Contacts of the helix formed by residues 862 - 897 (chain A) in PDB entry 1ZUC
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 862 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860A GLN 3.6 0.2 - - - -
861A LYS* 1.3 80.7 - - - +
863A VAL* 1.3 56.2 + - - -
864A VAL 3.2 2.7 - - - -
865A SER* 4.1 10.9 - - - -
866A SER* 2.8 37.0 + - - -
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Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A LYS 4.0 0.6 + - - +
862A GLY* 1.3 71.5 - - - -
864A VAL* 1.3 70.2 + - + +
866A SER* 3.7 5.7 - - - -
867A SER* 2.8 35.5 + - - -
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Residues in contact with VAL 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A GLY* 3.2 0.6 - - - -
863A VAL* 1.3 88.6 - - + +
865A SER* 1.3 59.6 + - - +
867A SER* 3.2 5.2 + - - -
868A GLN* 2.9 66.2 + - - +
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Residues in contact with SER 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A GLN* 2.9 33.1 + - - +
861A LYS 4.8 0.6 + - - -
862A GLY* 3.8 18.1 - - - -
864A VAL* 1.3 77.7 - - - +
866A SER* 1.3 56.7 + - - -
868A GLN* 3.4 9.8 + - - +
869A ARG* 2.9 31.2 + - - +
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Residues in contact with SER 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A ILE* 6.6 0.7 - - - -
856A ILE* 3.8 12.3 - - - +
857A GLY* 4.7 3.8 - - - -
860A GLN* 2.7 36.4 + - - +
861A LYS 4.5 0.3 + - - -
862A GLY 2.8 21.8 + - - -
863A VAL* 3.7 7.9 - - - -
865A SER* 1.3 71.9 - - - +
867A SER* 1.3 58.6 + - - +
869A ARG* 3.5 2.1 + - - +
870A PHE* 3.1 27.5 + - - +
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Residues in contact with SER 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A VAL* 2.8 24.6 + - - +
864A VAL* 3.2 4.5 + - - -
866A SER* 1.3 72.8 - - - +
868A GLN* 1.3 61.8 + - - +
870A PHE* 3.4 7.8 + - - +
871A TYR* 3.0 26.9 + - - +
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Residues in contact with GLN 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A VAL* 2.9 46.0 + - - +
865A SER* 3.9 7.6 - - - +
867A SER* 1.3 78.6 - - - +
869A ARG* 1.3 57.6 + - - +
871A TYR* 3.4 8.2 + - - +
872A GLN* 3.0 36.5 + - - +
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Residues in contact with ARG 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A LEU* 2.6 45.8 + - - +
812A GLN 3.3 14.3 + - - -
813A VAL* 3.6 4.2 - - - +
817A GLU* 2.9 37.6 + - - +
856A ILE* 3.7 21.1 - - + -
860A GLN* 3.7 31.6 + - + +
865A SER 2.9 17.8 + - - +
866A SER 3.6 5.6 - - - +
868A GLN* 1.3 74.5 - - - +
870A PHE* 1.3 58.5 + - - +
872A GLN* 3.2 19.8 + - - +
873A LEU* 2.9 39.4 + - + +
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Residues in contact with PHE 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A ILE* 3.7 26.7 - - + -
852A LEU* 4.1 11.7 - - + -
853A ILE* 3.8 34.8 - - + -
856A ILE* 3.6 19.7 - - + +
866A SER 3.1 16.6 + - - +
867A SER* 3.7 8.1 - - - +
868A GLN 3.3 0.2 - - - -
869A ARG* 1.3 72.2 - - - +
871A TYR* 1.3 68.5 + - - +
873A LEU* 4.8 0.7 - - - -
874A THR* 2.8 58.1 + - + +
930A PHE* 4.7 7.2 - + - -
931A HIS* 5.6 3.8 - + - -
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Residues in contact with TYR 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A SER 3.0 13.7 + - - +
868A GLN* 3.5 12.3 - - - +
870A PHE* 1.3 78.5 - - - +
872A GLN* 1.3 65.4 + - + +
874A THR* 3.2 5.9 + - - -
875A LYS* 2.8 62.5 + - + +
931A HIS* 3.4 35.7 + + + +
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Residues in contact with GLN 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A LEU* 3.7 37.9 - - + +
868A GLN* 3.0 18.7 + - - +
869A ARG* 3.2 30.5 + - - +
871A TYR* 1.3 84.9 - - + +
873A LEU* 1.3 60.7 + - + +
875A LYS* 3.4 4.5 + - - +
876A LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A LEU* 4.1 15.9 - - + -
813A VAL* 4.0 26.0 - - + -
817A GLU* 3.6 39.3 - - + +
821A MET* 3.6 24.0 - - + +
852A LEU* 4.3 11.4 - - + -
856A ILE* 3.9 18.6 - - + -
869A ARG* 2.9 30.2 + - - +
870A PHE* 4.2 2.7 - - - +
872A GLN* 1.3 77.9 - - + +
874A THR* 1.3 56.9 + - - +
876A LEU* 3.3 7.4 + - + +
877A LEU* 3.2 30.2 + - - +
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Residues in contact with THR 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A LEU* 4.3 10.8 - - + -
870A PHE* 2.8 55.2 + - + +
871A TYR* 3.2 0.5 + - - -
873A LEU* 1.3 74.0 - - - +
875A LYS* 1.3 58.6 + - - +
877A LEU* 3.5 6.5 + - + +
878A ASP* 3.0 31.9 + - - +
930A PHE* 3.5 32.7 - - + +
931A HIS* 2.6 30.8 + - - -
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Residues in contact with LYS 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A TYR* 2.8 50.9 + - + +
872A GLN* 3.7 5.6 - - - +
874A THR* 1.3 73.4 + - - +
876A LEU* 1.3 61.1 + - - +
878A ASP* 3.3 10.3 + - - +
879A ASN* 2.9 61.5 + - - +
931A HIS* 3.6 25.3 + - + +
932A LYS 4.5 9.9 + - - -
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Residues in contact with LEU 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761A PHE* 4.0 26.5 - - + -
804A ILE* 5.3 4.3 - - + -
807A GLU* 3.9 32.1 - - + +
808A PHE* 4.0 20.9 - - + -
811A LEU* 4.3 15.5 - - + -
813A VAL* 5.1 1.8 - - + -
821A MET* 4.0 11.2 - - + -
872A GLN 3.0 13.4 + - - +
873A LEU* 3.4 10.3 - - + +
874A THR 3.3 0.2 - - - -
875A LYS* 1.3 77.6 - - - +
877A LEU* 1.3 63.7 + - - +
879A ASN* 3.3 11.1 + - - +
880A LEU* 3.1 33.5 + - + +
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Residues in contact with LEU 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761A PHE* 4.3 2.9 - - + -
821A MET* 3.8 42.6 - - + +
824A LEU* 4.0 28.3 - - + -
825A LEU* 3.9 22.4 - - + +
828A ASN* 3.9 21.5 + - - +
852A LEU* 5.1 0.9 - - + -
873A LEU 3.2 13.8 + - - +
874A THR* 3.6 12.3 - - + +
875A LYS 3.3 0.2 - - - -
876A LEU* 1.3 76.1 - - - +
878A ASP* 1.3 66.2 + - - +
880A LEU* 3.0 27.4 + - + +
881A HIS* 4.0 1.9 + - - -
930A PHE* 3.9 23.1 - - + -
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Residues in contact with ASP 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ASN* 5.5 0.2 + - - -
874A THR 3.0 18.7 + - - +
875A LYS* 3.4 16.9 + - + +
877A LEU* 1.3 73.1 - - - +
879A ASN* 1.3 67.1 + - - +
880A LEU 3.1 1.2 + - - -
881A HIS* 3.2 24.6 + - - +
882A ASP* 4.5 2.6 + - - +
928A LEU 4.3 1.2 - - - +
929A LEU* 3.4 24.0 - - + +
930A PHE* 2.9 27.1 + - - -
931A HIS* 3.0 39.8 + - - +
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Residues in contact with ASN 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875A LYS* 2.9 53.8 + - - +
876A LEU* 3.3 9.2 + - - +
878A ASP* 1.3 75.4 - - - +
880A LEU* 1.3 63.7 + - + +
881A HIS 3.3 1.0 + - - -
882A ASP* 3.5 14.2 + - - +
883A LEU* 3.4 18.8 + - - +
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Residues in contact with LEU 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A SER* 5.6 1.1 - - - +
760A VAL* 5.4 0.7 - - + -
761A PHE* 3.7 26.7 - - + -
804A ILE* 3.4 36.6 - - + -
825A LEU* 3.7 31.4 - - + -
876A LEU* 3.1 26.2 + - + +
877A LEU* 3.0 14.3 + - + +
879A ASN* 1.3 78.1 - - + +
881A HIS* 1.3 64.4 + - - +
883A LEU* 3.9 12.6 - - + -
884A VAL* 2.9 34.0 + - + +
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Residues in contact with HIS 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A LEU* 6.5 0.4 - - + -
828A ASN* 3.1 39.0 + - - +
829A THR* 3.7 10.3 + - - -
877A LEU 4.0 1.1 + - - -
878A ASP* 3.2 20.4 + - - +
880A LEU* 1.3 77.6 - - - +
882A ASP* 1.3 65.6 + - - +
884A VAL* 3.9 3.6 - - - +
885A LYS* 3.0 23.4 + - - +
927A PRO* 3.4 28.2 - - + +
928A LEU 2.8 29.6 + - - -
929A LEU* 3.8 11.9 - - + +
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Residues in contact with ASP 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878A ASP 5.2 1.5 - - - +
879A ASN* 3.5 15.1 + - - +
880A LEU 3.3 0.4 - - - -
881A HIS* 1.3 79.2 - - - +
883A LEU* 1.3 65.0 + - - +
885A LYS* 3.4 22.9 + - - +
886A GLN* 3.6 12.0 + - - +
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Residues in contact with LEU 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760A VAL* 4.4 8.1 - - + -
800A THR* 3.5 44.0 - - + +
803A GLN* 3.7 16.2 - - + +
804A ILE* 3.6 35.4 - - + -
879A ASN 3.4 10.5 + - - +
880A LEU* 3.3 16.5 + - + +
882A ASP* 1.3 79.8 - - - +
884A VAL* 1.3 72.3 + - + +
886A GLN* 3.2 20.9 + - - +
887A LEU* 3.5 16.3 + - + +
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Residues in contact with VAL 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A MET* 4.1 12.6 - - + -
757A SER* 3.9 34.1 - - - +
760A VAL* 4.1 15.5 - - + -
880A LEU* 2.9 25.8 + - + +
881A HIS* 4.0 4.5 - - - +
883A LEU* 1.3 78.5 - - + +
885A LYS* 1.3 60.4 + - - +
887A LEU* 3.1 6.2 + - + +
888A HIS* 2.8 60.3 + - + +
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Residues in contact with LYS 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A HIS 3.0 14.3 + - - +
882A ASP* 3.5 19.4 + - - +
884A VAL* 1.3 77.6 - - - +
886A GLN* 1.3 62.0 + - - +
888A HIS* 3.3 10.7 + - - +
889A LEU* 2.9 29.7 + - + +
921A LEU* 3.7 16.7 - - + +
922B ALA* 3.0 39.7 + - + +
923B GLY 5.1 1.4 + - - -
924B MET* 4.1 18.9 - - - -
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Residues in contact with GLN 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A LEU* 3.9 8.6 - - + +
800A THR* 4.5 19.1 - - + +
882A ASP 3.6 11.1 + - - +
883A LEU* 3.2 9.9 + - - +
885A LYS* 1.3 85.4 + - - +
887A LEU* 1.3 57.3 + - - +
889A LEU* 3.5 14.9 + - - +
890A TYR* 3.0 29.8 + - - +
924B MET* 3.4 37.4 - - - +
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Residues in contact with LEU 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A T98 3.8 8.5 - - + +
756A MET* 3.7 30.3 - - + -
760A VAL* 3.6 39.7 - - + -
797A LEU* 3.2 32.1 - - + +
800A THR* 4.7 4.3 - - + -
801A MET* 3.6 26.2 - - + -
883A LEU* 3.5 18.1 + - + +
884A VAL* 3.1 9.7 + - - +
886A GLN* 1.3 73.8 - - - +
888A HIS* 1.3 59.8 + - - +
890A TYR* 3.5 1.4 + - - +
891A CYS* 2.9 32.0 + - - +
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Residues in contact with HIS 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A GLN 5.8 0.4 + - - -
753A TYR 4.3 17.3 + - - -
755A TRP* 4.9 2.7 - + - -
756A MET* 3.4 35.8 + - + +
757A SER 5.2 0.2 + - - -
884A VAL* 2.8 35.4 + - + +
885A LYS* 3.5 8.3 - - - +
887A LEU* 1.3 72.2 - - - +
889A LEU* 1.3 59.6 + - - +
891A CYS* 3.3 1.9 + - - +
892A LEU* 2.8 31.5 + - - +
917A LEU* 3.4 34.3 - - + +
920A ILE* 3.8 28.7 - - + +
921A LEU* 3.7 18.1 - - + +
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Residues in contact with LEU 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A LYS* 2.9 17.6 + - + +
886A GLN* 3.9 15.5 - - - +
888A HIS* 1.3 78.0 - - - +
890A TYR* 1.3 63.5 + - - +
892A LEU* 3.3 0.9 + - - -
893A ASN* 3.0 36.9 + - - +
921A LEU* 3.8 14.1 - - + +
918B PRO* 3.5 42.8 - - + +
919B LYS* 3.5 11.2 - - + +
922B ALA* 4.2 6.7 - - + -
924B MET* 3.7 34.1 - - + -
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Residues in contact with TYR 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A T98 3.5 22.4 - - - -
711A SER* 5.3 1.0 + - - -
715A LEU* 3.8 29.7 - - + +
793A SER* 3.8 35.4 - - - -
794A PHE* 4.0 18.1 + + - +
797A LEU* 3.7 32.5 - - + -
886A GLN 3.0 18.1 + - - +
887A LEU 3.8 3.4 - - - +
889A LEU* 1.3 75.0 - - - +
891A CYS* 1.3 59.1 + - - +
893A ASN* 3.7 8.2 - - - +
894A THR* 2.8 48.1 + - - -
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Residues in contact with CYS 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A T98 3.8 27.5 - - + -
755A TRP* 4.0 14.6 - - - -
756A MET* 3.8 14.6 - - + -
887A LEU 2.9 18.3 + - - +
888A HIS 3.6 3.8 - - - +
890A TYR* 1.3 76.9 - - - +
892A LEU* 1.3 58.9 + - - +
894A THR* 3.3 3.1 + - - -
895A PHE* 2.9 28.4 + - - +
905A PHE* 4.2 3.8 - - - -
913A ILE* 3.6 36.3 - - - -
917A LEU* 4.1 4.3 - - + -
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Residues in contact with LEU 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A HIS 2.8 20.2 + - - +
889A LEU 3.3 2.7 + - - +
891A CYS* 1.3 74.4 - - - +
893A ASN* 1.3 55.5 + - - +
895A PHE* 3.2 9.5 + - + +
896A ILE* 2.8 39.5 + - + +
913A ILE* 3.8 21.5 - - + -
917A LEU* 4.2 7.6 - - + +
918A PRO* 3.9 28.9 - - + -
921A LEU* 3.5 24.9 - - + -
892B LEU* 4.0 15.5 - - + -
896B ILE* 4.0 23.1 - - + -
918B PRO* 4.1 14.6 - - + -
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Residues in contact with ASN 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A LEU* 3.0 38.8 + - - +
890A TYR* 3.7 6.9 - - - +
892A LEU* 1.3 75.6 - - - +
894A THR* 1.3 63.7 + - - +
896A ILE* 3.5 6.6 + - - +
897A GLN* 3.1 42.8 + - - +
914B ALA 4.3 6.4 - - - +
915B ALA 5.0 4.3 + - - +
918B PRO* 3.4 27.4 - - - +
919B LYS* 4.7 8.9 + - - +
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Residues in contact with THR 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A T98 3.4 27.8 - - - -
715A LEU* 4.5 8.0 - - + +
890A TYR* 2.8 36.9 + - - -
893A ASN* 1.3 79.9 - - - +
895A PHE* 1.3 56.2 + - - +
897A GLN 3.2 1.7 + - - -
898A SER* 2.8 31.4 + - - -
901A LEU* 4.1 22.8 - - + +
903A VAL* 4.2 18.2 - - + -
905A PHE* 3.9 9.6 - - + -
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Residues in contact with PHE 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A CYS 2.9 17.9 + - - +
892A LEU* 3.5 12.3 - - + +
894A THR* 1.3 74.9 - - - +
896A ILE* 1.3 70.1 + - + +
898A SER* 3.2 20.8 + - - -
905A PHE* 3.5 35.8 - + + -
910A SER* 3.4 45.3 - - - -
913A ILE* 3.6 26.9 - - + -
914A ALA* 4.4 5.6 - - + -
896B ILE* 4.1 25.4 - - + -
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Residues in contact with ILE 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU* 2.8 31.4 + - + +
893A ASN* 3.5 5.4 - - - +
895A PHE* 1.3 82.2 - - + +
897A GLN* 1.3 62.1 + - + +
898A SER 3.7 0.5 + - - -
899A ARG 5.4 0.2 + - - -
892B LEU* 4.4 17.3 - - + -
895B PHE* 4.0 23.8 - - + -
896B ILE* 3.5 33.0 - - + -
914B ALA* 3.6 40.7 - - + +
918B PRO* 4.5 6.5 - - + -
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Residues in contact with GLN 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A ASN* 3.1 33.2 + - - +
894A THR 3.2 2.7 + - - -
896A ILE* 1.3 86.3 - - + +
898A SER* 1.3 54.0 + - - +
899A ARG 3.4 2.5 - - - -
900A ALA* 3.1 13.3 + - + -
901A LEU* 2.8 61.4 + - + +
914B ALA* 4.0 21.7 - - + +
915B ALA* 5.4 1.4 - - - -
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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
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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) + - + + + + + -
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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