Contacts of the helix formed by residues 846 - 873 (chain B) in PDB entry 5J3V
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 LYS 846 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808B GLU* 5.7 8.2 - - - +
811B ASP* 3.5 32.2 + - - +
815B ARG* 3.6 24.4 - - - +
842B TRP* 5.0 0.6 - - + -
844B ASN 3.8 1.5 + - - +
845B PRO* 1.3 74.6 - - - +
847B ASP* 1.3 55.6 + - - +
848B ASP* 3.3 11.7 - - - +
849B LEU* 3.2 8.0 + - + +
850B ARG* 2.8 33.1 + - - +
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Residues in contact with ASP 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B PRO 4.4 4.2 - - - +
846B LYS* 1.3 75.2 - - - +
848B ASP* 1.3 60.9 + - - +
850B ARG* 3.6 11.3 + - - +
851B ASP* 2.9 31.9 + - - +
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Residues in contact with ASP 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B ARG* 2.7 42.2 + - - -
846B LYS* 3.9 8.7 - - - +
847B ASP* 1.3 76.8 + - - +
849B LEU* 1.3 71.2 + - - +
851B ASP* 3.4 11.4 + - - +
852B MET* 3.2 29.7 + - - +
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Residues in contact with LEU 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B ASP* 3.4 24.0 - - - +
814B PHE* 4.2 4.0 - - + -
815B ARG* 4.1 28.7 - - + +
818B CYS* 4.1 17.9 - - - -
842B TRP* 3.9 28.5 - - + -
845B PRO* 4.7 1.6 - - + -
846B LYS* 3.2 20.5 + - + +
848B ASP* 1.3 85.6 + - - +
850B ARG* 1.3 63.8 + - - +
852B MET* 3.1 19.2 + - - +
853B PHE* 3.2 37.3 + - + -
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Residues in contact with ARG 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B PRO* 4.3 18.8 - - + +
846B LYS 2.8 16.9 + - - +
847B ASP* 3.8 11.9 + - - +
849B LEU* 1.3 77.8 - - - +
851B ASP* 1.3 74.0 + - - +
853B PHE* 3.3 14.5 + - - -
854B CYS* 3.4 11.5 + - - -
886B ALA 5.0 1.8 + - - -
887B PHE* 3.3 42.9 - - - +
888B TYR* 3.2 35.8 - - + +
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Residues in contact with ASP 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B ASP* 2.9 19.6 + - - +
848B ASP* 3.6 11.6 - - - +
849B LEU 3.2 0.8 - - - -
850B ARG* 1.3 94.1 + - - +
852B MET* 1.3 62.1 + - + +
854B CYS* 3.5 23.5 + - - +
855B LYS* 3.6 25.2 - - - +
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Residues in contact with MET 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B ARG* 5.1 9.6 - - - +
818B CYS* 3.6 41.1 - - + +
819B THR* 4.8 11.7 - - + +
848B ASP* 3.2 22.2 - - - +
849B LEU* 3.1 19.4 + - - +
851B ASP* 1.3 78.0 - - + +
853B PHE* 1.3 62.2 + - - +
854B CYS 3.3 0.4 + - - -
855B LYS* 3.7 11.2 + - + +
856B ILE* 3.1 30.5 + - + +
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Residues in contact with PHE 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B PHE* 3.5 31.2 - + - -
818B CYS* 3.7 26.9 - - - -
835B PHE* 4.4 10.5 - + - -
839B VAL* 3.6 29.4 - - + -
842B TRP* 4.0 18.2 - + - -
845B PRO* 4.7 3.6 - - + -
849B LEU* 3.2 35.1 + - + -
850B ARG* 3.3 4.6 + - - +
852B MET* 1.3 76.3 - - - +
854B CYS* 1.3 63.3 + - - +
856B ILE* 3.5 3.4 + - + +
857B LEU* 3.0 30.8 + - + +
888B TYR* 3.2 40.4 - - + -
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Residues in contact with CYS 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850B ARG* 3.4 18.8 + - - -
851B ASP* 3.5 16.6 - - - +
853B PHE* 1.3 79.8 - - - +
855B LYS* 1.3 58.8 + - + +
856B ILE 3.1 0.3 + - - -
857B LEU 3.2 0.3 + - - -
858B HIS* 2.8 50.9 + - + +
888B TYR* 3.4 37.5 - - - -
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Residues in contact with LYS 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851B ASP* 3.6 25.8 + - - +
852B MET* 3.7 10.3 + - + +
853B PHE 3.5 0.4 - - - -
854B CYS* 1.3 76.4 - - + +
856B ILE* 1.3 60.4 + - + +
858B HIS* 4.9 2.9 - - - -
859B GLY* 3.4 20.1 + - - +
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Residues in contact with ILE 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B CYS* 4.0 27.1 - - + +
821B ILE* 3.6 46.4 - - + -
832B PHE* 3.8 12.7 - - + -
835B PHE* 3.7 29.6 - - + -
852B MET* 3.1 21.1 - - + +
853B PHE* 4.0 4.3 - - - +
854B CYS 3.1 0.8 - - - -
855B LYS* 1.3 81.6 - - + +
857B LEU* 1.3 63.3 + - - +
859B GLY* 3.5 2.1 + - - -
860B PHE* 3.3 20.8 + - - +
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Residues in contact with LEU 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B PHE* 3.6 30.3 - - + -
835B PHE* 4.3 14.1 - - + -
836B CYS* 3.9 15.5 - - + -
839B VAL* 4.9 6.3 - - + -
853B PHE* 3.0 17.3 + - + +
854B CYS 4.0 1.1 - - - +
856B ILE* 1.3 75.8 - - - +
858B HIS* 1.3 66.0 - - + +
860B PHE* 3.1 14.0 + - - +
861B LYS* 3.2 13.0 + - - +
869B TRP* 5.0 11.3 - - + -
883B ARG* 3.6 24.5 - - + +
888B TYR* 3.5 44.9 - - + -
889B GLY* 5.1 2.2 - - - +
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Residues in contact with HIS 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B CYS* 2.8 32.6 + - + +
855B LYS* 4.9 2.5 - - - -
857B LEU* 1.3 76.3 - - - +
859B GLY* 1.3 56.1 + - - +
861B LYS* 3.4 11.4 + - + +
862B ASN* 2.9 45.9 + - - +
888B TYR* 3.5 11.9 - - + -
889B GLY* 3.2 46.0 + - - -
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Residues in contact with GLY 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B LYS 3.4 20.5 + - - -
856B ILE 3.5 4.0 + - - -
857B LEU 3.1 0.8 - - - -
858B HIS* 1.3 78.4 - - - +
860B PHE* 1.3 57.0 + - - +
862B ASN* 4.2 4.7 - - - +
863B GLN* 3.3 29.1 + - - +
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Residues in contact with PHE 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829B ILE* 4.0 35.9 - - + -
832B PHE* 3.5 52.3 - + + -
856B ILE 3.3 4.2 + - - +
857B LEU 3.1 9.7 + - - +
859B GLY* 1.3 78.4 - - - +
861B LYS* 1.3 63.7 + - - +
862B ASN 3.3 0.4 - - - -
863B GLN* 3.2 12.0 + - + +
864B VAL* 3.3 40.5 + - + +
869B TRP* 3.5 23.8 - + - -
872B PHE* 3.8 37.9 - + + -
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Residues in contact with LYS 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B LEU 3.2 9.3 + - - +
858B HIS* 4.0 11.6 - - + +
860B PHE* 1.3 76.4 - - - +
862B ASN* 1.3 68.9 + - - +
863B GLN 3.1 5.2 - - - -
864B VAL* 4.1 6.1 - - - -
865B GLY* 3.1 30.3 + - - +
866B ASP* 4.3 18.3 - - - +
869B TRP* 3.6 50.0 - - + +
884B LEU* 4.2 4.8 - - - +
889B GLY* 3.1 37.2 + - - -
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Residues in contact with ASN 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858B HIS* 2.9 27.2 + - - +
859B GLY* 4.2 5.1 - - - +
860B PHE 3.3 0.2 - - - -
861B LYS* 1.3 90.1 - - - +
863B GLN* 1.3 63.1 + - - +
865B GLY* 4.6 2.7 - - - -
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Residues in contact with GLN 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B ILE* 6.4 1.8 - - + -
859B GLY 3.3 21.5 - - - +
860B PHE* 3.7 8.3 - - + +
861B LYS 3.1 0.8 - - - -
862B ASN* 1.3 83.0 - - - +
864B VAL* 1.3 65.7 + - + +
865B GLY 3.7 0.7 - - - -
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Residues in contact with VAL 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829B ILE* 6.0 1.8 - - + -
860B PHE* 3.3 48.7 - - + +
861B LYS* 3.8 3.1 - - - +
863B GLN* 1.3 82.9 - - + +
865B GLY* 1.3 70.6 + - - +
868B ASN* 2.8 42.9 + - + +
869B TRP* 3.9 21.5 - - + +
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Residues in contact with GLY 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861B LYS 3.1 14.4 + - - +
862B ASN* 4.6 1.9 - - - -
863B GLN 3.7 1.4 - - - +
864B VAL* 1.3 86.8 - - - +
866B ASP* 1.3 66.7 + - - -
867B GLU* 3.2 3.4 - - - -
869B TRP* 3.2 17.7 + - - +
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Residues in contact with ASP 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B LYS* 4.3 18.9 - - - +
865B GLY* 1.3 73.9 - - - -
867B GLU* 1.3 61.7 + - - +
869B TRP* 3.8 5.9 - - - +
870B ARG* 3.1 49.4 + - - +
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Residues in contact with GLU 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B GLY* 3.2 1.2 - - - -
866B ASP* 1.3 79.4 - - - +
868B ASN* 1.3 66.0 + - - +
870B ARG* 3.4 17.5 + - - +
871B ARG* 3.3 64.0 + - - +
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Residues in contact with ASN 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864B VAL* 2.8 39.6 + - + +
865B GLY 3.6 1.6 + - - -
866B ASP 3.5 0.2 - - - -
867B GLU* 1.3 78.6 - - - +
869B TRP* 1.3 60.7 + - - +
871B ARG* 3.3 25.2 + - - +
872B PHE* 2.9 27.9 + - - +
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Residues in contact with TRP 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832B PHE* 4.7 2.9 - + - -
836B CYS* 5.0 4.7 - - - -
857B LEU* 5.0 14.8 - - + -
860B PHE* 3.5 30.1 - + - -
861B LYS* 3.6 38.5 - - + +
864B VAL* 3.9 5.6 - - + +
865B GLY 3.2 18.9 + - - +
866B ASP* 3.8 5.4 - - - +
868B ASN* 1.3 76.4 - - - +
870B ARG* 1.3 66.9 + - + +
872B PHE* 3.5 35.8 - + - -
873B SER* 2.9 31.9 + - - -
876B PHE* 4.6 9.4 - + - -
883B ARG* 4.8 14.8 - - + -
884B LEU* 3.4 49.2 - - + +
889B GLY* 5.3 3.1 - - - -
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Residues in contact with ARG 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B ASP* 3.1 35.8 + - - +
867B GLU* 3.8 16.2 + - - +
868B ASN 3.3 0.2 - - - -
869B TRP* 1.3 83.9 - - + +
871B ARG* 1.3 59.1 + - + +
873B SER* 3.3 10.1 + - - -
874B ASP* 2.9 28.6 - - - +
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Residues in contact with ARG 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B GLU* 3.3 46.3 + - - +
868B ASN* 3.6 21.5 + - - +
869B TRP 3.1 0.2 - - - -
870B ARG* 1.3 79.8 - - + +
872B PHE* 1.3 62.9 + - - +
873B SER 3.2 0.4 - - - -
874B ASP* 3.4 23.6 + - - +
875B GLN* 4.3 8.8 + - - +
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Residues in contact with PHE 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B PHE* 3.8 18.2 - + + -
833B ILE* 3.5 50.7 - - + -
836B CYS* 4.3 0.7 - - - -
860B PHE* 3.8 20.0 - + + -
864B VAL* 6.1 0.2 - - + -
868B ASN 2.9 18.0 + - - +
869B TRP* 3.5 36.3 - + + +
871B ARG* 1.3 78.3 - - - +
873B SER* 1.3 59.6 + - - +
874B ASP 3.4 0.5 + - - -
875B GLN* 3.6 28.5 + - - +
876B PHE* 3.6 25.1 - + - -
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Residues in contact with SER 873 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B TRP* 2.9 23.5 + - - -
870B ARG* 3.3 15.6 + - - +
872B PHE* 1.3 74.0 - - - +
874B ASP* 1.3 63.8 + - - +
875B GLN 3.1 2.5 - - - -
876B PHE* 3.3 26.0 + - - +
880B LEU* 3.3 37.5 - - - +
884B LEU* 3.8 16.7 - - - +
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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