Contacts of the helix formed by residues 573 - 597 (chain D) in PDB entry 5MG3
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 GLY 573 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572D THR* 1.4 58.3 - - - +
574D ALA* 1.4 61.9 + - - -
576D LYS* 3.1 21.8 + - - +
577D GLY* 3.5 4.0 + - - -
142F LEU* 4.6 7.5 - - - +
197F LEU* 4.3 4.3 - - - -
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Residues in contact with ALA 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D PRO* 3.3 32.3 - - + +
572D THR 3.2 2.2 + - - -
573D GLY* 1.4 70.1 - - - -
575D ILE* 1.3 51.7 + - - +
577D GLY* 3.2 2.9 + - - +
578D PHE* 2.7 37.0 + - - +
51F ASP* 5.2 3.8 - - - +
197F LEU* 3.8 33.1 - - + +
198F THR* 4.8 3.8 - - + +
201F ALA* 5.6 2.0 - - + -
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Residues in contact with ILE 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567D LEU* 3.4 50.5 - - + +
571D GLY* 4.1 13.2 - - - -
572D THR 3.5 15.0 - - - +
574D ALA* 1.3 72.9 - - - +
576D LYS* 1.3 56.9 + - - +
578D PHE* 3.7 9.4 - - + +
579D ALA* 2.8 30.2 + - - +
149F ALA* 4.9 2.7 - - + -
197F LEU* 3.6 37.2 - - + +
200F VAL* 3.9 16.4 - - + -
201F ALA* 3.9 19.3 - - + +
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Residues in contact with LYS 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D TYR* 2.8 59.4 + - + +
569D ALA 4.2 7.5 + - - -
571D GLY 3.2 26.2 + - - -
572D THR* 4.1 5.4 + - - +
573D GLY* 3.1 13.5 + - - +
575D ILE* 1.3 77.0 - - - +
577D GLY* 1.3 55.5 + - - +
579D ALA* 4.2 0.2 - - - +
580D ILE* 2.9 42.4 + - + +
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Residues in contact with GLY 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503D SER* 4.5 11.7 - - - -
505D PRO* 4.7 0.9 - - - -
506D GLY* 3.5 20.2 - - - -
573D GLY 3.5 4.2 + - - -
574D ALA* 3.2 7.6 + - - -
576D LYS* 1.3 77.5 - - - +
578D PHE* 1.3 58.3 + - - +
580D ILE* 3.5 20.4 - - - +
581D THR* 3.7 7.3 + - - +
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Residues in contact with PHE 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D PRO* 3.1 22.2 + - + +
508D ALA* 3.9 8.5 - - + -
509D GLY* 3.5 19.8 - - - -
512D LEU* 3.3 32.8 - - + -
564D VAL* 5.6 0.9 - - + -
567D LEU* 4.0 25.8 - - + -
574D ALA 2.7 20.2 + - - +
575D ILE* 3.7 13.0 - - + +
577D GLY* 1.3 70.6 - - - +
579D ALA* 1.4 72.6 + - - +
581D THR* 3.5 4.2 + - - -
582D THR* 2.9 27.0 + - - -
201F ALA* 3.5 35.2 - - + -
204F MET 4.5 0.4 - - - -
205F SER* 3.2 32.8 - - - -
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Residues in contact with ALA 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D VAL* 3.4 40.3 - - + +
567D LEU* 4.7 4.5 - - + -
568D TYR* 3.9 20.4 - - + +
575D ILE 2.8 20.5 + - - +
576D LYS 4.2 1.3 - - - +
578D PHE* 1.4 75.9 - - + +
580D ILE* 1.3 58.0 + - - +
582D THR* 3.3 2.8 + - - -
583D GLY* 2.8 28.6 + - - -
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Residues in contact with ILE 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D ALA* 4.2 24.9 - - + -
501D THR 5.6 2.7 - - - +
568D TYR* 3.6 28.9 - - + +
576D LYS* 2.9 38.0 + - + +
577D GLY* 3.5 15.3 - - - +
579D ALA* 1.3 71.4 - - - +
581D THR* 1.4 75.4 + - + +
583D GLY* 3.3 7.3 + - - -
584D ILE* 3.8 13.7 + - - +
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Residues in contact with THR 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D ILE* 5.5 1.9 - - - +
494D MET* 4.4 20.7 - - + +
502D LEU* 6.4 2.2 - - + -
506D GLY* 2.7 35.2 + - - +
509D GLY* 3.5 5.1 - - - -
510D ILE* 4.6 11.0 - - + -
513D THR* 4.7 5.2 - - - +
577D GLY 3.7 10.7 + - - +
578D PHE 3.5 9.0 + - - -
579D ALA 3.6 0.4 - - - -
580D ILE* 1.4 86.4 - - + +
582D THR* 1.3 63.2 + - - +
584D ILE* 3.3 22.8 - - - +
585D GLY* 3.7 4.7 + - - -
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Residues in contact with THR 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D GLY* 3.2 21.0 - - - -
512D LEU* 3.5 33.8 - - + +
513D THR* 4.3 13.7 - - - -
516D VAL* 6.6 0.2 - - + -
560D THR* 4.9 3.6 - - + -
564D VAL* 3.9 17.9 - - + -
578D PHE 2.9 20.4 + - - -
579D ALA 3.3 4.2 + - - -
580D ILE 3.3 0.4 - - - -
581D THR* 1.3 78.1 + - - +
583D GLY* 1.4 50.9 + - - +
585D GLY* 3.1 4.2 + - - -
586D VAL* 2.8 43.0 + - + +
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Residues in contact with GLY 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D LEU* 4.9 4.3 - - - +
564D VAL* 4.0 8.0 - - - +
565D ILE* 5.8 2.7 - - - -
579D ALA 2.8 18.6 + - - -
580D ILE* 3.3 3.7 + - - -
582D THR* 1.4 66.6 - - - +
584D ILE* 1.4 63.7 + - - +
586D VAL* 3.4 12.2 + - - +
587D ALA* 3.1 25.8 + - - +
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Residues in contact with ILE 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D ILE* 4.5 11.2 - - + +
493D ILE* 4.0 30.5 - - + -
494D MET* 3.4 37.5 - - + -
497D LEU* 5.0 8.3 - - + -
580D ILE 3.8 10.6 + - - +
581D THR* 3.3 19.1 - - - +
583D GLY* 1.4 71.8 - - - +
585D GLY* 1.3 61.4 + - - +
587D ALA* 3.7 4.5 - - - +
588D THR* 2.7 39.3 + - - +
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Residues in contact with GLY 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D ILE* 3.4 29.9 - - - +
513D THR* 3.4 14.0 + - - -
581D THR 3.7 4.0 + - - -
582D THR 3.1 7.4 + - - -
584D ILE* 1.3 84.8 - - - +
586D VAL* 1.4 54.6 + - - +
588D THR* 3.7 1.1 - - - -
589D SER* 2.9 30.5 + - - -
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Residues in contact with VAL 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D THR* 3.9 1.5 + - - +
516D VAL* 4.8 5.4 - - + -
557D ASN* 3.6 35.4 - - - +
560D THR* 4.0 18.8 - - + -
561D LEU* 3.7 29.8 - - + +
564D VAL* 5.1 3.8 - - + -
582D THR* 2.8 31.9 + - + +
583D GLY* 3.4 18.6 - - - +
584D ILE 3.3 0.2 - - - -
585D GLY* 1.4 69.7 - - - +
587D ALA* 1.3 63.1 + - - +
589D SER* 4.5 3.1 - - - +
590D MET* 3.6 24.1 + - + +
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Residues in contact with ALA 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D LEU* 4.9 6.0 - - + +
583D GLY 3.1 16.6 + - - +
584D ILE* 3.7 4.9 - - - +
586D VAL* 1.3 78.8 - - - +
588D THR* 1.3 63.9 + - - +
590D MET* 4.1 9.4 - - - +
591D PHE* 3.5 29.8 + - + +
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Residues in contact with THR 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D ASN* 3.9 14.8 - - - +
489D LEU* 3.7 39.7 - - + -
490D ILE* 4.4 5.4 - - + +
493D ILE* 3.4 23.6 - - + +
584D ILE 2.7 22.3 + - - -
585D GLY* 3.7 6.5 - - - -
587D ALA* 1.3 80.8 - - - +
589D SER* 1.4 60.4 + - - +
591D PHE* 3.8 2.3 + - - +
592D THR* 2.9 26.2 + - - +
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Residues in contact with SER 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D ASN* 2.7 32.1 + - - +
513D THR* 5.2 1.1 - - - -
516D VAL* 4.0 12.1 + - - +
517D ALA* 3.9 17.7 + - - -
520D ALA* 5.4 1.2 - - - +
557D ASN* 4.0 12.1 + - - -
585D GLY 2.9 21.1 + - - -
586D VAL 4.6 0.9 - - - -
587D ALA 3.5 0.2 - - - -
588D THR* 1.4 71.1 - - - +
590D MET* 1.3 56.1 + - - +
592D THR* 3.1 2.1 + - - -
593D ALA* 2.8 37.7 + - - +
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Residues in contact with MET 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ILE* 5.9 1.3 - - + -
554D PHE* 4.4 28.9 - - + +
557D ASN* 3.9 31.5 + - + +
558D ILE* 4.9 13.5 - - + -
561D LEU* 4.9 18.4 - - + -
586D VAL* 3.6 20.3 + - + +
587D ALA* 4.1 7.4 - - - +
588D THR 3.4 0.6 - - - -
589D SER* 1.3 74.7 - - - +
591D PHE* 1.3 89.2 + - + +
593D ALA* 3.2 3.7 + - - +
594D ILE* 3.1 31.6 + - + +
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Residues in contact with PHE 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D PHE* 6.1 2.7 - + - -
587D ALA* 3.5 18.1 + - + -
588D THR* 3.8 5.4 + - - +
589D SER 3.6 0.2 - - - -
590D MET* 1.3 95.8 - - + +
592D THR* 1.3 65.4 + - - +
594D ILE* 3.8 21.1 - - + -
595D VAL* 3.7 24.6 + - + +
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Residues in contact with THR 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ALA* 3.4 30.0 - - + +
485D ALA* 4.1 12.1 - - + -
486D ASN* 3.9 21.3 - - + +
489D LEU* 4.1 18.8 - - + +
588D THR* 2.9 23.2 + - - +
589D SER 3.1 8.8 + - - -
591D PHE* 1.3 74.1 - - - +
593D ALA* 1.3 59.3 + - - +
596D GLY* 2.8 34.0 + - - -
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Residues in contact with ALA 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ALA* 4.9 2.2 - - + -
520D ALA* 4.6 14.8 - - + -
553D ILE* 4.3 18.6 - - + -
557D ASN* 5.6 1.6 - - - +
589D SER* 2.8 20.6 + - - +
590D MET* 3.9 2.9 - - - +
591D PHE 3.1 0.4 - - - -
592D THR* 1.3 81.1 - - + +
594D ILE* 1.3 56.6 + - - +
597D THR* 2.8 52.4 + - + -
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Residues in contact with ILE 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D PHE* 3.6 24.9 - - + -
553D ILE* 3.9 20.0 - - + -
554D PHE* 3.4 51.4 - - + -
590D MET* 3.1 23.1 + - + +
591D PHE* 3.8 26.2 - - + -
593D ALA* 1.3 74.0 - - - +
595D VAL* 1.4 79.6 + - + +
598D ARG* 3.3 22.3 + - - +
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Residues in contact with VAL 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591D PHE* 3.7 15.5 + - + +
593D ALA 3.2 0.2 - - - -
594D ILE* 1.4 101.8 - - + +
596D GLY* 1.4 60.3 + - - +
597D THR 3.5 0.9 - - - -
598D ARG* 3.3 42.0 - - - +
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Residues in contact with GLY 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.1 35.1 + - - -
481D SER* 4.2 3.3 + - - -
482D ALA* 3.7 14.4 - - - +
592D THR* 2.8 25.5 + - - -
595D VAL* 1.4 74.1 - - - +
597D THR* 1.3 56.5 + - - +
598D ARG 3.3 1.0 + - - -
599D ALA* 5.2 0.7 + - - +
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Residues in contact with THR 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ALA* 3.5 24.0 - - + -
520D ALA* 5.4 1.3 - - + +
521D ASN* 4.7 17.0 - - + +
524D ILE* 3.9 31.8 - - + +
550D PHE* 3.6 14.8 - - - -
553D ILE* 5.6 1.9 - - - +
593D ALA* 2.8 39.0 + - + +
596D GLY* 1.3 71.0 - - - +
598D ARG* 1.3 61.1 + - - +
599D ALA* 3.6 2.2 - - - -
600D ILE* 3.4 25.8 - - + +
601D VAL 4.5 0.3 + - - -
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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
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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