Contacts of the helix formed by residues 888 - 912 (chain A) in PDB entry 2RD0
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 GLU 888 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-18A ASP* 3.1 30.1 - - + +
887A GLY* 1.3 68.5 - - - -
889A ILE* 1.3 65.6 + - - +
890A TYR 3.3 0.4 + - - -
891A ASP* 3.7 21.6 + - + +
892A ALA* 4.0 3.1 + - - +
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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
----------------------------------------------------------
-19A HIS* 3.8 39.9 - - + +
-18A ASP* 4.9 6.5 - - + -
884A LYS 4.7 4.0 - - - +
885A ASN* 3.4 37.5 - - + +
886A LYS 3.7 17.9 - - - +
888A GLU* 1.3 75.5 - - - +
890A TYR* 1.3 65.0 + - - +
892A ALA* 2.9 18.8 + - - +
893A ALA 3.0 9.5 + - - -
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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
----------------------------------------------------------
878A HIS* 2.9 25.0 + + - -
881A LEU 4.5 3.4 - - - -
882A LYS* 3.7 36.4 - - + -
885A ASN* 3.1 31.8 + - - +
887A GLY 3.1 15.0 + - - +
889A ILE* 1.3 73.5 - - - +
891A ASP* 1.3 74.4 + - - +
893A ALA* 3.0 4.6 + - + +
894A ILE* 2.8 60.2 + - + +
965A SER* 3.5 22.2 + - - -
966A LYS 4.7 0.5 + - - -
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Residues in contact with ASP 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A GLY 4.5 0.2 + - - -
888A GLU* 3.7 18.0 + - + +
889A ILE 3.1 1.0 + - - -
890A TYR* 1.3 94.7 - - - +
892A ALA* 1.3 57.2 + - - +
894A ILE* 3.3 6.6 + - - +
895A ASP* 3.0 28.1 + - - +
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Residues in contact with ALA 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-19A HIS* 3.5 31.4 - - + +
-18A ASP* 4.4 14.6 - - - +
888A GLU 4.0 1.7 + - - +
889A ILE 2.9 10.5 + - - +
891A ASP* 1.3 78.6 - - - +
893A ALA* 1.3 58.1 + - - +
895A ASP* 3.2 9.3 + - - +
896A LEU* 2.9 27.7 + - - +
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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
----------------------------------------------------------
-19A HIS* 3.6 9.1 + - + -
881A LEU* 4.2 12.8 - - + +
885A ASN* 3.3 42.6 - - + +
889A ILE 3.0 5.5 + - - +
890A TYR* 3.0 8.6 + - + +
892A ALA* 1.3 76.0 - - - +
894A ILE* 1.3 64.5 + - + +
896A LEU* 3.5 2.2 + - - +
897A PHE* 3.1 23.7 + - - +
926A ASP 4.0 7.4 - - - +
927A GLY* 3.9 5.0 - - - -
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Residues in contact with ILE 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A HIS* 4.1 6.3 - - + -
881A LEU* 5.1 8.1 - - + -
890A TYR* 2.8 64.8 + - + +
891A ASP* 3.7 6.3 - - - +
893A ALA* 1.3 73.2 - - + +
895A ASP* 1.3 55.4 + - - +
897A PHE* 3.6 5.3 - - - +
898A THR* 2.6 44.4 + - - +
963A VAL* 3.1 39.3 - - + +
964A ILE* 4.6 1.6 - - - -
965A SER* 4.1 14.8 - - - +
976A GLU* 4.8 5.8 - - - +
979A ARG* 4.9 5.6 - - - +
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Residues in contact with ASP 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ARG* 4.4 7.4 + - - -
891A ASP 3.0 13.3 + - - +
892A ALA* 3.3 13.5 - - - +
893A ALA 3.2 0.2 - - - -
894A ILE* 1.3 75.0 - - - +
896A LEU* 1.3 57.8 + - - +
898A THR* 2.9 3.3 + - - -
899A ARG* 2.7 68.5 + - - -
979A ARG* 3.5 22.8 + - - +
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Residues in contact with LEU 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-21A HIS* 3.5 26.5 - - + +
-19A HIS* 4.1 5.8 - - + +
832A ARG* 3.5 46.0 - - + +
892A ALA 2.9 16.5 + - - +
893A ALA* 3.7 7.0 - - - +
894A ILE 3.4 0.2 - - - -
895A ASP* 1.3 75.9 + - - +
897A PHE* 1.3 67.6 + - - +
899A ARG* 3.3 4.7 - - + +
900A SER* 2.8 26.7 + - - +
926A ASP* 3.0 34.5 - - - +
927A GLY 4.2 0.7 - - - -
928A GLN* 3.8 19.7 - - + +
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Residues in contact with PHE 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A LEU* 4.8 3.1 - - + -
881A LEU* 3.9 14.4 - - + -
893A ALA 3.1 12.6 + - - +
894A ILE* 3.6 5.2 - - - +
896A LEU* 1.3 79.0 - - - +
898A THR* 1.3 60.7 + - - +
900A SER* 2.8 6.1 + - - -
901A CYS* 2.7 57.6 + - + +
923A VAL* 4.3 16.2 - - + -
927A GLY 3.3 25.9 + - - +
929A LEU* 3.9 17.3 - - + -
960A PHE* 3.7 35.0 - + - -
963A VAL* 3.6 44.2 - - + -
964A ILE* 5.0 5.2 - - + -
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Residues in contact with THR 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A ILE* 2.6 30.0 + - - +
895A ASP 2.9 1.3 + - - -
897A PHE* 1.3 79.6 - - - +
899A ARG* 1.3 64.8 + - - +
901A CYS* 3.6 3.4 - - - +
902A ALA* 3.0 23.6 + - - +
964A ILE* 4.1 15.9 - - + +
979A ARG* 3.3 38.7 + - - +
980A PHE* 3.7 32.9 - - + -
983A MET* 4.8 7.0 - - - -
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Residues in contact with ARG 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A ASP* 3.1 60.8 + - - +
831A LEU* 3.9 13.7 - - - +
832A ARG* 4.2 16.8 - - + +
895A ASP* 2.7 52.1 + - - -
896A LEU* 3.3 13.0 - - + +
898A THR* 1.3 71.2 - - - +
900A SER* 1.3 52.8 + - - +
902A ALA* 3.0 6.9 + - - +
903A GLY* 2.8 31.9 + - - -
979A ARG* 5.3 4.2 - - - +
983A MET* 3.3 34.3 - - + +
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Residues in contact with SER 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ARG* 3.4 28.9 - - - +
896A LEU* 2.8 11.3 + - - -
897A PHE* 2.8 19.4 + - - -
899A ARG* 1.3 77.0 - - - +
901A CYS* 1.3 62.4 + - - +
903A GLY* 3.1 1.3 + - - +
904A TYR* 2.9 31.2 + - - -
928A GLN* 4.0 6.1 - - - -
929A LEU* 3.1 40.7 + - - +
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Residues in contact with CYS 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A PHE* 2.7 42.5 + - + +
898A THR* 3.6 4.9 - - - +
900A SER* 1.3 72.6 + - - +
902A ALA* 1.3 57.8 + - - +
904A TYR* 4.0 0.2 - - - -
905A CYS* 2.9 30.8 + - - +
929A LEU* 3.8 30.7 - - + -
954A PHE* 3.7 8.6 - - - -
956A LEU* 4.0 24.9 - - - -
960A PHE* 4.7 5.2 - - - -
964A ILE* 6.0 3.1 - - + -
980A PHE* 4.5 7.6 - - + -
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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
----------------------------------------------------------
831A LEU* 4.2 14.4 - - + -
898A THR 3.0 12.9 + - - +
899A ARG* 3.4 8.5 - - - +
901A CYS* 1.3 71.6 - - - +
903A GLY* 1.3 70.5 + - - +
905A CYS* 3.3 3.6 + - - +
906A VAL* 3.1 25.7 + - - +
980A PHE* 3.5 24.6 - - + -
983A MET* 4.3 8.7 - - + -
984A CYS* 3.8 16.8 - - - +
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Residues in contact with GLY 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824A TRP* 3.8 14.4 - - - -
831A LEU* 4.2 11.5 - - - +
833A MET* 3.7 19.7 - - - -
899A ARG 2.8 12.9 + - - -
900A SER 3.1 4.0 + - - -
902A ALA* 1.3 78.6 - - - +
904A TYR* 1.3 66.3 + - - +
906A VAL* 3.0 8.9 + - - +
907A ALA* 3.0 11.3 + - - +
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Residues in contact with TYR 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A ILE* 4.2 19.1 - - + +
832A ARG 4.5 0.4 - - - -
833A MET* 3.6 40.2 - - + +
834A LEU 2.9 35.2 + - - -
900A SER 2.9 24.0 + - - +
901A CYS 4.0 2.5 - - - +
903A GLY* 1.3 69.8 - - - -
905A CYS* 1.3 67.6 + - - +
906A VAL 2.7 2.1 + - - -
907A ALA* 2.9 3.0 + - + -
908A THR* 2.7 27.9 + - - +
929A LEU* 3.7 15.3 - - + -
930A PHE* 3.5 16.3 - - - +
931A HIS* 3.0 63.6 + + + +
934A PHE* 4.3 3.4 - + - -
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Residues in contact with CYS 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A CYS 2.9 19.6 + - - +
902A ALA* 3.4 10.1 - - - +
904A TYR* 1.3 74.5 - - - +
906A VAL* 1.3 61.4 + - - +
908A THR* 3.3 12.4 - - - +
909A PHE* 3.5 11.4 + - - +
954A PHE* 3.4 35.6 - - + +
956A LEU* 3.7 33.9 - - - -
980A PHE* 5.0 2.7 - - + -
984A CYS* 4.8 8.1 - - - -
1039A PHE* 5.4 4.3 - - + -
1047A HIS* 5.5 2.7 - - - -
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Residues in contact with VAL 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824A TRP* 4.4 6.1 - - + -
902A ALA 3.1 11.6 + - - +
903A GLY 3.0 7.8 + - - +
904A TYR 2.7 2.8 + - - -
905A CYS* 1.3 72.0 - - - +
907A ALA* 1.3 69.0 + - - +
908A THR 2.9 1.3 - - - -
909A PHE* 2.7 17.4 + - - +
910A ILE* 2.9 29.7 + - + +
984A CYS* 3.7 35.4 - - + +
987A ALA* 3.9 14.4 - - + -
988A TYR* 3.8 31.4 - - + +
1039A PHE* 4.5 9.0 - - + -
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Residues in contact with ALA 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A ILE* 4.5 11.2 - - + -
820A MET* 3.7 30.5 - - - -
824A TRP* 4.5 2.9 - - + -
833A MET* 3.7 26.9 - - + -
903A GLY 3.0 3.3 + - - +
904A TYR* 2.9 9.8 + - + +
906A VAL* 1.3 76.9 - - - +
908A THR* 1.3 61.5 + - - +
910A ILE* 3.5 1.3 + - - +
911A LEU* 3.1 33.0 + - + +
913A ILE* 5.0 0.4 - - - -
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Residues in contact with THR 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A TYR* 2.7 26.0 + - - +
905A CYS* 3.3 8.5 - - - +
907A ALA* 1.3 72.2 - - - +
909A PHE* 1.3 62.4 + - + +
912A GLY* 3.0 20.8 + - - -
913A ILE* 3.5 22.1 + - - +
916A ARG* 4.3 11.1 - - - +
931A HIS* 4.4 10.4 - - - -
934A PHE* 5.9 0.7 - - - -
953A PRO* 3.2 23.4 - - + +
954A PHE* 3.2 35.7 - - + +
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Residues in contact with PHE 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A CYS 3.6 10.5 - - - +
906A VAL* 2.7 14.3 + - - +
908A THR* 1.3 74.1 - - + +
910A ILE* 1.3 67.6 + - + +
912A GLY* 3.1 12.5 + - - -
951A ARG* 4.7 8.1 - - + -
952A VAL* 4.0 35.8 + - + -
953A PRO* 3.9 8.1 - - + -
988A TYR* 4.1 7.4 - + - -
1021A TYR* 4.6 2.9 + - - -
1025A THR* 3.4 40.6 + - + +
1038A TYR* 4.3 13.7 - + - -
1039A PHE* 3.7 34.8 - + + -
1042A GLN* 4.0 35.0 - - + -
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Residues in contact with ILE 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A MET* 4.0 18.6 - - + -
906A VAL* 2.9 36.3 + - + +
907A ALA 3.8 4.0 - - - +
909A PHE* 1.3 77.9 - - + +
911A LEU* 1.3 59.6 + - + +
912A GLY 3.6 0.2 + - - -
988A TYR* 4.2 17.7 - - + -
991A ILE* 3.6 33.0 - - + -
1021A TYR* 4.6 1.2 - - - -
1022A ILE* 3.9 33.8 - - + +
1025A THR* 3.3 22.6 + - + +
1026A LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A THR* 4.9 12.3 - - - +
816A ILE* 3.9 29.4 - - + -
817A ILE* 5.1 4.7 - - + -
820A MET* 4.3 15.3 - - + -
907A ALA* 3.1 20.0 + - + +
910A ILE* 1.3 81.3 - - + +
912A GLY* 1.3 66.3 + - - +
913A ILE* 3.5 25.8 - - + -
937A PHE 2.8 16.5 - - - +
938A LEU* 3.5 19.0 - - + +
998A PHE* 5.9 0.4 - - + -
1002A PHE* 3.5 38.4 - - + -
1021A TYR* 4.8 0.9 - - - -
1022A ILE* 4.9 5.2 - - + -
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Residues in contact with GLY 912 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A THR 3.0 13.3 + - - -
909A PHE 3.1 11.3 + - - -
910A ILE 3.3 0.2 - - - -
911A LEU* 1.3 76.7 - - - +
913A ILE* 1.3 60.7 + - - -
937A PHE 2.9 10.4 - - - +
939A ASP* 3.0 26.6 + - - +
951A ARG* 5.9 0.2 - - - -
952A VAL 5.8 0.4 - - - -
953A PRO* 3.8 7.9 - - - -
1021A TYR* 4.1 20.4 - - - -
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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
------------------------------------------------------------
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