Contacts of the helix formed by residues 798 - 833 (chain B) in PDB entry 5FLZ
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 798 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B LEU* 5.5 4.8 - - - +
780B ASN* 6.0 0.8 + - - +
799B ASN* 1.4 76.4 + - - +
800B GLY 3.4 2.3 - - - +
801B LEU* 3.3 30.6 + - - +
802B LEU* 3.2 20.4 + - - +
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Residues in contact with ASN 799 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B SER* 1.4 84.0 - - - +
800B GLY* 1.3 63.8 + - - +
802B LEU* 3.2 10.5 + - - +
803B GLY* 3.0 19.9 + - - -
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Residues in contact with GLY 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B SER 3.4 1.6 - - - +
799B ASN* 1.3 76.4 - - - +
801B LEU* 1.3 62.8 + - - +
803B GLY* 3.4 1.8 + - - -
804B LYS* 3.1 41.4 + - - +
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Residues in contact with LEU 801 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B VAL* 5.1 3.1 - - + +
778B ASN* 3.5 46.9 - - + +
779B LEU* 4.1 22.8 - - + +
798B SER 3.4 29.8 - - - +
799B ASN 3.2 0.4 - - - -
800B GLY* 1.3 78.4 - - - +
802B LEU* 1.4 57.5 + - - +
804B LYS* 3.5 23.1 - - - +
805B PHE* 3.0 29.6 + - - +
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Residues in contact with LEU 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B LYS* 4.3 9.9 - - + +
779B LEU* 4.5 10.3 - - + +
798B SER 3.2 9.4 + - - +
799B ASN* 3.2 12.1 + - - +
801B LEU* 1.4 79.4 - - - +
803B GLY* 1.4 62.3 + - - +
805B PHE* 3.3 17.7 + - + +
806B ASN* 3.1 55.3 + - - +
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Residues in contact with GLY 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B ASN 3.0 13.7 + - - -
800B GLY* 3.4 3.1 + - - -
802B LEU* 1.4 77.2 - - - +
804B LYS* 1.3 61.2 + - - +
806B ASN* 3.6 6.1 + - - +
807B THR* 3.3 27.7 + - - +
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Residues in contact with LYS 804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B VAL* 5.5 3.4 - - + -
800B GLY* 3.1 29.7 + - - +
801B LEU* 3.5 25.9 - - - +
803B GLY* 1.3 76.0 - - - +
805B PHE* 1.4 56.4 + - - +
807B THR* 2.8 22.7 + - - -
808B ASN* 2.9 28.4 + - - +
----------------------------------------------------------
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Residues in contact with PHE 805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B LYS* 4.1 35.4 - - + -
634B ILE* 4.9 8.5 - - + -
772B PHE* 3.9 32.8 - + - -
775B VAL* 4.2 15.0 - - + -
776B TYR* 6.1 5.4 - + - -
779B LEU* 4.5 22.0 - - + -
801B LEU 3.0 14.5 + - - +
802B LEU* 3.3 18.6 + - + +
804B LYS* 1.4 78.7 - - - +
806B ASN* 1.4 76.5 + - - +
808B ASN* 3.3 8.7 + - - +
809B LEU* 2.9 45.8 + - + +
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Residues in contact with ASN 806 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B LYS* 3.1 31.6 + - - +
802B LEU* 3.1 30.0 + - - +
803B GLY* 3.9 9.0 - - - +
805B PHE* 1.4 79.4 - - - +
807B THR* 1.4 68.0 + - + +
809B LEU* 3.4 8.3 + - - +
810B LYS* 3.3 22.5 + - - +
----------------------------------------------------------
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Residues in contact with THR 807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B GLY 3.3 12.1 + - - +
804B LYS* 2.8 23.9 + - - -
806B ASN* 1.4 77.8 - - + +
808B ASN* 1.3 67.5 + - - +
810B LYS* 3.4 5.9 + - - +
811B GLU* 3.2 22.2 + - - +
----------------------------------------------------------
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Residues in contact with ASN 808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B GLU* 3.4 24.0 + - - +
772B PHE* 3.7 12.1 - - + -
775B VAL* 3.3 31.3 - - + +
804B LYS* 2.9 29.8 + - - +
805B PHE* 3.5 5.4 - - - +
807B THR* 1.3 83.4 + - - +
809B LEU* 1.4 60.1 + - - +
811B GLU* 3.3 12.9 + - - +
812B ILE* 3.2 27.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B LYS* 4.9 12.6 - - + +
633B ARG* 4.3 15.3 - - + -
634B ILE* 4.8 9.9 - - + +
637B LEU* 3.8 19.1 - - + -
772B PHE* 3.8 14.3 - - + -
805B PHE* 2.9 37.0 + - + +
806B ASN* 3.7 8.7 - - - +
807B THR 3.3 0.4 - - - -
808B ASN* 1.4 74.3 - - - +
810B LYS* 1.3 62.4 + - - +
812B ILE* 3.3 26.6 - - + +
813B VAL* 3.3 25.3 + - - +
445D TYR* 3.9 22.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B ASN 3.3 15.0 + - - +
807B THR* 4.0 5.2 - - - +
809B LEU* 1.3 74.4 - - - +
811B GLU* 1.3 64.2 + - - +
813B VAL* 3.2 28.9 + - - +
814B SER* 3.2 35.5 + - - +
445D TYR* 3.8 43.0 - - + +
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Residues in contact with GLU 811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768B SER* 5.5 4.9 + - - -
771B GLU* 3.4 25.0 - - - +
807B THR 3.2 12.6 + - - +
808B ASN* 3.4 14.7 + - - +
809B LEU 3.1 0.2 - - - -
810B LYS* 1.3 79.7 - - - +
812B ILE* 1.4 74.1 + - - +
814B SER* 3.3 15.0 + - - -
815B GLN* 3.3 34.9 + - + +
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Residues in contact with ILE 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ILE* 5.1 4.7 - - + -
637B LEU* 4.5 9.4 - - + -
768B SER* 5.2 13.0 - - - +
771B GLU* 4.2 7.2 - - - +
772B PHE* 3.1 53.4 - - + -
808B ASN 3.2 11.0 + - - +
809B LEU* 3.3 28.3 - - + +
811B GLU* 1.4 89.6 - - - +
813B VAL* 1.4 56.6 + - - +
815B GLN* 3.6 4.2 + - - +
816B TYR* 2.9 59.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 3.8 23.6 - - + -
809B LEU 3.3 14.7 + - - +
810B LYS* 3.2 18.3 + - - +
812B ILE* 1.4 77.2 - - - +
814B SER* 1.4 61.9 + - - +
816B TYR* 3.1 8.3 + - + +
817B LYS* 3.0 24.9 + - + +
443D ASP* 4.8 13.0 - - + +
445D TYR* 3.5 41.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B LYS* 3.2 34.9 + - - +
811B GLU* 3.3 7.1 + - - -
813B VAL* 1.4 72.3 - - - +
815B GLN* 1.4 65.2 + - - +
817B LYS* 3.3 9.8 + - - +
818B ASN* 3.2 35.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B LEU* 4.5 19.8 - - - +
768B SER* 5.4 5.6 + - - +
811B GLU* 3.3 34.9 + - + +
812B ILE* 3.8 5.8 - - - +
814B SER* 1.4 78.9 - - - +
816B TYR* 1.3 62.0 + - + +
818B ASN* 3.6 17.4 + - - +
819B PHE* 3.2 46.4 + - + -
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Residues in contact with TYR 816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 3.4 53.3 + - + +
638B ARG* 4.2 3.1 + - - -
640B GLN* 4.3 19.5 - - + -
641B PHE* 3.3 56.6 - + + +
644B PHE* 6.3 0.7 - + - -
768B SER* 5.9 0.9 - - - -
769B VAL* 5.6 0.3 - - - +
812B ILE* 2.9 55.6 + - + +
813B VAL* 3.1 8.0 + - + +
815B GLN* 1.3 79.3 - - + +
817B LYS* 1.4 56.7 + - - +
819B PHE* 3.3 8.3 + + - +
820B LYS* 2.9 39.9 + - + +
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Residues in contact with LYS 817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B VAL* 3.0 14.8 + - + +
814B SER* 3.3 11.8 + - - +
816B TYR* 1.4 72.7 - - - +
818B ASN* 1.3 63.8 + - - +
820B LYS* 3.3 14.2 + - - +
821B ASP* 2.9 39.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 818 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B SER* 3.2 18.2 + - - +
815B GLN* 3.8 22.5 + - - +
817B LYS* 1.3 83.2 - - - +
819B PHE* 1.3 63.6 + - + +
821B ASP* 3.3 15.2 + - - +
822B ARG* 3.3 46.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 819 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B PHE* 4.0 21.5 - + + -
761B SER* 5.3 11.4 - - - -
764B LEU* 4.6 18.4 - - + -
765B LEU* 3.3 39.0 - - + -
768B SER* 5.1 4.0 - - - -
815B GLN* 3.2 45.3 + - + -
816B TYR* 3.3 7.2 + - - +
818B ASN* 1.3 78.9 - - + +
820B LYS* 1.3 58.1 + - + +
822B ARG* 3.2 24.8 + - + +
823B LEU* 2.9 27.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 820 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B GLN* 4.3 22.3 + - - +
644B PHE* 5.1 14.8 - - + -
816B TYR* 2.9 31.3 + - + +
817B LYS* 3.4 13.5 - - - +
818B ASN 3.3 0.4 - - - -
819B PHE* 1.3 73.5 - - + +
821B ASP* 1.3 60.1 + - - +
823B LEU* 3.1 14.9 + - + +
824B TYR* 3.1 60.6 + - + +
350D SER* 4.3 28.3 + - - +
443D ASP* 5.2 7.5 + - - -
----------------------------------------------------------
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Residues in contact with ASP 821 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B LYS* 2.9 29.5 + - - +
818B ASN* 3.5 16.6 - - - +
819B PHE 3.3 0.4 - - - -
820B LYS* 1.3 74.2 - - - +
822B ARG* 1.3 66.2 + - + +
823B LEU 3.3 0.3 + - - -
824B TYR* 3.4 25.0 + - - +
825B ILE* 3.5 18.9 + - + +
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Residues in contact with ARG 822 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B SER* 5.5 7.2 - - - -
818B ASN* 3.3 43.2 + - - +
819B PHE* 3.2 25.8 + - - +
821B ASP* 1.3 76.3 - - + +
823B LEU* 1.4 58.0 + - - +
825B ILE* 3.2 14.1 + - + +
826B PHE* 3.0 25.8 + - - +
841B LEU* 4.4 29.4 - - + +
----------------------------------------------------------
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Residues in contact with LEU 823 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B PHE* 3.6 46.2 - - + -
647B LYS* 4.2 2.9 - - - +
648B MET* 3.7 29.4 - - + -
758B TYR* 4.3 12.1 - - - +
819B PHE 2.9 14.3 + - - +
820B LYS* 3.1 18.6 + - + +
822B ARG* 1.4 75.1 - - - +
824B TYR* 1.4 61.5 + - + +
826B PHE* 3.3 8.8 + - + +
827B ARG* 2.9 56.0 + - + +
----------------------------------------------------------
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Residues in contact with TYR 824 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B LYS* 3.1 50.2 + - + -
821B ASP* 3.7 19.7 - - - +
822B ARG 3.3 0.4 - - - -
823B LEU* 1.4 78.6 - - + +
825B ILE* 1.4 62.7 + - + +
827B ARG* 3.3 43.4 + - - +
828B ALA* 3.2 21.3 + - - +
350D SER 5.3 2.3 + - - -
352D MET* 6.0 4.8 - - + +
----------------------------------------------------------
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Residues in contact with ILE 825 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B ASP* 3.5 16.6 - - + +
822B ARG* 3.2 14.3 + - + +
824B TYR* 1.4 73.7 - - + +
826B PHE* 1.3 58.0 + - - +
828B ALA* 3.2 10.2 - - - +
829B ASP* 3.1 22.7 + - - +
835B ASP* 3.3 3.2 - - - +
837B GLU* 3.7 30.3 - - + +
838B LEU* 3.4 38.4 - - + +
841B LEU* 4.6 17.9 - - + -
----------------------------------------------------------
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Residues in contact with PHE 826 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B MET* 3.6 26.9 - - + -
652B TYR* 3.6 21.3 - + - -
742B ALA* 4.8 16.8 - - + -
757B PRO* 6.5 0.2 - - + -
758B TYR* 3.6 46.0 - + + +
822B ARG 3.0 13.6 + - - +
823B LEU* 3.4 13.0 - - + +
824B TYR 3.2 0.2 - - - -
825B ILE* 1.3 75.5 - - - +
827B ARG* 1.4 58.4 + - - +
829B ASP* 3.1 20.7 + - - +
830B LEU* 3.0 44.8 + - + +
838B LEU* 4.1 24.0 - - + -
----------------------------------------------------------
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Residues in contact with ARG 827 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B PHE* 3.7 19.4 - - - -
647B LYS* 4.4 11.9 - - - +
648B MET* 5.6 2.5 - - + -
823B LEU* 2.9 55.2 + - + +
824B TYR* 3.4 37.6 - - - +
826B PHE* 1.4 69.1 - - - +
828B ALA* 1.3 65.1 + - - +
830B LEU* 3.4 12.1 + - + +
831B LYS 3.2 14.4 + - - -
340D GLN* 5.3 5.8 + - - +
341D ARG* 3.1 39.9 + - - +
343D LYS* 5.9 0.4 - - - +
352D MET* 4.9 9.1 - - - +
353D HIS* 3.8 37.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 828 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824B TYR 3.2 8.0 + - - +
825B ILE* 3.2 8.1 - - - +
827B ARG* 1.3 78.0 - - - +
829B ASP* 1.3 55.3 + - - +
831B LYS* 3.2 4.7 + - - +
832B ASN* 2.8 38.3 + - - +
835B ASP* 3.0 25.1 - - + +
341D ARG* 4.2 4.9 - - - +
----------------------------------------------------------
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Residues in contact with ASP 829 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B ALA* 5.7 2.8 - - - +
825B ILE 3.1 7.1 + - - +
826B PHE* 3.1 25.1 + - + +
828B ALA* 1.3 76.1 - - - +
830B LEU* 1.3 65.2 + - - +
833B ASP 2.9 31.9 + - - +
834B GLY* 3.2 9.8 - - - -
835B ASP* 2.8 44.7 + - - +
838B LEU* 3.4 30.3 - - + +
839B PHE* 3.8 4.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU 830 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B LYS* 6.0 0.2 - - - -
648B MET* 4.2 17.0 - - + -
651B TYR* 3.8 44.4 - - + -
652B TYR* 5.9 5.2 - - + -
655B CYS* 6.3 1.6 - - - -
826B PHE* 3.0 36.9 + - + +
827B ARG* 3.4 11.8 + - + +
829B ASP* 1.3 76.9 - - - +
831B LYS* 1.3 61.6 + - - +
833B ASP* 3.5 12.1 + - - +
337D LYS* 3.6 24.2 + - - +
340D GLN* 6.0 4.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 831 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B ARG 3.2 14.7 + - - +
828B ALA* 3.2 9.8 + - - +
830B LEU* 1.3 74.5 - - - +
832B ASN* 1.4 65.0 + - - +
833B ASP* 3.1 6.8 - - - +
337D LYS* 3.1 52.4 + - + +
338D LEU* 3.4 16.5 - - - +
340D GLN* 4.4 2.7 - - - +
341D ARG* 3.9 38.3 - - + +
----------------------------------------------------------
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Residues in contact with ASN 832 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LYS* 5.2 4.2 + - - +
828B ALA* 2.8 24.2 + - - +
831B LYS* 1.4 76.9 - - - +
833B ASP* 1.3 71.1 + - - +
834B GLY 3.2 8.5 + - - +
835B ASP* 3.6 33.3 - - - +
----------------------------------------------------------
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Residues in contact with ASP 833 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LYS* 4.2 18.0 + - - +
829B ASP* 2.9 15.3 + - - +
830B LEU* 3.6 6.9 - - - +
831B LYS 3.1 5.5 - - - +
832B ASN* 1.3 85.9 - - - +
834B GLY* 1.3 53.6 - - - +
337D LYS* 3.6 25.3 + - - -
----------------------------------------------------------
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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