Contacts of the helix formed by residues 865 - 898 (chain A) in PDB entry 4K6J
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 ASN 865 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A ASP* 5.2 7.3 - - - -
812A LYS* 4.1 14.0 - - + +
813A GLU* 2.9 24.4 + - - +
816A ARG* 3.3 6.8 + - - -
861A VAL 3.3 17.5 - - - +
862A THR 3.3 3.8 + - - +
863A VAL 3.0 7.2 + - - +
864A HIS* 1.3 79.5 + - - +
866A PRO* 1.3 68.3 - - - +
867A GLU* 3.5 4.3 - - - +
868A ASN* 2.8 45.6 + - - +
869A GLN* 3.1 25.2 + - - +
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Residues in contact with PRO 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A HIS* 3.6 7.9 - - - +
865A ASN* 1.3 88.6 - - - +
867A GLU* 1.3 57.8 + - + +
869A GLN* 3.2 20.4 + - - +
870A SER* 2.8 32.2 + - - -
944A ASN* 5.2 1.4 + - - -
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Residues in contact with GLU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A GLU* 4.9 4.4 - - - +
816A ARG* 3.3 41.8 + - - +
865A ASN* 3.2 4.4 - - - +
866A PRO* 1.3 79.8 - - + +
868A ASN* 1.3 58.1 + - - +
870A SER* 3.1 8.3 + - - -
871A TYR* 2.8 29.5 + - - +
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Residues in contact with ASN 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A LYS 3.0 22.8 + - - -
816A ARG* 2.7 39.9 + - - +
821A LEU* 3.6 9.9 - - + +
861A VAL* 2.7 39.9 + - + +
862A THR* 3.9 8.3 - - + -
865A ASN* 2.8 27.9 + - - +
867A GLU* 1.3 70.1 - - - +
869A GLN* 1.3 65.6 + - - +
871A TYR* 3.8 4.2 - - - +
872A LEU* 3.0 30.0 + - - +
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Residues in contact with GLN 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A THR* 2.9 33.8 + - + +
864A HIS* 4.6 3.0 - - - +
865A ASN 3.1 19.7 + - - +
866A PRO* 3.2 17.3 + - - +
868A ASN* 1.3 76.5 - - - +
870A SER* 1.3 62.1 + - - +
872A LEU 3.4 0.2 + - - -
873A ILE* 3.0 37.2 + - + +
939A ASN* 3.3 26.5 + - - +
940A LEU* 3.7 16.3 - - + +
942A ASN* 6.1 2.0 - - - +
943A ASP* 5.2 6.8 + - - +
944A ASN* 4.4 18.4 + - + +
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Residues in contact with SER 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A PRO 2.8 17.5 + - - -
867A GLU* 3.4 7.4 - - - -
869A GLN* 1.3 78.7 - - - +
871A TYR* 1.3 61.2 + - - +
873A ILE* 3.2 5.8 + - - +
874A ALA* 3.1 24.8 + - - +
944A ASN* 4.3 15.8 + - - +
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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
----------------------------------------------------------
816A ARG* 3.8 43.1 + - + -
819A GLY* 5.3 0.7 - - - -
821A LEU* 4.5 18.2 - - + -
822A ASP* 2.5 38.3 + - - -
867A GLU 2.8 19.3 + - - +
868A ASN* 3.8 6.1 - - - +
870A SER* 1.3 74.7 - - - +
872A LEU* 1.3 64.2 + - + +
874A ALA* 3.3 5.3 + - + +
875A TYR* 2.9 43.4 + + + +
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Residues in contact with LEU 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A LEU* 4.2 20.9 - - + -
825A VAL* 3.5 31.9 - - + -
858A LEU* 4.1 24.9 - - + +
861A VAL* 4.5 6.1 - - + -
862A THR* 3.6 22.2 - - + -
868A ASN 3.0 22.0 + - - +
869A GLN 4.0 3.1 - - - +
871A TYR* 1.3 79.9 - - + +
873A ILE* 1.3 62.1 + - - +
874A ALA 3.3 0.2 - - - -
875A TYR* 4.2 9.6 + - + +
878A SER* 4.6 5.7 - - - -
880A LEU* 3.9 39.0 - - + +
881A ILE* 5.1 1.2 + - - +
936A VAL* 5.9 0.4 - - + -
940A LEU* 4.3 8.3 - - + +
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Residues in contact with ILE 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A GLN 3.0 24.3 + - - +
870A SER* 3.2 5.4 + - - +
872A LEU* 1.3 80.8 - - - +
874A ALA* 1.3 57.6 + - - +
878A SER* 2.3 41.0 + - - +
881A ILE* 4.2 12.8 - - + -
940A LEU* 3.7 20.0 - - + +
944A ASN* 3.4 38.1 - - + +
946A TRP* 4.3 12.1 - - + +
947A GLY* 3.6 29.4 - - - +
950A LYS* 4.8 2.5 - - + -
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Residues in contact with ALA 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A SER* 3.1 16.3 + - - +
871A TYR* 3.9 5.4 - - + +
873A ILE* 1.3 78.9 - - - +
875A TYR* 1.3 67.6 + - - +
876A LYS 3.3 1.9 + - - -
877A ASP* 3.3 12.0 + - - -
878A SER 3.5 2.3 + - - -
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Residues in contact with TYR 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A ASP* 3.2 45.2 + - - +
825A VAL* 3.6 42.2 - - + -
826A ASP* 2.7 34.2 + - - -
871A TYR* 2.9 33.4 + + + +
872A LEU* 4.2 9.4 + - + +
873A ILE 3.6 0.8 - - - -
874A ALA* 1.3 74.7 - - - +
876A LYS* 1.3 104.8 + - + +
878A SER* 2.9 13.0 + - - -
879A GLN 3.1 10.0 + - - -
880A LEU 4.8 0.6 + - - -
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Residues in contact with LYS 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ASP* 3.8 14.7 + - - +
829A LYS* 6.2 1.8 - - + -
874A ALA 3.3 1.0 + - - -
875A TYR* 1.3 110.5 + - + +
877A ASP* 1.3 74.5 + - - +
879A GLN* 3.1 33.7 + - + +
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Residues in contact with ASP 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A ALA 3.3 6.7 + - - -
875A TYR 3.3 1.0 - - - -
876A LYS* 1.3 78.8 - - - +
878A SER* 1.3 70.0 + - - +
879A GLN* 4.3 0.3 - - - -
882A VAL* 4.1 9.2 - - - +
950A LYS* 4.8 5.9 - - - +
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Residues in contact with SER 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LEU 4.6 2.9 - - - -
873A ILE* 2.3 37.8 + - - +
874A ALA 3.5 5.9 + - - -
875A TYR 2.9 7.5 + - - -
877A ASP* 1.3 78.4 - - - +
879A GLN* 1.3 63.7 + - - +
880A LEU 3.2 3.1 - - - +
881A ILE* 3.3 9.2 + - - +
882A VAL* 3.0 25.2 + - - +
950A LYS* 3.3 38.4 - - - +
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Residues in contact with GLN 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A VAL* 4.1 16.8 - - + -
826A ASP* 5.4 1.3 - - - +
829A LYS* 3.6 41.0 - - + +
875A TYR 3.1 4.9 + - - +
876A LYS* 3.1 38.7 + - + +
877A ASP 4.3 0.9 - - - -
878A SER* 1.3 76.2 - - - +
880A LEU* 1.3 57.9 + - - +
882A VAL* 4.4 12.7 - - - +
883A SER* 2.8 58.5 + - - +
886A LYS* 5.9 1.4 - - - +
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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
----------------------------------------------------------
825A VAL* 4.0 19.0 - - + +
828A VAL* 4.3 12.6 - - + -
855A LEU* 4.1 12.6 - - + -
858A LEU* 3.6 32.8 - - + -
872A LEU* 3.9 42.1 + - + +
875A TYR* 4.8 0.8 + - + -
878A SER 3.2 0.6 - - - -
879A GLN* 1.3 78.6 - - - +
881A ILE* 1.3 54.9 + - + +
883A SER* 3.8 2.3 - - - -
884A SER* 2.6 48.9 + - - +
936A VAL* 3.8 21.8 - - + -
937A LEU* 6.4 0.2 - - + -
940A LEU* 4.0 8.1 - - + -
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Residues in contact with ILE 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LEU 5.3 1.1 - - - +
873A ILE* 4.2 18.6 - - + -
878A SER* 3.3 21.5 + - - +
879A GLN 3.3 0.2 - - - -
880A LEU* 1.3 77.3 - - + +
882A VAL* 1.3 68.0 + - - +
884A SER* 3.7 6.0 - - - -
885A ALA* 3.0 24.5 + - + +
937A LEU* 4.3 6.6 - - + +
940A LEU* 3.7 29.2 - - + -
947A GLY* 4.0 9.2 - - - +
950A LYS* 3.9 12.1 - - + +
951A THR* 3.4 44.4 - - + +
954A GLN* 3.8 12.3 - - + +
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Residues in contact with VAL 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A ASP 4.1 11.4 - - - +
878A SER* 3.0 22.9 + - - +
879A GLN* 3.7 15.5 - - - +
881A ILE* 1.3 77.9 - - - +
883A SER* 1.3 62.0 + - - +
885A ALA* 3.6 2.6 + - - +
886A LYS* 3.3 46.2 + - - +
950A LYS* 5.8 2.0 - - - -
954A GLN* 3.4 32.5 - - - +
----------------------------------------------------------
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Residues in contact with SER 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A VAL 6.0 0.2 - - - -
828A VAL* 4.4 12.8 - - - -
829A LYS* 3.7 24.9 - - - +
832A VAL* 3.5 16.8 - - - +
833A ASP* 5.3 1.2 + - - -
879A GLN* 2.8 39.6 + - - -
880A LEU* 3.9 3.4 - - - -
882A VAL* 1.3 74.7 - - - +
884A SER* 1.3 59.7 + - - +
886A LYS* 3.4 5.3 + - - +
887A ALA* 2.9 31.8 + - - +
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Residues in contact with SER 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A VAL* 5.2 1.8 - - - +
832A VAL* 5.7 0.2 - - - -
855A LEU* 4.2 11.7 - - - +
880A LEU* 2.6 40.1 + - - +
881A ILE 3.7 4.3 - - - -
883A SER* 1.3 77.4 - - - +
885A ALA* 1.3 55.7 + - - +
887A ALA* 3.3 5.2 + - - +
888A LEU* 2.9 25.6 + - - +
933A ILE* 3.4 24.5 + - - +
936A VAL* 4.8 2.9 - - - +
937A LEU* 4.0 23.7 - - - +
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Residues in contact with ALA 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A ILE* 3.0 16.3 + - + +
882A VAL 3.9 3.1 - - - +
884A SER* 1.3 74.0 - - - +
886A LYS* 1.3 66.0 + - + +
888A LEU* 3.3 4.0 + - - +
889A GLN* 3.2 23.7 + - - +
937A LEU* 5.1 0.4 - - + +
954A GLN* 3.5 33.4 - - + +
955A ASP 5.4 3.8 - - - +
957A LEU* 3.6 29.9 - - + +
960A THR* 5.4 0.9 + - - +
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Residues in contact with LYS 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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832A VAL* 4.3 10.3 - - + -
833A ASP* 5.1 11.0 + - - +
879A GLN* 5.9 0.8 - - - +
882A VAL* 3.3 35.5 + - + +
883A SER* 3.7 9.6 - - - +
885A ALA* 1.3 76.5 - - + +
887A ALA* 1.3 63.7 + - - +
889A GLN* 3.0 9.5 + - - +
890A HIS* 2.9 35.5 + - + +
----------------------------------------------------------
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Residues in contact with ALA 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A VAL* 3.5 28.2 - - + +
835A LEU* 4.4 12.7 - - + +
855A LEU* 6.0 0.4 - - + -
883A SER 2.9 18.4 + - - +
884A SER* 3.6 6.5 - - - +
886A LYS* 1.3 77.3 - - - +
888A LEU* 1.3 56.6 + - - +
889A GLN 3.2 0.2 + - - -
890A HIS* 3.2 3.3 + - - +
891A CYS* 2.9 33.3 + - - +
929A CYS* 5.4 2.2 - - - -
933A ILE* 3.6 19.1 - - + -
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Residues in contact with LEU 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A SER 2.9 17.8 + - - +
885A ALA* 3.7 6.5 - - - +
886A LYS 3.3 0.2 - - - -
887A ALA* 1.3 76.4 - - - +
889A GLN* 1.3 57.9 + - - +
891A CYS* 3.5 3.9 + - - +
892A GLU* 3.0 26.5 + - - +
930A MET* 4.0 22.0 - - + +
933A ILE* 3.8 17.6 - - + +
934A ILE* 3.8 31.4 - - + -
937A LEU* 4.8 6.1 - - + -
957A LEU* 4.1 18.8 - - + -
960A THR* 3.7 20.9 - - + -
961A ALA* 4.7 8.3 - - - +
964A CYS* 4.2 13.2 - - - -
987A LEU* 4.9 4.3 - - + -
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Residues in contact with GLN 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ALA 3.2 12.2 + - - +
886A LYS* 3.0 13.3 + - - +
888A LEU* 1.3 74.9 - - - +
890A HIS* 1.3 67.7 + - + +
892A GLU* 3.1 18.4 + - - +
893A GLU* 3.2 28.9 + - - +
955A ASP 3.6 19.0 + - - +
956A GLY* 3.9 7.9 - - - +
957A LEU* 4.7 0.5 + - - -
960A THR* 3.4 26.3 + - - +
----------------------------------------------------------
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Residues in contact with HIS 890 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A VAL* 4.1 7.1 + - + +
835A LEU* 3.6 34.2 - - + +
836A SER* 3.3 45.8 + - - -
886A LYS* 2.9 27.8 + - + -
887A ALA* 3.6 7.1 + - - +
889A GLN* 1.3 76.0 - - + +
891A CYS* 1.3 51.6 + - - +
893A GLU* 3.0 20.6 + - - +
894A LEU* 2.7 44.9 + - + +
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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
----------------------------------------------------------
835A LEU* 5.2 2.9 - - - -
848A LEU* 3.9 28.5 - - - -
887A ALA 2.9 20.1 + - - +
888A LEU* 3.5 3.6 - - - +
890A HIS* 1.3 74.5 - - - +
892A GLU* 1.3 65.4 + - - +
894A LEU* 4.3 2.5 - - - -
895A ILE* 2.9 28.4 + - - +
926A VAL* 3.6 24.6 - - + +
929A CYS* 4.2 13.9 - - - -
930A MET* 3.5 26.0 - - + -
933A ILE* 4.2 3.4 - - - -
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Residues in contact with GLU 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LEU 3.0 15.7 + - - +
889A GLN* 3.1 15.4 + - - +
891A CYS* 1.3 75.7 - - - +
893A GLU* 1.3 63.9 + - + +
895A ILE* 3.2 23.3 - - - +
896A GLN* 3.5 19.7 + - - +
930A MET* 4.7 2.2 - - - -
960A THR* 3.4 28.5 + - + +
963A ASN* 2.7 44.0 + - + +
964A CYS* 5.5 0.7 - - - -
967A GLN* 5.3 2.4 - - + +
968A VAL* 4.4 19.6 - - + +
----------------------------------------------------------
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Residues in contact with GLU 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A GLN* 3.2 31.0 + - + +
890A HIS* 3.0 22.6 + - - +
892A GLU* 1.3 81.5 - - + +
894A LEU* 1.3 66.6 + - + +
895A ILE 3.2 0.2 - - - -
896A GLN* 3.2 28.4 + - - +
897A GLN* 3.6 4.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LEU* 4.4 17.5 - - + +
844A LEU* 3.7 39.7 - - + -
848A LEU* 4.6 5.2 - - + -
890A HIS* 2.7 31.6 + - + +
891A CYS* 3.9 4.5 - - - +
893A GLU* 1.3 74.2 - - + +
895A ILE* 1.3 57.3 + - - +
897A GLN* 2.9 29.3 + - + +
898A TYR* 3.2 20.8 - - + -
926A VAL* 4.1 23.6 - - + -
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Residues in contact with ILE 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 14.6 + - - +
892A GLU* 3.2 21.8 - - - +
894A LEU* 1.3 77.5 - - - +
896A GLN* 1.3 68.3 + - + +
898A TYR* 3.3 19.7 + - - +
899A ASN 3.5 1.7 + - - -
900A ARG* 4.3 3.4 - - - +
923A GLY* 3.8 27.1 - - - +
926A VAL* 4.0 15.5 - - + +
927A GLU* 4.3 4.7 - - + +
930A MET* 5.2 3.6 - - - -
968A VAL* 4.3 21.8 - - + -
971A TYR* 3.7 22.4 - - + +
972A LEU* 3.7 32.5 - - + -
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Residues in contact with GLN 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A GLU* 3.5 27.9 + - - +
893A GLU* 3.5 15.9 - - - +
894A LEU 3.2 0.2 - - - -
895A ILE* 1.3 78.5 - - + +
897A GLN* 1.3 61.3 + - - +
898A TYR 3.3 0.7 + - - -
899A ASN* 3.8 12.1 + - - +
906A CYS* 5.0 0.9 - - - -
911A LYS* 4.0 21.0 + - - +
967A GLN* 6.3 1.2 - - - +
971A TYR* 3.5 52.0 + - + -
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Residues in contact with GLN 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A GLU 3.6 2.8 + - - +
894A LEU* 2.9 21.9 + - + +
896A GLN* 1.3 80.6 - - - +
898A TYR* 1.3 82.1 + - + +
899A ASN 3.7 1.0 + - - -
910A SER* 3.9 13.2 + - - -
911A LYS* 3.9 26.6 - - - +
912A PRO* 3.5 33.2 - - - +
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Residues in contact with TYR 898 (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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839A GLU 5.7 1.0 + - - -
841A GLU* 5.7 3.0 + - + -
844A LEU* 3.9 17.2 - - + +
894A LEU* 3.2 27.3 + - + +
895A ILE* 3.3 10.2 + - - +
896A GLN 3.2 0.4 - - - -
897A GLN* 1.3 104.4 + - + +
899A ASN* 1.3 64.6 + - - +
900A ARG* 3.5 18.4 + - - +
912A PRO* 4.0 23.3 - - + -
918A VAL* 4.4 12.6 - - + -
919A THR* 4.0 11.0 - - + +
922A VAL* 3.7 43.1 - - + +
923A GLY* 3.9 19.9 - - - +
926A VAL* 5.1 0.4 - - + -
971A TYR 4.5 1.0 - - - +
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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) + - + + + + + -
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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