Contacts of the helix formed by residues 710 - 742 (chain B) in PDB entry 3E7C
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 GLN 710 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B SER* 1.3 78.8 - - - +
711B ASN* 1.3 57.8 + - - +
712B TRP 3.4 2.5 - - - -
713B GLN* 3.3 15.1 + - + +
714B ARG* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GOL 3.7 21.3 + - - +
701B ILE* 3.8 21.0 - - + +
702B VAL* 4.1 31.6 + - + +
709B SER* 2.6 32.2 + - - +
710B GLN* 1.3 74.8 + - - +
712B TRP* 1.3 65.5 + - + +
714B ARG* 3.3 3.4 + - - +
715B PHE* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GOL 4.0 39.0 + - - -
709B SER 4.1 4.6 + - - -
710B GLN 3.4 0.6 - - - -
711B ASN* 1.3 81.6 - - + +
713B GLN* 1.3 58.2 + - - +
715B PHE* 3.2 39.0 + + + +
716B TYR* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B GLN* 3.3 20.3 + - + +
711B ASN 3.2 0.2 - - - -
712B TRP* 1.3 76.1 - - - +
714B ARG* 1.3 64.2 + - - +
716B TYR* 3.3 9.1 + - - +
717B GLN* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B LEU* 2.8 36.2 + - - +
657B GLN* 3.3 11.7 + - - +
658B VAL* 3.4 6.7 - - - +
662B GLU* 2.8 40.1 + - - -
701B ILE* 4.0 15.5 - - + -
710B GLN 2.9 16.4 + - - +
711B ASN* 3.3 4.9 + - - +
713B GLN* 1.3 75.5 - - - +
715B PHE* 1.3 58.1 + - - +
717B GLN* 2.9 20.0 + - + +
718B LEU* 2.8 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GOL 4.9 3.6 - - - +
694B ILE* 3.7 41.5 - - + -
697B LEU* 4.4 8.3 - - + -
698B GLY* 4.6 9.9 - - - -
701B ILE* 3.4 25.7 - - + +
711B ASN 3.0 15.0 + - - +
712B TRP* 3.2 36.8 + + + +
714B ARG* 1.3 75.2 - - - +
716B TYR* 1.3 57.3 + - - +
718B LEU* 4.7 0.7 - - - +
719B THR* 2.6 62.7 + - + +
774B PHE* 4.6 6.3 - + - -
775B HIS* 5.5 4.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B TRP 3.0 12.7 + - - +
713B GLN* 3.6 12.3 - - - +
715B PHE* 1.3 78.8 - - - +
717B GLN* 1.3 66.4 + - + +
719B THR* 3.4 5.7 + - - -
720B LYS* 2.9 66.3 + - + +
775B HIS* 3.4 35.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B ARG* 4.4 10.2 + - - +
656B LEU* 3.8 37.7 - - + +
713B GLN* 3.1 24.0 + - - +
714B ARG* 2.9 24.2 + - + +
716B TYR* 1.3 85.1 - - + +
718B LEU* 1.3 58.9 + - + +
720B LYS* 3.1 8.3 + - - +
721B LEU* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B LEU* 4.0 13.0 - - + -
658B VAL* 3.9 28.0 - - + -
662B GLU* 3.7 37.9 - - + +
666B MET* 3.4 26.1 - - + +
697B LEU* 4.1 15.5 - - + -
701B ILE* 3.7 20.4 - - + -
714B ARG* 2.8 35.0 + - + +
715B PHE* 4.2 2.9 - - - +
717B GLN* 1.3 72.2 - - + +
719B THR* 1.3 58.0 + - - +
721B LEU* 3.3 3.0 + - - -
722B LEU* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 4.2 12.6 - - + -
715B PHE* 2.6 55.8 + - + +
716B TYR* 3.4 0.7 + - - -
718B LEU* 1.3 73.1 - - - +
720B LYS* 1.3 60.8 + - - +
722B LEU* 3.6 7.9 - - + +
723B ASP* 3.1 33.3 + - - +
774B PHE* 3.6 28.3 - - + -
775B HIS* 2.6 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B TYR* 2.9 51.1 + - + +
717B GLN* 3.2 9.4 - - - +
719B THR* 1.3 75.7 - - - +
721B LEU* 1.3 64.6 + - - +
723B ASP* 3.3 9.3 + - + +
724B SER* 3.0 22.9 + - - -
775B HIS* 3.4 38.6 + - + +
776B GLN 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B PHE* 4.6 7.9 - - + -
648B TYR* 4.2 6.1 - - + +
649B VAL* 5.1 3.8 - - + +
652B GLU* 3.6 40.8 - - + +
653B LEU* 3.8 30.3 - - + +
656B LEU* 4.4 16.8 - - + -
658B VAL* 4.8 0.9 - - + -
666B MET* 4.1 13.9 - - + -
717B GLN 3.0 12.4 + - - +
718B LEU* 3.3 11.2 + - - +
720B LYS* 1.3 76.4 - - - +
722B LEU* 1.3 63.7 + - - +
724B SER* 2.6 37.6 + - - +
725B MET* 3.2 15.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TYR* 5.7 0.2 - - - -
606B PHE* 4.9 3.1 - - + -
666B MET* 3.7 42.0 - - + +
669B LEU* 3.8 26.5 - - + -
670B LEU* 3.9 24.3 - - + +
673B SER* 5.9 0.3 - - - -
697B LEU* 4.5 10.1 - - + -
718B LEU 3.0 19.2 + - - +
719B THR* 3.6 11.4 - - - +
720B LYS 3.3 0.4 - - - -
721B LEU* 1.3 74.1 - - - +
723B ASP* 1.3 64.9 + - - +
725B MET* 3.2 22.7 + - - +
726B HIS* 4.3 5.9 + - - -
774B PHE* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B THR 3.1 15.6 + - - +
720B LYS* 3.5 12.1 - - + +
722B LEU* 1.3 76.6 - - - +
724B SER* 1.3 63.9 + - - +
726B HIS* 3.1 30.4 + - - +
727B GLU 4.6 0.2 + - - -
772B LEU 4.2 1.9 - - - +
773B LEU* 3.6 18.6 - - + +
774B PHE* 2.8 28.8 + - - -
775B HIS* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B TYR* 3.2 31.8 + - - -
720B LYS 3.0 11.8 + - - -
721B LEU* 2.6 31.3 + - - +
723B ASP* 1.3 77.3 - - - +
725B MET* 1.3 62.1 + - - +
726B HIS 3.0 1.7 + - - -
727B GLU* 3.1 17.1 + - - +
728B VAL* 3.3 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TYR* 3.8 25.8 - - + +
605B ALA* 4.1 15.7 - - + -
606B PHE* 4.1 19.7 - - + +
649B VAL* 3.6 34.5 - - + -
670B LEU* 4.1 17.9 - - + -
721B LEU* 3.7 17.0 - - - +
722B LEU* 3.2 17.9 - - - +
723B ASP 3.1 1.0 - - - -
724B SER* 1.3 81.3 + - - +
726B HIS* 1.3 60.6 + - - +
728B VAL* 3.9 14.8 - - + -
729B VAL* 3.0 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TYR* 2.8 31.9 + + - -
673B SER* 3.2 38.9 - - - -
674B SER* 4.1 1.1 - - - -
722B LEU 4.4 4.5 + - - -
723B ASP* 3.1 25.7 + - - +
724B SER 3.0 1.6 + - - -
725B MET* 1.3 77.7 - - - +
727B GLU* 1.3 59.5 + - - +
729B VAL* 3.8 1.6 - - - +
730B GLU* 2.8 30.1 + - - +
771B LYS* 3.8 39.4 + - + +
772B LEU 3.0 23.2 + - - -
773B LEU* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B ASP 4.6 0.4 + - - -
724B SER* 3.1 10.0 + - - +
726B HIS* 1.3 77.4 - - - +
728B VAL* 1.3 63.9 + - - +
730B GLU* 3.2 21.0 + - - +
731B ASN* 3.1 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B HIS* 4.1 16.8 - - + +
648B TYR* 3.5 34.8 - - + -
649B VAL* 3.9 22.9 - - + -
724B SER 3.3 12.8 + - - +
725B MET* 3.5 20.2 - - + +
727B GLU* 1.3 79.9 - - + +
729B VAL* 1.3 57.3 + - - +
731B ASN* 3.2 9.0 + - - +
732B LEU* 3.0 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TYR 5.4 0.4 - - - +
601B MET* 3.9 20.4 - - + +
602B TYR* 3.6 56.3 - - + +
725B MET* 3.0 27.3 + - + +
726B HIS 4.0 2.2 - - - +
728B VAL* 1.3 75.2 - - + +
730B GLU* 1.3 66.5 + - - +
732B LEU* 4.0 7.2 - - + -
733B LEU* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TYR* 5.7 0.2 + - - -
726B HIS 2.8 16.7 + - - +
727B GLU* 3.3 22.2 - - - +
729B VAL* 1.3 77.6 - - - +
731B ASN* 1.3 63.9 + - - +
733B LEU* 3.6 4.9 + - - +
734B ASN* 3.0 34.7 + - - +
764B TYR* 5.9 8.1 - - + -
771B LYS* 3.7 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B GLN* 3.8 4.9 - - - +
645B HIS* 3.3 41.1 + - + +
727B GLU* 3.1 36.8 + - - +
728B VAL* 3.5 5.7 - - - +
730B GLU* 1.3 77.6 - - - +
732B LEU* 1.3 66.6 + - - +
733B LEU 3.0 1.6 - - - -
734B ASN* 3.0 19.2 + - - +
735B TYR* 3.2 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B MET* 4.1 20.8 - - + +
605B ALA* 3.6 30.7 - - + -
642B GLN* 2.8 53.4 + - + +
645B HIS* 3.8 19.1 - - + -
646B MET* 3.7 22.2 - - + -
728B VAL* 3.0 32.0 + - + +
729B VAL* 3.6 8.5 - - - +
731B ASN* 1.3 75.5 - - - +
733B LEU* 1.3 62.6 + - - +
736B CYS* 3.2 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TYR 5.5 2.5 - - - +
600B TRP* 3.6 34.8 - - + +
601B MET* 4.0 18.2 - - + -
729B VAL* 2.9 38.9 + - + +
730B GLU* 4.1 4.5 - - - +
731B ASN 3.0 0.2 + - - -
732B LEU* 1.3 73.1 - - - +
734B ASN* 1.3 58.3 + - - +
736B CYS* 4.1 3.1 - - + -
737B PHE* 2.6 64.3 + - + -
764B TYR* 3.0 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B GLU* 3.0 31.7 + - - +
731B ASN* 3.0 11.3 + - - +
733B LEU* 1.3 76.3 - - - +
735B TYR* 1.3 57.3 + - - +
737B PHE* 4.1 5.3 - - - +
738B GLN* 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 2.1 47.9 - + - +
556B THR* 5.6 1.4 - - - +
560B MET* 5.7 1.5 - - - -
638B GLY* 2.7 38.8 + - - -
641B ASP* 4.0 20.1 - - + +
642B GLN* 2.8 45.3 - - + +
731B ASN 3.2 4.8 + - - +
734B ASN* 1.3 79.6 - - + +
736B CYS* 1.3 49.9 - - - +
738B GLN* 4.2 15.0 - - + -
739B THR* 2.7 26.2 + - - -
745B MET* 5.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 736 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.0 44.4 - - + +
600B TRP* 4.5 7.4 - - - -
601B MET* 4.8 3.8 - - + -
732B LEU 3.2 18.1 + - - +
733B LEU* 3.0 7.3 + - - +
735B TYR* 1.3 78.6 - - - +
737B PHE* 1.3 69.2 + - - +
739B THR* 3.3 5.2 + - - -
740B PHE* 3.0 18.9 + - - +
749B PHE* 4.2 6.4 - - - -
757B ILE* 3.8 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 737 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B TRP* 4.8 3.6 - + - -
733B LEU* 2.6 54.4 + - + +
734B ASN* 4.1 5.4 - - - +
736B CYS* 1.3 74.6 - - - +
738B GLN* 1.3 61.6 + - - +
740B PHE* 2.8 22.3 + - - +
741B LEU* 2.9 21.9 + - + +
757B ILE* 3.6 30.7 - - + -
760B GLN* 4.0 12.3 - - + -
761B ILE* 3.3 37.0 - - + -
764B TYR* 3.8 41.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 738 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B ASN* 2.8 26.5 + - - +
735B TYR* 4.4 14.4 - - + +
737B PHE* 1.3 75.8 - - - +
739B THR* 1.3 62.6 + - - +
741B LEU* 3.2 9.3 + - - +
742B ASP* 3.1 26.2 + - + +
745B MET* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.4 26.4 - - + +
560B MET* 4.4 9.3 - - + -
735B TYR* 2.7 31.8 + - - -
736B CYS 3.3 9.2 + - - -
737B PHE 3.3 0.4 - - - -
738B GLN* 1.3 78.4 - - - +
740B PHE* 1.3 61.3 + - - +
741B LEU 3.6 0.2 + - - -
742B ASP* 3.7 12.0 + - - +
745B MET* 4.0 28.8 - - + +
747B ILE* 3.6 30.8 - - + +
749B PHE* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B CYS 3.0 12.9 + - - +
737B PHE* 2.8 16.2 + - - +
739B THR* 1.3 79.7 - - - +
741B LEU* 1.3 74.9 + - + +
742B ASP 3.7 2.8 + - - +
747B ILE* 5.2 1.1 - - - +
749B PHE* 3.3 40.6 - + + -
754B ALA* 3.9 40.4 - - + -
757B ILE* 3.6 24.9 - - + -
758B THR* 4.4 18.6 - - + -
761B ILE* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B PHE* 2.9 20.8 + - + +
738B GLN* 3.2 6.5 + - - +
740B PHE* 1.3 92.5 - - + +
742B ASP* 1.3 63.2 + - - +
743B LYS* 3.4 24.1 + - - +
761B ILE* 4.3 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 742 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B GLN* 3.1 17.0 + - + +
739B THR 3.9 6.5 - - - +
740B PHE 3.4 2.8 - - - +
741B LEU* 1.3 75.9 - - - +
743B LYS* 1.3 72.2 + - - +
744B THR* 2.8 31.8 + - - +
745B MET* 3.1 50.5 - - - +
747B ILE* 5.1 0.3 - - - +
----------------------------------------------------------
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