 76.1 - - - +
504D LEU* 1.3 59.9 + - - +
506D GLN* 3.4 18.7 - - - +
507D LEU* 3.0 32.1 + - + +
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Residues in contact with LEU 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C HIS* 3.8 26.9 - - + +
504C LEU* 4.3 12.8 - - + -
505C ALA* 4.5 2.9 - - + -
483D THR* 4.0 13.0 - - + +
486D LEU* 3.7 37.9 - - + -
487D ILE* 4.0 20.4 - - + -
490D MET* 3.9 7.8 - - + +
500D GLN 3.3 13.5 + - - +
501D HIS* 3.4 9.2 - - - +
502D GLN 3.1 0.4 - - - -
503D ARG* 1.3 76.6 - - - +
505D ALA* 1.3 60.1 + - - +
507D LEU* 3.1 3.9 + - + +
508D LEU* 2.8 49.7 + - + +
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Residues in contact with ALA 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C ASP* 5.7 0.2 - - - +
483C THR* 3.2 40.6 - - + +
504C LEU* 4.7 1.3 - - + -
508C LEU* 3.3 29.6 - - + +
501D HIS 3.1 2.9 + - - +
502D GLN 3.3 4.2 + - - +
504D LEU* 1.3 81.1 - - - +
506D GLN* 1.3 55.7 + - + +
508D LEU 3.9 0.3 - - - -
509D LEU* 2.9 41.2 + - + +
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Residues in contact with GLN 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C TYR* 4.9 1.4 + - - -
476C HIS* 5.9 5.7 - - + +
479C LEU* 6.4 1.8 - - + -
480C ASP* 3.0 32.5 - - - +
434D ARG* 3.8 17.6 - - - +
438D MET* 2.9 30.9 - - + +
502D GLN* 2.9 28.1 + - - +
503D ARG* 3.4 18.5 + - - +
504D LEU 3.2 0.2 - - - -
505D ALA* 1.3 77.3 - - + +
507D LEU* 1.3 60.4 + - - +
509D LEU* 3.5 9.2 + - - +
510D ILE* 3.2 27.1 + - - +
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Residues in contact with LEU 507 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D PHE* 5.1 0.9 - - + -
438D MET* 4.0 25.1 - - + -
440D LEU* 3.5 27.6 - - + -
444D GLU* 3.9 20.4 - - + +
448D LEU* 4.0 26.0 - - + +
486D LEU* 4.8 8.5 - - + -
490D MET* 3.5 31.2 - - + -
503D ARG* 3.0 21.7 + - + +
504D LEU* 3.6 5.2 - - + +
506D GLN* 1.3 75.0 - - - +
508D LEU* 1.3 64.5 + - + +
510D ILE* 3.1 24.4 + - + +
511D LEU* 3.6 10.2 + - - +
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Residues in contact with LEU 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C ALA* 3.4 46.0 - - + +
508C LEU* 4.2 24.1 - - + +
509C LEU* 4.2 12.3 - - + +
512C SER* 5.7 1.0 - - - -
448D LEU* 4.1 8.1 - - + -
451D ILE* 4.1 21.8 - - + -
486D LEU* 4.9 0.9 - - + -
504D LEU* 2.8 36.8 + - + +
505D ALA 4.1 3.1 - - - +
507D LEU* 1.3 77.6 - - + +
509D LEU* 1.3 61.8 + - - +
511D LEU* 3.3 40.0 + - + +
512D SER* 3.9 3.3 + - - -
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Residues in contact with LEU 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ILE* 3.8 34.1 - - + -
455C ASN* 3.3 40.0 + - + +
479C LEU* 4.6 13.9 - - + -
483C THR* 5.6 1.6 - - - +
508C LEU* 4.4 15.0 - - + +
511C LEU* 4.0 19.3 - - + -
505D ALA* 2.9 33.5 + - + +
506D GLN* 3.8 7.9 - - - +
507D LEU 3.2 0.4 - - - -
508D LEU* 1.3 77.3 - - - +
510D ILE* 1.3 61.9 + - + +
511D LEU 3.1 1.3 - - - -
512D SER* 3.3 21.4 + - - +
513D HIS* 3.7 5.9 + - - -
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Residues in contact with ILE 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ASN* 6.2 0.2 - - - +
459C TYR* 3.7 19.3 - - + +
431D THR* 4.3 9.6 - - + -
434D ARG* 3.5 25.1 - - + -
435D PHE* 3.4 42.2 - - + -
438D MET* 3.8 18.2 - - - -
506D GLN 3.2 13.9 - - - +
507D LEU* 3.1 12.6 + - + +
509D LEU* 1.3 76.2 - - - +
511D LEU* 1.3 60.8 + - + +
512D SER 3.1 0.7 - - - -
513D HIS* 3.2 11.7 + - + +
514D ILE* 3.0 32.2 + - + +
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Residues in contact with LEU 511 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C LEU* 4.0 18.2 - - + -
512C SER* 4.1 8.1 + - - +
385D GLU* 4.2 3.7 - - - +
389D ILE* 4.2 12.6 - - + -
448D LEU* 3.9 23.6 - - + -
451D ILE* 4.3 11.7 - - + -
452D ILE* 3.8 35.9 - - + -
507D LEU 3.7 10.8 - - - +
508D LEU* 3.5 32.8 - - + +
509D LEU 3.1 0.2 - - - -
510D ILE* 1.3 80.2 - - + +
512D SER* 1.3 58.8 + - - +
514D ILE* 3.1 8.9 + - + +
515D ARG* 2.8 28.6 + - - +
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Residues in contact with SER 512 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU* 4.7 0.2 + - - -
455C ASN* 4.3 6.6 + - - -
508C LEU 5.7 0.7 - - - -
511C LEU* 3.9 8.7 + - - +
512C SER* 4.2 22.8 + - - +
515C ARG* 3.0 41.4 + - - +
508D LEU 3.9 2.3 + - - -
509D LEU* 3.3 20.3 + - - -
511D LEU* 1.3 80.3 - - - +
513D HIS* 1.3 62.7 + - - +
515D ARG* 3.2 5.5 + - - +
516D HIS 3.1 17.2 + - - -
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Residues in contact with HIS 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ASN* 2.7 47.4 + - - -
456C SER 3.7 2.5 - - - -
458C VAL* 3.8 0.4 - - - +
459C TYR* 3.0 62.0 + + + +
460C THR* 6.2 0.9 - - + -
515C ARG* 3.3 20.6 + - - -
431D THR* 4.8 11.0 - - - +
509D LEU 3.9 5.9 + - - -
510D ILE* 3.2 12.0 + - + +
511D LEU 3.2 0.4 - - - -
512D SER* 1.3 74.6 - - - +
514D ILE* 1.3 60.4 + - + +
515D ARG 3.0 1.8 - - - -
516D HIS* 3.2 9.2 + - - +
517D MET* 2.9 34.2 + - + +
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Residues in contact with ILE 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D GLU* 3.7 36.3 - - + +
388D MET* 4.7 3.8 - - + +
389D ILE* 3.6 42.6 - - + +
392D VAL* 5.7 0.2 - - + -
431D THR* 4.6 4.9 - - + -
435D PHE* 4.3 5.6 - - + -
452D ILE* 4.4 5.4 - - + -
510D ILE* 3.0 28.6 + - + +
511D LEU* 3.1 14.8 + - + +
513D HIS* 1.3 73.3 - - + +
515D ARG* 1.3 64.2 + - - +
517D MET* 3.8 25.9 - - + +
518D SER* 3.2 21.1 + - - -
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Residues in contact with ARG 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C SER* 2.9 45.5 + - - +
513C HIS* 3.5 18.5 + - - -
515C ARG* 4.7 0.4 - - + -
516C HIS* 3.3 44.4 + - + +
381D SER* 5.2 3.0 + - - -
385D GLU* 3.1 34.4 + - - +
455D ASN* 4.7 1.6 + - - -
456D SER* 3.0 38.4 + - - +
460D THR* 5.9 2.0 - - - +
511D LEU 2.8 11.5 + - - +
512D SER 3.2 10.8 - - - +
513D HIS 3.0 0.2 - - - -
514D ILE* 1.3 74.9 - - - +
516D HIS* 1.3 66.7 + - - +
518D SER* 3.0 6.7 + - - -
519D ASN* 3.0 28.8 + - - +
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Residues in contact with HIS 516 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C SER* 6.1 1.1 - - - -
460C THR* 5.8 6.2 - - + +
515C ARG* 3.3 36.7 + - - +
519C ASN* 3.1 36.1 + - - +
427D MET* 4.0 19.2 - - - -
512D SER 3.1 4.3 + - - +
513D HIS* 3.3 10.8 - - - +
515D ARG* 1.3 80.4 - - - +
517D MET* 1.3 62.3 + - + +
519D ASN* 3.2 3.5 + - - +
520D LYS* 3.1 48.0 + - + +
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Residues in contact with MET 517 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D MET* 3.8 19.0 - - + +
392D VAL* 4.5 2.2 - - + -
424D ILE* 4.5 4.3 - - + +
427D MET* 3.6 26.9 - - + +
428D LEU* 3.5 48.2 - - + -
431D THR* 3.1 27.8 - - + +
513D HIS* 2.9 16.9 + - + +
514D ILE* 3.8 35.4 - - + +
515D ARG 3.2 0.2 - - - -
516D HIS* 1.3 77.4 - - + +
518D SER* 1.3 52.6 - - - +
520D LYS* 3.3 7.0 + - - +
521D GLY* 2.8 31.7 + - - -
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Residues in contact with SER 518 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D SER 5.2 3.8 + - - -
384D LEU* 3.5 21.9 - - - +
385D GLU* 3.4 39.2 + - - +
388D MET* 4.0 8.3 - - - -
514D ILE 3.2 3.9 + - - -
515D ARG* 3.0 8.6 + - - -
517D MET* 1.3 75.9 - - - +
519D ASN* 1.3 67.0 + - - +
521D GLY* 3.4 0.9 + - - -
522D MET* 3.0 34.6 + - - +
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Residues in contact with ASN 519 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C HIS* 3.1 40.9 + - - +
519C ASN* 2.4 51.2 - - + +
520C LYS* 4.9 4.3 - - - +
523C GLU* 5.0 3.7 - - - +
515D ARG* 3.0 22.1 + - - -
516D HIS 3.4 6.1 - - - +
518D SER* 1.3 78.3 + - - +
520D LYS* 1.3 62.1 + - + +
522D MET* 3.1 18.0 + - - +
523D GLU* 3.2 23.0 + - - +
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Residues in contact with LYS 520 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C ASN* 5.0 2.9 - - - +
424D ILE* 3.4 21.6 - - + +
427D MET* 3.6 21.1 - - + -
516D HIS* 3.1 35.9 + - + +
517D MET 3.8 3.8 - - - +
519D ASN* 1.3 78.4 - - + +
521D GLY* 1.3 63.6 + - - +
523D GLU* 3.4 32.8 + - - +
524D HIS* 3.3 23.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 521 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D I0G 5.5 7.0 - - - +
384D LEU* 3.9 15.5 - - - +
388D MET* 4.4 6.7 - - - -
424D ILE* 3.7 11.4 - - - +
517D MET 2.8 21.6 + - - -
518D SER 3.7 2.2 - - - -
520D LYS* 1.3 74.0 - - - +
522D MET* 1.3 56.3 + - - +
524D HIS* 3.7 5.8 + - - +
525D LEU* 3.0 28.8 + - - +
----------------------------------------------------------
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Residues in contact with MET 522 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D GLU 5.0 4.0 - - - +
381D SER 6.1 0.9 - - - +
383D TRP* 3.4 40.6 - - + +
384D LEU* 3.8 12.6 - - + -
518D SER* 3.0 27.7 + - - +
519D ASN* 3.1 7.5 + - - +
521D GLY* 1.3 75.4 - - - +
523D GLU* 1.3 55.6 + - - +
524D HIS 3.1 1.3 - - - -
525D LEU* 3.5 7.7 - - + +
526D TYR* 2.6 36.3 + - - +
536D LEU* 5.7 1.6 - - + -
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Residues in contact with GLU 523 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C ASN* 4.9 3.6 - - - +
523C GLU* 3.2 42.3 - - - +
519D ASN* 3.2 16.9 + - - +
520D LYS* 3.6 41.4 + - - +
522D MET* 1.3 74.5 - - - +
524D HIS* 1.3 57.8 + - - +
526D TYR* 3.2 9.0 + - - +
527D SER* 2.9 29.5 + - - -
----------------------------------------------------------
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Residues in contact with HIS 524 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D I0G 3.3 30.0 + - - -
343D MET* 3.8 28.7 - - + +
418D VAL* 4.1 5.0 - - + +
419D GLU 3.0 27.1 + - - -
420D GLY* 3.9 17.0 - - - +
421D MET* 3.9 10.3 + - + -
424D ILE* 5.2 4.3 - - + -
520D LYS 3.3 15.1 + - - +
521D GLY* 3.7 6.8 + - - +
523D GLU* 1.3 76.7 - - - +
525D LEU* 1.3 66.7 + - - +
527D SER* 3.0 24.1 + - - -
528D MET* 3.5 22.0 - - - +
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Residues in contact with LEU 525 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D I0G 3.4 40.6 - - + -
343D MET* 4.2 9.0 - - + -
347D THR* 5.2 5.4 - - - +
383D TRP* 5.1 11.2 - - + -
384D LEU* 5.7 0.7 - - + -
521D GLY 3.0 18.7 + - - +
522D MET* 3.2 10.7 + - + +
524D HIS* 1.3 76.3 + - - +
526D TYR* 1.3 63.6 + - - +
528D MET* 3.1 34.7 + - + +
----------------------------------------------------------
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Residues in contact with TYR 526 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D MET 2.6 21.8 + - - +
523D GLU* 3.3 10.8 - - - +
524D HIS 3.2 0.2 - - - -
525D LEU* 1.3 74.7 - - - +
527D SER* 1.3 59.4 + - - +
528D MET 3.2 7.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 527 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D GLU 2.9 13.0 + - - -
524D HIS* 3.0 19.5 + - - -
526D TYR* 1.3 79.1 - - - +
528D MET* 1.3 63.5 + - - +
----------------------------------------------------------
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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