Contacts of the helix formed by residues 723 - 757 (chain A) in PDB entry 2YEV
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 723 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A VAL* 4.3 2.6 - - - +
649A THR 3.7 14.8 + - - +
651A PRO* 4.0 16.7 - - - +
718A SER* 4.1 5.8 - - - +
719A SER 3.2 11.4 + - - +
720A TRP 3.9 4.8 - - - +
721A GLN 3.6 0.8 - - - -
722A GLU* 1.3 82.3 + - - +
724A LEU* 1.3 64.0 + - - +
725A TRP* 3.1 12.1 + - - +
726A THR* 2.8 41.2 + - - +
727A ALA* 3.1 20.6 + - - +
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Residues in contact with LEU 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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228A SER 3.5 24.5 - - - +
229A TRP* 3.8 20.6 - - + +
234A VAL* 3.6 24.6 + - + +
235A GLY 3.5 29.8 - - - +
236A GLY* 3.8 7.6 - - - +
642A LEU* 4.0 23.8 - - + -
647A ALA* 3.8 22.4 - - + +
648A ALA* 4.1 7.9 - - + -
722A GLU 4.4 0.2 - - - -
723A ASN* 1.3 70.7 + - - +
725A TRP* 1.3 62.6 + - - +
727A ALA* 3.2 7.2 + - + +
728A ALA* 2.9 26.8 + - + +
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Residues in contact with TRP 725 (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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639A TYR* 2.9 34.2 + + - -
643A ARG* 3.6 7.9 - - - +
648A ALA* 4.0 12.0 - - + +
649A THR 3.4 25.5 - - - +
650A PRO* 3.6 30.3 - - + +
651A PRO* 3.5 19.1 - - + -
654A ARG* 3.9 26.2 - - + -
655A PRO* 4.4 2.7 - - + -
714A PHE* 3.7 22.4 - + - -
723A ASN* 3.1 3.2 + - - +
724A LEU* 1.3 77.6 - - - +
726A THR* 1.3 61.7 + - - +
728A ALA* 3.1 5.0 + - - +
729A PHE* 2.8 50.0 + + + -
788A PHE* 3.5 37.0 - + - -
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Residues in contact with THR 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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651A PRO* 3.7 3.5 - - - +
714A PHE* 3.5 15.3 - - + -
718A SER* 2.8 33.1 + - - +
719A SER 4.1 0.9 - - - -
720A TRP* 3.9 17.3 - - - +
723A ASN* 2.8 25.1 + - - -
725A TRP* 1.3 82.6 - - - +
727A ALA* 1.3 62.2 + - - +
729A PHE* 3.3 2.1 + - - +
730A PHE* 3.0 56.4 + - + -
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Residues in contact with ALA 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.8 17.8 - - + +
228A SER 3.7 21.1 - - - +
229A TRP* 4.1 2.9 - - + -
720A TRP* 3.6 30.0 - - - +
723A ASN 3.1 8.0 + - - +
724A LEU* 3.2 10.3 + - + +
726A THR* 1.3 78.3 - - - +
728A ALA* 1.3 53.7 + - - +
730A PHE 3.5 0.2 + - - -
731A THR* 2.7 38.4 + - - -
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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
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229A TRP* 3.8 26.1 - - + +
639A TYR* 3.7 30.3 - - + -
642A LEU* 5.7 3.8 - - + -
648A ALA* 5.6 2.0 - - + -
724A LEU* 2.9 13.4 + - + +
725A TRP* 3.1 10.1 + - - +
727A ALA* 1.3 75.8 - - - +
729A PHE* 1.3 63.5 + - - +
731A THR* 3.2 0.9 + - - -
732A ILE* 2.9 29.5 + - - +
788A PHE* 3.8 2.6 - - + -
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Residues in contact with PHE 729 (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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655A PRO* 3.6 21.1 - - + -
710A GLU* 4.0 4.0 - - - -
711A PHE* 3.9 26.0 - + - -
714A PHE* 3.8 28.0 - + + -
725A TRP* 2.8 49.0 + + + +
726A THR 3.6 4.5 - - - +
728A ALA* 1.3 73.3 - - - +
730A PHE* 1.3 64.9 + + - +
733A VAL* 2.8 54.4 + - + +
788A PHE* 3.6 19.0 - + + -
789A TYR* 3.3 38.4 - + - -
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Residues in contact with PHE 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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227A LEU* 4.0 18.6 - - + -
711A PHE* 3.6 44.5 - + + -
714A PHE* 3.5 25.6 - + + -
715A TYR* 3.7 35.4 - + + -
718A SER 4.8 0.9 - - - -
720A TRP* 3.8 26.9 - + + -
726A THR* 3.0 41.7 + - + +
729A PHE* 1.3 81.5 - + - +
731A THR* 1.3 57.5 + - - +
734A GLY* 3.0 27.4 + - - +
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Residues in contact with THR 731 (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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217A LEU* 5.4 6.9 - - + +
218A LEU* 3.7 23.6 - - + -
221A LEU* 4.7 11.5 - - + +
227A LEU* 3.2 17.1 - - - +
229A TRP* 2.9 25.5 + - + +
635A LEU* 4.6 12.3 - - + -
727A ALA 2.7 22.5 + - - -
728A ALA 3.6 2.7 - - - -
729A PHE 3.1 0.2 - - - -
730A PHE* 1.3 78.0 - - - +
732A ILE* 1.3 60.4 + - - +
735A LEU* 2.9 30.9 + - + +
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Residues in contact with ILE 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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229A TRP* 3.8 16.4 - - + -
632A PHE* 4.0 16.1 - - + -
635A LEU* 3.6 45.8 - - + +
636A ILE* 4.1 12.1 - - + +
639A TYR* 3.9 6.5 - - + -
728A ALA 2.9 15.3 + - - +
731A THR* 1.3 73.7 - - + +
733A VAL* 1.3 62.5 + - - +
735A LEU* 3.4 4.9 + - - +
736A HIS* 3.0 25.5 + - - +
784A ILE* 4.2 18.2 - - + -
788A PHE* 3.7 33.9 - - + -
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Residues in contact with VAL 733 (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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707A GLN* 3.5 23.6 + - - +
711A PHE* 3.5 24.4 - - + -
729A PHE* 2.8 44.8 + - + +
732A ILE* 1.3 69.3 - - - +
734A GLY* 1.3 59.9 + - - +
736A HIS* 3.2 7.6 + - + +
737A GLY* 2.9 24.9 + - - -
781A TRP* 4.3 7.4 - - + -
784A ILE* 3.7 23.3 - - + -
788A PHE* 4.0 12.6 - - + -
789A TYR* 3.7 8.3 - - - +
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Residues in contact with GLY 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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711A PHE* 3.6 19.8 - - - -
729A PHE 3.7 0.2 + - - -
730A PHE 3.0 22.1 + - - -
733A VAL* 1.3 79.3 - - - +
735A LEU* 1.3 60.6 + - - +
737A GLY* 3.0 12.3 + - - -
738A LEU* 3.0 12.5 + - - +
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Residues in contact with LEU 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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217A LEU* 4.5 21.5 - - + -
631A LEU* 3.7 24.7 - - + -
632A PHE* 4.3 11.7 - - + -
635A LEU* 3.7 30.1 - - + -
731A THR* 2.9 21.3 + - + +
732A ILE 3.7 4.5 - - - +
733A VAL 3.3 0.2 - - - -
734A GLY* 1.3 75.0 - - - +
736A HIS* 1.3 62.8 + - - +
738A LEU* 3.1 29.9 + - + +
739A HIS* 2.8 36.0 + - + -
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Residues in contact with HIS 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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632A PHE* 4.0 12.0 - + + -
667A LEU* 4.3 0.9 - - + -
703A PHE* 3.7 12.0 - + - -
707A GLN* 5.3 1.0 + - - -
732A ILE 3.0 8.4 + - - +
733A VAL* 3.4 8.8 + - - +
735A LEU* 1.3 76.0 - - - +
737A GLY* 1.3 63.7 + - - +
739A HIS* 3.0 15.9 + - + +
740A VAL* 3.0 34.4 + - + +
777A VAL* 3.0 33.9 + - + +
780A VAL* 3.9 22.7 - - + -
781A TRP* 3.6 32.0 - + + +
784A ILE* 3.4 26.0 - - + -
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Residues in contact with GLY 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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703A PHE* 5.5 3.8 - - - -
704A PHE* 4.5 10.4 - - - -
707A GLN* 6.0 5.8 - - - -
711A PHE* 6.1 1.1 - - - -
733A VAL 2.9 14.7 + - - -
734A GLY* 3.0 6.2 + - - -
736A HIS* 1.3 80.1 + - - +
738A LEU* 1.3 61.3 + - - +
740A VAL* 3.0 19.2 + - - +
741A VAL* 3.1 17.6 + - - +
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Residues in contact with LEU 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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734A GLY 3.0 10.5 + - - +
735A LEU* 3.3 27.6 - - + +
737A GLY* 1.3 76.0 - - - +
739A HIS* 1.3 59.0 + - + +
741A VAL* 3.3 15.6 + - + +
742A ILE* 3.0 47.0 + - + +
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Residues in contact with HIS 739 (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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628A GLU* 2.9 32.1 + - - -
631A LEU* 4.6 5.6 - - + +
632A PHE* 3.7 25.8 - + + -
735A LEU* 2.8 46.5 + - + +
736A HIS* 3.0 13.1 + - + +
738A LEU* 1.3 79.2 - - + +
740A VAL* 1.3 55.8 + - - +
742A ILE* 3.7 8.3 - - + +
743A GLY* 2.7 33.6 + - - -
773A TYR* 3.0 27.5 - + - +
776A LEU* 6.0 2.5 - - + -
777A VAL* 3.8 21.3 - - + +
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Residues in contact with VAL 740 (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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667A LEU* 5.0 3.8 - - + -
700A GLY 4.1 20.9 - - - +
703A PHE* 3.7 22.4 - - + -
704A PHE* 4.3 13.7 - - + -
736A HIS* 3.0 29.6 + - + +
737A GLY* 3.0 10.7 + - - +
739A HIS* 1.3 74.8 - - - +
741A VAL* 1.3 54.6 + - - +
744A GLY* 2.7 32.4 + - - -
774A TRP* 3.6 14.9 - - + -
777A VAL* 3.6 26.5 - - + -
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Residues in contact with VAL 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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704A PHE* 3.5 37.2 - - + -
737A GLY 3.1 8.9 + - - +
738A LEU* 3.4 21.1 - - + +
739A HIS 3.2 0.2 - - - -
740A VAL* 1.3 77.2 - - - +
742A ILE* 1.3 60.1 + - + +
744A GLY* 3.3 1.7 + - - -
745A PHE* 2.9 30.3 + - + +
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Residues in contact with ILE 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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165A PHE* 6.3 3.6 - - + -
738A LEU* 3.0 43.5 + - + +
739A HIS* 3.2 9.8 + - + +
741A VAL* 1.3 75.4 - - + +
743A GLY* 1.3 60.7 + - - +
745A PHE* 3.2 8.5 + - - +
746A GLY* 2.9 24.6 + - - -
773A TYR* 3.9 25.8 - - + +
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Residues in contact with GLY 743 (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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739A HIS 2.7 20.7 + - - -
740A VAL 3.9 0.7 - - - -
742A ILE* 1.3 74.3 - - - +
744A GLY* 1.3 60.5 + - - +
746A GLY* 3.2 3.0 + - - -
747A LEU* 3.0 27.4 + - - +
770A ALA* 5.0 3.4 - - - +
773A TYR* 3.7 22.6 - - - -
774A TRP* 3.7 16.3 - - - -
777A VAL* 5.1 0.2 - - - -
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Residues in contact with GLY 744 (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 ILE* 4.7 5.2 - - - +
740A VAL 2.7 23.0 + - - -
741A VAL* 3.7 1.8 - - - -
743A GLY* 1.3 73.6 - - - +
745A PHE* 1.3 55.1 + - - +
747A LEU* 3.1 9.5 + - - +
748A ILE* 2.9 36.2 + - - +
774A TRP* 3.5 11.3 - - - -
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Residues in contact with PHE 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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590A ALA* 3.7 40.6 - - + -
593A LEU* 4.0 23.1 - - + -
594A VAL* 4.0 15.9 - - + -
741A VAL* 2.9 19.5 + - + +
742A ILE* 3.5 7.6 - - - +
744A GLY* 1.3 76.1 - - - +
746A GLY* 1.3 55.9 + - - +
748A ILE* 3.0 23.0 + - + +
749A LEU* 2.8 55.0 + - + +
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Residues in contact with GLY 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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742A ILE 2.9 14.7 + - - -
743A GLY* 3.2 4.7 + - - -
744A GLY 3.2 0.2 - - - -
745A PHE* 1.3 77.2 - - - +
747A LEU* 1.3 60.9 + - - +
749A LEU* 3.3 15.6 + - - +
750A ALA* 3.3 15.9 + - - +
766A THR* 4.4 2.7 - - - +
770A ALA* 3.5 23.0 - - - +
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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
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674A VAL* 4.1 16.6 - - + -
693A LEU* 3.7 24.3 - - + +
696A THR* 3.6 29.2 - - + -
697A ILE* 3.9 20.5 - - + +
743A GLY 3.0 12.4 + - - +
744A GLY* 3.5 9.2 - - - +
746A GLY* 1.3 75.3 - - - +
748A ILE* 1.3 58.7 + - - +
750A ALA* 3.2 6.5 + - - +
751A TYR* 3.0 26.9 + - - +
767A LEU* 5.0 2.7 - - + -
770A ALA* 4.1 25.8 - - + +
771A SER* 4.3 1.6 - - - +
774A TRP* 3.6 31.2 - - + -
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Residues in contact with ILE 748 (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 ILE* 3.9 33.2 - - + -
701A VAL* 6.1 2.9 - - + -
744A GLY 2.9 20.0 + - - +
745A PHE* 3.3 26.5 - - + +
747A LEU* 1.3 74.1 - - - +
749A LEU* 1.3 60.7 + - + +
751A TYR* 3.5 5.7 - - + +
752A LEU* 2.9 47.0 + - + +
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Residues in contact with LEU 749 (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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593A LEU* 3.8 13.0 - - + +
594A VAL* 3.8 40.2 - - + -
597A ALA* 3.9 20.7 - - + +
745A PHE* 2.8 42.8 + - + +
746A GLY* 3.5 14.4 - - - +
747A LEU 3.3 0.2 - - - -
748A ILE* 1.3 77.2 - - - +
750A ALA* 1.3 57.2 + - - +
752A LEU* 3.3 10.4 + - + +
753A GLN* 3.0 33.0 + - - +
766A THR* 4.3 9.4 - - + -
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Residues in contact with ALA 750 (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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693A LEU* 3.9 13.6 - - + +
746A GLY 3.3 8.0 + - - +
747A LEU* 3.2 11.8 + - - +
749A LEU* 1.3 78.8 - - - +
751A TYR* 1.3 58.4 + - - +
753A GLN* 3.2 15.8 - - - +
754A ALA* 2.9 26.5 + - - +
759A ILE* 3.9 5.0 - - + +
766A THR* 4.1 4.2 - - + +
767A LEU* 4.1 33.7 - - + +
770A ALA* 5.1 1.1 - - + -
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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
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690A ARG* 3.6 28.5 - - + -
693A LEU* 3.5 16.3 - - + +
694A LEU* 3.8 42.9 - - + +
697A ILE* 4.0 13.0 - - + -
747A LEU 3.0 13.2 + - - +
748A ILE* 3.5 11.0 - - + +
750A ALA* 1.3 74.1 - - - +
752A LEU* 1.3 67.5 + - + +
754A ALA* 3.0 8.7 + - + +
755A LEU* 2.9 67.4 + - + +
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Residues in contact with LEU 752 (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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594A VAL* 4.0 36.3 - - + -
597A ALA* 6.5 0.2 - - + -
598A LEU* 4.0 15.3 - - + -
748A ILE* 2.9 37.3 + - + +
749A LEU* 3.7 8.7 - - + +
751A TYR* 1.3 82.8 - - + +
753A GLN* 1.3 62.1 + - - +
755A LEU* 3.3 15.3 + - + +
756A ARG* 3.2 28.2 + - - +
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Residues in contact with GLN 753 (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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597A ALA* 2.8 34.9 + - + +
598A LEU* 3.9 12.3 - - + -
749A LEU 3.0 17.9 + - - +
750A ALA* 3.2 9.1 - - - +
751A TYR 3.1 0.2 - - - -
752A LEU* 1.3 77.6 - - - +
754A ALA* 1.3 56.9 + - - +
756A ARG* 3.2 2.1 + - - -
757A GLY 2.9 24.1 + - - -
758A LYS* 3.0 23.3 + - + +
759A ILE* 3.4 25.9 - - + +
766A THR* 3.1 43.2 + - - +
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Residues in contact with ALA 754 (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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689A PHE* 4.1 17.5 - - + -
690A ARG* 3.9 43.8 + - + +
693A LEU* 5.1 2.0 - - + -
750A ALA 2.9 13.2 + - - +
751A TYR* 3.0 15.0 + - + +
753A GLN* 1.3 77.3 - - - +
755A LEU* 1.3 63.4 + - + +
757A GLY* 3.3 12.2 + - - +
759A ILE* 3.8 9.6 - - + +
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Residues in contact with LEU 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ARG* 5.3 13.5 - - + +
751A TYR* 2.9 59.8 + - + +
752A LEU* 3.7 16.8 - - + +
753A GLN 3.3 0.4 - - - -
754A ALA* 1.3 77.4 - - + +
756A ARG* 1.3 62.0 + - + +
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Residues in contact with ARG 756 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A ARG* 4.9 12.3 - - - +
598A LEU* 3.9 34.1 - - + +
752A LEU* 3.2 17.3 + - + +
753A GLN 3.8 3.4 - - - +
754A ALA 3.1 0.4 - - - -
755A LEU* 1.3 79.7 - - + +
757A GLY* 1.3 61.9 + - - +
758A LYS* 3.4 20.0 + - + +
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Residues in contact with GLY 757 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690A ARG* 5.3 6.3 - - - -
753A GLN 2.9 4.9 + - - -
754A ALA* 3.3 11.6 + - - -
755A LEU 3.5 0.2 - - - -
756A ARG* 1.3 79.3 - - - +
758A LYS* 1.3 63.6 + - - +
759A ILE 3.1 12.0 + - - +
760A THR* 4.3 7.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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