Contacts of the helix formed by residues 719 - 755 (chain A) in PDB entry 3M62
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 719 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLU 3.4 4.3 - - - -
718A GLU* 1.3 83.8 - - - +
720A ASP* 1.3 63.6 + - - +
721A LYS* 3.3 36.8 + - + +
722A GLU* 2.6 33.8 + - + +
723A LEU* 2.9 11.3 + - - +
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Residues in contact with ASP 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU* 4.6 16.1 - - - +
717A GLU* 3.5 16.6 + - + +
719A GLU* 1.3 76.4 + - - +
721A LYS* 1.3 62.5 + - - +
723A LEU* 3.2 20.6 + - - +
724A GLN* 3.2 30.5 + - - +
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Residues in contact with LYS 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A GLU* 3.1 27.4 + - + +
720A ASP* 1.3 75.3 - - - +
722A GLU* 1.3 64.9 + - + +
724A GLN* 3.3 13.2 + - - +
725A THR* 2.8 36.6 + - - -
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Residues in contact with GLU 722 (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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716A ARG* 4.9 0.9 + - - -
718A GLU* 3.4 27.6 - - + +
719A GLU* 2.6 29.4 + - + +
721A LYS* 1.3 80.0 - - + +
723A LEU* 1.3 48.6 + - - -
725A THR* 3.4 12.6 - - + -
726A ARG* 2.7 69.8 + - - +
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Residues in contact with LEU 723 (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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701A ILE* 3.8 27.3 - - + +
704A GLU* 4.5 17.5 - - + -
705A LEU* 4.0 22.7 - - + -
716A ARG 4.9 1.6 - - - +
717A GLU* 3.6 42.0 - - + +
718A GLU* 3.3 24.9 - - - +
719A GLU 2.9 5.5 + - - +
720A ASP* 3.2 17.9 - - + +
722A GLU* 1.3 75.4 - - - +
724A GLN* 1.3 54.2 + - - +
726A ARG* 3.1 5.5 + - + +
727A LEU* 2.5 38.7 + - - +
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Residues in contact with GLN 724 (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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416A GLU* 4.5 15.9 + - - +
705A LEU* 5.1 13.2 - - + -
720A ASP* 3.2 24.0 + - - +
721A LYS* 3.3 14.0 + - - +
723A LEU* 1.3 77.9 - - - +
725A THR* 1.3 56.9 + - - +
727A LEU* 3.8 11.6 - - + +
728A ALA* 2.9 31.0 + - - +
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Residues in contact with THR 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LYS* 2.8 22.8 + - - -
722A GLU* 3.4 15.9 - - + -
724A GLN* 1.3 78.6 - - - +
726A ARG* 1.3 57.5 + - - +
728A ALA* 3.5 4.4 + - - +
729A SER* 2.8 31.5 + - - -
732A ARG* 5.6 0.3 + - - -
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Residues in contact with ARG 726 (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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697A GLU* 5.3 5.9 + - + +
701A ILE* 3.6 17.7 - - + +
718A GLU* 4.3 19.3 + - - +
722A GLU* 2.7 59.4 + - - +
723A LEU* 3.7 7.0 - - + +
725A THR* 1.3 74.5 - - - +
727A LEU* 1.3 57.6 + - - +
729A SER* 3.5 7.2 + - - -
730A ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A VAL* 4.2 12.8 - - + +
701A ILE* 3.5 29.8 - - + +
702A GLN* 3.5 42.2 - - + +
705A LEU* 4.9 4.9 - - + -
723A LEU 2.5 21.0 + - - +
724A GLN* 3.8 12.3 - - + +
726A ARG* 1.3 71.2 - - - +
728A ALA* 1.3 61.5 + - + +
730A ALA* 3.5 4.3 + - - +
731A SER* 2.7 39.2 + - - +
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Residues in contact with ALA 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A GLN 2.9 20.3 + - - +
725A THR* 3.9 4.9 - - - +
727A LEU* 1.3 75.5 - - + +
729A SER* 1.3 58.7 + - - +
731A SER* 3.1 8.4 + - - -
732A ARG* 2.8 43.4 + - - +
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Residues in contact with SER 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A THR* 2.8 21.5 + - - -
726A ARG* 3.6 10.8 - - - -
727A LEU 3.3 0.2 - - - -
728A ALA* 1.3 77.8 - - - +
730A ALA* 1.3 61.5 + - - +
732A ARG* 3.5 27.9 + - - +
733A GLN* 3.1 24.6 + - - +
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Residues in contact with ALA 730 (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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694A ASN* 3.6 28.2 - - - +
697A GLU* 4.4 12.3 - - + -
698A VAL* 3.7 27.4 - - + +
701A ILE* 5.1 0.4 - - + -
726A ARG 2.9 20.2 + - - +
727A LEU* 4.0 2.0 - - - +
728A ALA 3.4 0.2 - - - -
729A SER* 1.3 72.9 - - - +
731A SER* 1.3 55.8 + - - +
734A ALA* 2.9 30.8 + - - +
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Residues in contact with SER 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A VAL* 3.9 14.1 - - - +
727A LEU* 2.7 26.8 + - - +
728A ALA* 3.4 11.6 - - - -
730A ALA* 1.3 73.0 - - - +
732A ARG* 1.3 66.1 + - - +
734A ALA* 3.4 5.9 + - - +
735A LYS* 3.1 23.7 + - - +
795A TYR* 4.1 25.6 + - - -
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Residues in contact with ARG 732 (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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633A GLN* 5.0 18.1 + - - +
634A PHE* 3.9 31.0 - - + -
725A THR 5.6 0.2 + - - -
728A ALA* 2.8 33.2 + - - +
729A SER* 3.6 30.3 + - - +
730A ALA 3.4 0.2 - - - -
731A SER* 1.3 74.6 - - - +
733A GLN* 1.3 58.7 + - - +
735A LYS* 3.2 5.4 + - + +
736A SER* 2.9 32.2 + - - -
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Residues in contact with GLN 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A GLN* 3.7 19.4 - - - +
636A ASP* 4.5 8.6 + - - +
638A PHE* 5.1 13.4 - - - -
687A LEU* 6.1 0.2 - - - +
690A GLU* 4.5 11.3 - - - +
694A ASN* 3.4 31.6 - - - +
729A SER 3.1 14.4 + - - +
732A ARG* 1.3 80.2 - - - +
734A ALA* 1.3 61.8 + - - +
736A SER* 4.3 13.3 + - - -
737A SER* 3.0 52.3 + - - -
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Residues in contact with ALA 734 (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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691A GLY* 3.9 5.8 - - - +
694A ASN* 3.8 14.5 - - + +
695A LEU* 3.7 36.3 - - + +
698A VAL* 5.5 0.4 - - + -
730A ALA 2.9 19.1 + - - +
731A SER* 3.7 6.1 - - - +
733A GLN* 1.3 78.5 - - - +
735A LYS* 1.3 56.3 + - - +
737A SER* 4.0 0.7 - - - -
738A CYS* 3.0 35.6 + - - -
795A TYR* 4.2 5.6 - - + -
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Residues in contact with LYS 735 (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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731A SER 3.1 16.8 + - - +
732A ARG* 3.7 4.9 - - + +
734A ALA* 1.3 72.5 - - - +
736A SER* 1.3 61.9 + - - +
739A GLY* 2.7 32.6 + - - -
793A GLN 4.8 2.2 - - - -
794A SER 3.1 27.6 + - - +
795A TYR* 3.3 20.1 - - + +
796A SER* 3.9 18.6 - - - +
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Residues in contact with SER 736 (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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636A ASP* 5.2 1.7 + - - -
638A PHE* 4.4 14.9 - - - +
639A ASN* 3.1 26.0 + - - -
642A TYR* 5.3 3.1 - - - +
687A LEU* 5.7 0.2 - - - -
732A ARG* 2.9 18.1 + - - -
733A GLN* 3.9 14.3 + - - -
735A LYS* 1.3 80.5 - - - +
737A SER* 1.3 55.9 + - - +
739A GLY* 5.2 0.2 - - - -
740A LEU* 3.1 30.8 + - - +
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Residues in contact with SER 737 (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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638A PHE* 6.4 0.2 - - - -
687A LEU* 3.4 41.7 - - - +
690A GLU* 3.6 14.6 - - - +
691A GLY* 3.7 11.4 - - - -
733A GLN* 3.0 36.0 + - - +
736A SER* 1.3 75.0 + - - +
738A CYS* 1.3 65.1 + - - +
740A LEU* 4.0 0.5 - - - +
741A ALA* 3.0 24.1 + - - +
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Residues in contact with CYS 738 (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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687A LEU 5.2 0.7 - - - -
688A LEU* 5.0 9.2 - - + -
691A GLY* 4.0 18.4 - - - -
692A LEU 4.9 0.2 - - - -
695A LEU* 4.3 8.7 - - - -
734A ALA 3.0 25.4 + - - +
737A SER* 1.3 73.1 - - - +
739A GLY* 1.3 57.2 + - - +
741A ALA* 3.2 8.0 + - - +
742A ASP* 2.9 33.5 + - - +
795A TYR 3.6 8.7 - - - +
796A SER 3.4 19.3 - - - +
797A PHE* 3.7 29.6 - - + -
802A LEU* 5.7 0.6 - - - +
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Residues in contact with GLY 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A TYR* 3.7 18.6 - - - -
735A LYS 2.7 23.4 + - - -
736A SER* 4.0 0.4 - - - -
738A CYS* 1.3 71.1 - - - +
740A LEU* 1.3 61.7 + - - +
742A ASP* 3.1 8.6 + - - +
743A LYS* 3.0 23.0 + - - +
796A SER* 3.7 18.3 - - - -
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Residues in contact with LEU 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A TYR* 4.3 3.1 - - - +
638A PHE* 3.5 50.0 - - + +
641A ARG* 3.8 17.5 - - + +
642A TYR* 3.7 36.1 - - + +
645A SER* 4.2 6.1 - - - +
683A ASP* 4.6 4.5 - - + +
687A LEU* 3.6 21.3 - - + -
736A SER 3.1 17.8 + - - +
737A SER 4.1 2.2 - - - +
739A GLY* 1.3 74.6 - - - +
741A ALA* 1.3 52.6 + - - +
743A LYS* 3.1 3.1 + - + +
744A SER* 2.6 49.1 + - - +
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Residues in contact with ALA 741 (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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684A LEU* 3.8 25.3 - - + +
687A LEU* 4.0 11.8 - - + +
688A LEU* 4.5 10.1 - - + +
737A SER 3.0 20.6 + - - +
738A CYS* 3.2 8.9 + - - +
740A LEU* 1.3 75.3 - - - +
742A ASP* 1.3 61.4 + - - +
745A MET* 3.0 27.2 + - - +
802A LEU* 3.5 18.2 - - + +
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Residues in contact with ASP 742 (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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738A CYS* 2.9 12.5 + - - +
739A GLY* 3.4 11.2 - - - +
741A ALA* 1.3 76.3 - - - +
743A LYS* 1.3 68.8 + - + +
745A MET* 3.7 1.9 - - - +
746A LYS* 2.9 22.8 + - - +
796A SER* 3.6 10.5 - - - +
798A ASN* 3.5 32.3 + - - +
801A ASP* 3.9 12.3 - - - +
802A LEU* 3.9 34.4 + - - +
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Residues in contact with LYS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A TYR* 3.5 42.8 - - + +
645A SER* 3.5 26.7 - - - +
646A ILE* 3.9 21.6 - - + +
649A GLU* 3.1 28.9 + - - +
739A GLY 3.0 9.6 + - - +
740A LEU* 3.6 7.0 - - - +
742A ASP* 1.3 79.1 - - + +
744A SER* 1.3 65.0 + - - +
746A LYS* 3.0 8.7 + - + +
747A LEU* 2.9 24.8 + - + +
----------------------------------------------------------
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Residues in contact with SER 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A TYR* 3.8 10.2 + - - -
645A SER* 4.9 0.9 + - - -
680A MET* 3.8 21.7 + - - +
683A ASP* 5.9 0.7 - - - +
684A LEU* 3.4 26.5 - - - -
687A LEU* 4.6 3.2 - - - +
740A LEU* 2.6 39.7 + - - +
741A ALA 4.1 1.1 - - - -
743A LYS* 1.3 72.0 - - - +
745A MET* 1.3 63.6 + - - +
747A LEU* 3.2 6.4 + - - +
748A PHE* 2.9 25.6 + - - -
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Residues in contact with MET 745 (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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684A LEU* 3.9 28.7 - - + +
741A ALA 3.0 19.0 + - - +
742A ASP 3.7 2.0 - - - +
744A SER* 1.3 77.1 - - - +
746A LYS* 1.3 57.2 + - - +
748A PHE* 3.2 9.7 + - - +
749A GLU* 3.0 26.5 + - - +
771A MET* 4.6 4.0 - - - +
772A LEU* 4.3 9.2 - - - -
775A ASN* 4.3 17.9 - - + -
802A LEU* 3.6 23.8 - - + -
805A ALA* 3.8 8.7 - - + -
806A LEU* 3.7 55.2 - - + +
809A VAL* 4.2 5.9 - - - +
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Residues in contact with LYS 746 (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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649A GLU* 3.4 23.6 - - + +
653A TYR* 3.1 22.4 - - - +
742A ASP 2.9 13.2 + - - +
743A LYS* 3.0 12.5 + - + +
745A MET* 1.3 74.9 - - - +
747A LEU* 1.3 65.0 + - - +
749A GLU* 3.1 39.6 + - - +
750A ILE* 2.9 32.9 + - + +
805A ALA* 4.4 7.8 - - + +
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Residues in contact with LEU 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A SER* 3.5 36.3 - - - +
648A LEU* 4.0 16.8 - - + -
649A GLU* 4.0 37.5 - - + +
676A PHE* 4.6 2.7 - - + -
680A MET* 3.9 23.6 - - - -
743A LYS 2.9 15.7 + - - +
744A SER* 3.6 6.5 - - - +
746A LYS* 1.3 75.5 - - + +
748A PHE* 1.3 62.2 + - - +
750A ILE* 4.1 11.7 - - + -
751A TYR* 3.1 51.6 + - + +
----------------------------------------------------------
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Residues in contact with PHE 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A VAL* 4.1 9.4 - - + -
680A MET* 3.8 22.9 - - + +
681A LEU* 3.9 31.2 - - + -
684A LEU* 3.7 25.6 - - + -
744A SER 2.9 27.1 + - - -
745A MET* 3.2 12.3 + - - +
747A LEU* 1.3 72.3 - - - +
749A GLU* 1.3 57.9 + - - +
751A TYR* 4.3 1.7 - - - +
752A SER* 2.8 35.5 + - - -
759A PHE* 3.5 34.5 - + - -
768A LEU* 3.7 24.9 - - + -
771A MET* 3.9 10.8 - - + -
772A LEU* 5.8 0.7 - - + -
809A VAL* 3.7 19.1 - - + -
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Residues in contact with GLU 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A MET 3.0 13.4 + - - +
746A LYS* 3.1 40.1 + - - +
748A PHE* 1.3 77.0 - - - +
750A ILE* 1.3 67.8 + - - +
752A SER* 3.2 5.3 + - - -
753A LYS* 3.3 4.0 + - - +
804A LYS* 5.0 1.2 - - - +
805A ALA* 3.4 27.7 - - - +
808A THR* 3.7 31.3 + - + +
809A VAL* 3.6 15.5 - - + -
812A ASN* 3.0 23.0 + - - +
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Residues in contact with ILE 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A GLU* 4.4 6.7 - - + -
652A TYR* 3.6 47.6 - - + -
653A TYR* 4.1 28.0 - - + +
746A LYS* 2.9 33.7 + - + +
747A LEU* 3.7 26.2 - - + +
749A GLU* 1.3 82.9 - - + +
751A TYR* 1.3 73.3 + - + +
753A LYS* 3.2 18.3 - - - +
754A ASP* 3.7 3.8 - - - +
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Residues in contact with TYR 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A LEU* 5.2 0.7 - - - +
648A LEU* 3.8 31.9 + - - +
652A TYR* 3.5 31.9 - + + -
662A LEU* 2.8 41.1 - - + +
673A PHE* 4.6 7.2 - + - -
676A PHE* 3.9 25.8 - + - -
677A VAL* 5.9 0.2 - - + -
680A MET* 4.9 3.1 - - + -
747A LEU* 3.1 35.0 + - + +
750A ILE* 1.3 79.9 - - + +
752A SER* 1.4 57.6 + - - +
753A LYS 3.0 4.9 - - - -
754A ASP* 3.0 4.9 + - - +
755A ILE* 2.8 35.7 + - + +
759A PHE* 3.7 23.8 - + + -
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Residues in contact with SER 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A PHE* 2.8 25.5 + - - -
749A GLU* 3.2 1.9 + - - -
751A TYR* 1.4 75.6 - - - +
753A LYS* 1.3 60.6 + - - +
754A ASP 3.3 0.2 - - - -
756A PRO* 3.4 24.8 - - - +
759A PHE* 3.8 19.3 - - - -
809A VAL* 4.0 10.6 - - - -
812A ASN* 3.1 32.2 + - - +
813A LEU* 3.8 23.3 - - - -
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Residues in contact with LYS 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A GLU 3.4 10.1 - - - +
750A ILE* 3.2 18.6 - - - +
752A SER* 1.3 83.1 + - - +
754A ASP* 1.3 68.6 + - - +
756A PRO* 4.2 4.2 - - - +
808A THR* 6.3 0.2 - - + -
812A ASN* 3.6 24.6 + - - +
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Residues in contact with ASP 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A TYR* 2.4 36.0 + - - +
659A LYS* 3.2 28.3 + - - -
663A ILE* 4.6 13.3 - - + +
750A ILE 3.7 3.6 - - - +
751A TYR 3.0 3.5 + - - +
753A LYS* 1.3 86.2 - - - +
755A ILE* 1.3 66.8 + - + +
756A PRO* 3.3 9.9 - - - +
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Residues in contact with ILE 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A TYR* 5.2 0.2 - - - +
662A LEU* 4.0 24.0 - - + -
663A ILE* 4.2 25.1 - - + -
666A SER* 3.2 42.6 - - - +
667A GLN* 4.4 10.8 - - + +
673A PHE* 4.0 10.8 - - + -
751A TYR* 2.8 20.0 + - + +
754A ASP* 1.3 83.4 - - + +
756A PRO* 1.3 68.2 - - - +
757A ALA 2.8 5.0 + - - -
758A ALA* 3.0 18.7 + - + +
759A PHE* 3.5 11.7 - - + -
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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