Contacts of the helix formed by residues 723 - 755 (chain A) in PDB entry 4FE1
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 723 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 5.7 10.5 - - - +
694A ARG* 3.8 8.2 - - - +
721A ALA 3.7 1.0 + - - -
722A LEU* 1.3 78.4 - - - +
724A ILE* 1.3 54.4 + - - +
725A ILE* 3.6 7.7 + - - +
726A GLN* 3.0 29.2 + - - +
727A GLY* 2.7 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A PRO* 3.6 30.3 - - + -
578A CYS* 5.3 5.8 - - - -
694A ARG* 3.5 30.9 - - + +
723A SER* 1.3 72.5 - - - +
725A ILE* 1.3 63.0 + - - +
727A GLY* 3.2 3.8 + - - -
728A ARG* 3.1 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ARG* 3.7 26.7 - - + +
576A PHE* 3.5 32.1 - - - +
577A PRO* 3.5 26.9 - - + +
592A TRP* 3.5 40.7 - - + -
593A ASP* 4.0 0.2 - - - +
723A SER* 3.2 6.7 + - - +
724A ILE* 1.3 73.1 - - - +
726A GLN* 1.3 63.0 + - - +
728A ARG* 3.1 15.4 + - - +
729A ALA* 2.9 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 6.2 0.2 - - - +
49A TRP* 3.3 53.5 - - - +
722A LEU* 3.3 29.3 - - + +
723A SER* 3.0 29.2 + - - +
725A ILE* 1.3 78.9 - - - +
727A GLY* 1.3 63.0 + - - +
729A ALA* 3.1 7.4 + - + -
730A VAL* 2.8 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A PHE* 3.5 31.2 - - - +
722A LEU* 4.4 6.6 - - - +
723A SER 2.7 18.6 + - - -
724A ILE* 3.2 5.6 + - - -
726A GLN* 1.3 72.1 - - - +
728A ARG* 1.3 58.2 + - - +
730A VAL* 3.8 3.5 - - - +
731A GLY* 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A PRO* 3.3 36.0 + - - +
587A CYS* 4.0 10.9 - - - +
588A GLN* 3.3 32.9 - - - +
592A TRP* 4.0 7.4 - - + -
593A ASP* 2.6 39.8 + - - -
596A PHE* 3.2 37.3 - - + -
689A PHE 5.4 1.6 - - - +
690A LEU* 4.8 4.0 - - + -
724A ILE* 3.1 34.3 + - + +
725A ILE* 3.5 9.7 - - - +
727A GLY* 1.3 75.9 - - - +
729A ALA* 1.3 58.7 + - - +
731A GLY* 3.4 0.5 + - - -
732A VAL* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A TRP* 3.8 21.0 - - + -
725A ILE* 2.9 16.4 + - + +
726A GLN* 3.7 9.0 - - + +
728A ARG* 1.3 76.0 - - - +
730A VAL* 1.3 57.7 + - + +
732A VAL* 3.1 12.7 - - - +
733A ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A PHE* 3.4 38.6 - - + -
722A LEU* 4.1 10.3 - - + -
726A GLN* 2.8 40.5 + - + +
727A GLY 3.8 2.9 - - - +
729A ALA* 1.3 74.9 - - + +
731A GLY* 1.3 67.2 + - - +
733A ALA* 3.1 5.6 + - - +
734A HIS* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A SER* 3.1 13.9 - - - -
689A PHE* 3.7 11.2 - - - -
690A LEU* 3.6 27.6 - - - -
727A GLY 3.0 14.5 + - - -
730A VAL* 1.3 78.5 - - - +
732A VAL* 1.3 56.0 + - - +
735A TYR* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A TRP* 5.8 1.3 - - + -
596A PHE* 3.8 16.2 - - + +
599A LEU* 3.9 37.9 - - + -
600A PHE* 3.8 26.0 - - + -
690A LEU* 3.7 1.4 - - - +
728A ARG 2.9 16.6 + - - +
729A ALA* 3.1 24.9 - - - +
731A GLY* 1.3 76.7 - - - +
733A ALA* 1.3 56.9 + - + +
735A TYR* 4.1 4.7 - - + -
736A LEU* 2.9 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A ALA 2.9 19.4 + - - +
730A VAL* 3.1 8.7 + - - +
732A VAL* 1.3 78.6 - - + +
734A HIS* 1.3 63.1 + - + +
736A LEU* 4.0 5.5 - - - +
737A LEU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A ILE* 3.3 34.0 - - + +
685A PHE* 3.2 38.7 - + - -
686A SER* 3.3 21.3 - - - -
689A PHE* 5.3 0.4 - + - -
730A VAL* 2.9 33.2 + - + +
733A ALA* 1.3 80.8 - - + +
735A TYR* 1.3 62.2 + - - +
737A LEU* 4.4 3.4 - - + -
738A GLY* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.9 29.5 - + + -
603A TYR* 4.1 29.9 - + - -
683A TRP* 3.1 44.0 + + - +
686A SER* 3.2 18.7 - - - +
687A LEU* 3.8 12.3 - - + -
690A LEU* 3.7 15.7 - - + -
731A GLY 2.9 20.1 + - - +
732A VAL* 3.7 7.9 - - - +
734A HIS* 1.3 76.5 - - - +
736A LEU* 1.3 65.9 + - + +
739A GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A PHE* 3.5 40.4 - - + -
599A LEU* 4.3 22.0 - - + +
600A PHE* 5.4 1.1 - - + +
602A MET* 4.6 2.2 - - + -
603A TYR* 3.9 35.7 - - + -
732A VAL* 2.9 43.2 + - + +
733A ALA* 4.0 5.2 - - - +
735A TYR* 1.3 79.0 - - + +
737A LEU* 1.3 66.5 + - - +
740A ILE* 3.0 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A ILE* 4.3 23.8 - - + -
733A ALA 2.9 20.0 + - - +
734A HIS* 4.1 6.1 - - + +
736A LEU* 1.3 74.4 - - - +
738A GLY* 1.3 57.8 + - - +
740A ILE* 4.4 1.3 - - - +
741A ALA* 2.9 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ALA* 3.1 27.3 - - - +
682A ILE* 4.0 6.0 - - - +
683A TRP* 4.0 7.6 - - - -
734A HIS 2.9 18.3 + - - -
737A LEU* 1.3 76.2 - - - +
739A GLY* 1.3 53.5 + - - +
742A THR* 2.5 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A TYR* 3.1 25.7 + - - -
683A TRP* 4.0 10.5 - - - -
735A TYR 2.9 17.2 + - - -
738A GLY* 1.3 74.6 - - - +
740A ILE* 1.3 63.8 + - - +
742A THR* 3.2 8.4 + - - -
743A THR* 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A TRP* 3.6 55.4 - - + +
403A PHE* 3.7 26.7 - - + -
603A TYR* 3.7 19.7 - - + -
736A LEU* 3.0 21.2 + - + +
737A LEU* 4.4 1.8 - - + +
739A GLY* 1.3 72.6 - - - +
741A ALA* 1.3 60.5 + - - +
743A THR* 3.1 8.7 + - - +
744A TRP* 2.9 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A LEU* 5.4 11.1 - - + +
679A ALA* 3.5 17.7 - - + -
737A LEU* 2.9 32.4 + - + +
740A ILE* 1.3 76.7 - - - +
742A THR* 1.3 63.6 + - - +
744A TRP* 3.1 14.7 + - + +
745A ALA* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A PHE* 4.0 7.8 - - + -
679A ALA* 3.0 15.7 - - - +
680A HIS* 3.1 44.9 + - + +
683A TRP* 5.3 0.5 - - - +
738A GLY 2.5 21.1 + - - -
739A GLY* 3.2 11.7 - - - -
740A ILE 3.1 0.2 - - - -
741A ALA* 1.3 77.3 - - - +
743A THR* 1.3 64.8 + - - +
744A TRP 3.3 0.2 + - - -
745A ALA* 3.4 4.4 + - - +
746A PHE* 3.0 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A THR* 5.6 1.1 - - - +
399A TRP* 5.0 6.3 - - - +
603A TYR* 4.8 4.3 + - - -
607A SER* 4.9 5.5 + - - -
610A ILE* 3.6 30.4 - - + +
611A PHE* 4.3 17.5 - - + -
739A GLY 3.0 13.3 + - - -
740A ILE* 3.1 10.6 + - - -
742A THR* 1.3 77.8 - - - +
744A TRP* 1.3 57.5 + - - +
746A PHE* 3.7 6.9 - - - +
747A PHE* 2.9 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A TYR* 3.3 35.7 - + - -
675A LEU* 4.3 35.4 - - + -
740A ILE* 2.9 14.6 + - + +
741A ALA* 3.1 19.3 + - + +
743A THR* 1.3 74.7 - - - +
745A ALA* 1.3 87.8 + - + +
747A PHE* 3.8 2.4 - - - +
748A LEU* 2.9 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A VAL* 3.7 3.1 - - - +
672A TYR* 3.6 31.3 - - - +
675A LEU 4.4 1.3 - - - -
676A PHE* 3.8 23.1 - - + +
741A ALA 2.9 16.8 + - - +
742A THR 3.9 2.0 - - - +
744A TRP* 1.3 88.7 - - + +
746A PHE* 1.3 66.0 + - - +
748A LEU* 4.1 0.3 - - - +
749A ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A PHE* 4.3 9.0 - + - -
653A PHE* 4.4 10.3 - + - -
654A LEU* 4.2 28.0 - - + -
657A GLN* 3.4 46.9 - - + -
658A ALA* 3.7 17.5 - - + -
661A VAL* 4.0 13.2 + - + +
676A PHE* 3.6 14.7 - + + -
742A THR* 3.0 16.4 + - + +
743A THR* 3.7 8.7 - - - +
745A ALA* 1.3 79.7 - - - +
747A PHE* 1.3 98.2 + + - +
749A ALA* 3.9 1.6 - - - +
750A ARG* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LEU* 3.9 22.6 - - + +
395A THR* 3.8 32.3 - - + -
610A ILE* 3.6 32.8 - - + -
611A PHE* 3.7 22.7 - + - -
614A SER* 3.6 19.3 - - - -
653A PHE* 4.4 1.8 - + - -
743A THR* 2.9 27.7 + - + +
744A TRP* 3.8 3.4 - - - +
746A PHE* 1.3 105.4 - + - +
748A LEU* 1.3 71.5 + - + +
750A ARG* 3.2 5.7 + - + +
751A ILE* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 4.0 21.5 - - + +
388A PRO 4.8 1.6 - - - +
391A LEU* 5.8 1.6 - - + -
392A SER* 3.2 28.9 - - - +
672A TYR* 3.4 35.0 - - + +
744A TRP* 2.9 51.5 + - + +
747A PHE* 1.3 82.6 - - + +
749A ALA* 1.3 64.9 + - - +
751A ILE* 4.5 6.7 - - + -
752A ILE* 2.9 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLN* 3.7 5.4 - - - +
661A VAL* 3.6 34.3 - - + +
664A SER* 5.3 2.0 - - - -
669A LEU* 4.3 9.0 - - + +
672A TYR* 4.0 20.7 - - + -
745A ALA 2.9 19.3 + - - +
748A LEU* 1.3 74.5 - - - +
750A ARG* 1.3 64.1 + - - +
752A ILE* 4.0 2.3 - - - +
753A SER* 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A SER* 5.8 0.2 - - - +
618A GLN* 3.3 25.3 + - - +
634A ILE* 3.9 13.7 + - - +
635A THR* 3.7 27.5 - - - +
656A ALA* 3.9 7.1 + - - +
657A GLN* 3.4 48.8 - - + +
659A SER* 5.3 1.0 - - - -
660A GLN* 2.9 59.6 + - - +
746A PHE* 3.0 23.1 + - + +
747A PHE* 3.2 6.5 + - + +
749A ALA* 1.3 76.5 - - - +
751A ILE* 1.3 60.1 + - - +
753A SER 3.0 2.6 + - - -
754A VAL* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR* 3.7 25.6 - - + +
388A PRO* 3.4 28.8 - - + +
391A LEU* 3.6 24.7 - - + -
618A GLN* 3.5 27.4 - - + +
622A TRP* 3.9 21.1 - - + -
634A ILE* 4.2 12.1 - - + -
747A PHE 3.0 18.2 + - - +
748A LEU* 4.1 7.0 - - + +
750A ARG* 1.3 72.7 - - - +
752A ILE* 1.3 63.8 + - - +
754A VAL* 4.1 4.5 - - + -
755A GLY* 2.7 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 5.4 5.7 - - - -
138A GLN* 3.9 37.6 + - + +
140A THR* 4.1 15.7 - - + -
388A PRO* 3.6 27.1 - - + -
669A LEU* 3.9 27.1 - - + -
672A TYR* 3.8 28.7 - - + +
748A LEU* 2.9 25.8 + - + +
749A ALA* 4.2 0.7 - - - +
751A ILE* 1.3 79.0 - - - +
753A SER* 1.3 61.7 + - - +
755A GLY* 4.0 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLN* 3.2 28.7 + - - +
669A LEU* 4.5 11.2 - - - -
749A ALA 3.0 21.2 + - - -
750A ARG 3.5 0.7 - - - -
752A ILE* 1.3 81.3 - - - +
754A VAL* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR* 4.8 0.5 - - - -
523A LYS* 5.4 2.8 - - - -
618A GLN* 4.8 0.2 - - - +
634A ILE* 3.7 37.8 - - + +
660A GLN* 3.1 20.9 - - - +
750A ARG* 3.0 40.3 + - - +
751A ILE* 4.1 11.7 - - + -
753A SER* 1.3 81.6 - - - +
755A GLY* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 4.3 14.9 + - - -
138A GLN* 5.5 1.2 + - - -
385A THR 3.9 8.5 - - - +
387A TYR* 3.4 39.1 - - - -
388A PRO* 4.1 9.7 - - - +
523A LYS* 2.7 29.3 + - - -
751A ILE* 2.7 28.1 + - - +
752A ILE 4.0 8.0 - - - +
753A SER 3.8 0.2 - - - -
754A VAL* 1.3 76.5 - - - +
----------------------------------------------------------
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