Contacts of the helix formed by residues 712 - 737 (chain A) in PDB entry 1IVS
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 ASP 712 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ARG* 4.1 24.1 + - - +
612A SER* 2.7 21.0 + - - -
616A ARG* 5.3 0.7 - - - -
711A ARG* 1.3 71.9 - - - +
713A GLU* 1.3 70.2 + - - +
714A GLU* 3.3 26.0 - - - +
715A ALA* 3.3 25.1 - - + +
716A GLU* 3.1 21.6 + - - +
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Residues in contact with GLU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ARG* 4.2 16.3 + - - +
711A ARG* 3.6 9.4 + - + +
712A ASP* 1.3 76.7 + - - +
714A GLU* 1.3 70.5 + - - +
716A GLU* 3.2 9.9 + - - +
717A ARG* 3.2 42.2 + - - +
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Residues in contact with GLU 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ASP* 3.3 17.8 - - - +
713A GLU* 1.3 74.5 - - - +
715A ALA* 1.3 65.8 - - + +
717A ARG* 2.5 50.2 + - - +
718A ALA* 2.8 13.6 + - + -
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Residues in contact with ALA 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 4.3 8.5 - - + +
608A ARG* 4.4 22.7 - - + +
609A PHE* 4.7 3.1 - - - +
712A ASP* 3.3 33.4 - - + +
713A GLU 3.4 0.4 - - - -
714A GLU* 1.3 81.6 - - + +
716A GLU* 1.3 57.5 + - - +
718A ALA* 3.0 9.0 + - - +
719A PHE* 2.8 32.7 + - - +
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Residues in contact with GLU 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PHE* 3.9 22.6 - - + -
612A SER* 2.6 37.9 + - - +
613A ARG* 3.6 18.3 + - - +
616A ARG* 3.1 31.0 + - - -
712A ASP 3.1 17.6 + - - +
713A GLU* 3.6 4.9 - - - +
714A GLU 2.7 4.0 + - - -
715A ALA* 1.3 76.4 - - - +
717A ARG* 1.3 56.0 + - - +
719A PHE* 3.7 2.1 + - - +
720A GLU* 3.2 25.1 + - - +
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Residues in contact with ARG 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A GLU* 3.2 30.5 + - - +
714A GLU* 2.5 41.2 + - - +
716A GLU* 1.3 74.0 - - - +
718A ALA* 1.3 62.7 + - - +
720A GLU* 3.5 7.5 + - + +
721A ALA* 3.4 16.3 + - - +
751A GLU* 4.0 19.5 - - - +
785A ARG* 5.9 3.1 - - + +
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Residues in contact with ALA 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 4.0 20.4 - - + -
714A GLU* 2.8 12.4 + - + +
715A ALA* 3.3 13.2 - - - +
717A ARG* 1.3 77.3 - - - +
719A PHE* 1.3 59.1 + - - +
721A ALA* 2.9 27.9 + - - +
722A LEU 3.2 3.3 + - - -
751A GLU* 4.5 5.4 - - - -
754A PRO* 3.5 19.4 - - + +
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Residues in contact with PHE 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 3.4 28.4 - - + +
606A ALA* 4.0 24.7 - - + -
609A PHE* 3.5 54.7 - + + -
648A TRP* 4.2 21.3 - + + -
649A TYR* 5.2 0.9 - + - -
652A ALA* 4.2 18.2 - - + -
715A ALA 2.8 7.6 + - - +
718A ALA* 1.3 72.7 - - - +
720A GLU* 1.3 60.3 + - - +
722A LEU* 3.3 27.8 + - + +
723A LYS* 2.9 48.3 + - + +
765A LEU* 5.9 0.4 - - + -
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Residues in contact with GLU 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PHE* 6.1 0.6 - - - -
716A GLU 3.2 17.7 + - - +
717A ARG* 3.7 9.9 - - - +
718A ALA 3.1 1.0 - - - -
719A PHE* 1.3 74.2 - - - +
721A ALA* 1.3 69.6 + - - +
723A LYS* 3.0 31.6 + - - +
724A GLN* 2.9 51.5 + - - +
785A ARG* 5.8 4.0 - - + -
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Residues in contact with ALA 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A ARG 3.4 3.6 + - - +
718A ALA 2.9 15.2 + - - +
720A GLU* 1.3 80.6 - - - +
722A LEU* 1.3 60.7 + - - +
724A GLN* 3.1 8.7 + - - +
725A ALA* 3.0 20.4 + - - +
751A GLU* 3.9 35.7 - - + +
754A PRO* 3.6 18.8 - - + -
755A VAL* 5.5 0.7 - - - -
785A ARG* 4.8 10.5 - - + +
786A VAL* 4.3 4.6 - - + +
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Residues in contact with LEU 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 5.3 4.3 - - + -
648A TRP* 6.0 0.9 - - + -
718A ALA 3.2 2.9 + - - +
719A PHE* 3.4 40.6 - - + +
721A ALA* 1.3 76.1 - - - +
723A LYS* 1.3 69.4 + - - +
725A ALA* 2.8 16.2 + - - +
726A VAL* 2.9 26.4 + - + +
754A PRO* 4.2 10.4 - - + +
755A VAL* 3.9 34.5 - - + +
758A ASN* 4.8 12.6 - - + +
761A VAL* 4.3 21.5 - - + -
762A PHE* 4.4 16.2 - - + +
765A LEU* 5.4 2.0 - - + -
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Residues in contact with LYS 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PHE* 4.2 7.0 - - - -
644A GLU* 3.0 31.5 + - - -
648A TRP* 3.5 63.8 - - + +
719A PHE* 2.9 35.4 + - + +
720A GLU* 3.0 31.7 + - - +
722A LEU* 1.3 72.2 - - - +
724A GLN* 1.3 52.1 + - + +
726A VAL* 3.4 2.3 + - - +
727A THR* 2.5 39.7 + - + +
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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
----------------------------------------------------------
720A GLU* 2.9 45.4 + - - +
721A ALA 3.3 6.5 - - - +
722A LEU 2.8 0.6 + - - -
723A LYS* 1.3 73.9 - - + +
725A ALA* 1.3 56.3 + - - +
727A THR* 3.0 7.2 + - - +
728A ALA* 2.6 37.2 + - - +
783A MET* 3.8 14.0 - - + +
784A PRO* 3.6 25.3 - - - +
785A ARG* 3.0 46.0 + - - +
786A VAL* 3.8 9.5 - - + +
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Residues in contact with ALA 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ALA 3.0 9.4 + - - +
722A LEU 2.8 11.3 + - - +
724A GLN* 1.3 73.0 - - - +
726A VAL* 1.3 63.6 + - - +
728A ALA* 3.3 4.4 - - - +
729A VAL* 3.0 28.2 + - - +
748A LEU* 4.2 17.2 - - + +
751A GLU 6.1 0.2 - - - +
755A VAL* 3.6 30.3 - - + -
762A PHE* 4.1 7.4 - - + -
786A VAL* 3.7 16.7 - - + +
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Residues in contact with VAL 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TRP* 3.9 11.4 - - + -
722A LEU* 2.9 24.5 + - + +
723A LYS 3.5 7.6 - - - +
725A ALA* 1.3 77.5 - - - +
727A THR* 1.3 60.6 + - - +
729A VAL* 3.4 2.8 + - - +
730A ARG* 3.0 62.3 + - - +
762A PHE* 3.9 26.2 - - + +
765A LEU* 3.9 33.9 - - + -
766A SER* 4.5 2.4 - - - -
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Residues in contact with THR 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TRP* 4.1 20.6 - - + -
723A LYS 2.5 27.5 + - - +
724A GLN* 3.0 15.9 + - - +
726A VAL* 1.3 70.6 - - - +
728A ALA* 1.3 67.0 + - - +
730A ARG* 3.3 11.2 - - - +
731A ALA* 2.8 26.7 + - - +
783A MET* 4.5 10.1 - - - +
941C A 3.3 26.0 - - - +
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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 2.6 23.1 + - - +
725A ALA* 3.3 8.5 - - - +
727A THR* 1.3 72.5 + - - +
729A VAL* 1.3 65.1 + - - +
731A ALA* 2.9 6.0 + - - +
732A LEU* 2.9 22.8 + - - +
781A LYS* 3.8 18.8 - - + +
783A MET* 3.8 25.3 - - + -
786A VAL* 5.2 2.2 - - + -
788A ALA* 4.1 17.7 - - + +
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Residues in contact with VAL 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A ALA 3.0 15.3 + - - +
726A VAL 3.7 4.0 - - - +
728A ALA* 1.3 79.2 - - - +
730A ARG* 1.3 57.7 + - - +
732A LEU* 3.0 13.3 + - - +
733A LYS* 2.9 36.4 + - + +
744A VAL* 5.0 1.3 - - + -
746A VAL* 4.0 28.9 - - + -
748A LEU* 4.9 1.1 - - + -
762A PHE* 3.7 23.6 - - + -
766A SER* 3.6 26.9 - - - +
768A ALA* 3.8 13.7 - - + -
788A ALA* 4.8 5.2 - - + -
790A MET* 5.2 0.7 - - + -
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Residues in contact with ARG 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ASP 5.8 1.6 + - - -
648A TRP* 4.1 17.2 - - - -
726A VAL* 3.0 34.8 + - - +
727A THR* 3.3 18.4 - - - +
729A VAL* 1.3 78.8 - - - +
731A ALA* 1.3 58.4 + - - +
733A LYS* 4.1 11.7 - - + +
734A ALA* 3.4 19.9 + - - +
765A LEU* 2.6 44.1 + - - +
766A SER* 5.3 6.3 - - - +
940C G 3.4 56.9 + - - +
941C A 4.0 12.6 + - - +
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Residues in contact with ALA 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A THR 2.8 17.7 + - - +
728A ALA* 3.3 4.9 - - - +
730A ARG* 1.3 76.0 - - - +
732A LEU* 1.3 69.5 + - - +
734A ALA* 3.4 1.6 + - - +
735A GLU* 3.1 29.7 + - - +
781A LYS* 3.8 23.6 - - - +
783A MET* 5.8 2.2 - - + -
941C A 3.8 26.7 - - - +
942C G 4.3 2.9 - - - +
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Residues in contact with LEU 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A ALA 2.9 7.9 + - - +
729A VAL* 3.3 9.6 - - - +
731A ALA* 1.3 73.5 - - - +
733A LYS* 1.3 67.3 - - - +
735A GLU* 3.0 8.0 + - - +
736A ALA* 2.8 24.3 + - - +
746A VAL* 4.8 4.3 - - + -
779A LEU* 4.2 10.0 - - + +
780A VAL 4.0 12.3 - - - +
781A LYS* 3.4 40.8 - - + -
788A ALA* 4.1 22.9 - - + +
790A MET* 3.9 38.4 - - + +
801A TRP* 4.0 16.5 - - + -
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Residues in contact with LYS 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A VAL* 2.9 22.7 + - + +
730A ARG* 4.2 7.9 - - - +
732A LEU* 1.3 75.5 - - - +
734A ALA* 1.3 67.5 + - - +
736A ALA* 3.1 4.2 + - - -
737A GLY 3.0 14.7 + - - -
738A LEU* 3.1 31.0 + - + +
739A PRO 4.3 6.7 - - - +
740A PRO* 3.4 17.0 + - + +
742A GLN 2.7 23.7 + - - +
744A VAL* 3.6 27.8 - - + -
766A SER 2.9 12.1 + - - +
767A ARG* 2.9 34.8 + - - +
790A MET* 4.2 12.5 - - + +
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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
----------------------------------------------------------
730A ARG 3.4 14.8 + - - +
731A ALA 3.4 10.3 - - - +
732A LEU 3.1 0.6 - - - -
733A LYS* 1.3 76.8 - - - +
735A GLU* 1.3 59.1 + - - +
737A GLY* 2.9 22.7 + - - -
738A LEU 5.0 2.9 - - - -
804A ARG* 5.6 0.7 - - - +
940C G 5.3 6.3 - - - +
941C A 3.8 31.9 - - - +
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Residues in contact with GLU 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A ALA 3.2 13.9 - - - +
732A LEU* 3.0 10.9 + - - +
734A ALA* 1.3 80.4 - - + +
736A ALA* 1.3 63.1 + - - +
737A GLY* 3.0 1.6 + - - -
781A LYS* 3.0 24.9 + - - -
797A ASP* 3.4 6.6 - - - +
800A GLU* 3.1 30.3 - - - +
801A TRP* 3.8 24.7 - - + +
804A ARG* 3.2 48.8 + - + +
805A GLN* 3.3 19.6 + - - +
941C A 5.0 0.2 - - - +
942C G 4.0 7.1 + - - -
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Residues in contact with ALA 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A LEU 2.8 19.5 + - - +
733A LYS* 3.1 5.4 + - - +
735A GLU* 1.3 72.0 - - - +
737A GLY* 1.3 60.6 + - - +
738A LEU* 3.5 25.2 + - + +
779A LEU* 4.2 18.1 - - + +
790A MET* 4.9 1.8 - - - -
795A LEU 4.3 1.6 - - - +
796A LEU* 3.6 16.7 - - + -
797A ASP* 2.7 34.2 + - - +
801A TRP* 5.3 0.8 - - - +
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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
----------------------------------------------------------
734A ALA 2.9 16.2 + - - -
735A GLU 3.0 2.5 - - - -
736A ALA* 1.3 79.5 - - - +
738A LEU* 1.3 65.1 + - - +
739A PRO* 3.7 6.1 - - - +
795A LEU 5.8 0.2 - - - -
797A ASP* 4.5 6.1 - - - -
929C G 5.4 1.9 + - - -
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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