Contacts of the helix formed by residues 588 - 613 (chain A) in PDB entry 1Y8B
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 SER 588 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ASN* 3.2 8.0 + - - -
587A TRP* 1.3 74.2 - - - +
589A ALA* 1.3 67.8 + - - +
590A GLN* 3.0 10.4 + - - -
591A GLU* 3.1 10.7 + - - +
592A ILE* 2.8 23.6 + - - +
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Residues in contact with ALA 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER* 1.3 75.3 - - - +
590A GLN* 1.3 57.7 + - - +
592A ILE* 4.4 9.4 - - - +
593A GLN* 2.7 42.4 + - + +
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Residues in contact with GLN 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER* 3.0 7.5 - - - -
589A ALA* 1.3 78.7 - - - +
591A GLU* 1.3 67.1 + - - +
593A GLN* 3.9 2.9 - - - +
594A GLN* 3.1 36.3 + - + +
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Residues in contact with GLU 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TRP* 4.1 23.6 - - + -
588A SER* 3.1 21.2 + - - +
590A GLN* 1.3 80.5 - - - +
592A ILE* 1.3 52.0 + - - +
594A GLN* 3.0 10.7 + - - +
595A GLU* 2.6 62.8 + - + +
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Residues in contact with ILE 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TRP* 3.2 42.8 - - + +
588A SER 2.8 22.1 + - - +
589A ALA* 4.2 6.7 - - - +
591A GLU* 1.3 71.0 - - - +
593A GLN* 1.3 62.0 + - + +
595A GLU* 2.6 7.4 + - - +
596A LEU* 2.3 48.2 + - + +
649A GLY 4.2 18.6 - - - +
650A ILE* 5.1 2.2 - - + +
651A LEU* 3.9 25.4 - - + -
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Residues in contact with GLN 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A ALA* 2.7 34.1 + - + +
590A GLN* 3.9 4.3 - - - +
592A ILE* 1.3 80.4 - - + +
594A GLN* 1.3 51.3 + - + +
596A LEU* 4.2 11.2 - - - +
597A ASP* 2.4 38.4 + - - +
655A GLN* 5.4 3.8 - - - +
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Residues in contact with GLN 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLN* 3.1 28.9 + - + +
591A GLU* 3.0 11.2 + - - +
593A GLN* 1.3 74.5 - - + +
595A GLU* 1.3 53.4 + - + +
597A ASP* 2.4 29.3 + - - +
598A ASN* 2.6 40.3 + - - +
623A ILE* 4.9 8.7 - - - +
624A HIS* 4.8 17.6 + - - -
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Residues in contact with GLU 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A PRO* 3.8 21.2 - - - +
513A ASP* 5.3 1.2 - - - +
587A TRP* 6.1 2.5 - - + -
591A GLU* 2.6 46.7 + - + +
592A ILE* 2.6 8.6 + - - +
594A GLN* 1.3 74.6 - - + +
596A LEU* 1.3 61.2 + - - +
597A ASP 3.3 0.4 - - - -
598A ASN* 4.0 9.8 + - - +
599A ASN* 2.5 43.8 + - - +
645A TRP* 3.2 35.1 - - + -
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Residues in contact with LEU 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 2.3 41.2 + - + +
593A GLN* 4.2 11.0 - - - +
595A GLU* 1.3 68.4 - - - +
597A ASP* 1.3 60.1 + - + +
599A ASN* 3.8 4.2 - - - +
600A VAL* 2.9 45.0 + - + +
646A LEU* 5.0 13.2 - - + -
651A LEU* 3.8 38.8 - - + -
656A VAL* 4.5 11.7 - - + -
659A SER* 3.3 37.2 - - - +
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Residues in contact with ASP 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A GLN 2.4 20.5 - - - +
594A GLN* 2.4 38.8 + - - +
596A LEU* 1.3 78.4 - - + +
598A ASN* 1.3 73.8 + - - +
599A ASN 2.9 0.5 + - - -
600A VAL* 2.9 2.6 + - - +
601A GLN* 2.6 38.7 + - + +
623A ILE* 4.1 16.4 - - + +
659A SER* 5.8 0.2 - - - -
663A MET* 4.2 31.2 - - + +
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Residues in contact with ASN 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A MET* 4.4 12.8 - - - +
512A PRO 3.8 15.7 + - - +
513A ASP* 3.1 34.1 + - - +
594A GLN* 2.6 37.0 + - - +
595A GLU* 3.7 12.6 + - - +
597A ASP* 1.3 89.9 + - - +
599A ASN* 1.3 64.6 + - - +
601A GLN* 3.2 25.3 - - - +
602A GLY* 3.6 1.6 + - - -
623A ILE* 4.2 14.2 - - - +
624A HIS* 5.4 0.2 - - - -
638A SER* 5.2 0.2 + - - -
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Residues in contact with ASN 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A MET 4.7 7.7 - - - +
512A PRO* 5.3 1.7 - - - +
595A GLU* 2.5 34.4 + - - +
596A LEU* 3.8 4.9 - - - +
598A ASN* 1.3 77.9 - - - +
600A VAL* 1.3 67.8 + - - +
602A GLY* 3.4 8.1 + - - -
603A ILE* 3.5 13.7 + - - +
634A THR* 4.6 0.2 - - - +
638A SER* 4.1 24.8 + - - +
641A HIS* 6.5 0.4 - - - -
642A ILE* 3.7 27.7 - - + +
645A TRP* 3.6 31.5 - - - -
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU* 2.9 45.1 + - + +
597A ASP* 2.9 4.0 + - - +
599A ASN* 1.3 72.9 - - + +
601A GLN* 1.3 57.1 + - - +
602A GLY 2.9 1.1 - - - -
603A ILE* 2.4 38.5 + - + +
604A LEU* 3.1 25.5 + - + -
642A ILE* 4.4 8.3 - - + -
646A LEU* 6.6 0.4 - - + -
656A VAL* 5.1 1.8 - - + -
659A SER* 4.9 0.7 - - - +
660A LEU* 3.2 33.2 - - + +
663A MET* 5.3 3.4 - - + -
697A ILE* 4.2 22.4 - - + -
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Residues in contact with GLN 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A MET* 4.7 6.6 - - - +
597A ASP* 2.6 30.6 + - + +
598A ASN* 3.2 18.4 - - - +
600A VAL* 1.3 74.3 - - - +
602A GLY* 1.3 89.1 + - - +
604A LEU* 4.6 2.7 - - - +
605A GLY* 2.8 23.4 + - - -
621A PRO 4.9 0.2 + - - -
622A ASP* 4.5 23.6 - - - +
623A ILE* 5.1 4.2 - - + +
628A LEU* 5.8 1.2 - - - +
630A GLU* 3.5 14.9 + - - +
663A MET* 4.6 12.5 - - + +
667A VAL* 4.4 21.7 - - + +
670A GLN* 4.4 14.3 + - - -
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Residues in contact with GLY 602 (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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511A MET* 5.5 2.5 - - - -
598A ASN 3.6 2.2 + - - -
599A ASN 3.4 8.1 + - - -
600A VAL 2.7 5.5 + - - -
601A GLN* 1.3 98.2 + - - +
603A ILE* 1.3 58.9 + - - -
606A TYR* 3.2 24.8 + - - +
630A GLU* 3.4 17.7 - - - +
634A THR* 3.6 14.4 - - - +
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Residues in contact with ILE 603 (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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599A ASN 3.5 11.2 - - - +
600A VAL* 2.4 27.8 + - + +
602A GLY* 1.3 65.2 - - - -
604A LEU* 1.3 60.8 + - + +
605A GLY 3.0 1.1 - - - -
606A TYR* 2.9 2.5 + - - -
607A VAL* 2.4 59.6 + - + +
634A THR* 4.0 9.9 - - + -
635A LEU* 4.7 5.4 - - + -
639A SER* 2.9 36.8 - - - +
642A ILE* 3.6 23.6 - - + -
693A ALA 4.5 7.6 - - - +
696A LEU* 4.0 19.5 - - + -
697A ILE* 4.5 12.8 - - + -
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Residues in contact with LEU 604 (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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600A VAL* 3.1 31.3 + - + +
601A GLN 4.3 0.9 - - - +
603A ILE* 1.3 76.9 - - + +
605A GLY* 1.3 57.5 + - - +
607A VAL* 4.3 4.3 - - - -
608A VAL* 2.7 37.4 + - + +
660A LEU* 4.1 20.0 - - + +
663A MET* 4.0 22.9 - - + -
664A ALA* 4.1 13.9 - - + +
667A VAL* 3.8 15.9 - - + -
690A PHE 5.6 0.4 - - - +
693A ALA* 3.5 37.0 - - + +
694A SER* 4.6 4.9 - - - +
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Residues in contact with GLY 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A GLN 2.8 17.7 + - - -
604A LEU* 1.3 79.0 - - - +
606A TYR* 1.3 59.5 + - - +
608A VAL* 3.4 9.8 - - - +
609A ARG* 3.0 30.3 + - - -
630A GLU* 4.3 2.7 - - - -
667A VAL* 3.5 6.0 - - - +
670A GLN* 3.4 25.6 - - - -
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Residues in contact with TYR 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 6.1 0.2 - - - -
602A GLY 3.2 17.9 + - - +
603A ILE 2.9 1.6 + - - -
605A GLY* 1.3 74.8 - - - +
607A VAL* 1.3 64.1 + - + +
609A ARG* 4.2 3.4 - - - +
610A TRP* 2.8 75.3 + + + +
615A ILE 4.2 6.5 - - - -
616A GLY* 5.3 0.7 - - - -
630A GLU* 3.8 21.6 - - + +
631A ASP* 3.5 23.8 - - - +
632A ARG* 3.1 49.1 + - + -
634A THR* 4.3 1.3 - - - +
635A LEU* 3.6 32.3 - - + -
712A LEU* 4.2 12.6 - - + -
713A HIS* 5.2 3.6 - + - -
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Residues in contact with VAL 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 2.4 53.1 + - + +
604A LEU* 4.3 0.4 - - - -
606A TYR* 1.3 78.7 - - + +
608A VAL* 1.3 59.4 + - - +
610A TRP* 4.5 1.6 - - - -
611A VAL* 2.8 53.1 + - + +
635A LEU* 4.5 0.7 - - + -
689A ALA* 4.8 3.1 - - + +
693A ALA* 3.4 33.4 - - + +
696A LEU* 4.0 5.4 - - + -
712A LEU* 3.7 27.8 - - + -
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Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A LEU* 2.7 32.4 + - + +
605A GLY* 3.4 12.1 - - - +
607A VAL* 1.3 75.0 - - - +
609A ARG* 1.3 67.6 + - + +
611A VAL* 4.9 1.3 - - - -
612A GLU* 2.4 48.7 + - - +
667A VAL* 4.0 14.8 - - + +
668A ASP* 6.0 5.4 - - - +
670A GLN* 4.9 1.3 - - - +
671A ASN* 6.1 2.7 - - + -
689A ALA* 5.6 8.9 - - + +
693A ALA* 6.1 1.3 - - + -
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Residues in contact with ARG 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU* 5.7 3.4 - - - -
605A GLY 3.0 27.2 + - - +
606A TYR* 4.4 3.4 - - - +
608A VAL* 1.3 87.1 - - + +
610A TRP* 1.3 60.3 + - - +
611A VAL 3.4 0.2 - - - -
612A GLU* 3.6 18.7 - - - +
613A GLN 3.3 7.1 + - - -
614A GLY 3.2 17.2 + - - -
615A ILE* 3.4 30.2 + - + +
616A GLY* 4.6 13.7 - - - +
617A CYS 5.8 1.2 + - - -
620A VAL* 3.6 32.1 - - - +
630A GLU* 3.1 39.2 + - - +
670A GLN* 3.8 20.1 - - + +
671A ASN* 4.9 13.2 - - + +
674A ASP* 5.4 2.9 - - - -
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Residues in contact with TRP 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 4.1 19.7 - - + -
123A ASN* 3.5 33.4 - - - -
282A ASP* 6.5 0.9 - - + -
606A TYR* 2.8 60.6 + + + +
607A VAL* 4.2 1.6 - - - +
609A ARG* 1.3 80.4 - - - +
611A VAL* 1.3 63.3 + - + +
614A GLY* 3.0 24.6 + - - -
615A ILE 3.4 31.4 + - - +
632A ARG* 4.3 7.6 - - - -
712A LEU* 5.4 2.0 - - + -
713A HIS* 5.4 3.5 + + - -
716A ARG* 3.2 50.7 - - - +
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Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A VAL* 2.8 39.4 + - + +
608A VAL 4.7 0.2 - - - +
610A TRP* 1.3 81.0 - - + +
612A GLU* 1.3 62.9 + - - +
614A GLY 4.6 0.2 - - - -
689A ALA* 3.6 27.6 - - + -
712A LEU* 4.5 4.3 - - + -
716A ARG* 4.0 27.1 - - + +
719A GLU* 3.0 42.3 - - - +
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Residues in contact with GLU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A VAL* 2.4 41.8 + - + +
609A ARG* 3.6 19.7 - - - +
611A VAL* 1.3 82.9 - - - +
613A GLN* 1.3 85.3 + - + +
671A ASN* 2.7 27.1 + - - +
678A ARG* 2.7 38.7 + - - +
689A ALA* 5.8 0.2 - - - +
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Residues in contact with GLN 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ARG* 6.0 1.8 - - - +
609A ARG 3.3 4.2 + - - +
612A GLU* 1.3 97.5 - - + +
614A GLY* 1.3 70.4 + - - +
615A ILE* 3.5 28.3 - - + +
671A ASN* 4.6 3.5 + - - +
676A ALA* 5.2 8.7 + - - +
678A ARG* 3.6 36.5 - - - +
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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