Contacts of the helix formed by residues 882 - 910 (chain A) in PDB entry 5QSY
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 ASP 882 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826A GLN* 2.8 16.9 + - + +
830A LEU* 4.5 6.7 - - + +
879A ASP* 4.7 3.1 - - - +
881A VAL* 1.3 72.8 - - - +
883A MET* 1.3 66.6 + - - +
884A HIS* 3.4 17.6 + - - +
885A ALA* 3.4 30.4 + - + +
886A ALA* 3.4 19.9 + - - +
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Residues in contact with MET 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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876A ILE* 3.7 40.2 - - + +
877A ILE* 5.1 5.4 - - - +
879A ASP* 3.3 30.2 + - + +
881A VAL 3.0 5.8 + - - -
882A ASP* 1.3 72.6 + - - +
884A HIS* 1.3 81.9 + - + +
886A ALA* 3.5 3.3 - - - +
887A ALA* 3.0 28.2 + - - +
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Residues in contact with HIS 884 (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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882A ASP* 3.2 13.0 + - - +
883A MET* 1.3 97.3 - - + +
885A ALA* 1.3 66.6 + - - +
886A ALA 3.1 1.5 + - - -
887A ALA* 3.2 8.0 + - + +
888A ASP* 3.0 31.9 + - - +
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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
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830A LEU* 4.0 15.7 - - + +
882A ASP* 3.4 27.6 + - + +
884A HIS* 1.3 76.5 - - - +
886A ALA* 1.3 61.7 + - - +
888A ASP* 3.6 12.9 + - - +
889A ILE* 3.3 27.7 + - - +
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Residues in contact with ALA 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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830A LEU* 3.9 12.3 - - + +
872A PHE* 4.3 10.3 - - + -
876A ILE* 3.8 34.3 - - + -
882A ASP 3.4 12.9 + - - +
883A MET 3.5 9.6 - - - +
884A HIS 3.1 0.6 - - - -
885A ALA* 1.3 77.2 - - - +
887A ALA* 1.3 61.1 + - - +
889A ILE* 3.0 8.1 + - - +
890A PHE* 3.0 32.3 + - + -
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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
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883A MET 3.0 17.1 + - - +
884A HIS* 3.2 7.8 + - + +
886A ALA* 1.3 74.3 - - - +
888A ASP* 1.3 53.1 + - - +
890A PHE* 2.9 17.2 + - + +
891A LYS* 2.6 37.7 + - - +
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Residues in contact with ASP 888 (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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884A HIS* 3.0 27.7 + - - +
885A ALA* 3.6 10.9 - - - +
886A ALA 3.2 0.2 - - - -
887A ALA* 1.3 77.6 - - - +
889A ILE* 1.3 61.2 + - + +
891A LYS* 3.4 14.9 + - + +
892A HIS* 3.0 28.2 + - - +
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Residues in contact with ILE 889 (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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830A LEU* 3.9 18.8 - - + -
833A VAL* 4.8 5.4 - - + -
834A MET* 3.5 36.6 - - + -
838A PHE* 4.3 14.4 - - + -
885A ALA 3.3 14.6 + - - +
886A ALA 3.0 8.8 + - - +
888A ASP* 1.3 81.0 - - + +
890A PHE* 1.3 63.9 + - + +
892A HIS* 3.2 7.5 + - + +
893A TYR* 3.0 49.8 + - + -
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Residues in contact with PHE 890 (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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833A VAL* 4.7 4.9 - - + -
838A PHE* 3.9 26.5 - + - -
869A LEU* 3.7 34.5 - - + -
872A PHE* 4.7 3.8 - + - -
873A SER* 5.2 3.1 - - - -
876A ILE* 3.8 32.3 - - + -
886A ALA* 3.0 19.8 + - + -
887A ALA* 2.9 15.9 + - + +
889A ILE* 1.3 74.4 - - + +
891A LYS* 1.3 65.2 + - - +
893A TYR* 3.9 2.8 - - - -
894A MET* 3.0 36.3 + - + +
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Residues in contact with LYS 891 (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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887A ALA 2.6 16.9 + - - +
888A ASP* 3.5 18.2 - - - +
890A PHE* 1.3 70.8 - - - +
892A HIS* 1.3 85.0 + - + +
894A MET* 2.9 16.3 + - - +
895A LYS* 3.0 37.9 + - - +
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Residues in contact with HIS 892 (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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888A ASP 3.0 14.6 + - - +
889A ILE* 3.2 14.1 + - + +
891A LYS* 1.3 91.0 - - + +
893A TYR* 1.3 93.4 + + + +
895A LYS* 3.4 27.1 + - + +
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Residues in contact with TYR 893 (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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834A MET* 3.0 32.3 + - + +
838A PHE* 3.5 60.1 + + + -
889A ILE* 3.0 49.0 + - + +
890A PHE* 4.5 2.0 - - - +
892A HIS* 1.3 103.5 - + - +
894A MET* 1.3 70.3 + - + +
895A LYS 3.5 0.4 - - - -
896A TYR 5.3 0.5 + - - -
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Residues in contact with MET 894 (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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838A PHE* 4.8 13.0 - - + -
890A PHE* 3.0 27.4 + - + +
891A LYS* 2.9 6.5 + - - +
893A TYR* 1.3 103.7 - - + +
895A LYS* 1.3 66.8 + - - +
896A TYR 3.3 2.5 - - - -
897A TYR* 2.8 33.5 + - + +
898A ASN* 3.2 19.4 + - - +
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Residues in contact with LYS 895 (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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891A LYS* 3.0 35.8 + - - +
892A HIS* 3.4 24.9 + - + +
893A TYR 3.5 0.8 - - - -
894A MET* 1.3 73.4 - - - +
896A TYR* 1.3 72.3 + - + +
898A ASN* 2.8 13.2 + - - +
899A ASP* 2.7 57.8 + - - +
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Residues in contact with TYR 896 (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 TYR 5.3 0.6 + - - -
894A MET 3.1 1.0 + - - -
895A LYS* 1.3 99.8 + - + +
897A TYR* 1.3 60.5 + - - +
899A ASP* 4.1 1.1 - - + -
900A TYR* 3.3 52.3 + + + +
901A GLY* 3.8 2.8 + - - -
904A ILE* 4.7 4.7 - - - +
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Residues in contact with TYR 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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894A MET* 2.8 32.5 + - + +
896A TYR* 1.3 71.8 - - - +
898A ASN* 1.3 80.5 + - - +
901A GLY* 3.1 32.7 + - - +
902A ASP 4.5 0.5 + - - -
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Residues in contact with ASN 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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894A MET* 3.2 14.8 + - - +
895A LYS* 2.8 17.4 + - - +
897A TYR* 1.3 94.5 - - - +
899A ASP* 1.3 67.3 + - - +
900A TYR 3.5 0.3 + - - -
902A ASP* 4.3 9.0 - - - +
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Residues in contact with ASP 899 (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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895A LYS* 2.7 48.8 + - - +
898A ASN* 1.3 79.3 - - - +
900A TYR* 1.3 91.4 + - + +
902A ASP* 4.7 3.4 - - - +
903A ILE* 5.0 4.3 - - - +
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Residues in contact with TYR 900 (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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896A TYR* 3.3 45.2 + + + +
899A ASP* 1.3 106.9 + - + +
901A GLY* 1.3 60.0 + - - +
902A ASP* 3.5 6.3 - - - -
903A ILE* 3.3 20.0 + - + +
904A ILE* 3.0 38.4 + - + +
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Residues in contact with GLY 901 (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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896A TYR 3.8 1.7 + - - -
897A TYR* 3.1 36.3 + - - -
900A TYR* 1.3 75.5 - - - +
902A ASP* 1.3 58.2 + - - +
904A ILE* 3.2 11.8 + - - +
905A LYS* 2.7 37.3 + - - +
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Residues in contact with ASP 902 (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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897A TYR 4.5 1.4 + - - -
898A ASN 4.3 10.1 - - - +
899A ASP 4.7 1.7 - - - +
900A TYR* 3.8 4.2 - - - -
901A GLY* 1.3 78.4 + - - -
903A ILE* 1.3 74.2 + - - +
905A LYS* 3.2 8.8 + - - +
906A GLU* 3.2 27.5 + - - +
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Residues in contact with ILE 903 (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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899A ASP 5.0 4.5 - - - +
900A TYR* 3.3 23.5 + - + +
901A GLY 3.2 0.4 - - - -
902A ASP* 1.3 85.9 - - - +
904A ILE* 1.3 61.2 + - + +
906A GLU* 3.8 12.7 - - + +
907A THR* 2.4 41.1 + - - +
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Residues in contact with ILE 904 (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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896A TYR* 4.7 5.2 - - + +
897A TYR* 6.2 0.2 - - - -
900A TYR* 3.0 36.5 + - + +
901A GLY* 3.2 9.8 + - - +
903A ILE* 1.3 76.1 - - + +
905A LYS* 1.3 67.0 + - - +
907A THR* 3.7 6.8 + - - -
908A LEU* 3.1 42.2 + - + +
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Residues in contact with LYS 905 (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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901A GLY 2.7 21.1 + - - +
902A ASP* 3.2 10.7 + - - +
904A ILE* 1.3 74.5 - - - +
906A GLU* 1.3 63.4 + - - +
908A LEU* 3.1 8.7 + - - +
909A SER* 3.1 21.2 + - - -
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Residues in contact with GLU 906 (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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902A ASP 3.2 14.9 + - - +
903A ILE* 3.8 13.8 - - + +
905A LYS* 1.3 78.3 - - - +
907A THR* 1.3 68.2 + - - +
909A SER* 3.3 24.7 + - - +
910A LYS* 3.4 28.3 + - - +
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Residues in contact with THR 907 (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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903A ILE* 2.4 34.9 + - - +
904A ILE* 3.7 8.0 - - - -
906A GLU* 1.3 78.9 - - - +
908A LEU* 1.3 62.4 + - + +
909A SER 3.6 0.2 + - - -
910A LYS* 3.6 8.6 + - - +
911A THR* 3.6 18.3 - - + +
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Residues in contact with LEU 908 (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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904A ILE* 3.1 32.9 + - + +
905A LYS* 3.1 4.9 + - - +
907A THR* 1.3 80.4 - - + +
909A SER* 1.3 66.4 + - - +
911A THR* 3.4 30.5 + - + +
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Residues in contact with SER 909 (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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905A LYS* 3.1 12.7 + - - -
906A GLU* 3.3 15.5 + - - +
908A LEU* 1.3 78.2 - - - +
910A LYS* 1.3 67.3 + - - +
911A THR 3.1 12.0 + - - +
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Residues in contact with LYS 910 (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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906A GLU* 3.4 32.0 + - - +
907A THR* 3.6 5.2 + - - +
908A LEU 3.3 0.8 - - - -
909A SER* 1.3 85.3 + - - +
911A THR* 1.3 64.9 + - - +
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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