Contacts of the helix formed by residues 720 - 746 (chain A) in PDB entry 3IAY
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 CYS 720 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 3.7 15.5 - - + -
624A TYR* 3.5 25.1 - - + -
627A LEU* 3.8 28.3 - - - -
711A THR* 2.8 14.8 + - - +
718A LEU 3.5 1.6 + - - -
719A PRO* 1.3 75.2 - - - +
721A LEU* 1.3 59.4 + - - +
722A ALA* 3.1 10.3 - - - -
723A ILE* 2.9 43.4 + - + +
724A SER 3.2 8.1 + - - -
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TYR* 4.3 20.2 - - + +
649A ASN* 5.3 0.2 - - - -
711A THR 3.7 11.0 - - - +
712A GLY* 4.0 15.9 - - - +
714A THR* 4.4 21.8 - - + -
719A PRO* 4.0 6.3 - - + -
720A CYS* 1.3 68.5 - - - +
722A ALA* 1.3 66.2 + - - +
723A ILE 3.1 0.2 - - - -
724A SER* 3.3 17.0 - - - +
725A SER* 2.8 37.3 + - - +
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Residues in contact with ALA 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LEU* 3.8 27.1 - - + -
649A ASN* 4.7 1.6 - - - +
651A ASP* 3.2 29.6 - - - +
653A PHE* 4.0 2.4 - - + -
720A CYS* 3.1 11.6 - - - -
721A LEU* 1.3 77.7 - - - +
723A ILE* 1.3 57.7 + - - +
726A SER* 2.8 34.5 + - - -
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Residues in contact with ILE 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A MET* 4.0 24.9 - - + -
622A LEU* 4.5 9.9 - - + -
623A CYS* 3.6 6.7 - - - +
624A TYR* 3.4 31.6 - - + +
653A PHE* 3.8 23.6 - - + -
663A LEU* 4.0 2.9 - - + -
711A THR* 3.7 24.7 - - + +
720A CYS* 2.9 35.3 + - + +
722A ALA* 1.3 75.0 - - - +
724A SER* 1.3 61.2 + - - +
726A SER* 3.2 2.8 + - - -
727A VAL* 2.8 40.6 + - + +
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Residues in contact with SER 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TYR* 3.5 38.7 - - - -
708A TYR* 3.6 15.8 - - - -
711A THR* 3.4 18.8 - - - -
712A GLY* 3.6 8.3 - - - -
720A CYS 3.2 2.6 + - - -
721A LEU* 3.3 21.3 - - - +
723A ILE* 1.3 80.1 - - - +
725A SER* 1.3 59.7 + - - +
727A VAL* 3.3 3.8 + - - +
728A THR* 3.1 25.3 + - - +
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Residues in contact with SER 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TYR* 3.5 28.1 - - - +
588A GLU 5.1 0.6 + - - -
649A ASN* 3.5 26.7 - - - +
721A LEU* 2.8 29.2 + - - +
724A SER* 1.3 70.5 + - - +
726A SER* 1.3 63.7 + - - -
728A THR* 3.3 9.8 + - - -
729A ALA* 3.0 25.6 + - - +
732A ARG* 5.0 0.7 + - - -
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Residues in contact with SER 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 4.5 6.7 - - - -
647A THR* 2.7 41.7 + - - +
648A PRO* 4.9 0.2 - - - +
649A ASN* 3.8 7.6 - - - +
651A ASP* 2.8 19.6 + - - +
653A PHE* 3.7 5.6 - - - -
722A ALA 2.8 17.7 + - - -
723A ILE* 3.7 3.4 - - - -
725A SER* 1.3 75.8 - - - +
727A VAL* 1.3 58.9 + - - +
729A ALA* 3.2 2.2 + - - +
730A TYR* 2.8 37.5 + - - -
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Residues in contact with VAL 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A TYR* 3.4 49.0 - - + +
616A ILE* 3.7 18.0 - - + +
617A MET* 3.5 32.8 - - + -
622A LEU* 3.7 11.4 - - + +
708A TYR* 3.9 10.3 - - + -
723A ILE* 2.8 22.9 + - + +
724A SER 3.4 7.0 - - - +
726A SER* 1.3 77.3 - - - +
728A THR* 1.3 63.4 + - - +
730A TYR* 3.4 0.3 + - - +
731A GLY* 3.0 17.2 + - - -
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Residues in contact with THR 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TYR* 4.0 4.2 - - + -
588A GLU 2.8 28.2 + - - +
589A GLY* 4.0 13.6 - - - +
590A ALA* 5.4 0.5 - - - -
613A TYR* 3.8 24.6 + - + +
708A TYR* 3.2 27.1 - - + +
724A SER 3.1 11.0 + - - +
725A SER* 3.3 12.0 + - - -
727A VAL* 1.3 74.7 - - - +
729A ALA* 1.3 58.5 + - - +
731A GLY* 3.1 2.0 + - - +
732A ARG* 3.0 40.2 + - - +
6T T 5.5 0.4 - - - +
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Residues in contact with ALA 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PRO* 3.9 9.0 - - + -
649A ASN* 3.8 27.8 - - + +
725A SER 3.0 19.4 + - - +
726A SER 3.5 3.6 - - - +
728A THR* 1.3 74.7 + - - +
730A TYR* 1.3 67.5 + - - +
731A GLY 3.2 0.2 + - - -
732A ARG* 3.2 27.8 + - - +
733A THR* 3.1 28.1 + - - +
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Residues in contact with TYR 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ILE* 3.7 33.9 - - + -
620A HIS* 3.5 47.0 + + + +
622A LEU* 4.3 7.4 - - + +
645A VAL* 3.5 27.2 - - - +
646A ILE 4.6 0.9 + - - -
647A THR* 3.8 24.5 - - + +
648A PRO* 3.5 25.1 - - + +
726A SER 2.8 30.1 + - - +
727A VAL 3.7 0.2 - - - +
729A ALA* 1.3 70.9 - - - +
731A GLY* 1.3 59.0 + - - +
733A THR* 2.6 25.4 + - - -
734A MET* 2.9 24.0 + - + +
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Residues in contact with GLY 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ALA* 6.3 0.7 - - - -
591A THR 6.0 0.4 - - - -
612A LEU* 4.4 11.5 - - - +
613A TYR* 4.9 4.9 - - - -
616A ILE* 3.8 13.2 - - - +
727A VAL 3.0 14.7 + - - -
728A THR 3.5 4.5 - - - -
729A ALA 3.1 0.6 - - - -
730A TYR* 1.3 77.2 - - - +
732A ARG* 1.3 61.4 + - - +
734A MET* 3.2 4.7 + - - +
735A ILE* 3.1 25.8 + - - +
763A THR 4.1 7.0 - - - +
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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
----------------------------------------------------------
588A GLU* 3.5 43.9 + - - +
589A GLY 3.0 29.8 + - - +
590A ALA* 4.4 1.5 - - - +
591A THR* 3.5 31.9 + - - +
648A PRO 5.7 1.0 + - - -
649A ASN* 5.4 4.2 + - - +
725A SER 5.0 0.8 + - - -
728A THR* 3.0 33.4 + - - +
729A ALA* 3.2 30.3 + - - +
731A GLY* 1.3 73.9 - - - +
733A THR* 1.3 65.6 + - + +
735A ILE* 3.3 7.5 - - - +
736A LEU* 3.2 24.1 + - - +
----------------------------------------------------------
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Residues in contact with THR 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PRO* 4.0 25.5 - - + +
729A ALA 3.1 13.5 + - - +
730A TYR* 2.6 25.5 + - - -
732A ARG* 1.3 77.6 - - + +
734A MET* 1.3 60.6 + - - +
736A LEU* 3.5 8.7 + - - +
737A LYS* 2.9 30.2 + - - +
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Residues in contact with MET 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PHE* 3.8 15.9 - - + -
612A LEU* 3.6 21.5 - - + -
616A ILE* 3.6 31.9 - - - -
620A HIS* 5.5 1.3 - - - -
730A TYR* 2.9 25.3 + - + +
731A GLY* 3.2 4.9 + - - +
733A THR* 1.3 79.3 - - - +
735A ILE* 1.3 60.7 + - - +
737A LYS* 3.4 1.4 + - - +
738A THR* 2.7 35.0 + - - -
793A PHE* 3.7 26.0 - - + -
797A ILE* 3.5 44.6 - - + -
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Residues in contact with ILE 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A THR* 3.8 30.3 - - + +
593A ILE* 4.0 25.8 - - + -
609A PHE* 5.0 3.8 - - + -
731A GLY 3.1 11.4 + - - +
732A ARG* 3.3 13.5 - - - +
734A MET* 1.3 73.2 - - - +
736A LEU* 1.3 63.7 + - + +
738A THR* 3.6 5.6 - - - -
739A LYS* 2.9 30.0 + - - +
762A ASP 4.2 0.9 - - - +
763A THR 3.7 40.4 - - - +
764A ASP* 4.1 3.1 - - - +
765A SER 3.4 26.9 - - - +
766A VAL* 4.4 5.2 - - + -
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Residues in contact with LEU 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A ARG 3.2 19.3 + - - +
733A THR* 3.7 7.6 - - - +
735A ILE* 1.3 78.5 - - + +
737A LYS* 1.3 57.4 + - - +
739A LYS* 3.4 15.1 + - + +
740A THR* 2.8 44.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A THR 2.9 21.9 + - - +
734A MET 3.7 4.3 - - - +
736A LEU* 1.3 73.7 - - - +
738A THR* 1.3 57.1 + - - +
740A THR* 3.8 5.2 - - - -
741A ALA* 2.8 30.9 + - + +
792A LEU* 3.5 50.6 + - + +
793A PHE* 3.6 22.8 - - + -
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Residues in contact with THR 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PHE* 3.3 26.3 - - + -
734A MET 2.7 26.3 + - - -
735A ILE* 3.6 8.7 - - - -
737A LYS* 1.3 70.7 - - - +
739A LYS* 1.3 67.5 + - - +
741A ALA* 3.3 1.3 + - - +
742A VAL* 3.0 33.4 + - + +
766A VAL* 4.0 25.1 - - + -
789A VAL* 3.8 15.5 - - + +
793A PHE* 4.0 1.6 - - - -
799A LEU* 3.9 26.2 - - + -
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Residues in contact with LYS 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A ILE* 4.2 31.0 - - + +
735A ILE 2.9 17.2 + - - +
736A LEU* 3.7 14.8 - - + +
738A THR* 1.3 76.2 - - - +
740A THR* 1.3 65.5 + - - +
742A VAL* 3.5 1.0 + - - +
743A GLN* 3.0 51.7 + - - +
758A VAL* 3.9 35.7 - - + -
766A VAL* 4.5 8.9 - - + +
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Residues in contact with THR 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A LEU* 2.8 34.9 + - - +
737A LYS* 3.8 6.2 - - - -
739A LYS* 1.3 78.6 - - - +
741A ALA* 1.3 57.3 + - - +
743A GLN* 3.3 5.9 + - - +
744A GLU* 2.9 60.5 + - + +
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Residues in contact with ALA 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A LYS* 2.8 23.7 + - + +
738A THR* 3.9 2.7 - - - +
740A THR* 1.3 75.1 - - - +
742A VAL* 1.3 63.0 + - - +
744A GLU* 4.0 6.1 - - - +
745A LYS* 3.0 27.0 + - - +
788A TYR* 4.2 15.2 + - + +
789A VAL* 4.4 6.1 - - + -
792A LEU* 3.8 28.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 4.5 17.9 - - + -
738A THR* 3.0 24.4 + - + +
739A LYS 3.9 3.4 - - - +
741A ALA* 1.3 77.0 - - - +
743A GLN* 1.3 62.9 + - + +
745A LYS* 4.9 0.2 - - - -
746A TYR* 3.1 41.0 + - + +
756A ALA* 4.3 6.2 - - + +
758A VAL* 4.5 8.3 - - + -
766A VAL* 5.1 1.8 - - + -
768A VAL* 3.9 35.2 - - + -
770A PHE* 4.8 2.9 - - + -
785A ALA* 4.6 7.0 - - + -
788A TYR* 5.7 0.4 - - - -
789A VAL* 4.0 19.3 - - + -
----------------------------------------------------------
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Residues in contact with GLN 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A LYS* 3.0 41.9 + - - +
740A THR* 4.0 4.9 - - - +
742A VAL* 1.3 78.5 - - + +
744A GLU* 1.3 62.9 + - + +
746A TYR 4.1 3.1 + - - +
747A CYS* 3.8 18.9 - - - +
755A ASP* 6.1 0.3 - - - +
756A ALA* 3.7 22.2 - - - +
757A VAL* 3.9 5.7 - - - +
758A VAL* 3.1 36.7 + - + +
----------------------------------------------------------
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Residues in contact with GLU 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A THR* 2.9 42.4 + - + +
741A ALA* 4.1 4.8 - - - +
743A GLN* 1.3 77.2 - - + +
745A LYS* 1.3 60.8 + - - +
747A CYS* 3.6 8.4 - - - -
750A ASN* 3.0 18.9 + - - -
----------------------------------------------------------
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Residues in contact with LYS 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A ALA 3.0 17.7 + - - +
744A GLU* 1.3 77.5 - - - +
746A TYR* 1.3 96.3 + - + +
747A CYS 3.0 8.1 + - - -
750A ASN* 3.1 19.7 + - - +
752A TYR* 3.4 26.3 + - + +
784A GLU* 4.3 5.6 - - - -
788A TYR* 3.5 47.1 - - + +
----------------------------------------------------------
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Residues in contact with TYR 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A VAL* 3.1 26.4 + - + +
743A GLN 4.1 3.2 - - - +
745A LYS* 1.3 98.5 - - + +
747A CYS* 1.3 58.7 + - - +
752A TYR* 3.5 37.2 - + + -
754A HIS 3.5 5.4 - - - +
756A ALA* 2.8 42.5 + - + +
770A PHE* 3.8 20.2 - + + -
781A LEU* 4.0 11.9 - - + -
784A GLU* 2.7 34.0 + - - +
785A ALA* 3.3 42.5 + - + -
788A TYR* 4.9 2.5 - + - -
----------------------------------------------------------
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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