Contacts of the helix formed by residues 647 - 671 (chain C) in PDB entry 3F7F
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 PHE 647 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579C ILE* 3.6 33.0 - - + -
580C PRO* 3.8 29.4 - - + -
583C LEU* 3.9 5.2 - - + -
637C PHE* 3.6 29.6 - + + -
642C LEU* 4.0 28.7 - - + -
643C ASP 3.0 20.0 + - - +
644C THR 4.1 1.1 - - - -
646C ILE* 1.3 95.9 - - + +
648C GLY* 1.3 54.0 + - - +
649C GLN 3.1 3.5 + - - -
650C HIS* 3.2 22.6 + + + +
651C ILE* 2.7 42.4 + - + +
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Residues in contact with GLY 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644C THR 3.2 19.6 + - - -
645C GLU* 3.2 8.8 + - - -
646C ILE 3.1 5.9 - - - -
647C PHE* 1.3 77.6 - - - +
649C GLN* 1.3 61.9 + - - +
651C ILE* 3.9 5.0 - - - +
652C SER* 3.1 24.8 + - - -
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Residues in contact with GLN 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C GLU 4.8 0.6 + - - -
646C ILE 4.3 5.6 + - - +
647C PHE 3.1 0.6 - - - -
648C GLY* 1.3 75.3 - - - +
650C HIS* 1.3 71.8 + - + +
652C SER* 3.0 14.4 + - - -
653C THR* 2.9 47.0 + - - +
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Residues in contact with HIS 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C PRO* 4.4 5.9 + - + +
583C LEU* 4.2 14.5 - - + +
584C ASN* 4.1 39.8 + - - -
587C ILE* 3.4 31.4 - - + +
588C ASN* 4.2 9.9 - - - -
637C PHE* 5.0 1.1 - - + -
646C ILE 5.7 0.9 - - - -
647C PHE* 3.2 36.8 + + + +
649C GLN* 1.3 84.3 - - + +
651C ILE* 1.3 57.4 + - - +
653C THR* 3.1 3.9 + - - -
654C LEU* 2.8 41.0 + - + +
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Residues in contact with ILE 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C THR* 4.4 8.5 - - + +
550C PHE* 3.7 32.5 - - + -
634C LEU* 4.1 3.5 - - + +
637C PHE* 3.9 34.1 - - + -
642C LEU 5.4 1.1 - - - +
644C THR* 4.0 27.8 - - - +
647C PHE* 2.7 37.9 + - + +
648C GLY* 3.9 4.9 - - - +
650C HIS* 1.3 73.5 - - - +
652C SER* 1.3 57.2 + - - +
654C LEU* 3.7 7.8 - - - +
655C LEU* 3.0 40.5 + - + +
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Residues in contact with SER 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C GLY 3.1 12.3 + - - -
649C GLN* 3.0 24.2 + - - -
651C ILE* 1.3 79.3 - - - +
653C THR* 1.3 63.8 + - - +
655C LEU* 4.0 8.4 - - - +
656C ASP* 3.2 23.4 + - - +
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Residues in contact with THR 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C ILE* 3.8 27.4 - - + -
592C LYS* 3.9 30.8 + - - +
649C GLN* 2.9 37.5 + - - +
650C HIS* 3.6 8.1 + - - -
652C SER* 1.3 76.9 + - - +
654C LEU* 1.3 60.3 + - - +
656C ASP* 3.4 6.0 + - + +
657C LEU* 2.9 32.0 + - + +
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Residues in contact with LEU 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C LEU* 5.2 0.4 - - + -
586C LEU* 5.7 1.3 - - + -
587C ILE* 3.7 30.3 - - + -
591C MET* 5.0 8.5 - - - -
630C THR* 3.7 23.3 - - + +
633C VAL* 3.9 31.0 - - + -
634C LEU* 3.5 25.4 - - + -
637C PHE* 4.0 13.9 - - + -
650C HIS* 2.8 26.6 + - + +
651C ILE* 3.7 0.9 - - - +
653C THR* 1.3 75.2 - - - +
655C LEU* 1.3 59.7 + - - +
657C LEU* 3.0 9.3 + - + +
658C HIS* 2.7 32.4 + - - +
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Residues in contact with LEU 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C PHE* 3.7 45.7 - - + +
535C ILE* 4.1 28.3 - - + -
536C ILE* 3.6 20.9 - - + +
546C THR* 6.4 0.2 - - + -
550C PHE* 4.7 4.5 - - + -
634C LEU* 3.7 19.1 - - + -
651C ILE* 3.0 38.1 + - + +
652C SER* 4.1 7.6 - - - +
653C THR 3.4 0.2 - - - -
654C LEU* 1.3 76.0 - - - +
656C ASP* 1.3 61.3 + - - +
658C HIS* 3.8 5.4 + - - +
659C TYR* 3.2 22.3 + - - +
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Residues in contact with ASP 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C ILE* 4.4 10.2 - - + +
592C LYS* 6.0 0.9 - - - -
652C SER 3.2 19.3 + - - +
653C THR* 3.6 6.2 - - - +
654C LEU 3.1 0.6 - - - -
655C LEU* 1.3 76.7 - - - +
657C LEU* 1.3 69.3 + - - +
659C TYR* 3.5 4.5 + - - +
660C LYS* 2.6 63.7 + - - +
714C ILE* 3.7 14.9 - - - +
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Residues in contact with LEU 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C ILE* 4.9 4.9 - - + -
591C MET* 4.4 22.7 - - + -
592C LYS* 4.3 22.7 - - + -
630C THR* 4.8 1.6 - - + -
653C THR* 2.9 37.6 + - + +
654C LEU* 3.0 9.2 + - + +
656C ASP* 1.3 80.4 - - - +
658C HIS* 1.3 60.9 + - - +
660C LYS* 3.4 4.5 + - + +
661C GLN* 2.8 45.5 + - - +
710C TYR* 3.4 51.9 - - + +
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Residues in contact with HIS 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C SER* 2.8 47.3 + - - -
532C PHE* 3.6 17.3 - - + +
533C LEU* 4.0 17.9 - - + +
627C TYR* 3.5 24.9 - + - -
630C THR* 3.7 8.9 - - + +
631C LEU* 3.7 21.6 - - + +
634C LEU* 3.9 13.9 - - + -
654C LEU 2.7 16.9 + - - +
655C LEU 3.8 5.8 + - - +
657C LEU* 1.3 78.1 - - - +
659C TYR* 1.3 58.1 + - - +
661C GLN* 3.1 14.8 + - - +
662C PHE* 2.8 30.6 + - + +
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Residues in contact with TYR 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C LEU* 3.4 27.6 - - + -
536C ILE* 3.6 33.7 - - + -
537C THR* 3.9 20.1 - - + +
655C LEU 3.2 15.6 + - - +
656C ASP* 3.7 5.6 - - - +
657C LEU 3.3 0.2 - - - -
658C HIS* 1.3 80.3 + - - +
660C LYS* 1.3 64.1 + - - +
662C PHE* 3.3 2.4 + - - +
663C LEU* 3.0 50.5 + - + +
714C ILE* 3.7 37.3 + - + -
716C GLU* 3.7 6.6 + - - -
725C ARG* 3.1 30.4 - - - +
729C ILE* 4.1 9.6 - - + -
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Residues in contact with LYS 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C ASP* 2.6 48.9 + - - +
657C LEU* 3.9 4.3 - - + +
659C TYR* 1.3 79.3 - - + +
661C GLN* 1.3 57.2 + - - +
663C LEU* 3.4 5.6 + - - +
664C LEU* 2.9 32.0 + - - +
709C VAL* 3.6 31.8 - - + +
710C TYR* 2.9 34.4 + - + +
711C ASN 4.8 0.4 - - - -
712C ALA* 3.5 20.5 + - + +
714C ILE* 3.9 25.6 - - + -
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Residues in contact with GLN 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C MET* 3.5 8.1 - - - +
623C LEU* 4.2 21.3 - - + +
626C HIS* 3.7 1.2 + - - +
627C TYR* 3.2 35.7 - - + -
630C THR* 2.8 28.1 + - - -
657C LEU* 2.8 30.9 + - - +
658C HIS* 3.3 15.1 - - - +
660C LYS* 1.3 73.0 - - - +
662C PHE* 1.3 69.6 + - - +
664C LEU* 3.3 4.3 + - - +
665C LEU* 2.9 27.9 + - - +
710C TYR* 3.0 31.1 + - + +
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Residues in contact with PHE 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C ILE* 5.0 3.8 - - + -
398C VAL* 4.1 26.7 - - + -
529C SER* 4.1 9.2 - - - -
533C LEU* 3.5 37.7 - - + -
627C TYR* 3.6 33.6 - + + -
658C HIS* 2.8 19.1 + - + +
659C TYR 3.5 3.8 - - - +
661C GLN* 1.3 75.8 - - - +
663C LEU* 1.3 67.5 + - - +
665C LEU* 2.9 6.3 + - - +
666C ASN* 2.7 43.0 + - - +
729C ILE* 3.8 26.9 - - + -
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Residues in contact with LEU 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659C TYR* 3.0 46.8 + - + +
660C LYS* 3.6 6.3 - - - +
662C PHE* 1.3 78.4 - - + +
664C LEU* 1.3 57.9 + - - +
666C ASN* 3.0 9.5 + - + +
667C LEU* 2.8 43.0 + - + +
714C ILE* 4.9 8.7 - - + -
725C ARG* 5.3 6.5 - - + -
729C ILE* 3.3 41.7 - - + -
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Residues in contact with LEU 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C LEU* 6.3 0.2 - - + -
619C LEU* 4.0 20.0 - - + +
620C HIS* 5.4 2.7 - - + -
623C LEU* 2.9 40.4 - - + -
660C LYS 2.9 20.7 + - - +
661C GLN 3.8 3.4 - - - +
663C LEU* 1.3 72.8 - - - +
665C LEU* 1.3 61.1 + - + +
667C LEU* 3.1 9.8 + - + +
668C TYR* 2.8 29.5 + - + +
675C LEU* 4.0 31.0 - - + -
679C LEU* 4.4 7.9 - - + -
709C VAL* 4.1 22.0 - - + -
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Residues in contact with LEU 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C VAL* 3.9 30.5 - - + -
620C HIS* 3.4 27.4 - - + +
623C LEU* 4.3 10.5 - - + +
624C SER* 3.3 34.5 - - - +
627C TYR* 3.9 30.3 - - + -
661C GLN 2.9 19.7 + - - +
662C PHE* 2.9 4.8 + - - +
664C LEU* 1.3 77.8 - - + +
666C ASN* 1.3 61.2 + - - +
668C TYR* 3.5 5.2 + - - +
669C ARG* 3.0 35.6 + - - +
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Residues in contact with ASN 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C VAL* 4.1 14.2 - - + +
400C LYS* 4.0 15.4 + - - +
662C PHE* 2.7 35.9 + - + +
663C LEU* 3.2 14.4 - - - +
665C LEU* 1.3 76.0 - - - +
667C LEU* 1.3 65.2 + - + +
669C ARG* 3.4 7.8 + - - +
670C GLN* 3.1 48.1 + - - +
728C ILE* 3.4 26.8 + - - +
729C ILE* 4.2 5.2 - - + +
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Residues in contact with LEU 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C LEU* 2.8 33.4 + - + +
664C LEU* 3.7 7.6 - - + +
666C ASN* 1.3 73.0 - - + +
668C TYR* 1.3 64.3 + - - +
670C GLN* 3.8 6.6 - - + +
671C ASP* 3.1 26.5 + - - +
675C LEU* 4.2 28.0 - - + +
678C VAL* 5.8 4.0 - - + -
728C ILE* 4.2 28.7 - - + -
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Residues in contact with TYR 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C VAL* 4.1 11.8 - - + +
616C LEU* 4.1 24.9 - - + -
617C GLU* 2.5 42.2 + - - -
620C HIS* 3.1 56.3 - + + -
664C LEU* 2.8 18.3 + - + +
665C LEU* 3.5 4.5 - - - +
666C ASN 3.2 0.2 - - - -
667C LEU* 1.3 79.0 - - - +
669C ARG* 1.3 72.3 + - + +
672C LYS* 3.3 54.5 + - + +
675C LEU* 3.6 13.0 - - + +
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Residues in contact with ARG 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C GLN* 5.0 5.5 + - - -
396C ASP* 3.0 32.9 + - - -
398C VAL* 3.5 13.4 - - - +
399C THR* 3.1 40.4 + - + +
400C LYS 5.7 0.2 - - - +
406C ARG* 5.5 3.1 + - - -
410C ASN* 5.7 3.0 - - - +
413C SER* 2.8 28.6 + - - +
414C ARG* 6.5 0.7 - - - -
620C HIS* 2.6 38.9 + - - -
624C SER* 4.5 2.0 + - - -
665C LEU* 3.0 29.6 + - - +
666C ASN* 3.8 10.1 - - - +
668C TYR* 1.3 86.5 - - + +
670C GLN* 1.3 59.6 + - - +
672C LYS* 4.4 2.9 - - - +
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Residues in contact with GLN 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C LYS* 3.5 14.3 - - - +
406C ARG* 3.8 33.1 - - - +
413C SER* 4.7 4.0 + - - -
666C ASN* 3.1 35.7 + - - +
667C LEU* 3.8 9.6 - - + +
668C TYR 3.3 0.4 - - - -
669C ARG* 1.3 81.5 - - - +
671C ASP* 1.3 66.8 + - + +
728C ILE* 3.9 19.9 - - + +
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Residues in contact with ASP 671 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C SER* 5.3 1.6 - - - -
667C LEU 3.1 10.4 + - - +
669C ARG 3.4 0.8 - - - -
670C GLN* 1.3 86.1 - - + +
672C LYS* 1.3 63.4 + - - +
673C CYS* 3.4 9.0 + - - +
674C LEU* 3.0 40.5 + - + +
675C LEU* 3.0 18.4 + - - +
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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