Contacts of the helix formed by residues 885 - 912 (chain A) in PDB entry 4C3I
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 885 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A GLU 3.7 3.6 + - - +
882A ILE 2.9 20.1 + - - +
883A LEU 4.6 1.6 - - - -
884A ARG* 1.3 79.1 - - - +
886A ASN* 1.3 62.4 + - - +
887A ASN* 3.3 15.9 + - - +
888A LYS* 3.0 59.2 + - + +
889A SER* 3.1 18.5 + - - -
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Residues in contact with ASN 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A ARG 4.2 1.4 + - - -
885A ASP* 1.3 73.7 + - - +
887A ASN* 1.3 62.5 + - - +
889A SER* 4.7 0.4 - - - -
890A GLY 3.4 1.6 + - - -
955A ARG* 2.8 53.3 + - - +
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Residues in contact with ASN 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ASP* 3.3 13.9 + - - +
886A ASN* 1.3 79.8 - - - +
888A LYS* 1.4 69.4 + - - +
890A GLY* 3.0 12.9 + - - -
891A ILE* 3.2 34.0 + - - +
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Residues in contact with LYS 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A VAL* 4.7 2.8 - - - +
881A GLU* 3.6 47.3 - - + +
882A ILE* 3.5 28.3 - - + +
885A ASP* 3.0 34.5 + - + +
887A ASN* 1.4 77.7 - - - +
889A SER* 1.4 61.1 + - - +
891A ILE* 3.3 12.6 + - + +
892A LEU* 3.2 17.0 + - - +
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Residues in contact with SER 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ILE* 2.7 31.7 + - - +
883A LEU* 3.8 11.4 + - - +
885A ASP 3.1 13.6 + - - -
887A ASN 3.3 0.2 - - - -
888A LYS* 1.4 74.4 - - - +
890A GLY* 1.3 53.5 + - - +
892A LEU* 3.3 5.8 + - - +
893A ASP* 2.8 41.2 + - - +
955A ARG* 3.3 22.2 - - - -
959A VAL* 5.6 4.7 - - - +
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Residues in contact with GLY 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A ASN 3.4 5.4 + - - -
887A ASN* 3.0 9.4 + - - -
889A SER* 1.3 76.0 - - - +
891A ILE* 1.4 60.3 + - - +
893A ASP* 3.4 4.0 + - - +
894A ALA* 3.0 32.8 + - - +
955A ARG* 3.4 24.7 - - - +
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Residues in contact with ILE 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A VAL* 4.1 16.6 - - + -
887A ASN* 3.2 37.2 + - - +
888A LYS* 3.3 10.3 + - + +
890A GLY* 1.4 73.8 - - - +
892A LEU* 1.4 62.8 + - - +
894A ALA* 3.7 3.7 + - - +
895A VAL* 3.2 39.3 + - + +
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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
----------------------------------------------------------
858A ALA* 4.1 28.3 - - + +
861A VAL* 3.8 22.3 - - + +
879A LEU* 4.2 19.5 - - + -
882A ILE* 3.8 31.6 - - + -
888A LYS 3.2 5.4 + - - +
889A SER* 3.3 9.6 + - - +
891A ILE* 1.4 72.5 - - - +
893A ASP* 1.3 64.2 + - - +
895A VAL* 4.1 1.2 - - - +
896A THR* 2.7 36.9 + - - +
956A ARG* 3.8 22.0 - - - +
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Residues in contact with ASP 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A SER* 2.8 24.5 + - - +
890A GLY* 3.8 4.7 - - - +
892A LEU* 1.3 77.4 - - - +
894A ALA* 1.4 56.2 + - - +
896A THR* 3.9 1.0 - - - -
897A SER* 2.9 36.8 + - - -
955A ARG* 3.4 37.0 + - + +
956A ARG* 2.9 53.7 + - + +
957A VAL 5.3 2.4 - - - +
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Residues in contact with ALA 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A GLY 3.0 18.6 + - - +
891A ILE* 4.1 4.3 - - - +
893A ASP* 1.4 75.8 - - - +
895A VAL* 1.4 62.9 + - + +
897A SER* 4.0 5.1 - - - -
898A SER* 3.2 24.8 + - - -
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Residues in contact with VAL 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A ALA* 4.0 9.0 - - + +
860A GLU* 3.7 23.8 - - - +
861A VAL* 3.7 25.4 - - + -
891A ILE* 3.2 27.6 + - + +
892A LEU 4.1 0.2 - - - +
893A ASP 3.3 0.2 - - - -
894A ALA* 1.4 73.7 - - + +
896A THR* 1.4 63.2 + - - +
898A SER* 2.7 22.6 + - - +
899A LYS* 3.2 26.7 + - - +
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Residues in contact with THR 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A THR* 4.8 0.9 - - + +
854A GLY* 4.5 20.0 - - - +
857A ALA* 3.5 28.2 - - + +
858A ALA* 4.7 0.7 + - - +
892A LEU* 2.7 31.9 + - - +
893A ASP 4.0 2.0 - - - -
895A VAL* 1.4 75.2 - - - +
897A SER* 1.4 56.6 + - - +
899A LYS* 3.4 2.8 + - - +
900A VAL* 3.0 40.8 + - + +
949A GLN* 5.8 0.7 - - - +
956A ARG* 3.5 32.5 + - - +
976A ALA* 5.4 2.0 - - - -
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Residues in contact with SER 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A ASP 2.9 24.6 + - - -
894A ALA* 4.0 5.8 - - - -
896A THR* 1.4 74.9 - - - +
898A SER* 1.4 53.2 + - - +
900A VAL* 3.2 10.6 + - - +
901A ASN* 2.8 51.7 + - - +
949A GLN* 3.9 9.9 - - - +
955A ARG 5.2 2.6 - - - -
956A ARG* 3.4 21.3 + - - +
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Residues in contact with SER 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A ALA 3.2 13.6 + - - -
895A VAL* 2.7 23.9 + - - +
897A SER* 1.4 76.9 - - - +
899A LYS* 1.3 58.7 + - - +
901A ASN* 4.0 6.9 - - - +
902A ALA* 3.2 26.3 + - - +
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Residues in contact with LYS 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A THR* 3.7 21.7 - - + +
856A GLU* 5.0 6.3 - - + -
857A ALA* 3.8 24.5 - - + +
860A GLU* 3.0 37.1 + - - -
895A VAL* 3.2 25.9 + - - +
896A THR* 3.7 3.8 - - - +
898A SER* 1.3 81.9 + - - +
900A VAL* 1.4 63.0 + - - +
902A ALA* 3.4 14.0 - - - +
903A ILE* 3.4 18.5 - - - +
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Residues in contact with VAL 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A SER* 5.1 0.7 - - - +
853A THR* 3.8 18.6 - - + -
854A GLY 5.3 0.2 - - - +
896A THR* 3.0 30.7 + - + +
897A SER* 3.3 15.7 - - - +
899A LYS* 1.4 73.3 - - - +
901A ASN* 1.4 57.7 + - - +
903A ILE* 3.1 8.8 + - + +
904A THR* 3.0 28.9 + - - -
949A GLN* 3.9 19.1 - - + +
976A ALA* 3.8 28.9 - - + -
981A TYR* 3.3 32.3 + - + -
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Residues in contact with ASN 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A SER* 2.8 40.4 + - - +
898A SER* 4.0 7.6 - - - +
900A VAL* 1.4 71.7 - - - +
902A ALA* 1.3 58.2 + - - +
903A ILE 3.3 0.2 - - - -
904A THR* 3.4 11.1 + - - +
905A SER* 2.9 29.3 + - - -
948A GLY* 5.5 0.2 - - - -
949A GLN* 3.7 27.7 + - - +
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Residues in contact with ALA 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A SER 3.2 14.9 + - - +
899A LYS* 3.4 13.9 - - - +
900A VAL 3.2 0.4 - - - -
901A ASN* 1.3 74.9 - - - +
903A ILE* 1.4 62.6 + - + +
905A SER* 2.7 21.8 + - - -
906A GLN* 3.2 26.7 + - - +
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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
----------------------------------------------------------
846A ILE* 3.7 29.2 - - + +
847A LEU* 4.7 2.5 - - - -
849A THR* 4.0 14.6 - - - +
850A SER* 4.0 14.8 - - - -
853A THR* 4.1 20.6 - - + +
899A LYS 3.4 16.2 - - - +
900A VAL* 3.1 12.0 + - - +
902A ALA* 1.4 76.6 - - + +
904A THR* 1.4 62.1 + - - +
906A GLN* 3.4 25.8 + - - +
907A VAL* 3.2 27.9 + - + +
981A TYR* 3.9 11.7 - - + +
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Residues in contact with THR 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A VAL 3.0 14.4 + - - -
901A ASN* 3.3 17.0 + - - +
903A ILE* 1.4 73.9 - - - +
905A SER* 1.4 62.6 + - - +
907A VAL* 3.0 15.0 + - - +
908A VAL* 3.1 25.1 + - + +
946A LEU* 3.8 28.7 - - + +
947A LEU 5.5 0.2 - - - -
948A GLY* 4.2 10.2 - - - -
981A TYR* 3.0 25.7 + - - -
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Residues in contact with SER 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A ASN 2.9 13.3 + - - -
902A ALA* 2.7 28.1 + - - -
904A THR* 1.4 74.6 - - - +
906A GLN* 1.4 56.7 + - - +
908A VAL* 3.5 7.6 + - - +
909A SER* 2.9 32.6 + - - -
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Residues in contact with GLN 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A ILE* 3.8 22.8 - - + +
849A THR* 5.4 0.7 + - - -
902A ALA* 3.2 25.3 + - - +
903A ILE* 3.4 27.6 - - - +
904A THR 3.2 0.8 - - - -
905A SER* 1.4 78.7 + - - +
907A VAL* 1.4 65.3 + - - +
909A SER* 3.4 5.6 + - - -
910A LYS* 3.1 25.8 + - - +
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Residues in contact with VAL 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A ARG* 4.0 24.2 - - + +
846A ILE* 3.7 29.6 - - + +
847A LEU* 4.0 25.1 - - + -
903A ILE 3.2 15.7 - - - +
904A THR 3.0 6.7 + - - +
906A GLN* 1.4 74.8 - - - +
908A VAL* 1.4 54.3 + - - +
910A LYS* 3.8 0.3 - - - +
911A CYS* 2.9 44.6 + - - +
945A CYS* 3.9 14.4 - - + -
946A LEU* 3.8 20.0 - - + -
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Residues in contact with VAL 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A THR* 3.1 30.0 + - + +
905A SER* 3.8 6.3 - - - +
907A VAL* 1.4 74.0 - - - +
909A SER* 1.4 57.1 + - - +
912A VAL* 2.9 39.3 + - + +
937A ASN* 5.0 5.6 - - + +
941A SER* 3.7 36.6 - - - +
945A CYS* 4.3 16.4 - - + -
946A LEU* 4.7 2.9 - - + +
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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
----------------------------------------------------------
905A SER 2.9 19.4 + - - -
906A GLN* 3.8 6.1 - - - -
908A VAL* 1.4 76.5 - - - +
910A LYS* 1.3 62.2 + - - +
912A VAL 3.7 11.3 - - - +
913A PRO* 5.3 0.7 - - - +
914A ASP* 5.2 4.5 - - - +
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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
----------------------------------------------------------
842A TRP* 3.6 71.0 - - + +
846A ILE* 3.8 16.6 - - + -
906A GLN 3.1 17.6 + - - +
909A SER* 1.3 79.8 - - - +
911A CYS* 1.3 62.4 + - - +
912A VAL 3.7 0.2 + - - -
914A ASP* 3.9 13.2 + - - +
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Residues in contact with CYS 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LEU* 4.2 10.5 - - + -
839A GLY 3.4 23.3 - - - +
842A TRP* 4.1 8.5 - - - -
843A ARG* 3.7 30.3 - - - -
846A ILE* 5.1 0.2 - - - -
907A VAL* 2.9 26.4 + - - +
910A LYS* 1.3 75.5 - - - +
912A VAL* 1.3 58.8 + - - +
915A GLY* 2.9 28.9 + - - +
916A THR* 3.4 10.4 + - - +
945A CYS* 3.8 16.8 - - - -
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Residues in contact with VAL 912 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A TYR* 5.6 1.3 - - - +
835A LEU* 5.1 0.7 - - + -
908A VAL* 2.9 27.8 + - + +
909A SER* 3.7 12.3 - - - +
910A LYS 4.7 0.2 - - - -
911A CYS* 1.3 81.0 - - - +
913A PRO* 1.4 67.5 - - + +
914A ASP 3.7 0.7 - - - -
916A THR* 4.1 12.6 - - + -
926A GLN* 3.9 16.2 - - - +
937A ASN* 5.1 16.6 - - + +
940A VAL* 4.3 23.6 - - + -
941A SER* 5.1 4.3 - - - -
944A MET* 4.8 6.7 - - + -
945A CYS* 3.8 23.6 - - - -
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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