Contacts of the helix formed by residues 894 - 922 (chain C) in PDB entry 1XD2
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 PRO 894 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849C VAL* 5.4 2.0 - - + -
853C SER* 5.0 3.6 - - - +
892C GLN 3.6 6.9 - - - +
893C ILE* 1.3 90.5 - - + +
895C SER* 1.3 67.2 + - - +
896C ARG* 3.3 25.6 - - - +
897C GLN* 3.2 44.2 + - + +
898C LYS* 3.4 9.2 + - - +
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Residues in contact with SER 895 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893C ILE 3.5 1.9 + - - -
894C PRO* 1.3 72.7 - - - +
896C ARG* 1.3 64.7 + - - +
897C GLN 3.3 0.5 + - - -
898C LYS* 3.4 13.0 + - - +
899C LYS* 3.4 19.4 + - - +
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Residues in contact with ARG 896 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C GLN* 6.2 1.3 - - - +
894C PRO* 3.3 26.7 - - - +
895C SER* 1.3 78.4 + - - +
897C GLN* 1.3 79.3 + - + +
899C LYS* 3.4 10.7 + - - +
900C ILE* 3.3 27.5 + - + +
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Residues in contact with GLN 897 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853C SER* 2.9 53.1 + - - -
856C ILE* 3.9 18.9 - - + +
857C GLU* 3.6 19.6 + - - +
860C GLN* 5.4 3.5 - - - +
893C ILE* 3.8 15.3 - - + +
894C PRO* 3.2 24.8 + - + +
896C ARG* 1.3 96.3 - - + +
898C LYS* 1.3 64.8 + - - +
900C ILE* 3.1 13.3 + - + +
901C LEU* 3.0 23.4 + - - +
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Residues in contact with LYS 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856C ILE* 5.7 0.4 - - - -
890C PHE* 2.9 29.7 + - + +
891C GLU* 3.4 20.4 + - - +
893C ILE* 3.1 26.8 + - + +
894C PRO 3.4 7.3 + - - +
895C SER* 3.4 13.3 + - - +
897C GLN* 1.3 77.2 - - - +
899C LYS* 1.3 57.9 + - - +
901C LEU* 3.2 8.5 + - - +
902C GLU* 2.8 31.6 + - - +
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Residues in contact with LYS 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C SER 3.4 9.1 + - - +
896C ARG* 3.5 11.9 - - - +
897C GLN 3.2 0.4 - - - -
898C LYS* 1.3 81.2 - - - +
900C ILE* 1.3 55.1 + - + +
902C GLU* 3.3 6.4 + - - +
903C GLU* 2.7 60.2 + - + +
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Residues in contact with ILE 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856C ILE* 4.2 15.9 - - + +
859C LEU* 4.3 12.1 - - + -
860C GLN* 3.3 42.4 - - + +
863C GLN* 4.2 20.3 + - - +
896C ARG* 3.3 18.1 + - + +
897C GLN* 3.1 16.7 + - + +
899C LYS* 1.3 78.0 - - + +
901C LEU* 1.3 62.4 + - - +
903C GLU* 3.4 8.8 + - - +
904C ALA* 3.0 22.0 + - - +
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Residues in contact with LEU 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856C ILE* 4.3 16.2 - - + -
859C LEU* 3.8 23.8 - - + -
874C VAL* 4.7 3.4 - - + -
875C VAL* 4.8 10.8 - - + -
878C MET* 3.8 39.0 - - + -
879C ASN* 5.7 1.8 - - - +
890C PHE* 3.9 23.3 - - + -
897C GLN 3.0 15.5 + - - +
898C LYS* 3.7 8.1 - - - +
900C ILE* 1.3 77.9 - - - +
902C GLU* 1.3 56.5 + - - +
904C ALA* 3.5 3.9 + - - +
905C HIS* 2.9 29.5 + - + +
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Residues in contact with GLU 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C LYS 2.8 17.7 + - - +
899C LYS* 3.6 8.7 - - + +
901C LEU* 1.3 73.9 - - - +
903C GLU* 1.3 57.1 + - - +
905C HIS* 3.1 15.8 + - - +
906C GLU* 2.7 77.2 + - - +
909C GLU* 4.0 7.6 - - - +
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Residues in contact with GLU 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863C GLN* 4.8 7.4 - - - +
899C LYS* 2.7 53.8 + - + +
900C ILE* 3.7 7.6 - - - +
902C GLU* 1.3 75.7 - - - +
904C ALA* 1.3 64.8 + - - +
906C GLU* 3.2 33.1 + - - +
907C LEU* 3.3 16.2 + - - +
914C LYS* 5.9 0.2 - - - +
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Residues in contact with ALA 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859C LEU* 3.9 18.2 - - + -
863C GLN* 4.1 11.8 + - - +
871C VAL* 4.1 10.1 - - + -
872C LEU* 4.7 3.1 - - - +
875C VAL* 3.8 24.7 - - + +
900C ILE 3.0 15.6 + - - +
901C LEU 3.5 5.6 - - - +
903C GLU* 1.3 80.3 - - - +
905C HIS* 1.3 62.0 + - - +
907C LEU* 3.1 26.8 + - - +
908C SER* 4.1 1.0 + - - -
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Residues in contact with HIS 905 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLN* 4.6 8.8 + - - +
875C VAL* 3.9 17.0 - - + +
879C ASN* 3.9 31.9 + - - +
884C TYR* 6.4 0.2 - + - -
901C LEU* 2.9 20.4 + - + +
902C GLU* 3.5 16.6 + - - +
904C ALA* 1.3 75.6 - - - +
906C GLU* 1.3 63.3 + - - +
907C LEU 3.0 0.5 + - - -
908C SER* 2.9 32.5 + - - -
909C GLU* 3.2 29.4 + - + +
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Residues in contact with GLU 906 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902C GLU* 2.7 55.5 + - - +
903C GLU* 3.2 22.4 + - - +
905C HIS* 1.3 73.3 - - - +
907C LEU* 1.3 62.3 + - - +
908C SER 3.2 0.2 - - - -
909C GLU* 3.2 36.6 + - - +
914C LYS* 2.8 48.4 + - + +
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Residues in contact with LEU 907 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863C GLN* 4.5 8.1 - - + +
868C PHE* 4.5 19.7 - - + -
871C VAL* 4.2 21.5 - - + -
872C LEU* 5.0 7.9 - - + -
903C GLU 3.3 13.8 + - - +
904C ALA* 3.1 19.6 + - - +
905C HIS 3.0 1.0 - - - -
906C GLU* 1.3 79.1 - - - +
908C SER* 1.3 60.9 + - - +
909C GLU 3.6 1.0 + - - +
912C TYR* 3.3 12.3 - - - -
914C LYS* 3.9 12.9 + - + +
915C TYR* 3.2 52.7 + - + +
918C LYS* 4.2 14.8 - - + -
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Residues in contact with SER 908 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLN* 3.2 28.6 + - - -
71B TYR* 5.9 0.2 - - - -
872C LEU* 4.8 8.7 - - - +
875C VAL* 4.8 2.1 - - - +
904C ALA 4.1 0.4 + - - -
905C HIS* 2.9 22.4 + - - -
907C LEU* 1.3 76.6 - - - +
909C GLU* 1.3 67.7 + - - +
910C ASP 3.6 0.5 + - - -
911C HIS* 3.7 2.9 + - - -
912C TYR* 3.0 48.4 + - - -
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Residues in contact with GLU 909 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902C GLU* 4.0 8.2 - - - +
905C HIS* 3.2 42.8 + - + +
906C GLU* 3.2 35.1 + - - +
907C LEU 3.9 2.1 - - - +
908C SER* 1.3 82.7 + - - +
910C ASP* 1.3 70.9 + - + +
912C TYR* 3.2 4.2 + - - -
913C LYS* 3.5 8.0 + - - +
914C LYS* 4.6 1.0 + - - +
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Residues in contact with ASP 910 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 5.1 2.0 + - - -
41B ARG* 3.1 34.5 + - - -
54B ASP* 5.4 0.2 - - - +
908C SER 3.6 0.2 + - - -
909C GLU* 1.3 77.6 - - + +
911C HIS* 1.3 75.0 + - - +
913C LYS* 3.2 35.9 + - + +
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Residues in contact with HIS 911 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.2 56.4 + + + +
41B ARG* 3.7 9.9 - - - -
54B ASP* 3.0 22.3 + - - -
55B ILE 3.5 22.0 - - - -
56B LEU* 3.6 26.4 - - + +
57B ASP 4.9 3.2 + - - -
908C SER 3.7 2.9 + - - -
909C GLU 3.4 0.8 - - - -
910C ASP* 1.3 83.2 - - - +
912C TYR* 1.3 76.0 + - - +
913C LYS* 3.3 1.6 + - - -
916C LEU* 4.3 8.7 - - - +
932C ILE* 5.2 0.7 - - - +
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Residues in contact with TYR 912 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR* 5.9 0.7 - - + -
61B GLN* 5.2 2.9 - - - -
67B MET* 3.3 19.4 - - - +
70B GLN* 4.8 0.5 + - - -
71B TYR* 2.7 41.5 + + - -
872C LEU* 3.7 20.6 - - + -
907C LEU 3.3 11.4 - - - -
908C SER* 3.0 44.6 + - - -
909C GLU 3.2 0.4 + - - -
911C HIS* 1.3 81.2 - - - +
913C LYS* 1.3 63.8 + - - +
914C LYS 3.4 2.9 - - - -
915C TYR* 3.3 22.8 + + + -
916C LEU* 2.9 28.3 + - + +
929C PHE* 3.6 9.8 - + - -
932C ILE* 3.1 32.8 - - + -
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Residues in contact with LYS 913 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 3.3 30.9 + - - +
909C GLU 3.5 4.9 + - - +
910C ASP* 3.2 37.5 + - + +
911C HIS 3.2 1.7 - - - -
912C TYR* 1.3 79.1 - - - +
914C LYS* 1.3 68.2 + - + +
916C LEU* 3.4 9.0 + - - +
917C ALA* 3.2 18.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 914 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903C GLU 5.9 0.2 - - - +
906C GLU* 2.8 57.2 + - + +
907C LEU* 3.9 15.0 + - + +
909C GLU* 4.6 1.8 + - - +
912C TYR 3.4 0.2 - - - -
913C LYS* 1.3 81.5 - - + +
915C TYR* 1.3 61.5 + - - +
917C ALA* 3.0 9.5 + - + +
918C LYS* 2.8 28.8 + - - +
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Residues in contact with TYR 915 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868C PHE* 3.6 42.2 - + + -
872C LEU* 5.3 5.8 - - + -
907C LEU* 3.2 39.0 + - + +
912C TYR* 3.6 26.2 - + + +
914C LYS* 1.3 78.5 - - - +
916C LEU* 1.3 76.1 + - + +
918C LYS* 3.0 3.3 + - - +
919C LEU* 2.8 44.2 + - + +
928C PRO* 3.6 12.5 - - - +
929C PHE* 2.9 35.5 + - + -
932C ILE* 3.7 20.6 - - + -
933C TYR* 5.3 1.2 - - - -
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Residues in contact with LEU 916 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 5.9 2.7 - - - +
911C HIS 4.3 8.5 - - - +
912C TYR* 2.9 27.8 + - + +
913C LYS* 3.7 7.4 - - - +
915C TYR* 1.3 94.5 - - + +
917C ALA* 1.3 62.7 + - - +
919C LEU* 3.8 7.5 + - + +
920C ARG* 3.1 36.2 + - - +
932C ILE* 4.0 24.7 - - + -
933C TYR* 6.6 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 917 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913C LYS* 3.2 12.8 + - + +
914C LYS* 3.0 12.2 + - - +
916C LEU* 1.3 77.8 - - - +
918C LYS* 1.3 62.6 + - - +
920C ARG* 3.2 12.3 + - - +
921C SER* 3.2 22.5 + - - -
----------------------------------------------------------
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Residues in contact with LYS 918 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863C GLN* 6.0 7.6 - - - -
866C ASN* 5.3 1.3 - - - -
868C PHE* 3.5 26.5 - - + -
907C LEU* 4.2 13.5 - - + -
914C LYS 2.8 15.9 + - - +
915C TYR* 3.2 13.0 - - - +
917C ALA* 1.3 72.4 - - - +
919C LEU* 1.3 57.4 + - - +
921C SER* 2.9 31.8 + - - +
922C ILE* 3.1 28.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 919 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 3.0 21.0 + - - -
868C PHE* 3.9 18.6 - - + -
915C TYR* 2.8 51.6 + - + +
916C LEU* 4.2 7.9 - - + +
918C LYS* 1.3 73.8 - - - +
920C ARG* 1.3 59.4 + - + +
921C SER 3.3 0.5 + - - -
922C ILE* 3.6 8.6 - - + +
926C CYS* 3.8 29.6 - - - -
928C PRO* 4.2 5.6 - - + -
933C TYR* 3.8 22.7 - - + +
970C GLU* 4.7 5.4 - - - +
974C TYR* 3.3 20.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG 920 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.5 57.0 + - - +
43A GLN* 3.6 9.9 + - - -
50A THR* 3.3 19.8 - - - +
916C LEU* 3.1 30.3 + - + +
917C ALA* 3.2 9.4 + - - +
919C LEU* 1.3 79.9 - - + +
921C SER* 1.3 58.2 + - - +
974C TYR* 4.4 3.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 921 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.8 5.2 - - - +
50A THR* 2.8 25.9 + - - -
917C ALA 3.2 11.0 + - - -
918C LYS* 2.9 27.8 + - - +
920C ARG* 1.3 79.4 - - - +
922C ILE* 1.3 65.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 922 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 2.8 31.9 + - - +
45A VAL* 4.0 5.2 + - - +
50A THR* 4.5 0.3 - - - +
866C ASN* 3.3 25.1 - - - +
868C PHE* 3.9 22.9 - - + -
918C LYS* 3.1 32.6 + - + +
919C LEU* 3.6 12.0 + - + +
921C SER* 1.3 82.0 - - - +
923C ASN* 1.3 62.9 + - - +
924C PRO* 3.4 16.8 - - + +
926C CYS* 3.8 29.4 - - + -
974C TYR* 4.9 0.2 - - + -
----------------------------------------------------------
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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