Contacts of the helix formed by residues 880 - 918 (chain B) in PDB entry 6UZA
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 ASN 880 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875A GLU 3.6 15.8 + - - -
876A SER* 3.7 25.0 + - - +
877A ASP 3.3 15.7 - - - +
878A GLU* 4.2 1.3 - - - +
879A VAL* 4.0 8.7 - - - +
878B GLU 3.6 4.9 + - - +
879B VAL* 1.3 85.6 - - - +
881B GLU* 1.3 64.0 + - - +
882B GLY* 3.4 2.0 + - - -
883B GLU* 3.1 39.6 + - - +
884B LEU* 4.0 3.6 + - - +
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Residues in contact with GLU 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A LYS* 3.1 31.8 - - - +
875A GLU* 4.2 10.7 + - + +
877A ASP* 2.8 27.3 + - - +
878A GLU 5.3 1.4 - - - +
879A VAL* 4.6 7.9 - - - +
883A GLU* 3.3 37.2 - - - +
880B ASN* 1.3 74.0 - - - +
882B GLY* 1.3 59.6 + - - +
883B GLU 3.4 0.8 + - - -
884B LEU* 4.0 4.9 + - + +
885B LYS* 3.9 17.2 + - - +
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Residues in contact with GLY 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A GLU* 3.4 36.7 + - - -
171B LYS* 5.6 3.6 + - - -
173B TYR* 5.1 4.7 + - - -
880B ASN* 3.2 3.4 + - - -
881B GLU* 1.3 77.2 - - - +
883B GLU* 1.3 63.9 + - - +
884B LEU 3.6 0.4 - - - -
885B LYS* 4.2 13.6 + - - +
886B GLU* 4.3 11.4 + - - +
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Residues in contact with GLU 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B VAL* 3.4 27.5 - - + +
880B ASN* 3.1 25.1 + - - +
881B GLU 3.4 0.4 - - - -
882B GLY* 1.3 81.5 - - - +
884B LEU* 1.3 58.8 + - - +
885B LYS 3.4 0.4 - - - -
886B GLU* 3.8 21.2 + - - +
887B ILE* 3.4 11.6 - - - +
881C GLU* 3.3 42.7 - - - +
884C LEU* 3.3 18.7 - - + +
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Residues in contact with LEU 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A VAL* 3.8 28.7 - - + -
883A GLU* 3.3 33.7 - - + +
884A LEU* 3.8 20.9 - - + +
887A ILE* 3.9 16.2 - - + +
879B VAL* 5.5 1.8 - - + -
880B ASN 4.0 9.3 + - - +
881B GLU* 4.0 6.5 + - + +
883B GLU* 1.3 75.5 - - - +
885B LYS* 1.3 60.4 + - - +
886B GLU 3.2 1.6 - - - -
887B ILE* 3.2 10.1 + - + +
888B LYS* 3.0 26.3 + - - +
884C LEU* 3.8 26.9 - - + +
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Residues in contact with LYS 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A GLU* 3.3 28.6 + - - +
142B ALA 3.1 26.7 + - - -
143B ASN* 3.7 20.4 + - - +
171B LYS* 4.3 12.1 - - - +
173B TYR* 4.9 3.8 + - - -
881B GLU 3.9 15.0 + - - +
882B GLY* 4.4 10.0 + - - +
883B GLU 3.4 0.4 - - - -
884B LEU* 1.3 79.7 - - - +
886B GLU* 1.3 58.1 + - - +
888B LYS* 3.3 10.9 + - + +
889B GLN* 2.9 48.9 + - + +
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Residues in contact with GLU 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN 4.9 4.0 - - - +
144B GLU* 3.6 27.6 - - + +
173B TYR* 3.7 26.5 + - - +
882B GLY 4.3 7.1 + - - +
883B GLU* 3.8 22.3 + - - +
884B LEU 3.2 0.4 - - - -
885B LYS* 1.3 83.3 - - - +
887B ILE* 1.3 59.2 + - + +
889B GLN* 3.4 6.1 + - - +
890B ASP* 3.0 34.2 + - - +
888C LYS* 2.8 39.6 + - - +
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Residues in contact with ILE 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A ILE* 4.9 8.7 - - + -
883B GLU 3.4 20.4 - - - +
884B LEU* 3.2 12.5 + - + +
886B GLU* 1.3 77.7 - - + +
888B LYS* 1.3 64.5 + - - +
890B ASP* 3.2 5.5 + - - +
891B ILE* 3.0 35.5 + - + +
884C LEU* 3.9 27.6 - - + +
887C ILE* 4.8 11.0 - - + -
888C LYS* 3.7 39.3 - - + +
891C ILE* 3.7 24.2 - - + -
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Residues in contact with LYS 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLU* 3.3 17.7 + - - -
886A GLU* 2.8 37.4 + - - +
887A ILE* 3.7 17.0 - - + +
890A ASP* 2.9 33.3 + - - +
884B LEU 3.0 13.8 + - - +
885B LYS* 3.5 16.2 - - + +
887B ILE* 1.3 77.1 - - - +
889B GLN* 1.3 69.3 + - - +
891B ILE* 3.3 7.8 + - - +
892B SER* 3.0 26.9 + - - -
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Residues in contact with GLN 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 3.4 19.7 - - - +
108B TYR* 3.7 29.3 - - - +
143B ASN* 3.8 35.3 + - + +
145B HIS* 3.6 14.1 + - + -
885B LYS* 2.9 40.0 + - + +
886B GLU 3.9 2.7 - - - +
888B LYS* 1.3 87.3 - - - +
890B ASP* 1.3 61.9 + - - +
892B SER* 3.7 6.9 - - - -
893B SER* 3.0 31.0 + - - -
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Residues in contact with ASP 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN 5.3 0.2 - - - +
144B GLU* 3.2 23.8 - - - +
145B HIS* 5.7 0.2 + - - -
886B GLU 3.0 19.7 + - - +
887B ILE* 3.2 13.7 + - - +
889B GLN* 1.3 77.0 - - - +
891B ILE* 1.3 57.5 + - - +
893B SER* 3.5 4.8 + - - -
894B LEU* 3.0 29.2 + - - +
888C LYS* 2.9 36.6 + - - +
891C ILE* 4.5 19.5 - - + +
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Residues in contact with ILE 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A ILE* 3.7 31.0 - - + +
890A ASP* 4.5 22.7 - - + +
891A ILE* 3.8 24.9 - - + -
894A LEU* 4.1 21.8 - - + +
887B ILE* 3.0 16.3 + - + +
888B LYS* 3.3 6.7 + - - +
890B ASP* 1.3 76.4 - - - +
892B SER* 1.3 57.2 + - - +
894B LEU* 3.4 7.2 + - + +
895B ARG* 2.9 29.0 + - + +
891C ILE* 3.8 26.2 - - + -
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Residues in contact with SER 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 4.9 5.5 + - - -
108B TYR* 3.0 25.1 + - - +
888B LYS* 3.0 18.3 + - - -
889B GLN* 3.7 13.0 - - - -
891B ILE* 1.3 75.8 - - - +
893B SER* 1.3 62.1 + - - +
895B ARG* 3.3 9.2 + - - +
896B TYR* 3.1 36.4 + - - -
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Residues in contact with SER 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B TYR 4.5 0.6 + - - -
109B GLY* 3.7 20.6 - - - +
111B ILE* 3.6 22.3 - - - +
145B HIS* 4.2 16.4 - - - -
147B GLU* 3.8 7.8 + - - -
889B GLN 3.0 17.6 + - - -
890B ASP* 3.9 4.9 - - - -
892B SER* 1.3 75.3 - - - +
894B LEU* 1.3 62.8 + - - +
896B TYR* 3.4 2.1 + - - +
897B GLU* 3.0 28.1 + - - +
895C ARG* 5.3 2.1 + - - -
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Residues in contact with LEU 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 4.6 15.0 - - + -
890B ASP 3.0 17.7 + - - +
891B ILE* 3.7 7.0 - - + +
893B SER* 1.3 77.9 + - - +
895B ARG* 1.3 56.2 + - - +
897B GLU* 3.5 6.0 + - + +
898B LEU* 3.0 62.9 + - + +
891C ILE* 4.1 26.2 - - + +
894C LEU* 4.6 20.4 - - + -
895C ARG* 3.7 39.9 - - + +
898C LEU* 5.3 0.4 - - + -
899C LEU* 5.7 0.9 - - + -
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Residues in contact with ARG 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU* 3.7 35.1 + - - +
893A SER* 5.3 2.1 + - - -
894A LEU* 3.7 33.0 - - + +
897A GLU* 3.0 38.2 + - - +
891B ILE* 2.9 18.1 + - + +
892B SER* 3.3 9.2 + - - +
894B LEU* 1.3 77.4 - - - +
896B TYR* 1.3 94.3 + - - +
898B LEU* 4.0 1.0 - - - +
899B LEU* 3.0 43.4 + - + +
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Residues in contact with TYR 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 3.4 28.3 + - - -
108B TYR* 3.6 27.6 - - + +
109B GLY 4.0 2.7 - - - +
110B ASN* 3.8 53.8 - - + +
112B PRO* 4.6 5.4 - - + +
892B SER* 3.1 31.5 + - - +
893B SER 3.9 3.1 - - - +
894B LEU 3.4 0.2 - - - -
895B ARG* 1.3 100.4 + - - +
897B GLU* 1.3 62.8 + - - +
899B LEU* 4.1 3.2 - - + +
900B GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 3.6 28.2 - - + +
112B PRO* 4.8 6.9 - - + +
115B ARG* 4.7 17.1 + - - +
147B GLU* 5.2 0.3 - - - +
893B SER* 3.0 18.6 + - - +
894B LEU* 3.9 5.7 - - + +
896B TYR* 1.3 76.4 - - - +
898B LEU* 1.3 58.7 + - + +
900B GLU* 3.5 6.3 + - - +
901B GLU* 3.0 29.7 + - - +
895C ARG* 3.0 41.2 + - - +
899C LEU* 3.6 25.0 - - + +
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Residues in contact with LEU 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894A LEU* 5.3 1.3 - - + -
898A LEU* 3.7 34.3 - - + +
894B LEU* 3.0 43.9 + - + +
895B ARG* 4.1 2.0 - - - +
897B GLU* 1.3 73.0 - - - +
899B LEU* 1.3 63.0 + - - +
901B GLU* 3.3 5.3 + - + +
902B LYS* 3.0 29.1 + - - +
898C LEU* 3.7 43.1 - - + +
899C LEU* 3.9 23.6 - - + -
902C LYS* 5.8 2.5 - - + -
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Residues in contact with LEU 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894A LEU* 5.7 0.4 - - + -
897A GLU* 3.6 43.5 - - + +
898A LEU* 3.9 22.4 - - + -
901A GLU* 4.8 9.4 - - + -
895B ARG* 3.0 49.2 + - + +
896B TYR* 4.1 3.8 - - + +
898B LEU* 1.3 75.5 - - - +
900B GLU* 1.3 57.3 + - - +
902B LYS* 3.4 5.2 + - + +
903B SER* 3.0 28.8 + - - -
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Residues in contact with GLU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PRO* 3.4 39.2 - - + +
115B ARG* 4.4 9.6 + - - -
896B TYR 3.1 18.1 + - - +
897B GLU* 4.0 4.3 - - - +
899B LEU* 1.3 77.9 - - - +
901B GLU* 1.3 61.4 + - - +
903B SER* 2.9 23.4 + - - +
904B GLN* 2.9 37.2 + - - +
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Residues in contact with GLU 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B GLU 3.0 19.5 + - - +
898B LEU* 3.3 7.6 + - + +
900B GLU* 1.3 81.0 + - - +
902B LYS* 1.3 59.1 + - - +
904B GLN* 3.9 4.9 - - - +
905B ASN* 3.0 30.8 + - - +
899C LEU* 4.8 10.3 - - + -
902C LYS* 4.7 20.7 - - + +
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Residues in contact with LYS 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898A LEU* 5.8 2.7 - - + -
901A GLU* 4.7 22.0 - - + +
905A ASN* 5.6 2.3 - - - +
898B LEU 3.0 17.6 + - - +
899B LEU* 3.8 7.6 - - + +
900B GLU 3.3 0.2 - - - -
901B GLU* 1.3 77.5 - - - +
903B SER* 1.3 57.6 + - - +
905B ASN* 3.4 5.0 + - - +
906B THR* 3.0 30.2 + - - -
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Residues in contact with SER 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899B LEU 3.0 15.0 + - - -
900B GLU* 2.9 24.3 + - - +
902B LYS* 1.3 75.9 - - - +
904B GLN* 1.3 58.8 + - - +
906B THR* 3.4 5.8 + - - -
907B GLU* 2.9 29.8 + - - +
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Residues in contact with GLN 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900B GLU* 2.9 37.3 + - - +
901B GLU* 3.9 6.3 - - - +
903B SER* 1.3 80.4 + - - +
905B ASN* 1.3 57.6 + - - +
907B GLU* 3.4 10.2 + - - +
908B ASP* 2.9 34.6 + - + +
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Residues in contact with ASN 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B GLU 3.0 18.9 + - - +
902B LYS* 3.8 6.1 - - - +
904B GLN* 1.3 76.2 - - - +
906B THR* 1.3 57.6 + - - +
908B ASP* 3.4 4.9 + - - +
909B LEU* 3.0 30.5 + - - +
902C LYS* 5.6 4.5 - - + +
906C THR* 4.8 20.9 - - - +
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Residues in contact with THR 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905A ASN* 4.8 20.2 - - - +
908A ASP* 6.5 0.7 - - - -
902B LYS 3.0 18.5 + - - -
903B SER* 3.8 5.6 - - - -
905B ASN* 1.3 76.5 - - - +
907B GLU* 1.3 57.1 + - - +
909B LEU* 3.5 4.9 + - - +
910B ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B SER 2.9 18.6 + - - +
904B GLN* 3.8 13.2 - - - +
906B THR* 1.3 77.5 - - - +
908B ASP* 1.3 56.9 + - - +
910B ALA* 3.4 5.4 + - - +
911B GLU* 2.9 30.1 + - - +
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Residues in contact with ASP 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B GLN* 2.9 23.4 + - + +
905B ASN* 3.9 5.8 - - - +
907B GLU* 1.3 76.3 - - - +
909B LEU* 1.3 58.0 + - - +
911B GLU* 3.4 5.2 + - - +
912B LEU* 3.0 38.7 + - + +
906C THR* 6.5 0.9 - - - -
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Residues in contact with LEU 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A LEU* 5.8 8.1 - - + -
905B ASN 3.0 18.7 + - - +
906B THR* 3.9 5.2 - - - +
908B ASP* 1.3 77.7 - - - +
910B ALA* 1.3 56.9 + - - +
912B LEU* 3.5 4.2 + - - +
913B ILE* 2.9 38.5 + - + +
909C LEU* 5.8 7.6 - - + -
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Residues in contact with ALA 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912A LEU* 4.4 20.6 - - + +
906B THR 2.9 19.6 + - - +
907B GLU* 3.9 6.1 - - - +
909B LEU* 1.3 76.9 - - - +
911B GLU* 1.3 57.4 + - - +
913B ILE* 3.4 1.2 + - - +
914B ARG* 2.9 31.1 + - - +
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Residues in contact with GLU 911 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B GLU 2.9 18.1 + - - +
908B ASP* 3.9 6.3 - - - +
910B ALA* 1.3 77.5 - - - +
912B LEU* 1.3 63.7 + - + +
914B ARG* 3.3 18.0 + - - +
915B GLU* 3.0 30.3 + - - +
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Residues in contact with LEU 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908B ASP* 3.0 24.3 + - + +
909B LEU* 4.2 4.5 - - - +
911B GLU* 1.3 80.4 - - + +
913B ILE* 1.3 61.8 + - + +
915B GLU* 4.1 7.3 + - + +
916B LEU* 3.8 16.8 + - - +
910C ALA* 4.4 23.3 - - + +
913C ILE* 3.7 40.1 - - + +
914C ARG* 5.3 3.4 - - + +
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Residues in contact with ILE 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A LEU* 3.7 48.2 - - + +
913A ILE* 3.7 26.7 - - + -
916A LEU* 4.6 7.3 - - + +
909B LEU* 2.9 24.4 + - + +
910B ALA 4.0 2.7 - - - +
911B GLU 3.2 0.2 - - - -
912B LEU* 1.3 78.4 - - - +
914B ARG* 1.3 59.3 + - - +
916B LEU* 3.3 11.9 + - + +
917B GLY* 2.9 25.3 + - - -
913C ILE* 3.7 28.3 - - + -
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Residues in contact with ARG 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A LEU* 5.3 3.3 - - + +
910B ALA 2.9 19.2 + - - +
911B GLU* 3.8 19.6 + - - +
913B ILE* 1.3 78.1 - - - +
915B GLU* 1.3 86.3 + - - +
917B GLY* 3.7 1.9 - - - +
918B GLU* 3.0 48.2 + - + +
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Residues in contact with GLU 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B GLU 3.0 17.1 + - - +
912B LEU* 4.1 8.9 + - + +
913B ILE 3.3 0.4 - - - -
914B ARG* 1.3 95.5 - - - +
916B LEU* 1.3 57.2 + - - +
918B GLU* 4.3 5.7 + - - +
919B LYS* 3.7 25.3 + - - +
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Residues in contact with LEU 916 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A LEU* 3.1 43.7 - - + -
912B LEU 3.8 14.8 + - - +
913B ILE* 3.3 9.4 + - + +
914B ARG 3.1 0.4 - - - -
915B GLU* 1.3 76.2 - - - +
917B GLY* 1.3 59.7 + - - +
918B GLU 3.3 1.6 - - - -
919B LYS* 3.4 21.1 + - - +
920B LEU* 3.6 17.9 - - + +
913C ILE* 4.6 11.4 - - + +
916C LEU* 3.1 35.2 - - + +
917C GLY* 4.0 23.3 - - - +
920C LEU* 4.9 13.2 - - + -
----------------------------------------------------------
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Residues in contact with GLY 917 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A LEU* 4.0 14.7 - - - +
919A LYS* 5.5 5.7 - - - -
913B ILE 2.9 16.5 + - - -
914B ARG* 3.2 3.5 + - - -
916B LEU* 1.3 73.0 - - - +
918B GLU* 1.3 59.5 + - - +
919B LYS 3.2 6.4 + - - -
920B LEU* 4.0 15.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 918 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914B ARG* 3.0 42.0 + - + +
915B GLU 4.7 5.8 - - - +
916B LEU 3.3 0.8 - - - -
917B GLY* 1.3 78.7 - - - +
919B LYS* 1.3 62.3 + - + +
920B LEU 3.7 2.7 - - - -
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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