Contacts of the helix formed by residues 832 - 860 (chain D) in PDB entry 1DQ8
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 832 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D ASP* 5.2 2.7 - - - -
652D GLY 3.0 26.2 - - - -
653D ASP* 2.9 24.9 + - - -
704D LYS* 4.9 0.4 - - - -
831D PRO* 1.3 71.5 - - - +
833D GLU* 1.3 55.4 + - - +
835D ALA* 3.3 3.8 + - - +
836D ARG* 2.8 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 833 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827D CYS* 3.9 11.4 - - - -
830D ASN* 3.0 37.3 + - + +
831D PRO 3.4 1.0 + - - -
832D GLY* 1.3 74.5 - - - +
834D ASN* 1.3 61.4 + - - +
836D ARG* 2.5 34.4 + - - +
837D GLN* 2.9 28.4 + - + +
840D ARG* 3.1 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 834 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653D ASP* 2.8 10.5 + - - +
804D THR* 3.6 1.8 - - - +
822D GLY 4.1 11.2 + - - +
823D VAL* 2.7 50.0 + - - +
824D GLN 3.5 10.1 + - - -
825D GLY 2.9 23.1 + - - +
826D ALA 3.6 14.6 + - - -
827D CYS* 3.7 15.1 - - - +
833D GLU* 1.3 76.4 - - - +
835D ALA* 1.3 61.2 + - - +
837D GLN* 3.1 3.5 + - - +
838D LEU* 2.9 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 835 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D GLY 4.6 0.4 - - - +
653D ASP* 3.0 35.2 + - - +
704D LYS* 3.9 20.9 - - - +
802D ILE* 3.6 13.8 - - - +
803D GLY* 4.2 10.3 - - - -
804D THR* 4.0 10.8 + - - -
832D GLY 3.7 7.2 - - - +
834D ASN* 1.3 76.0 - - - +
836D ARG* 1.3 57.6 + - - +
838D LEU* 3.4 2.4 + - - +
839D ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 836 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D VAL* 3.9 24.7 - - + +
586D ASP* 3.7 15.2 + - - +
650D ARG* 4.0 20.0 - - - +
704D LYS* 4.0 18.8 - - - +
830D ASN* 3.4 21.4 + - - +
831D PRO 2.7 28.5 + - - -
832D GLY* 2.8 22.2 + - - +
833D GLU* 2.5 38.4 + - - +
835D ALA* 1.3 75.4 - - - +
837D GLN* 1.3 63.4 + - - +
839D ALA* 3.3 6.7 + - - +
840D ARG* 3.1 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 837 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D LEU* 4.6 2.4 - - - +
547D ASP* 5.2 2.4 + - - -
549D LYS* 3.3 24.2 + - - +
551D PHE* 3.6 30.9 - - + -
821D LEU 5.2 2.0 - - - +
822D GLY 5.9 1.3 - - - +
823D VAL* 4.3 9.4 - - + -
833D GLU* 2.9 20.7 + - + +
834D ASN* 3.1 6.9 + - - +
836D ARG* 1.3 73.1 - - - +
838D LEU* 1.3 67.3 + - - +
840D ARG* 3.1 39.1 + - - +
841D ILE* 3.0 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 838 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760D ILE* 4.5 9.6 - - + -
764D CYS* 4.7 4.0 - - + -
766D GLN* 3.9 11.7 - - + +
802D ILE* 3.5 29.8 - - + -
804D THR* 3.9 9.0 - - + -
818D LEU* 3.8 24.2 - - + -
821D LEU* 3.7 30.5 - - + -
823D VAL* 4.0 10.7 - - + +
834D ASN 2.9 13.3 + - - +
835D ALA* 3.6 8.3 - - - +
837D GLN* 1.3 77.8 - - - +
839D ALA* 1.3 57.0 + - - +
841D ILE* 3.2 11.3 + - + +
842D VAL* 2.9 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 839 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D VAL* 5.5 0.2 - - + -
704D LYS* 3.7 31.2 - - + -
706D VAL* 3.9 9.9 - - + -
800D ILE* 3.7 24.0 - - + +
802D ILE* 4.0 4.0 - - + +
835D ALA 3.0 17.1 + - - +
836D ARG 3.7 4.9 - - - +
837D GLN 3.2 0.2 - - - -
838D LEU* 1.3 78.8 - - - +
840D ARG* 1.3 60.7 + - - +
842D VAL* 3.3 4.5 + - - +
843D CYS* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 840 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D LEU* 3.5 11.4 - - + +
547D ASP* 4.3 6.1 - - - -
581D SER* 3.5 31.4 + - - +
582D ARG* 5.3 0.6 - - - +
583D VAL* 3.5 27.7 - - + +
706D VAL* 4.2 11.7 - - + -
833D GLU* 3.1 38.7 + - - -
836D ARG* 3.1 32.4 + - - +
837D GLN* 3.1 49.1 + - - +
839D ALA* 1.3 75.7 - - - +
841D ILE* 1.3 58.2 + - - +
843D CYS* 3.5 2.4 + - - +
844D GLY* 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 841 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 3.9 3.8 - - + +
546D LEU* 3.9 7.6 - - + -
551D PHE* 3.7 41.5 - - + -
553D VAL* 4.2 19.1 - - + -
760D ILE* 5.1 2.7 - - + -
821D LEU* 4.0 35.7 - - + +
823D VAL* 5.4 1.1 - - + -
837D GLN* 3.0 35.1 + - + +
838D LEU* 3.4 13.0 - - + +
840D ARG* 1.3 74.9 - - - +
842D VAL* 1.3 57.9 + - - +
845D THR* 2.6 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 842 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756D ILE* 4.5 0.7 - - - +
757D VAL* 4.1 32.3 - - + -
760D ILE* 4.1 32.5 - - + -
761D TYR* 4.3 9.0 - - + +
797D MET* 4.7 0.2 - - + -
800D ILE* 4.3 14.8 - - + -
802D ILE* 3.7 23.8 - - + -
838D LEU* 2.9 19.8 + - + +
839D ALA* 3.3 9.8 + - - +
841D ILE* 1.3 74.8 - - - +
843D CYS* 1.3 58.6 + - - +
845D THR* 3.3 1.9 + - - -
846D VAL* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 843 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D VAL* 3.6 29.2 - - + -
708D CYS* 3.8 14.5 - - + +
795D CYS* 3.8 25.2 - - - +
797D MET* 3.8 32.1 - - - -
800D ILE* 4.4 0.9 - - + -
839D ALA 3.0 16.6 + - - +
840D ARG 3.7 2.7 - - - +
842D VAL* 1.3 75.3 - - - +
844D GLY* 1.3 60.7 + - - +
846D VAL* 3.3 3.3 + - - +
847D MET* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 844 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 4.0 18.9 - - - +
546D LEU* 4.6 4.3 - - - -
573D ILE* 4.5 2.1 - - - +
708D CYS* 3.7 22.8 - - - -
840D ARG 2.9 15.6 + - - -
841D ILE 3.8 0.9 - - - -
843D CYS* 1.3 76.4 - - - +
845D THR* 1.3 57.0 + - - +
847D MET* 3.1 6.5 + - - +
848D ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 845 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 3.4 15.4 - - + +
553D VAL* 3.6 25.1 - - + +
555D MET* 4.6 2.7 - - - -
566D THR* 3.5 20.3 - - + +
570D CYS* 5.4 2.7 - - - -
756D ILE* 3.4 22.4 - - + +
760D ILE* 3.8 11.4 - - + -
841D ILE* 2.6 24.8 + - - +
842D VAL 3.7 3.6 - - - -
844D GLY* 1.3 74.1 - - - +
846D VAL* 1.3 64.7 + - - +
848D ALA* 3.1 6.7 + - + +
849D GLY* 2.8 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 846 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753D ALA* 3.7 33.0 - - + +
756D ILE* 3.8 24.9 - - + +
757D VAL* 4.1 5.6 - - + -
777D CYS* 4.2 8.7 - - - -
795D CYS* 4.4 2.7 - - - -
797D MET* 3.8 29.2 - - + -
842D VAL* 2.9 21.1 + - + +
843D CYS 3.5 5.6 - - - +
845D THR* 1.3 76.9 - - - +
847D MET* 1.3 53.4 + - - +
849D GLY* 3.0 3.6 + - - -
850D GLU* 2.8 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 847 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D ILE* 3.8 13.9 - - + -
579D ALA* 3.5 31.4 - - + -
708D CYS* 3.7 17.7 - - + +
709D GLU* 3.6 32.3 - - - +
710D ALA* 3.7 8.5 - - + -
793D ILE* 3.8 34.5 - - + +
794D SER* 4.4 1.1 - - - -
795D CYS* 3.6 20.0 - - + -
843D CYS 2.9 13.4 + - - +
844D GLY* 3.1 8.3 + - - +
846D VAL* 1.3 73.8 - - - +
848D ALA* 1.3 64.5 + - - +
850D GLU* 3.4 2.5 + - - +
851D LEU* 3.1 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 848 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 4.7 0.9 - - + -
566D THR* 3.9 9.6 - - + +
569D GLY* 3.4 13.0 - - - -
570D CYS* 3.7 35.7 - - - +
573D ILE* 4.0 15.6 - - + +
844D GLY 3.0 12.9 + - - +
845D THR* 3.4 9.6 - - - +
847D MET* 1.3 74.5 - - - +
849D GLY* 1.3 64.6 + - - +
851D LEU* 3.2 14.5 + - - +
852D SER* 3.2 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 849 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D SER* 4.5 1.8 + - - -
566D THR* 4.3 13.4 - - - +
752D HIS* 3.1 26.8 + - - -
756D ILE* 4.1 12.8 - - - -
845D THR 2.8 13.4 + - - -
846D VAL 3.0 4.0 + - - -
848D ALA* 1.3 77.6 - - - +
850D GLU* 1.3 60.2 + - - +
852D SER* 3.4 2.6 + - - -
853D LEU 3.1 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 850 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736D ASN* 4.1 0.7 + - - -
750D ASN* 3.3 6.3 - - - +
751D ALA* 2.7 27.2 + - - +
752D HIS* 2.8 40.8 + - - -
753D ALA 3.6 5.2 + - - -
779D THR* 2.6 42.3 + - + +
781D MET* 4.8 0.9 - - - -
793D ILE* 4.4 3.6 - - + -
795D CYS* 4.0 4.3 - - - -
846D VAL* 2.8 33.3 + - + +
847D MET* 3.7 6.3 - - - +
849D GLY* 1.3 69.8 - - - +
851D LEU* 1.3 67.3 + - - +
853D LEU* 5.0 0.4 - - - -
854D MET* 2.9 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 851 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569D GLY* 4.2 9.6 - - - +
572D ALA* 4.7 2.7 - - + -
573D ILE* 3.8 30.5 - - + -
712D ILE* 3.9 17.9 - - + -
721D LEU* 4.0 16.8 - - + -
728D MET* 3.3 29.6 - - + +
781D MET* 4.6 0.9 - - + -
791D LEU* 3.8 17.3 - - + -
793D ILE* 3.7 29.8 - - + +
847D MET 3.1 13.7 + - - +
848D ALA 3.2 9.2 + - - +
850D GLU* 1.3 76.3 - - - +
852D SER* 1.3 58.0 + - - +
854D MET* 4.8 0.2 - - - -
855D ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 852 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D COA 3.0 13.7 + - - -
565D SER* 2.7 43.4 + - - -
568D ARG* 3.0 31.6 + - - +
569D GLY* 4.0 6.7 - - - -
721D LEU* 4.3 5.2 - - - -
848D ALA 3.2 5.5 + - - -
849D GLY 3.4 1.5 + - - -
850D GLU 3.3 0.2 - - - -
851D LEU* 1.3 78.5 - - - +
853D LEU* 1.3 62.9 + - - +
855D ALA 3.4 0.3 + - - -
856D ALA* 3.0 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 853 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D COA 3.5 28.9 - - - +
203D MAH 3.6 28.5 - - + +
565D SER* 3.8 0.8 + - - -
751D ALA* 3.6 13.2 - - + -
752D HIS* 3.5 43.1 - - + +
849D GLY 3.1 8.0 + - - +
850D GLU 4.4 0.9 - - - +
852D SER* 1.3 76.8 - - - +
854D MET* 1.3 59.1 + - - +
856D ALA* 3.1 3.4 + - + +
857D LEU* 2.8 41.0 + - + +
862D LEU* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 854 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728D MET* 3.6 10.0 - - + +
731D VAL* 3.5 24.9 - - + +
732D ASN* 3.4 41.3 - - + +
735D LYS* 3.8 13.9 - - + -
736D ASN* 3.5 18.4 - - - +
751D ALA* 3.7 20.9 - - + -
781D MET* 3.8 20.0 - - + -
850D GLU* 2.9 29.7 + - + +
851D LEU 3.9 2.0 - - - +
853D LEU* 1.3 77.6 - - - +
855D ALA* 1.3 56.3 + - - +
857D LEU* 3.3 6.1 + - - +
858D ALA* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 855 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D ARG* 4.0 4.5 - - - +
721D LEU* 3.3 42.6 - - + +
723D THR* 3.7 7.4 - - + -
728D MET* 3.3 13.8 - - - -
851D LEU 2.9 18.0 + - - +
852D SER 3.6 5.8 - - - +
853D LEU 3.2 0.2 - - - -
854D MET* 1.3 75.2 - - - +
856D ALA* 1.3 63.5 + - - +
858D ALA* 3.2 3.1 + - - +
859D ALA* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 856 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D COA 3.6 35.2 - - - +
568D ARG* 4.1 6.7 - - - +
852D SER 3.0 9.4 + - - +
853D LEU* 3.5 8.5 - - + +
855D ALA* 1.3 78.1 - - - +
857D LEU* 1.3 61.0 + - - +
859D ALA 3.3 0.5 + - - -
860D GLY 3.1 4.3 + - - -
861D HIS* 2.9 45.2 + - + -
862D LEU* 3.8 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 857 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C LEU 3.8 12.7 - - - +
682C ALA* 4.2 14.8 - - + -
683C VAL* 4.3 9.4 + - + +
684C SER* 4.2 19.3 - - - +
203D MAH 3.8 7.4 - - - +
731D VAL* 4.5 4.3 - - + -
735D LYS* 3.5 41.5 - - + +
853D LEU* 2.8 35.5 + - + +
854D MET* 3.3 8.7 + - - +
856D ALA* 1.3 71.9 - - - +
858D ALA* 1.3 62.7 + - - +
859D ALA 3.4 0.5 + - - -
860D GLY* 3.5 10.1 + - - -
862D LEU* 3.7 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 858 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C LEU 4.6 2.8 - - - +
723D THR* 3.7 17.9 + - - +
727D ALA* 4.2 19.5 - - + +
728D MET* 4.4 3.4 - - - +
731D VAL* 3.7 27.3 - - + +
854D MET 2.9 18.1 + - - +
855D ALA* 3.6 5.8 - - - +
857D LEU* 1.3 77.5 - - - +
859D ALA* 1.3 59.9 + - - +
860D GLY 3.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 859 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722D LYS* 3.5 24.5 - - + +
723D THR* 4.4 3.8 - - - -
855D ALA 3.0 16.1 + - - +
856D ALA 4.2 0.2 - - - +
857D LEU 3.3 0.2 - - - -
858D ALA* 1.3 79.1 - - - +
860D GLY* 1.3 60.2 + - - +
861D HIS* 3.6 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 860 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C GLU* 4.8 12.0 - - - +
683C VAL* 5.8 5.2 - - - -
856D ALA 3.1 3.7 + - - -
857D LEU* 3.5 7.9 + - - -
858D ALA 3.4 3.6 + - - -
859D ALA* 1.3 78.9 - - - +
861D HIS* 1.3 62.6 + - - +
862D LEU 3.7 2.2 + - - -
863D VAL* 5.6 0.9 + - - +
864D LYS 4.8 4.2 - - - +
----------------------------------------------------------
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