Contacts of the helix formed by residues 890 - 918 (chain A) in PDB entry 3MPX
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 GLN 890 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A UNX 3.9 11.6 - - - -
891A SER* 1.3 62.2 + - - +
892A ARG* 3.3 10.9 - - - +
893A ALA* 3.8 13.1 - - - +
894A LEU* 3.1 25.8 + - - +
970A TRP* 4.8 4.3 + - - -
974A GLN* 6.0 5.1 - - - +
1056A ASN* 4.2 17.9 + - - +
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Residues in contact with SER 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A UNX 3.4 14.8 - - - -
890A GLN* 1.3 74.1 - - - +
892A ARG* 1.3 59.9 + - - +
894A LEU* 3.1 12.5 + - - +
895A VAL* 2.9 36.0 + - - +
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Residues in contact with ARG 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A UNX 3.7 20.2 - - - -
890A GLN 4.6 4.4 - - - +
891A SER* 1.3 80.5 - - - +
893A ALA* 1.4 59.7 + - - +
895A VAL* 3.6 6.3 + - - +
896A ILE* 3.2 29.8 + - + +
1056A ASN* 3.3 33.4 + - + +
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Residues in contact with ALA 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A GLN* 3.6 12.9 + - - +
891A SER 3.3 0.2 - - - -
892A ARG* 1.4 75.5 - - - +
894A LEU* 1.4 63.3 + - - +
896A ILE* 3.4 6.4 + - - +
897A ALA* 3.2 22.5 + - - +
970A TRP* 4.6 6.0 - - + -
1053A TYR* 3.8 30.0 - - + -
1056A ASN* 4.0 21.6 - - + +
1057A LEU* 4.4 13.0 - - + -
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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
----------------------------------------------------------
890A GLN 3.1 19.4 + - - +
891A SER* 3.1 11.2 + - - +
893A ALA* 1.4 76.0 - - - +
895A VAL* 1.3 62.5 + - + +
897A ALA* 3.3 3.3 + - - +
898A GLN* 3.1 50.5 + - + +
967A LEU* 4.3 7.2 - - + +
970A TRP* 3.4 48.9 - - + +
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Residues in contact with VAL 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A SER* 2.9 19.7 + - - +
892A ARG* 3.6 6.7 + - - +
893A ALA 3.4 0.2 - - - -
894A LEU* 1.3 76.9 - - + +
896A ILE* 1.3 57.1 + - + +
898A GLN* 3.4 21.6 + - - +
899A GLU* 2.8 34.6 + - + +
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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 ARG* 3.2 19.6 + - + +
893A ALA* 3.8 7.2 - - - +
894A LEU 3.3 0.8 - - - -
895A VAL* 1.3 78.6 - - + +
897A ALA* 1.4 54.6 + - - +
899A GLU* 3.1 14.6 + - - +
900A LEU* 2.8 32.9 + - + +
1049A LEU* 3.5 38.0 - - + +
1052A ASP* 3.3 39.0 - - + +
1053A TYR* 3.9 15.9 - - + +
1056A ASN* 3.5 11.0 - - - +
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Residues in contact with ALA 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A ALA 3.2 13.1 + - - +
894A LEU 3.7 7.4 - - - +
896A ILE* 1.4 73.7 - - - +
898A GLN* 1.3 57.1 + - - +
900A LEU* 3.2 13.2 + - - +
901A LEU 2.8 24.1 + - - -
967A LEU* 3.5 30.9 - - + +
970A TRP* 4.2 20.4 - - + -
976A VAL* 4.5 13.5 - - + -
1053A TYR* 4.8 2.6 - - + -
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Residues in contact with GLN 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 3.1 34.5 + - - +
895A VAL* 3.5 27.0 - - - +
897A ALA* 1.3 75.5 - - - +
899A GLU* 1.4 50.3 + - - +
901A LEU* 3.2 7.0 + - + +
902A SER* 2.8 37.2 + - - -
967A LEU* 3.7 17.3 - - + +
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Residues in contact with GLU 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A VAL* 2.8 21.0 + - + +
896A ILE* 3.1 19.3 + - - +
898A GLN* 1.4 71.0 - - - +
900A LEU* 1.3 53.3 + - - +
902A SER* 3.3 14.9 + - - +
903A SER* 2.7 29.7 + - - -
1049A LEU* 3.6 27.2 - - + +
1099A HIS* 5.1 13.4 + - - -
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Residues in contact with LEU 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A ILE* 2.8 14.5 + - + +
897A ALA* 3.2 10.3 + - - +
899A GLU* 1.3 76.0 - - - +
901A LEU* 1.4 58.9 + - - +
903A SER* 3.1 4.3 + - - -
904A GLU* 2.9 27.6 + - - +
963A LEU* 4.0 27.6 - - + -
976A VAL* 4.7 13.7 - - + -
980A PHE* 3.9 24.7 - - + -
1042A ARG* 3.2 17.4 + - - +
1046A TYR* 3.8 31.4 - - + -
1049A LEU* 3.9 22.9 - - + +
1050A LEU* 5.2 6.3 - - + -
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Residues in contact with LEU 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A ALA 2.8 16.2 + - - +
898A GLN* 3.7 5.8 - - - +
900A LEU* 1.4 74.0 - - - +
902A SER* 1.3 59.1 + - - +
904A GLU* 3.2 5.9 + - - +
905A LYS* 3.0 52.9 + - - +
960A LEU* 3.7 26.5 - - + -
963A LEU* 3.7 11.8 - - + +
964A GLU* 3.5 37.9 - - + +
967A LEU* 3.7 28.0 - - + -
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Residues in contact with SER 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A GLN 2.8 18.8 + - - -
899A GLU* 3.3 15.8 + - - +
901A LEU* 1.3 74.8 - - - +
903A SER* 1.4 57.5 + - - +
905A LYS* 3.4 19.0 - - - +
906A ALA* 3.3 21.3 + - - +
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Residues in contact with SER 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A GLU* 2.7 23.3 + - - -
900A LEU* 3.1 3.8 + - - -
902A SER* 1.4 76.4 + - - +
904A GLU* 1.3 63.9 + - - +
906A ALA* 3.5 8.0 + - - +
907A TYR* 3.1 22.9 + - - +
1042A ARG* 2.9 38.0 + - - -
1045A GLN* 5.2 1.3 - - - -
1049A LEU* 4.3 4.0 - - - +
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Residues in contact with GLU 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A LEU 2.9 19.9 + - - +
901A LEU 3.2 5.1 + - - +
903A SER* 1.3 73.9 - - - +
905A LYS* 1.4 58.8 + - - +
907A TYR* 3.0 8.4 + - - +
908A VAL* 2.9 28.8 + - + +
956A HIS* 2.8 38.7 + - - +
959A ILE* 3.6 21.9 - - + +
960A LEU* 4.2 18.4 - - + +
963A LEU* 4.1 12.1 - - + +
1042A ARG* 3.1 21.5 + - - +
1046A TYR* 2.6 23.4 + - - -
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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
----------------------------------------------------------
901A LEU* 3.0 45.7 + - - +
902A SER* 3.4 15.8 - - - +
903A SER 3.4 0.2 - - - -
904A GLU* 1.4 71.8 - - - +
906A ALA* 1.3 57.4 + - - +
908A VAL* 3.2 3.6 + - - +
909A GLU* 3.0 30.1 + - - +
960A LEU* 3.6 27.4 - - + +
964A GLU* 5.8 3.1 - - - -
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Residues in contact with ALA 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A SER 3.3 9.8 + - - +
903A SER* 3.7 11.9 - - - +
905A LYS* 1.3 78.9 - - - +
907A TYR* 1.4 55.8 + - - +
909A GLU* 3.6 9.9 - - - +
910A MSE 3.2 25.5 + - - +
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Residues in contact with TYR 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A UNX 3.7 11.0 - - - -
903A SER 3.1 13.2 + - - +
904A GLU* 3.0 15.0 + - - +
906A ALA* 1.4 73.2 - - - +
908A VAL* 1.3 56.1 - - - +
910A MSE 3.3 32.3 + - + +
911A LEU* 2.8 55.7 + - + +
952A ILE* 4.2 0.3 - - - +
956A HIS* 3.4 35.4 + + + -
990A HIS* 3.6 15.9 + - - -
1038A ARG 3.7 7.2 - - - -
1039A VAL* 2.7 26.4 + - - +
1042A ARG* 3.4 36.4 - - + +
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Residues in contact with VAL 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLU* 2.9 21.7 + - - +
905A LYS 3.7 4.0 - - - +
907A TYR* 1.3 72.1 - - - +
909A GLU* 1.3 58.7 + - - +
911A LEU* 3.3 7.9 + - - +
912A GLN* 3.0 34.0 + - - +
953A HIS* 4.0 5.0 - - + +
956A HIS* 3.5 39.5 - - + +
957A GLN* 3.9 26.7 - - + +
960A LEU* 3.8 26.0 - - + -
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Residues in contact with GLU 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A LYS 3.0 16.9 + - - +
906A ALA* 3.6 10.8 - - - +
908A VAL* 1.3 75.1 - - - +
910A MSE 1.3 59.9 + - - +
912A GLN* 3.2 15.3 - - - +
913A HIS* 2.8 53.0 + - - +
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Residues in contact with MSE 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A UNX 3.9 4.5 - - - -
906A ALA 3.2 16.1 + - - +
907A TYR* 3.3 33.0 + - + +
909A GLU* 1.3 76.2 - - - +
911A LEU* 1.3 72.1 + - + +
913A HIS* 3.6 4.6 + - - +
914A LEU* 3.1 28.2 + - - +
1035A ARG 5.1 3.4 - - - +
1038A ARG* 3.4 52.0 - - + +
1039A VAL* 3.9 10.1 - - + +
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Residues in contact with LEU 911 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A TYR* 2.8 61.3 + - + +
908A VAL* 3.3 2.2 + - - +
910A MSE 1.3 72.1 - - - +
912A GLN* 1.4 61.8 + - - +
914A LEU* 3.5 8.8 - - + +
915A ASN* 2.8 35.7 + - - +
949A LEU* 5.6 2.7 - - + +
952A ILE* 3.8 23.6 - - + -
953A HIS* 3.8 25.4 - - + +
956A HIS* 3.8 17.0 - - + -
1039A VAL* 3.8 28.5 - - + -
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Residues in contact with GLN 912 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A VAL* 3.0 18.1 + - - +
909A GLU* 3.2 16.3 - - - +
911A LEU* 1.4 74.0 - - - +
913A HIS* 1.4 68.6 + - + +
915A ASN* 3.0 21.1 + - - +
916A LEU* 3.1 14.2 + - + +
953A HIS* 3.2 34.9 + - - -
957A GLN* 4.0 10.8 + - - +
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Residues in contact with HIS 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A GLU* 2.8 55.8 + - - +
910A MSE 4.2 4.4 - - - +
912A GLN* 1.4 85.2 - - + +
914A LEU* 1.3 58.9 + - - +
916A LEU* 3.9 16.4 - - + +
917A ASP* 2.9 48.1 + - - +
1021A PHE* 5.0 1.5 - - - -
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Residues in contact with LEU 914 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A MSE 3.1 23.4 + - - +
911A LEU* 3.5 13.9 - - + +
912A GLN 3.2 0.2 - - - -
913A HIS* 1.3 76.8 - - - +
915A ASN* 1.3 56.1 + - - +
918A PHE* 2.7 42.7 + - + +
919A HIS* 3.0 8.8 + - - -
949A LEU* 4.2 17.7 - - + -
1021A PHE* 3.6 33.4 - - + -
1035A ARG* 4.8 7.0 - - + +
1036A LEU* 3.8 18.6 - - + -
1039A VAL* 3.5 31.9 - - + -
----------------------------------------------------------
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Residues in contact with ASN 915 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A LEU* 2.8 26.8 + - - +
912A GLN* 3.0 10.8 + - - +
914A LEU* 1.3 80.3 - - - +
916A LEU* 1.3 53.3 + - - +
919A HIS* 3.6 14.8 - - + +
920A GLY* 2.8 30.0 + - - -
949A LEU* 3.6 18.4 + - - +
950A PRO* 3.2 36.9 - - - +
953A HIS* 3.6 26.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 916 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A GLN* 3.1 13.8 + - + +
913A HIS* 4.2 16.4 - - + +
914A LEU 3.3 0.2 - - - -
915A ASN* 1.3 80.4 - - - +
917A ASP* 1.3 74.2 + - - +
918A PHE 3.6 0.2 - - - -
920A GLY* 3.8 3.1 - - - -
921A ALA 3.8 5.0 + - - -
924A ARG* 3.8 21.4 + - - +
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Residues in contact with ASP 917 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A HIS* 2.9 31.9 + - - +
916A LEU* 1.3 99.6 - - - +
918A PHE* 1.3 58.7 + - - +
921A ALA* 3.4 19.4 - - - +
924A ARG* 5.5 0.9 - - - +
1020A GLU 5.2 2.9 - - - +
1021A PHE* 3.4 31.9 + - + +
1024A SER 4.6 13.6 - - - +
----------------------------------------------------------
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Residues in contact with PHE 918 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A LEU* 2.7 27.3 + - + +
917A ASP* 1.3 74.5 - - - +
919A HIS* 1.3 66.2 + - - -
921A ALA 3.4 0.9 + - - -
922A VAL* 2.9 40.0 + - + +
946A LEU* 3.4 26.0 - - + -
949A LEU* 3.6 19.3 - - + -
1000A TYR* 4.6 3.8 - + - -
1001A LEU* 4.4 1.8 - - + -
1004A LEU* 3.5 33.2 - - + -
1018A VAL* 4.9 4.3 - - + -
1021A PHE* 3.4 42.6 - + + -
1032A ALA* 4.1 11.9 - - + -
1036A LEU* 3.6 24.2 - - + -
----------------------------------------------------------
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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