Contacts of the helix formed by residues 804 - 837 (chain F) in PDB entry 1TU3
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 ALA 804 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805F GLN* 1.3 64.8 + - - +
806F ARG* 3.3 25.9 + - + +
807F LEU* 3.5 26.2 - - - +
808F GLN* 3.6 16.8 + - - +
803G LYS* 6.3 1.9 - - - +
804G ALA* 4.1 16.6 - - - +
807G LEU* 5.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 805 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F ALA* 1.3 75.6 - - - +
806F ARG* 1.3 61.8 + - - +
808F GLN* 3.5 8.9 + - - +
809F THR* 3.2 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 806 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F ALA* 4.0 16.7 - - + +
805F GLN* 1.3 76.6 - - + +
807F LEU* 1.3 95.7 + - - +
808F GLN 3.1 1.8 - - - -
809F THR* 2.7 12.7 + - - +
810F GLU* 2.7 47.5 + - - +
808G GLN* 4.9 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 807 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F ALA 3.5 21.5 + - - +
805F GLN 3.4 0.2 - - - -
806F ARG* 1.3 107.1 - - - +
808F GLN* 1.3 57.6 + - - +
810F GLU* 3.1 22.4 - - - +
811F LEU* 3.0 22.9 + - - +
804G ALA* 4.1 14.6 - - + +
807G LEU* 3.3 29.5 - - + +
808G GLN* 3.3 39.9 - - + +
811G LEU* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 808 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F ALA 3.6 9.0 + - - +
805F GLN* 3.5 14.5 + - - +
806F ARG 3.1 0.2 - - - -
807F LEU* 1.3 78.9 - - - +
809F THR* 1.3 60.7 + - + +
811F LEU* 3.4 18.4 + - - +
812F ASP* 3.0 60.6 + - - +
807G LEU* 3.2 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 809 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805F GLN* 3.2 26.9 - - + +
806F ARG* 2.7 24.3 + - - +
808F GLN* 1.3 74.6 - - + +
810F GLU* 1.3 65.7 + - - +
812F ASP* 3.4 12.0 + - - +
813F VAL* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 810 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LYS* 6.0 1.2 - - - -
806F ARG* 2.7 31.8 + - - +
807F LEU* 3.1 22.6 - - - +
809F THR* 1.3 75.2 + - - +
811F LEU* 1.3 60.9 + - - +
813F VAL* 3.4 6.0 + - - +
814F SER* 3.0 22.2 + - - -
808G GLN* 4.2 2.6 + - - -
811G LEU* 3.0 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 811 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807F LEU 3.0 14.4 + - - +
808F GLN* 3.4 28.9 - - - +
810F GLU* 1.3 76.7 - - - +
812F ASP* 1.3 65.2 + - - +
814F SER* 3.1 4.0 - - - -
815F GLU* 2.9 42.0 + - - +
807G LEU* 4.7 13.0 - - + -
810G GLU* 3.3 32.5 - - + +
811G LEU* 3.5 45.1 - - + +
814G SER* 4.2 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 812 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808F GLN* 3.0 39.9 + - - +
809F THR* 3.7 15.3 - - - +
810F GLU 3.3 0.4 - - - -
811F LEU* 1.3 78.3 - - - +
813F VAL* 1.3 57.5 + - + +
815F GLU* 3.2 7.6 + - - +
816F GLN* 2.9 29.9 + - - +
819F ARG* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 813 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 4.0 34.8 - - + +
809F THR* 3.1 19.2 + - - +
810F GLU* 3.7 6.1 - - - +
812F ASP* 1.3 74.6 - - + +
814F SER* 1.3 64.6 + - - +
816F GLN* 3.2 16.4 + - - +
817F VAL* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 814 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810F GLU 3.0 14.0 + - - -
811F LEU* 3.1 14.4 - - - -
813F VAL* 1.3 78.6 - - - +
815F GLU* 1.3 57.1 + - - +
817F VAL* 4.9 0.7 - - - -
818F GLN* 2.9 25.6 + - - +
811G LEU* 4.1 6.4 - - - +
814G SER* 2.7 26.0 + - - -
815G GLU* 2.9 27.4 + - - +
818G GLN* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 815 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 5.4 6.3 + - - -
811F LEU* 2.9 40.6 + - + +
812F ASP* 3.8 5.6 - - - +
814F SER* 1.3 74.2 - - - +
816F GLN* 1.3 64.1 + - - +
818F GLN* 3.5 17.9 - - - +
819F ARG* 3.1 38.0 + - + +
810G GLU* 3.8 13.2 - - - +
814G SER* 3.4 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 816 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 2.5 46.0 - - - +
812F ASP 2.9 12.3 + - - +
813F VAL* 3.3 22.4 - - - +
815F GLU* 1.3 74.9 - - - +
817F VAL* 1.3 61.1 + - + +
819F ARG* 3.2 25.5 + - - +
820F ASP* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 817 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.5 42.6 - - + +
82B TYR* 3.8 14.8 - - + -
85B LEU* 3.5 33.0 - - + -
813F VAL* 3.0 16.8 + - + +
814F SER* 3.6 0.4 - - - +
816F GLN* 1.3 70.1 - - - +
818F GLN* 1.3 66.8 + - - +
819F ARG 3.0 1.6 - - - -
820F ASP* 2.8 21.6 + - - +
821F PHE* 3.0 16.6 + - + -
818G GLN* 3.4 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 818 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 4.4 8.3 + - - -
85A LEU* 3.6 28.2 - - + +
814F SER 2.9 16.3 + - - +
815F GLU* 3.5 17.7 - - - +
817F VAL* 1.3 76.5 - - - +
819F ARG* 1.3 59.2 + - + +
821F PHE* 3.4 3.7 + - - +
822F VAL* 3.0 26.2 + - + +
814G SER* 3.1 42.0 + - - +
817G VAL* 3.8 24.3 - - + +
818G GLN* 3.8 21.7 - - + +
821G PHE* 4.7 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 819 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.7 6.7 - - + -
88A MET* 3.6 34.5 - - + +
812F ASP 5.5 0.6 + - - -
815F GLU* 3.1 21.9 + - + +
816F GLN* 3.6 30.0 + - - +
817F VAL 3.0 0.8 - - - -
818F GLN* 1.3 75.9 - - + +
820F ASP* 1.3 68.1 + - - +
821F PHE 3.1 1.1 - - - -
822F VAL* 3.8 5.3 - - - +
823F LYS* 3.0 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 820 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 3.9 17.5 - - + +
81B ARG* 3.0 27.7 + - - -
82B TYR* 2.9 39.8 + - + +
816F GLN* 3.0 18.0 + - - +
817F VAL* 2.8 12.4 + - - +
819F ARG* 1.3 77.9 + - - +
821F PHE* 1.3 58.9 + - + +
823F LYS* 3.5 16.0 + - - +
824F LEU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 821 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY* 3.2 36.3 - - - -
82B TYR* 3.9 12.8 - + - -
85B LEU* 3.3 30.3 - - + -
89B TYR* 3.3 26.9 - + - -
817F VAL* 3.0 24.8 + - + +
818F GLN* 4.1 2.2 - - - +
820F ASP* 1.3 78.2 - - + +
822F VAL* 1.3 61.3 + - - +
824F LEU* 3.6 14.5 - - + +
825F SER* 2.8 31.2 + - - -
818G GLN* 4.9 2.0 - - + +
821G PHE* 4.0 22.4 - - + +
822G VAL* 3.9 16.2 - - + +
825G SER* 3.3 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 822 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.8 20.0 - - + -
88A MET* 4.0 20.4 - - + -
89A TYR* 3.9 21.3 - - + +
818F GLN* 3.0 21.3 + - + +
819F ARG* 3.8 7.0 - - - +
821F PHE* 1.3 76.5 - - - +
823F LYS* 1.3 62.5 - - - +
825F SER* 2.8 22.9 + - - -
826F GLN* 3.0 21.7 + - - +
821G PHE* 3.6 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 823 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 3.4 31.6 - - + -
91A ARG* 4.2 13.9 - - - +
53B ILE* 6.0 1.9 - - + +
819F ARG* 3.0 31.4 + - - +
820F ASP* 3.7 17.5 + - - +
822F VAL* 1.3 75.1 - - - +
824F LEU* 1.3 65.3 + - - +
826F GLN* 3.0 26.9 + - - +
827F THR* 3.1 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 824 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 3.6 37.0 - - + +
55B ALA 4.4 2.5 - - - +
820F ASP 3.0 17.9 + - - +
821F PHE* 3.6 21.3 - - + +
823F LYS* 1.3 75.8 - - - +
825F SER* 1.3 61.1 + - - +
827F THR* 3.3 8.5 + - + -
828F LEU* 3.1 50.6 + - + +
825G SER* 3.8 20.4 - - - +
829G GLN* 4.0 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 825 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 4.4 2.8 + - - -
821F PHE 2.8 18.1 + - - -
822F VAL 2.8 17.7 + - - -
824F LEU* 1.3 73.1 - - - +
826F GLN* 1.3 56.1 + - - +
828F LEU* 3.5 10.2 + - - -
829F GLN* 2.9 40.1 + - - +
821G PHE* 3.5 23.3 - - - -
824G LEU* 3.9 26.6 - - - +
825G SER* 4.8 2.4 - - - -
828G LEU* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 826 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 6.1 0.2 - - - +
74A TRP* 3.6 31.0 - - + -
88A MET* 3.3 25.8 + - - +
89A TYR* 3.2 36.0 - - + +
91A ARG* 5.6 1.4 + - - -
822F VAL* 3.0 22.8 + - - +
823F LYS* 3.0 28.3 + - - +
825F SER* 1.3 77.5 + - - +
827F THR* 1.3 63.0 + - - +
829F GLN* 3.6 2.4 + - - +
830F VAL* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 827 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823F LYS 3.1 13.2 + - - -
824F LEU* 3.6 12.1 - - + -
826F GLN* 1.3 74.4 - - - +
828F LEU* 1.3 69.1 + - + +
830F VAL* 3.1 8.0 + - - +
831F GLN* 2.9 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 828 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824F LEU* 3.1 51.1 + - + +
825F SER* 3.8 2.2 - - - +
827F THR* 1.3 85.2 - - + +
829F GLN* 1.3 56.6 + - - +
831F GLN* 3.4 10.9 + - - +
832F LEU* 2.8 34.4 + - - +
825G SER* 4.0 21.1 - - - +
828G LEU* 3.7 22.0 - - + -
829G GLN* 4.0 21.8 - - + +
832G LEU* 4.4 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 829 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 2.7 35.0 + - - +
56A ALA* 3.8 9.3 - - - +
57A PHE* 3.8 19.5 - - + +
74A TRP* 3.6 18.8 - - - -
89A TYR* 5.1 0.3 + - - -
825F SER* 2.9 31.0 + - - +
826F GLN* 3.9 4.4 - - - +
828F LEU* 1.3 72.9 - - - +
830F VAL* 1.3 57.4 + - - +
832F LEU* 3.4 8.1 + - - +
833F GLU* 3.0 27.7 + - - +
824G LEU* 4.2 18.1 - - - +
828G LEU* 3.7 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 830 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.9 16.4 - - + -
74A TRP* 3.8 24.9 - - + -
826F GLN 3.1 19.1 + - - +
827F THR* 3.1 11.8 + - - +
829F GLN* 1.3 71.5 - - - +
831F GLN* 1.3 67.6 + - - +
833F GLU* 3.1 3.8 + - - +
834F ARG* 3.0 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 831 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827F THR* 2.9 20.1 + - + +
828F LEU* 3.6 11.6 - - - +
830F VAL* 1.3 79.6 - - - +
832F LEU* 1.3 63.5 + - - +
834F ARG* 3.1 10.9 + - - +
835F ILE* 3.0 27.0 + - + +
847F ILE* 2.9 39.8 + - + +
848F LEU* 4.0 10.9 - - - +
849F ASN 5.0 1.0 + - - -
832G LEU* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 832 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828F LEU 2.8 21.9 + - - +
829F GLN* 3.7 6.5 - - + +
831F GLN* 1.3 71.9 - - - +
833F GLU* 1.3 58.6 + - - +
835F ILE* 3.3 6.9 + - + +
836F ARG* 3.0 27.4 + - - +
828G LEU* 3.5 43.5 - - + +
831G GLN* 4.7 15.3 - - + +
832G LEU* 3.2 31.0 - - + +
835G ILE* 3.9 22.7 - - + -
848G LEU* 3.9 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 833 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.6 23.9 - - + +
58A LEU* 4.1 7.6 - - - +
59A THR* 3.2 47.4 + - + +
829F GLN 3.0 14.1 + - - +
830F VAL 3.1 8.4 + - - +
832F LEU* 1.3 78.2 - - - +
834F ARG* 1.3 64.4 + - + +
836F ARG* 3.0 46.2 + - - +
837F GLN* 3.1 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 834 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 5.8 3.6 + - - +
57A PHE* 5.1 6.9 - - - -
70A LYS* 5.1 12.6 - - - +
830F VAL* 3.0 43.0 + - - +
831F GLN* 3.6 10.5 - - - +
833F GLU* 1.3 77.0 - - + +
835F ILE* 1.3 57.2 + - - +
837F GLN* 3.2 9.6 + - - +
838F ALA 3.0 21.1 + - - -
843F ARG* 3.7 6.8 + - - +
847F ILE* 3.6 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 835 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831F GLN* 3.0 13.3 + - + +
832F LEU* 3.4 10.5 - - + +
834F ARG* 1.3 76.1 - - - +
836F ARG* 1.3 61.7 + - - +
838F ALA* 3.1 18.3 + - - +
844F ILE* 4.3 13.7 - - + +
847F ILE* 3.9 20.4 - - + -
848F LEU* 3.8 27.8 - - + -
832G LEU* 3.5 32.5 - - + -
835G ILE* 4.1 18.6 - - + -
844G ILE* 4.2 12.0 - - + +
848G LEU* 4.1 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 836 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.0 13.3 + - - +
42A LYS* 4.0 24.5 - - - +
58A LEU* 4.1 12.9 - - - +
59A THR 3.7 11.9 + - - -
832F LEU 3.0 13.6 + - - +
833F GLU* 3.0 42.7 + - - +
835F ILE* 1.3 77.8 - - - +
837F GLN* 1.3 78.9 + - - +
838F ALA 3.6 3.5 + - - +
848G LEU* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 837 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.3 26.0 + - - +
60A GLN* 5.6 1.2 - - - +
70A LYS* 6.4 0.9 - - + -
833F GLU* 3.1 14.5 + - + +
834F ARG* 3.6 10.5 - - - +
835F ILE 3.2 0.4 - - - -
836F ARG* 1.3 108.7 - - - +
838F ALA* 1.3 62.5 + - - +
839F ASP* 3.6 3.6 + - - +
843F ARG* 3.7 12.2 + - - +
----------------------------------------------------------
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