Contacts of the helix formed by residues 638 - 666 (chain C) in PDB entry 1IW1
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 638 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632C LEU* 4.1 3.6 - - - +
637C LEU* 1.3 79.8 - - - +
639C VAL* 1.3 66.4 + - - -
640C ALA* 3.1 3.1 - - - -
641C GLU* 3.0 18.3 + - - +
642C PHE* 3.2 11.3 + - - +
751C TYR* 3.5 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 639 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C GLY* 1.3 68.4 - - - -
640C ALA* 1.3 67.5 + - - +
642C PHE* 3.2 7.9 + - + +
643C THR* 2.8 39.5 + - - +
690C LEU* 4.2 16.8 - - + +
751C TYR* 3.6 35.1 - - + +
753C VAL* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 640 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C GLY* 3.1 1.0 - - - -
639C VAL* 1.3 79.9 - - - +
641C GLU* 1.3 75.7 + - - +
643C THR* 3.1 7.2 + - - -
644C ARG* 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 641 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628C PHE* 3.7 22.5 - - + -
632C LEU* 4.2 1.1 - - + -
637C LEU* 3.7 41.4 - - + -
638C GLY* 3.0 27.1 + - - +
640C ALA* 1.3 82.8 - - - +
642C PHE* 1.3 66.4 + - - +
644C ARG* 3.3 22.4 + - - +
645C LEU 3.1 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 642 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632C LEU* 4.0 14.4 - - + +
638C GLY 3.2 9.1 + - - +
639C VAL* 3.2 11.1 + - - +
641C GLU* 1.3 77.4 - - - +
643C THR* 1.3 57.8 + - - +
645C LEU* 3.2 9.8 + - + +
646C GLN* 3.0 48.6 + - + +
690C LEU* 3.9 34.1 - - + -
743C ILE* 4.8 2.0 - - + -
747C MET* 3.6 36.3 - - + -
751C TYR* 5.2 0.2 - - + -
753C VAL* 4.6 8.7 - - + -
757C ALA 4.4 2.9 - - - -
758C LEU* 3.5 32.5 - - + -
761C TYR* 3.6 22.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 643 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639C VAL* 2.8 34.9 + - - +
640C ALA* 3.4 6.9 - - - -
642C PHE* 1.3 77.0 - - - +
644C ARG* 1.3 57.4 + - + +
646C GLN* 3.2 2.6 + - - +
647C GLU* 2.9 40.8 + - - +
687C LEU* 4.0 8.1 - - + -
690C LEU* 3.9 24.0 + - + +
691C ASN* 3.7 36.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 644 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628C PHE* 4.6 6.1 - - - -
640C ALA* 3.0 18.1 + - - +
641C GLU* 3.6 21.3 + - - +
642C PHE 3.3 0.2 - - - -
643C THR* 1.3 75.2 - - - +
645C LEU* 1.3 62.9 + - - +
647C GLU* 3.4 15.0 + - - +
648C GLN* 3.2 28.1 + - - +
810C ASP 5.2 2.6 + - - -
811C LEU* 2.6 51.0 + - + +
813C LYS* 5.0 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 645 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628C PHE* 4.2 4.3 - - + -
629C MET* 4.1 24.2 - - + -
632C LEU* 4.2 13.0 - - + -
641C GLU 3.1 13.1 + - - +
642C PHE* 3.2 15.0 + - + +
644C ARG* 1.3 75.6 - - - +
646C GLN* 1.3 72.3 + - - +
648C GLN* 3.1 3.8 + - - +
649C ALA* 2.9 29.9 + - + +
652C PHE* 5.7 3.8 - - + -
743C ILE* 5.8 1.8 - - + -
761C TYR* 4.7 7.4 - - - +
807C VAL* 5.1 5.6 - - + -
808C PHE* 3.7 20.0 - - + -
811C LEU* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 646 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C PHE* 3.0 52.3 + - + +
643C THR 3.2 4.0 + - - +
645C LEU* 1.3 92.9 + - - +
647C GLU* 1.3 57.7 + - - +
649C ALA* 3.6 12.2 - - - +
650C TRP* 2.9 28.4 + - - +
683C LEU* 3.7 25.6 - - + +
686C ASP* 4.8 4.4 - - + +
687C LEU* 3.8 18.2 - - + +
690C LEU* 4.5 6.7 - - + -
760C PHE* 3.9 10.5 - - - +
761C TYR* 3.6 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 647 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643C THR* 2.9 27.1 + - - +
644C ARG* 3.7 16.1 - - - +
645C LEU 3.3 0.2 - - - -
646C GLN* 1.3 76.0 - - - +
648C GLN* 1.3 67.2 + - - +
650C TRP* 3.3 9.5 + - - +
651C LEU* 3.3 9.5 + - - +
687C LEU* 3.6 21.5 - - + -
691C ASN* 3.8 19.1 + - - +
696C TRP* 3.9 13.4 - - + +
699C ARG* 6.1 1.4 - - - +
700C ILE* 3.4 47.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 648 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644C ARG 3.2 14.5 + - - +
645C LEU* 3.1 8.3 + - - +
647C GLU* 1.3 84.6 + - - +
649C ALA* 1.3 62.6 + - - +
651C LEU* 3.1 11.6 + - - +
652C PHE* 3.1 26.2 + - - -
700C ILE* 4.8 1.2 - - - +
701C THR 2.9 25.7 + - - -
702C ALA* 3.6 3.3 - - - -
703C SER* 2.9 31.4 + - - +
706C VAL* 3.1 29.4 - - + +
807C VAL* 4.5 10.5 - - + -
811C LEU* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 649 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C LEU* 2.9 18.4 + - + +
646C GLN* 3.6 18.4 - - - +
648C GLN* 1.3 74.1 - - - +
650C TRP* 1.3 60.2 + - - +
652C PHE* 3.6 24.3 - - + -
653C TYR* 2.8 42.2 + - + +
683C LEU* 3.7 14.4 - - + -
732C ARG* 5.9 0.9 - - - +
760C PHE* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 650 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TRP* 3.9 30.5 - + - -
397B ARG* 3.6 33.2 - - + -
646C GLN 2.9 14.5 + - - +
647C GLU 3.5 6.7 - - - +
649C ALA* 1.3 73.5 - - - +
651C LEU* 1.3 83.5 + - + +
653C TYR* 4.3 0.6 - - - +
654C THR* 2.7 44.6 + - - -
680C ALA* 3.3 29.7 + - - +
681C GLU* 5.6 2.0 + - - -
683C LEU* 3.7 11.6 - - + +
684C ALA* 3.7 21.6 - - + +
687C LEU* 4.0 9.9 - - + -
696C TRP* 3.6 35.2 - + - -
697C ARG* 5.0 2.0 - - + -
700C ILE* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 651 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B SER* 5.1 3.1 + - - +
397B ARG* 4.0 19.2 - - + +
398B SER* 3.9 13.5 - - - +
647C GLU 3.7 13.2 - - - +
648C GLN* 3.1 16.2 + - - +
650C TRP* 1.3 102.3 - - + +
652C PHE* 1.3 61.0 + - - +
654C THR* 3.5 5.1 + - - -
655C ALA* 3.3 17.0 + - - +
700C ILE* 4.0 16.2 - - + -
701C THR 4.1 0.2 - - - -
702C ALA* 3.7 38.1 - - + +
706C VAL* 4.0 9.6 - - + -
710C VAL* 3.9 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 652 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C LEU* 5.5 5.2 - - + -
648C GLN* 3.1 25.2 + - + -
649C ALA* 3.6 23.1 - - + -
651C LEU* 1.3 75.0 - - - +
653C TYR* 1.3 91.2 + + - +
655C ALA 3.3 0.2 + - - -
656C LEU* 2.7 31.8 + - + +
706C VAL* 4.2 11.2 - - + -
709C TYR* 3.5 44.0 - + + -
710C VAL* 4.0 16.8 - - + -
713C LEU* 3.5 6.4 - - + +
732C ARG* 4.1 18.8 - - + -
804C ASN* 4.1 11.7 - - - -
807C VAL* 4.1 22.0 - - + -
808C PHE* 6.2 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 653 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C ALA* 2.8 32.7 + - + +
650C TRP 4.3 0.9 - - - +
652C PHE* 1.3 93.6 - + - +
654C THR* 1.3 66.2 + - - +
656C LEU* 4.0 7.9 - - + -
657C GLU* 2.9 48.7 + - - +
679C ARG* 3.7 14.6 - - + -
680C ALA* 4.3 9.0 - - - +
683C LEU* 3.9 20.2 - - + -
732C ARG* 2.7 41.2 + - + +
733C TYR* 3.8 15.3 - + - -
736C ASP* 2.5 29.1 + - - -
760C PHE* 3.7 15.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 654 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B SER* 4.6 3.6 - - - -
397B ARG* 3.7 37.7 - - - +
650C TRP* 2.7 41.7 + - - -
651C LEU* 3.6 7.2 - - - -
652C PHE 3.3 0.2 - - - -
653C TYR* 1.3 76.8 - - - +
655C ALA* 1.3 63.7 + - - +
657C GLU* 3.9 2.5 - - - +
658C GLN* 3.1 35.1 + - - +
680C ALA* 3.8 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 655 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B SER* 4.4 8.1 - - - +
651C LEU 3.3 8.6 + - - +
652C PHE 3.8 6.1 - - - +
654C THR* 1.3 78.8 - - - +
656C LEU* 1.3 65.9 + - - +
658C GLN* 3.1 11.9 + - - +
659C ALA* 3.1 21.0 + - - +
710C VAL* 3.9 29.6 - - + +
713C LEU* 4.0 19.9 - - + +
714C GLU* 4.6 7.0 - - + +
717C ARG* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 656 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C PHE* 2.7 24.0 + - + +
653C TYR* 3.7 13.5 - - + +
654C THR 3.4 0.2 - - - -
655C ALA* 1.3 73.8 - - - +
657C GLU* 1.3 58.4 + - - +
659C ALA* 3.1 5.4 + - - +
660C VAL* 2.8 34.6 + - + +
709C TYR* 5.5 1.8 - - - +
713C LEU* 3.7 26.3 - - + +
725C LEU* 3.9 22.0 - - + -
728C HIS* 4.0 17.3 - - + +
729C HIS* 4.6 1.6 - - - +
732C ARG* 4.0 28.0 - - + -
733C TYR* 3.7 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 657 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C TYR* 2.9 29.8 + - - +
654C THR* 4.0 3.4 - - - +
656C LEU* 1.3 74.1 - - + +
658C GLN* 1.3 60.0 + - - +
660C VAL* 3.7 6.6 - - + +
661C ASP* 3.0 38.4 + - - +
678C ASN* 3.3 23.8 - - - +
679C ARG 2.7 26.2 + - - -
680C ALA* 2.9 30.1 + - + +
733C TYR* 2.5 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 658 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ASP* 3.0 31.1 + - - +
394B SER* 3.9 11.8 - - - -
397B ARG* 4.1 1.8 - - - +
654C THR* 3.1 33.3 + - + +
655C ALA* 3.1 11.3 + - - +
657C GLU* 1.3 76.1 - - - +
659C ALA* 1.3 62.3 + - - +
661C ASP* 3.5 9.8 + - - +
662C ALA* 3.1 17.5 + - - +
714C GLU* 5.0 0.7 - - + +
717C ARG* 2.8 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655C ALA 3.1 8.7 + - - +
656C LEU* 3.1 10.1 + - - +
658C GLN* 1.3 75.1 - - - +
660C VAL* 1.3 65.7 + - - +
662C ALA* 3.2 2.4 + - - +
663C VAL* 2.9 26.9 + - - +
713C LEU* 3.6 26.5 - - + +
716C ILE* 4.3 5.2 - - + -
717C ARG* 3.8 19.8 - - + +
725C LEU* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 660 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C LEU* 2.8 34.2 + - + +
657C GLU* 3.7 11.2 - - + +
658C GLN 3.4 0.2 - - - -
659C ALA* 1.3 72.2 - - - +
661C ASP* 1.3 58.2 + - - +
663C VAL* 3.2 1.2 + - - -
664C ARG* 2.8 54.6 + - - +
673C LEU* 3.9 21.8 - - + +
678C ASN* 5.4 4.0 - - - +
725C LEU* 3.9 21.3 - - + -
729C HIS* 4.0 21.8 - - + +
733C TYR* 4.6 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 661 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C GLU* 3.0 24.9 + - - +
658C GLN* 3.6 8.9 - - - +
659C ALA 3.2 0.2 - - - -
660C VAL* 1.3 76.9 - - - +
662C ALA* 1.3 61.9 + - - +
664C ARG* 3.0 29.3 + - - +
665C ALA* 3.1 24.8 + - - +
678C ASN* 5.1 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 662 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658C GLN 3.1 14.4 + - - +
659C ALA 3.2 7.4 + - - +
661C ASP* 1.3 76.1 - - - +
663C VAL* 1.3 62.9 + - + +
665C ALA* 3.3 7.9 + - - +
666C SER* 3.2 19.9 + - - -
717C ARG* 3.9 30.7 - - + +
720C VAL* 3.9 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 663 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659C ALA 2.9 19.5 + - - +
660C VAL 3.9 2.2 - - - +
662C ALA* 1.3 79.0 - - + +
664C ARG* 1.3 63.9 + - - +
666C SER* 2.7 25.3 + - - +
667C GLY 3.5 2.8 + - - -
668C PHE* 3.5 26.5 + - + +
669C ALA* 5.5 0.2 - - + -
673C LEU* 3.8 8.5 - - + -
716C ILE* 4.9 4.0 - - + +
720C VAL* 4.3 13.2 - - + -
721C ASP 4.1 6.1 - - - +
722C GLY* 3.8 29.4 - - - +
725C LEU* 3.7 28.3 - - + -
726C VAL* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 664 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660C VAL* 2.8 39.3 + - - +
661C ASP* 3.0 33.6 + - - +
663C VAL* 1.3 72.4 - - - +
665C ALA* 1.3 56.9 + - - +
667C GLY* 3.0 19.9 + - - -
668C PHE 4.3 3.8 - - - -
670C GLU* 3.9 25.4 - - + +
673C LEU* 2.9 46.1 + - + +
674C ASP 4.3 0.6 + - - -
675C PRO* 3.8 30.2 - - - +
678C ASN* 4.7 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 665 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 6.1 1.6 - - - +
661C ASP 3.1 18.0 + - - +
662C ALA* 3.6 7.4 - - - +
663C VAL 3.2 0.4 - - - -
664C ARG* 1.3 76.6 - - - +
666C SER* 1.3 59.1 + - - +
667C GLY* 3.1 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 666 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662C ALA 3.2 4.7 + - - -
663C VAL* 2.7 21.5 + - - +
665C ALA* 1.3 77.6 - - - +
667C GLY* 1.3 57.2 + - - +
668C PHE* 3.6 13.5 + - - +
720C VAL* 3.7 28.0 + - - +
722C GLY* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
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