Contacts of the helix formed by residues 790 - 827 (chain A) in PDB entry 5I4E
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 GLY 790 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734A ASN* 4.1 6.1 + - - -
788A ARG 3.4 0.6 + - - -
789A ALA* 1.3 72.5 - - - +
791A VAL* 1.4 61.0 + - - +
792A LEU 3.4 2.9 - - - -
793A ALA* 3.8 15.8 - - - +
794A GLN* 3.4 26.5 + - - +
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Residues in contact with VAL 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 5.3 9.2 - - + -
777A LEU* 3.9 48.0 - - + +
787A PHE* 3.5 32.1 - - + -
788A ARG* 3.2 22.7 + - + +
789A ALA 4.3 2.7 - - - +
790A GLY* 1.4 74.0 - - - +
792A LEU* 1.3 63.3 + - - +
794A GLN* 3.6 5.1 + - - +
795A LEU* 3.2 29.9 + - + +
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Residues in contact with LEU 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A ASN* 3.8 32.1 + - + +
735A ARG 4.8 4.9 - - - +
736A ILE* 4.5 19.1 - - + -
745A TYR* 3.7 32.4 + - + +
787A PHE* 3.7 37.6 - - + +
788A ARG 5.0 0.2 + - - -
790A GLY* 4.5 0.4 - - - -
791A VAL* 1.3 76.3 - - - +
793A ALA* 1.4 53.4 + - - +
795A LEU* 2.9 14.8 + - + +
796A GLU* 2.9 39.5 + - + +
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Residues in contact with ALA 793 (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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168A HIS* 4.6 26.4 - - + +
790A GLY* 3.8 18.5 + - - +
792A LEU* 1.4 75.7 - - - +
794A GLN* 1.3 60.1 + - - +
796A GLU* 3.9 9.0 - - - +
797A GLU* 3.3 28.1 + - - +
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Residues in contact with GLN 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A GLY 3.4 15.7 + - - +
791A VAL* 4.0 5.6 - - - +
792A LEU 3.2 0.8 - - - -
793A ALA* 1.3 77.5 - - - +
795A LEU* 1.4 60.6 + - + +
796A GLU 3.4 0.4 - - - -
797A GLU* 3.5 15.2 + - - +
798A GLU* 3.1 37.4 + - + +
880A GLU* 5.9 1.0 + - - -
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Residues in contact with LEU 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A PHE* 4.2 25.8 - - + -
745A TYR* 3.7 19.4 - - + -
748A LEU* 3.9 13.8 - - + +
771A LEU* 4.5 14.1 - - + -
773A LEU* 4.6 18.8 - - + -
787A PHE* 4.6 5.2 - - + -
791A VAL* 3.2 27.4 + - + +
792A LEU* 2.9 19.8 + - + +
794A GLN* 1.4 74.7 - - + +
796A GLU* 1.4 53.7 + - - +
798A GLU* 3.6 23.2 - - - +
799A ARG* 2.8 34.8 + - - +
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Residues in contact with GLU 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LYS* 6.0 6.5 - - - -
744A ARG* 2.7 47.3 + - - +
745A TYR* 2.8 23.5 + - - +
792A LEU* 2.9 22.0 + - + +
793A ALA* 3.9 10.1 - - - +
795A LEU* 1.4 73.5 - - - +
797A GLU* 1.4 61.9 + - + +
799A ARG* 3.9 11.9 + - - +
800A ALA* 3.2 26.7 + - - +
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Residues in contact with GLU 797 (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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168A HIS* 5.6 10.7 - - + -
169A GLU* 5.6 2.2 - - - +
793A ALA 3.3 16.3 + - - +
794A GLN* 3.5 21.2 + - - +
795A LEU 3.3 0.2 - - - -
796A GLU* 1.4 78.5 - - + +
798A GLU* 1.4 59.8 + - - +
800A ALA* 3.6 6.6 + - - +
801A SER* 3.0 26.7 + - - -
873A LYS* 4.5 21.3 + - - +
875A ARG* 5.5 4.5 + - - -
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Residues in contact with GLU 798 (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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748A LEU* 3.4 23.0 - - + +
771A LEU* 4.9 6.4 - - - +
794A GLN* 3.1 26.6 + - + +
795A LEU* 3.3 25.2 + - - +
797A GLU* 1.4 72.6 - - - +
799A ARG* 1.3 61.4 + - - +
801A SER* 3.4 7.7 - - - -
802A GLU* 3.0 24.1 + - - +
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Residues in contact with ARG 799 (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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743A GLN* 5.5 3.8 + - - +
744A ARG* 2.8 85.7 + - - +
745A TYR* 3.9 13.7 - - + -
747A ILE* 3.6 18.6 - - + +
748A LEU* 3.7 9.8 - - + +
795A LEU 2.8 17.4 + - - +
796A GLU* 3.9 12.9 + - - +
798A GLU* 1.3 74.3 - - - +
800A ALA* 1.4 54.7 + - - +
802A GLU* 3.3 2.4 + - - +
803A GLN* 2.9 72.4 + - - +
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Residues in contact with ALA 800 (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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796A GLU 3.2 20.4 + - - +
797A GLU* 3.8 11.2 - - - +
799A ARG* 1.4 75.8 - - - +
801A SER* 1.3 61.7 + - - +
803A GLN* 3.7 14.0 - - - +
804A THR* 3.0 29.5 + - - -
873A LYS* 4.5 16.9 - - - +
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Residues in contact with SER 801 (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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797A GLU 3.0 19.1 + - - -
798A GLU* 3.4 11.0 - - - -
800A ALA* 1.3 75.4 - - - +
802A GLU* 1.4 58.4 + - - +
804A THR* 3.4 4.3 + - - -
805A LYS* 2.9 28.4 + - - +
870A LEU* 3.8 16.7 - - - +
873A LYS* 4.5 7.2 - - - +
874A LEU* 3.2 30.6 - - - +
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Residues in contact with GLU 802 (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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747A ILE* 3.8 33.8 - - + +
748A LEU* 4.1 13.7 - - + -
750A PRO* 6.1 0.3 - - - +
798A GLU 3.0 19.1 + - - +
799A ARG 3.3 4.0 + - - +
801A SER* 1.4 72.2 - - - +
803A GLN* 1.3 56.0 + - - +
805A LYS* 3.5 43.5 + - - +
806A SER* 2.8 36.2 + - - -
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Residues in contact with GLN 803 (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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747A ILE* 3.9 20.3 - - + +
799A ARG* 2.9 58.4 + - - +
800A ALA* 3.7 13.9 - - - +
801A SER 3.3 0.2 - - - -
802A GLU* 1.3 74.8 - - - +
804A THR* 1.3 57.6 + - - +
806A SER* 3.6 2.6 + - - -
807A ASP* 3.1 28.1 + - - +
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Residues in contact with THR 804 (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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800A ALA 3.0 17.4 + - - -
801A SER 3.7 3.8 - - - -
802A GLU 3.3 0.2 - - - -
803A GLN* 1.3 74.3 - - - +
805A LYS* 1.3 60.3 + - - +
807A ASP* 3.4 5.5 + - - +
808A TYR* 3.0 29.8 + - - +
866A ILE* 4.1 18.9 - - + +
869A SER* 5.7 2.0 - - - +
870A LEU* 3.8 32.5 - - + -
873A LYS* 5.5 4.3 - - + +
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Residues in contact with LYS 805 (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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801A SER* 2.9 18.2 + - - +
802A GLU* 3.4 39.3 + - - +
804A THR* 1.3 76.8 - - - +
806A SER* 1.3 58.0 + - - +
808A TYR* 4.0 2.3 - - - +
809A LEU* 3.2 58.0 + - + +
870A LEU* 3.9 12.0 - - + +
883A VAL* 4.0 30.7 - - + -
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Residues in contact with SER 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ILE* 4.1 17.0 - - - +
802A GLU* 2.8 23.1 + - - -
803A GLN 3.8 4.9 - - - -
805A LYS* 1.3 74.9 - - - +
807A ASP* 1.4 57.5 + - - +
809A LEU* 3.5 5.6 + - - +
810A LYS* 3.1 29.5 + - - +
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Residues in contact with ASP 807 (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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803A GLN 3.1 18.0 + - - +
804A THR* 3.4 6.0 + - - +
806A SER* 1.4 71.6 - - - +
808A TYR* 1.4 64.8 + - - +
810A LYS* 3.6 9.1 + - - +
811A ARG* 3.1 58.6 + - - +
866A ILE* 5.2 4.2 - - - +
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Residues in contact with TYR 808 (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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804A THR 3.0 18.4 + - - +
805A LYS* 4.0 5.2 - - - +
807A ASP* 1.4 77.1 + - - +
809A LEU* 1.3 74.2 + - + +
810A LYS 3.4 0.2 + - - -
811A ARG* 3.8 0.6 - - - +
812A ALA* 2.9 48.1 + - + +
863A LEU* 3.2 54.4 - - + +
866A ILE* 4.1 18.5 - - + +
867A TYR* 3.5 24.1 - + + +
870A LEU* 5.4 5.8 - - + -
883A VAL* 6.2 2.0 - - + -
885A PRO* 5.1 5.6 - - + -
888A LEU* 2.9 29.5 + - + -
889A THR 4.2 0.2 - - - -
890A PRO* 3.5 22.9 - - - +
893A ILE* 4.8 2.8 - - - +
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Residues in contact with LEU 809 (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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805A LYS* 3.2 49.9 + - + +
806A SER* 3.8 6.1 - - - +
807A ASP 3.4 0.2 - - - -
808A TYR* 1.3 91.4 - - + +
810A LYS* 1.3 57.6 + - - +
812A ALA* 4.2 2.8 - - - +
813A ASN* 2.8 41.2 + - - +
883A VAL* 4.9 6.3 - - + -
885A PRO* 4.5 20.6 - - + -
888A LEU* 4.5 12.7 - - + +
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Residues in contact with LYS 810 (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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806A SER* 3.1 17.7 + - - +
807A ASP* 3.8 9.2 - - - +
808A TYR 3.3 0.2 - - - -
809A LEU* 1.3 76.3 - - - +
811A ARG* 1.3 64.7 + - + +
813A ASN* 3.3 6.9 + - - +
814A GLU* 3.1 62.1 + - + +
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Residues in contact with ARG 811 (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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807A ASP* 3.1 49.2 + - - +
810A LYS* 1.3 85.9 - - + +
812A ALA* 1.3 57.0 + - - +
814A GLU* 3.2 11.8 + - - +
815A LEU* 2.9 29.8 + - - +
859A GLU* 3.1 42.2 + - - +
862A GLU* 4.1 19.8 + - - +
863A LEU* 3.7 19.1 - - + +
866A ILE* 3.9 29.4 - - - +
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Residues in contact with ALA 812 (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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808A TYR* 2.9 43.5 + - + +
809A LEU 4.5 2.2 - - - +
811A ARG* 1.3 72.0 - - - +
813A ASN* 1.3 59.3 + - - +
815A LEU* 4.0 5.4 - - - +
816A VAL* 3.4 18.0 + - - +
863A LEU* 3.9 16.7 - - + +
888A LEU* 3.4 29.0 - - + +
893A ILE* 4.4 9.8 - - + +
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Residues in contact with ASN 813 (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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809A LEU* 2.8 32.3 + - - +
810A LYS* 3.6 6.4 - - - +
811A ARG 3.2 0.8 - - - -
812A ALA* 1.3 76.3 - - - +
814A GLU* 1.3 60.6 + - + +
816A VAL* 3.7 3.8 + - - +
817A GLN* 3.1 26.7 + - - +
888A LEU* 3.4 28.1 - - - +
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Residues in contact with GLU 814 (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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810A LYS* 3.1 52.2 + - + +
811A ARG* 3.2 14.6 + - - +
813A ASN* 1.3 77.0 - - + +
815A LEU* 1.4 57.3 + - - +
817A GLN* 3.5 7.8 + - - +
818A TRP* 3.0 28.8 + - - +
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Residues in contact with LEU 815 (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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811A ARG 2.9 16.5 + - - +
812A ALA* 4.0 5.8 - - - +
814A GLU* 1.4 74.3 - - - +
816A VAL* 1.4 59.4 + - + +
818A TRP* 3.3 5.6 + - - +
819A ILE* 3.0 43.9 + - + +
856A LYS* 4.0 27.6 - - + +
859A GLU* 3.8 26.7 - - + -
860A VAL* 3.8 26.9 - - + -
863A LEU* 3.9 20.9 - - + -
893A ILE* 3.9 24.0 - - + -
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Residues in contact with VAL 816 (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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812A ALA 3.4 18.1 + - - +
813A ASN* 4.1 4.0 - - - +
815A LEU* 1.4 74.3 - - + +
817A GLN* 1.3 60.4 + - - +
819A ILE* 3.6 15.0 - - + +
820A ASN* 3.0 50.8 + - - +
887A GLY 4.7 4.5 - - - +
888A LEU* 4.0 13.7 - - + -
893A ILE* 3.7 24.2 - - + -
896A THR* 4.9 6.1 - - + +
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Residues in contact with GLN 817 (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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813A ASN 3.1 18.8 + - - +
814A GLU* 3.6 9.6 - - - +
815A LEU 3.4 0.2 - - - -
816A VAL* 1.3 75.3 - - - +
818A TRP* 1.3 58.9 + - - +
820A ASN* 4.3 2.9 - - - +
821A ASP* 3.3 61.5 + - - +
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Residues in contact with TRP 818 (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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814A GLU 3.0 16.9 + - - +
815A LEU* 3.6 6.7 - - + +
816A VAL 3.2 0.2 - - - -
817A GLN* 1.3 76.5 - - - +
819A ILE* 1.4 82.8 + - + +
821A ASP* 3.5 3.8 + - - +
822A LYS* 3.1 41.5 + - + +
848A TYR* 3.8 34.5 - + - -
852A GLU* 4.0 27.7 + - + +
853A LYS* 4.7 4.7 - - + -
856A LYS* 3.4 58.6 - - + +
897A TRP* 5.5 0.7 - - - -
900A LEU* 4.3 13.2 - - + -
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Residues in contact with ILE 819 (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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815A LEU* 3.0 33.0 + - + +
816A VAL* 3.6 16.8 - - + +
818A TRP* 1.4 101.6 - - + +
820A ASN* 1.4 65.9 + - - +
823A GLN* 3.1 28.2 + - - +
856A LYS* 5.6 0.7 - - + -
893A ILE* 4.8 4.7 - - + +
896A THR* 3.4 46.4 - - - +
897A TRP* 4.1 16.2 - - + +
900A LEU* 3.4 26.4 - - + +
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Residues in contact with ASN 820 (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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816A VAL* 3.0 37.5 + - - +
817A GLN* 4.5 4.0 - - - +
819A ILE* 1.4 84.1 - - - +
821A ASP* 1.3 66.4 + - - +
823A GLN* 3.8 9.4 + - - +
824A ALA* 3.4 20.3 + - - +
896A THR* 5.1 8.3 - - - +
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Residues in contact with ASP 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A GLN* 3.3 40.8 + - - +
818A TRP* 3.8 5.6 - - + +
819A ILE 3.4 0.6 - - - -
820A ASN* 1.3 79.0 - - - +
822A LYS* 1.4 65.3 + - + +
824A ALA* 3.5 8.8 + - - +
825A SER* 3.3 18.5 + - - -
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Residues in contact with LYS 822 (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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818A TRP* 3.1 44.9 + - + +
819A ILE* 4.9 0.7 - - - -
821A ASP* 1.4 76.9 - - + +
823A GLN* 1.4 59.6 + - - +
825A SER* 3.1 19.8 + - - -
826A LEU* 3.0 33.7 + - - +
848A TYR* 3.7 42.1 - - + +
852A GLU* 4.3 13.3 + - - +
900A LEU* 4.3 6.7 - - + -
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Residues in contact with GLN 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A ILE 3.1 20.1 + - - +
820A ASN* 3.8 12.1 - - - +
822A LYS* 1.4 73.6 - - - +
824A ALA* 1.4 58.2 + - - +
826A LEU* 3.1 26.5 + - - +
827A GLU* 3.1 41.4 + - - +
896A THR 4.3 2.4 - - - +
899A ALA* 3.1 44.0 + - - +
900A LEU* 3.4 9.6 + - + +
903A ALA* 3.8 12.0 - - + +
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Residues in contact with ALA 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A ASN 3.4 10.8 + - - +
821A ASP* 3.6 11.7 - - - +
822A LYS 3.3 0.4 - - - -
823A GLN* 1.4 77.5 - - - +
825A SER* 1.3 59.0 + - - +
826A LEU 3.4 0.2 - - - -
827A GLU* 3.8 24.5 + - - +
828A SER* 4.1 6.6 + - - -
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Residues in contact with SER 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A ASP 3.3 10.5 + - - -
822A LYS* 3.1 30.4 + - - -
824A ALA* 1.3 77.3 - - - +
826A LEU* 1.3 60.9 + - - +
827A GLU 3.5 0.2 - - - -
828A SER* 3.8 15.6 + - - -
841A PHE* 5.8 2.8 - - - -
907A HIS* 4.2 9.4 - - - -
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Residues in contact with LEU 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A LYS* 3.0 20.5 + - + +
823A GLN* 3.1 8.7 + - - +
825A SER* 1.3 79.8 - - - +
827A GLU* 1.4 56.8 + - - +
828A SER 3.8 1.8 + - - -
829A ARG* 3.3 13.5 + - - -
845A HIS* 3.9 14.8 - - + -
848A TYR* 4.5 11.9 - - + +
900A LEU* 4.0 26.9 - - + +
903A ALA* 3.8 15.4 - - + +
904A GLU* 3.8 26.2 - - + -
907A HIS* 2.8 55.6 + - + +
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Residues in contact with GLU 827 (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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823A GLN* 3.1 45.2 + - + +
824A ALA* 3.8 11.9 + - - +
825A SER 3.5 0.2 - - - -
826A LEU* 1.4 76.2 - - + +
828A SER* 1.3 57.6 - - - +
829A ARG* 3.9 18.6 - - + +
903A ALA* 5.5 4.7 - - + -
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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) + - + + + + + -
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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