Contacts of the helix formed by residues 880 - 918 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878A GLU 3.6 4.6 + - - +
879A VAL* 1.3 85.2 - - - +
881A GLU* 1.3 64.1 + - - +
882A GLY* 3.4 1.7 + - - -
883A GLU* 3.1 38.6 + - - +
884A LEU* 4.0 4.0 + - - +
875D GLU 3.6 16.0 + - - -
876D SER* 3.7 25.0 + - - +
877D ASP 3.3 15.7 - - - +
878D GLU* 4.2 1.6 - - - +
879D VAL* 4.0 8.8 - - - +
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Residues in contact with GLU 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ASN* 1.3 74.8 - - - +
882A GLY* 1.3 58.4 + - - +
883A GLU 3.4 1.0 + - - -
884A LEU* 4.0 5.5 + - + +
885A LYS* 3.9 17.2 + - - +
874D LYS* 3.1 31.3 - - - +
875D GLU* 4.2 11.2 + - + +
877D ASP* 2.8 27.2 + - - +
878D GLU 5.3 1.2 - - - +
879D VAL* 4.3 7.4 - - - +
883D GLU* 3.3 38.7 - - - +
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Residues in contact with GLY 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LYS* 5.6 3.3 + - - -
173A TYR* 5.1 5.0 + - - -
880A ASN* 3.2 3.6 + - - -
881A GLU* 1.3 77.5 - - - +
883A GLU* 1.3 62.7 + - - +
884A LEU 3.6 0.4 - - - -
885A LYS* 4.2 12.9 + - - +
886A GLU* 4.3 11.8 + - - +
875D GLU* 3.4 36.5 + - - -
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Residues in contact with GLU 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A VAL* 3.4 27.6 - - + +
880A ASN* 3.1 24.7 + - - +
881A GLU 3.4 0.6 - - - -
882A GLY* 1.3 81.3 - - - +
884A LEU* 1.3 58.4 + - - +
885A LYS 3.4 0.4 - - - -
886A GLU* 3.8 19.0 + - - +
887A ILE* 3.4 12.0 - - - +
881B GLU* 3.3 42.3 - - - +
884B LEU* 3.3 19.4 - - + +
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Residues in contact with LEU 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A VAL* 5.5 1.8 - - + -
880A ASN 4.0 8.5 + - - +
881A GLU* 4.0 7.5 + - - +
883A GLU* 1.3 75.2 - - - +
885A LYS* 1.3 60.6 + - - +
886A GLU 3.2 2.0 - - - -
887A ILE* 3.2 10.7 + - + +
888A LYS* 3.0 26.0 + - - +
884B LEU* 3.8 28.0 - - + +
879D VAL* 3.8 28.7 - - + -
883D GLU* 3.3 33.9 - - + +
884D LEU* 3.8 21.1 - - + +
887D ILE* 3.9 17.3 - - + +
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Residues in contact with LYS 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA 3.1 27.1 + - - -
143A ASN* 3.7 21.9 + - - +
171A LYS* 4.3 11.5 - - - +
173A TYR* 4.9 4.2 + - - -
881A GLU 3.9 14.7 + - - +
882A GLY* 4.4 9.7 + - - +
883A GLU 3.4 0.2 - - - -
884A LEU* 1.3 79.0 - - - +
886A GLU* 1.3 57.9 + - - +
888A LYS* 3.3 12.7 + - + +
889A GLN* 2.9 47.5 + - + +
875D GLU* 3.3 28.0 + - - +
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Residues in contact with GLU 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN 4.9 3.6 - - - -
144A GLU* 3.6 28.8 - - + +
173A TYR* 3.7 26.0 + - - +
882A GLY 4.3 7.1 + - - +
883A GLU* 3.8 22.5 + - - +
884A LEU 3.2 0.6 - - - -
885A LYS* 1.3 83.4 - - + +
887A ILE* 1.3 59.4 + - + +
889A GLN* 3.4 5.8 + - - +
890A ASP* 3.0 33.8 + - - +
888B LYS* 2.8 41.1 + - - +
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Residues in contact with ILE 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883A GLU 3.4 18.8 - - - +
884A LEU* 3.2 12.1 + - + +
886A GLU* 1.3 76.2 - - + +
888A LYS* 1.3 65.7 + - - +
890A ASP* 3.2 6.1 + - - +
891A ILE* 3.0 35.0 + - + +
884B LEU* 3.9 28.0 - - + +
887B ILE* 4.9 11.0 - - + -
888B LYS* 3.7 40.2 - - + +
891B ILE* 3.7 24.5 - - + -
887D ILE* 4.8 8.7 - - + -
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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
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884A LEU 3.0 13.6 + - - +
885A LYS* 3.3 15.2 + - + +
887A ILE* 1.3 77.7 - - - +
889A GLN* 1.3 70.2 + - - +
891A ILE* 3.3 8.8 + - - +
892A SER* 3.0 27.1 + - - -
144D GLU* 3.3 18.5 + - - -
886D GLU* 2.8 38.1 + - - +
887D ILE* 3.7 17.4 - - + +
890D ASP* 2.9 33.9 + - - +
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Residues in contact with GLN 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.4 19.5 - - - +
108A TYR* 3.7 30.1 - - - +
143A ASN* 3.8 35.3 + - + +
145A HIS* 3.6 14.0 + - + -
885A LYS* 2.9 39.6 + - + +
886A GLU 3.9 2.5 - - - +
887A ILE 3.3 0.2 - - - -
888A LYS* 1.3 86.9 - - - +
890A ASP* 1.3 61.6 + - - +
892A SER* 3.7 6.5 - - - -
893A SER* 3.0 30.7 + - - -
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Residues in contact with ASP 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 3.2 24.2 - - - +
145A HIS* 5.7 0.2 + - - -
886A GLU* 3.0 20.0 + - - +
887A ILE* 3.2 12.5 + - - +
889A GLN* 1.3 77.9 - - - +
891A ILE* 1.3 56.7 + - - +
893A SER* 3.5 4.4 + - - -
894A LEU* 3.0 29.7 + - - +
888B LYS* 2.9 36.5 + - - +
891B ILE* 4.5 19.3 - - + +
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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
----------------------------------------------------------
887A ILE* 3.0 17.5 + - + +
888A LYS* 3.3 6.3 + - - +
890A ASP* 1.3 75.1 - - - +
892A SER* 1.3 58.6 + - - +
894A LEU* 3.4 7.2 + - + +
895A ARG* 2.9 29.2 + - + +
891B ILE* 3.8 27.4 - - + -
887D ILE* 3.7 31.2 - - + +
890D ASP* 4.5 22.2 - - + +
891D ILE* 3.8 23.3 - - + -
894D LEU* 4.1 22.3 - - + +
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Residues in contact with SER 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 3.0 24.6 + - - +
888A LYS* 3.0 17.8 + - - -
889A GLN* 3.7 13.4 + - - -
891A ILE* 1.3 76.2 - - - +
893A SER* 1.3 61.4 + - - +
895A ARG* 3.3 9.9 + - - +
896A TYR* 3.1 36.5 + - - -
175D ARG* 4.9 5.7 + - - -
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Residues in contact with SER 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR 4.5 0.6 + - - -
109A GLY* 3.7 20.6 - - - +
111A ILE* 3.6 21.7 - - - +
145A HIS* 4.2 15.7 - - - -
147A GLU* 3.8 7.5 + - - -
889A GLN 3.0 17.6 + - - -
890A ASP* 3.9 4.5 - - - -
892A SER* 1.3 75.9 + - - +
894A LEU* 1.3 63.2 + - - +
896A TYR* 3.4 2.3 + - - +
897A GLU* 3.0 28.5 + - - +
895B ARG* 5.3 2.3 + - - -
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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 ASP 3.0 18.1 + - - +
891A ILE* 3.7 7.0 - - + +
893A SER* 1.3 77.4 + - - +
895A ARG* 1.3 57.2 + - - +
897A GLU* 3.9 6.2 - - + +
898A LEU* 3.0 63.6 + - + +
891B ILE* 4.1 26.5 - - + +
894B LEU* 4.6 18.8 - - + -
895B ARG* 3.7 39.5 - - + +
898B LEU* 5.3 0.9 - - + -
899B LEU* 5.7 1.3 - - + -
894D LEU* 4.6 14.8 - - + -
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Residues in contact with ARG 895 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A ILE* 2.9 18.1 + - + +
892A SER* 3.3 9.4 + - - +
894A LEU* 1.3 77.1 - - - +
896A TYR* 1.3 92.6 + - - +
898A LEU* 4.0 0.6 - - - +
899A LEU* 3.0 42.4 + - + +
147D GLU* 3.7 35.1 + - - +
893D SER* 5.3 2.7 + - - -
894D LEU* 3.7 33.1 - - + +
897D GLU* 3.0 37.7 + - - +
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Residues in contact with TYR 896 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 3.6 27.7 - - + +
109A GLY 4.0 2.9 - - - +
110A ASN* 3.8 54.3 + - + +
112A PRO* 4.6 4.8 - - + +
892A SER* 3.1 31.1 + - - +
893A SER 3.9 3.6 - - - +
894A LEU 3.4 0.2 - - - -
895A ARG* 1.3 102.0 + - - +
897A GLU* 1.3 63.0 + - - +
899A LEU* 3.5 4.0 + - + +
900A GLU* 3.1 26.2 + - - +
175D ARG* 3.4 28.9 + - - -
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Residues in contact with GLU 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 3.6 27.9 - - + +
112A PRO* 4.8 6.5 - - + -
115A ARG* 4.7 16.5 + - - +
147A GLU* 5.2 0.5 - - - +
893A SER* 3.0 19.9 + - - +
894A LEU* 3.9 5.0 - - + +
896A TYR* 1.3 76.7 - - - +
898A LEU* 1.3 58.8 + - + +
900A GLU* 3.5 6.7 + - - +
901A GLU* 3.0 29.6 + - + +
895B ARG* 3.0 41.4 + - - +
899B LEU* 3.6 24.2 - - + +
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Residues in contact with LEU 898 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894A LEU* 3.0 42.6 + - + +
895A ARG* 4.1 2.5 - - - +
897A GLU* 1.3 72.1 - - - +
899A LEU* 1.3 61.9 + - - +
901A GLU* 3.3 6.2 + - + +
902A LYS* 3.0 29.3 + - - +
898B LEU* 3.7 44.0 - - + +
899B LEU* 3.9 22.4 - - + -
902B LYS* 5.8 2.5 - - + -
894D LEU* 5.3 2.0 - - + -
898D LEU* 3.7 35.2 - - + +
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Residues in contact with LEU 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895A ARG* 3.0 48.3 + - + +
896A TYR* 4.1 4.5 - - + +
898A LEU* 1.3 76.7 - - - +
900A GLU* 1.3 58.8 + - - +
902A LYS* 3.4 4.3 + - + +
903A SER* 3.0 28.6 + - - -
894D LEU* 5.7 0.4 - - + -
897D GLU* 3.6 43.1 - - + +
898D LEU* 3.9 23.6 - - + -
901D GLU* 4.8 10.1 - - + -
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Residues in contact with GLU 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 3.4 38.9 - - + +
115A ARG* 4.4 10.0 + - - -
896A TYR 3.1 18.9 + - - +
897A GLU* 4.0 4.9 - - - +
899A LEU* 1.3 78.2 - - - +
901A GLU* 1.3 61.6 + - - +
903A SER* 2.9 22.4 + - - +
904A GLN* 2.9 37.3 + - - +
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Residues in contact with GLU 901 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897A GLU* 3.0 18.7 + - + +
898A LEU* 3.3 8.0 + - + +
900A GLU* 1.3 81.1 + - - +
902A LYS* 1.3 57.2 + - - +
904A GLN* 3.9 4.4 - - - +
905A ASN* 3.0 30.3 + - - +
899B LEU* 4.8 10.3 - - + -
902B LYS* 4.7 20.7 - - + +
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Residues in contact with LYS 902 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898A LEU 3.0 16.8 + - - +
899A LEU* 3.8 8.7 - - + +
901A GLU* 1.3 77.7 - - - +
903A SER* 1.3 57.4 + - - +
905A ASN* 3.4 4.8 + - - +
906A THR* 3.0 29.3 + - - -
898D LEU* 5.8 3.4 - - + -
901D GLU* 4.7 20.9 - - + +
905D ASN* 5.6 2.6 - - - +
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Residues in contact with SER 903 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A LEU 3.0 15.0 + - - -
900A GLU* 2.9 23.4 + - - +
902A LYS* 1.3 75.6 - - - +
904A GLN* 1.3 58.3 + - - +
906A THR* 3.4 5.5 + - - -
907A GLU* 2.9 30.1 + - - +
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Residues in contact with GLN 904 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900A GLU* 2.9 36.0 + - - +
901A GLU* 3.9 6.1 - - - +
903A SER* 1.3 79.8 + - - +
905A ASN* 1.3 56.8 + - - +
907A GLU* 3.4 11.2 + - - +
908A ASP* 2.9 35.0 + - + +
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Residues in contact with ASN 905 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A GLU 3.0 18.5 + - - +
902A LYS* 3.8 6.3 - - - +
904A GLN* 1.3 76.8 - - - +
906A THR* 1.3 55.9 + - - +
908A ASP* 3.4 4.9 + - - +
909A LEU* 3.0 31.0 + - - +
902B LYS* 5.6 4.7 - - + +
906B THR* 4.8 20.6 - - - -
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Residues in contact with THR 906 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902A LYS 3.0 18.1 + - - -
903A SER* 3.8 5.6 - - - -
905A ASN* 1.3 75.7 - - - +
907A GLU* 1.3 58.9 + - - +
909A LEU* 3.5 5.0 + - - +
910A ALA* 2.9 30.5 + - - +
905D ASN* 4.8 19.3 - - - -
908D ASP* 6.5 0.7 - - - -
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Residues in contact with GLU 907 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A SER 2.9 17.7 + - - +
904A GLN* 3.8 13.9 - - - +
906A THR* 1.3 77.7 - - - +
908A ASP* 1.3 56.8 + - - +
910A ALA* 3.4 4.8 + - - +
911A GLU* 2.9 30.5 + - - +
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Residues in contact with ASP 908 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLN* 2.9 22.5 + - + +
905A ASN* 3.9 4.7 - - - +
907A GLU* 1.3 75.6 - - - +
909A LEU* 1.3 58.3 + - - +
911A GLU* 3.4 5.4 + - - +
912A LEU* 3.0 39.1 + - + +
906B THR* 6.5 0.7 - - - -
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Residues in contact with LEU 909 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905A ASN 3.0 18.8 + - - +
906A THR* 3.9 4.5 - - - +
908A ASP* 1.3 77.4 - - - +
910A ALA* 1.3 56.2 + - - +
912A LEU* 3.5 4.0 + - - +
913A ILE* 2.9 38.6 + - + +
909B LEU* 5.8 7.4 - - + -
909D LEU* 5.8 7.6 - - + -
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Residues in contact with ALA 910 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906A THR 2.9 19.1 + - - +
907A GLU* 3.9 5.6 - - - +
909A LEU* 1.3 75.2 - - - +
911A GLU* 1.3 57.6 + - - +
913A ILE* 3.4 1.2 + - - +
914A ARG* 2.9 30.8 + - - +
912D LEU* 4.4 20.6 - - + +
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Residues in contact with GLU 911 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907A GLU 2.9 18.4 + - - +
908A ASP* 3.9 5.2 - - - +
910A ALA* 1.3 77.9 - - - +
912A LEU* 1.3 63.9 + - + +
914A ARG* 3.3 17.1 + - - +
915A GLU* 3.0 30.5 + - - +
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Residues in contact with LEU 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908A ASP* 3.0 24.8 + - + +
909A LEU* 4.2 3.6 - - - +
911A GLU* 1.3 81.5 - - + +
913A ILE* 1.3 60.7 - - - +
915A GLU* 4.1 7.4 - - + +
916A LEU* 3.8 16.1 + - - +
910B ALA* 4.4 23.3 - - + +
913B ILE* 3.7 41.6 - - + +
914B ARG* 5.3 2.2 - - + +
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Residues in contact with ILE 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A LEU* 2.9 24.0 + - + +
910A ALA 4.0 2.9 - - - +
912A LEU* 1.3 79.9 - - - +
914A ARG* 1.3 59.1 + - - +
915A GLU 3.3 0.2 - - - -
916A LEU* 3.3 11.6 + - + +
917A GLY* 2.9 25.6 + - - -
913B ILE* 3.7 31.9 - - + -
912D LEU* 3.7 47.1 - - + +
913D ILE* 3.7 23.6 - - + -
916D LEU* 4.6 8.4 - - + +
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Residues in contact with ARG 914 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A ALA 2.9 19.0 + - - +
911A GLU* 3.8 18.7 + - - +
913A ILE* 1.3 79.0 - - - +
915A GLU* 1.3 86.5 + - - +
916A LEU 3.1 0.2 - - - -
917A GLY* 3.7 2.5 - - - +
918A GLU* 3.0 47.9 + - + +
912D LEU* 5.3 2.2 - - + +
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Residues in contact with GLU 915 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A GLU 3.0 17.5 + - - +
912A LEU* 4.5 8.7 - - + +
913A ILE 3.3 0.2 - - - -
914A ARG* 1.3 95.5 - - - +
916A LEU* 1.3 56.4 + - - +
918A GLU* 4.3 5.7 + - - +
919A LYS* 3.7 25.3 + - - +
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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 LEU 3.8 14.4 + - - +
913A ILE* 3.3 9.9 + - + +
914A ARG 3.1 0.4 - - - -
915A GLU* 1.3 75.5 - - - +
917A GLY* 1.3 60.6 + - - +
918A GLU 3.3 2.0 - - - -
919A LYS* 3.4 21.7 + - - +
920A LEU* 3.6 17.4 - - + +
913B ILE* 4.6 11.4 - - + +
916B LEU* 3.1 37.2 - - + +
917B GLY* 4.0 23.6 - - - +
920B LEU* 4.9 12.3 - - + -
916D LEU* 3.1 40.4 - - + -
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Residues in contact with GLY 917 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A ILE 2.9 16.1 + - - -
914A ARG* 3.2 4.2 + - - -
916A LEU* 1.3 73.5 - - - +
918A GLU* 1.3 59.0 + - - +
919A LYS 3.2 7.5 + - - -
920A LEU* 4.0 15.5 + - - +
916D LEU* 4.0 14.5 - - - +
919D LYS* 5.5 5.7 - - - -
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Residues in contact with GLU 918 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A ARG* 3.0 41.7 + - + +
915A GLU 4.7 6.5 - - - +
916A LEU 3.3 1.0 - - - -
917A GLY* 1.3 79.3 - - - +
919A LYS* 1.3 61.7 + - - +
920A LEU 3.7 3.1 - - - -
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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