Contacts of the helix formed by residues 833 - 861 (chain B) 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 PRO 833 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B LYS 4.8 0.2 - - - +
832B ALA* 1.3 75.4 - - + +
834B LYS* 1.3 58.4 + - + +
835B GLU* 4.3 13.7 - - + +
836B VAL* 2.5 43.6 + - + +
837B VAL* 3.2 7.3 + - - -
918D G 2.5 36.1 - - + +
955D C 5.2 0.2 - - - +
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Residues in contact with LYS 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B ALA 3.5 4.0 + - - +
833B PRO* 1.3 70.7 - - + +
835B GLU* 1.3 65.1 + - - +
836B VAL 2.8 2.1 + - - -
837B VAL* 2.8 18.5 + - - +
838B GLU* 2.8 29.5 + - + +
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Residues in contact with GLU 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B PRO* 4.4 12.8 - - + +
834B LYS* 1.3 79.6 - - - +
836B VAL* 1.3 58.4 + - + +
838B GLU* 3.9 16.6 - - - +
839B ALA* 3.4 19.6 - - - +
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Residues in contact with VAL 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B PHE* 3.8 24.0 - - + -
832B ALA* 3.9 18.6 - - + -
833B PRO* 2.5 23.7 + - + +
835B GLU* 1.3 77.7 - - + +
837B VAL* 1.3 64.5 + - - +
838B GLU 3.3 0.2 - - - -
839B ALA* 3.3 5.5 + - + +
840B GLU* 3.2 24.0 + - - +
918D G 3.6 42.0 - - + +
919D A 5.0 5.2 - - - +
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Residues in contact with VAL 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823B LEU* 4.3 18.1 - - + +
828B PHE* 3.7 29.2 - - + +
829B ARG* 3.6 34.1 - - - +
832B ALA* 3.8 22.0 - - + +
833B PRO 3.2 2.2 + - - +
834B LYS* 2.8 12.2 + - - +
836B VAL* 1.3 73.5 - - - +
838B GLU* 1.3 57.9 + - - +
839B ALA 3.1 0.2 - - - -
840B GLU* 3.5 1.9 + - - +
841B GLU* 2.9 41.0 + - + +
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Residues in contact with GLU 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B LYS* 2.8 40.2 + - + +
835B GLU* 3.9 13.7 - - - +
837B VAL* 1.3 74.8 - - + +
839B ALA* 1.3 58.1 + - - +
841B GLU* 4.1 18.5 - - - +
842B ALA* 3.6 16.4 + - - +
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Residues in contact with ALA 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B GLU 3.4 18.6 - - - +
836B VAL* 3.5 8.7 - - + +
837B VAL 3.1 0.4 - - - -
838B GLU* 1.3 77.2 - - + +
840B GLU* 1.3 64.1 + - - +
841B GLU 3.2 0.7 - - - -
842B ALA* 3.3 6.8 + - - +
843B ARG* 2.8 42.8 + - - +
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Residues in contact with GLU 840 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B ARG* 5.4 0.3 - - - +
819B SER* 3.0 32.8 + - - +
822B LYS* 3.7 26.0 - - + +
823B LEU* 3.3 28.7 - - + +
828B PHE* 4.1 14.1 - - + -
836B VAL* 3.2 14.1 + - - +
837B VAL 4.0 2.0 - - - +
839B ALA* 1.3 77.5 - - - +
841B GLU* 1.3 65.6 + - - +
843B ARG* 3.1 34.5 + - - +
844B LEU* 3.1 23.4 + - - +
919D A 4.2 5.2 - - - +
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Residues in contact with GLU 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A GLN* 4.6 5.2 + - - -
824A ALA* 3.3 34.2 - - + +
823B LEU* 3.4 20.6 - - + -
829B ARG* 2.6 32.8 + - - -
837B VAL* 2.9 30.2 + - - +
838B GLU* 4.1 16.2 - - - +
840B GLU* 1.3 80.4 - - - +
842B ALA* 1.3 62.1 + - - +
844B LEU* 3.4 7.1 + - - +
845B LYS* 3.1 21.0 + - - +
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Residues in contact with ALA 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B GLU 3.6 15.3 + - - +
839B ALA* 3.3 11.5 + - - +
840B GLU 3.2 0.2 - - - -
841B GLU* 1.3 76.1 - - - +
843B ARG* 1.3 68.8 + - + +
845B LYS* 3.0 16.9 + - - +
846B GLU* 3.2 16.3 + - - +
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Residues in contact with ARG 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B SER* 3.8 4.5 - - - +
822B LYS* 6.0 1.0 - - - +
839B ALA* 2.8 34.2 + - - +
840B GLU* 3.1 37.4 + - - +
841B GLU 3.3 0.2 - - - -
842B ALA* 1.3 74.0 - - - +
844B LEU* 1.3 66.0 + - - +
846B GLU* 3.2 7.3 + - - +
847B ASN* 2.9 31.1 + - - +
919D A 3.0 110.6 + - - +
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Residues in contact with LEU 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A GLN* 3.5 33.0 - - + -
823A LEU* 6.5 0.4 - - + -
824A ALA* 6.4 0.7 - - + -
844A LEU* 4.2 18.6 - - + -
848A LEU* 6.2 1.1 - - + -
816B ALA* 3.1 39.9 - - + +
819B SER* 3.7 17.8 + - - +
820B GLN* 3.8 10.3 - - + +
823B LEU* 5.5 7.4 - - + -
840B GLU 3.1 10.8 + - - +
841B GLU* 3.5 9.6 - - - +
843B ARG* 1.3 79.2 - - - +
845B LYS* 1.3 66.1 + - - +
847B ASN* 3.2 11.7 + - - +
848B LEU* 3.3 21.4 + - + +
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Residues in contact with LYS 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A GLU* 2.7 31.6 + - + +
820A GLN* 3.1 36.4 + - - +
821A ARG* 4.0 16.1 - - - +
841B GLU 3.1 9.8 + - - +
842B ALA* 3.0 14.4 + - - +
844B LEU* 1.3 81.4 - - - +
846B GLU* 1.3 61.8 + - + +
848B LEU* 3.8 3.5 + - - +
849B GLU* 3.3 41.7 + - - +
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Residues in contact with GLU 846 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B PRO* 3.8 30.2 - - - +
785B ARG* 6.0 1.0 - - - -
842B ALA* 3.6 8.4 - - - +
843B ARG* 3.4 13.7 - - - +
845B LYS* 1.3 78.0 - - + +
847B ASN* 1.3 74.0 + - - +
849B GLU* 3.3 18.3 - - - +
850B GLN* 3.0 46.3 + - + +
919D A 4.7 7.4 + - - -
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Residues in contact with ASN 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B LEU* 3.1 30.6 - - + +
815B LEU* 3.3 25.6 + - - +
816B ALA* 3.8 18.9 - - + +
819B SER* 4.3 1.2 + - - -
843B ARG 2.9 26.4 + - - +
844B LEU 3.6 4.7 - - - +
846B GLU* 1.3 83.8 - - - +
848B LEU* 1.3 63.7 + - - +
850B GLN* 4.5 2.8 + - - +
851B ALA* 3.0 20.5 + - - +
919D A 3.2 38.8 + - - -
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Residues in contact with LEU 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A LEU* 4.7 14.5 - - + +
816A ALA* 4.0 36.8 - - + +
817A GLU* 4.3 11.4 - - + +
820A GLN* 4.3 14.8 - - + -
844A LEU* 5.1 2.9 - - + -
848A LEU* 4.0 18.4 - - + -
813B LEU* 4.7 9.9 - - + -
816B ALA* 3.9 21.8 - - + -
844B LEU* 3.3 23.8 + - + +
845B LYS 4.1 3.4 - - - +
847B ASN* 1.3 75.1 - - - +
849B GLU* 1.3 55.6 + - - +
851B ALA* 3.0 6.2 + - - +
852B GLU* 2.8 35.2 + - - +
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Residues in contact with GLU 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A GLU* 6.4 2.7 - - + -
845B LYS* 3.3 40.9 + - - +
846B GLU* 3.3 23.9 - - + +
848B LEU* 1.3 81.1 - - - +
850B GLN* 1.3 61.0 + - + +
852B GLU* 3.5 16.0 - - - +
853B ARG* 3.4 36.1 + - - +
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Residues in contact with GLN 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B ALA* 3.5 26.2 - - + +
783B MET* 3.7 24.4 - - - +
784B PRO* 3.9 15.6 - - + +
808B ARG* 4.5 7.9 + - - +
812B LEU* 3.5 27.8 - - + +
846B GLU* 3.0 45.0 + - + +
847B ASN* 3.8 2.6 + - - +
849B GLU* 1.3 72.0 - - + +
851B ALA* 1.3 67.9 + - - +
852B GLU 2.7 6.1 + - - -
853B ARG* 3.0 15.0 + - - +
854B ILE* 2.9 25.6 + - - +
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Residues in contact with ALA 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A LEU* 4.1 6.6 - - + +
809B LEU* 3.2 28.7 - - + +
812B LEU* 3.7 16.5 - - + +
813B LEU* 4.3 15.5 - - + +
847B ASN 3.0 12.0 + - - +
848B LEU* 3.0 13.9 + - - +
850B GLN* 1.3 79.3 - - - +
852B GLU* 1.3 55.8 + - - +
854B ILE* 4.0 1.8 - - - -
855B ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A LYS* 4.7 7.3 - - - +
813A LEU* 4.4 16.5 - - + +
814A ALA* 5.3 1.7 + - - +
848B LEU 2.8 11.6 + - - +
849B GLU* 3.5 14.1 - - - +
850B GLN 2.7 3.8 + - - -
851B ALA* 1.3 71.2 - - - +
853B ARG* 1.3 62.7 + - + +
855B ARG* 2.5 67.1 + - - +
856B GLU* 2.7 23.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B GLU* 4.0 22.0 + - - +
780B VAL* 4.9 11.6 - - + +
782B ALA* 4.7 8.5 - - + -
783B MET 5.9 0.4 + - - -
787B THR* 3.6 26.5 + - + -
789B ARG* 5.1 9.7 + - - +
849B GLU* 3.4 38.4 + - - +
850B GLN* 3.0 14.6 + - - +
852B GLU* 1.3 80.0 - - + +
854B ILE* 1.3 57.3 + - - +
856B GLU* 3.5 14.0 + - - +
857B ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B VAL* 5.6 2.7 - - + -
781B LYS* 5.8 0.4 - - - +
782B ALA* 3.7 27.4 - - + +
805B GLN* 3.4 46.9 - - + +
808B ARG* 3.4 33.7 - - + -
809B LEU* 4.2 10.5 - - + +
812B LEU* 3.6 20.0 - - + -
850B GLN 2.9 11.2 + - - +
851B ALA* 3.9 5.4 - - - +
852B GLU 2.9 0.2 + - - -
853B ARG* 1.3 73.0 - - - +
855B ARG* 1.3 61.2 + - - +
857B ALA* 3.2 6.4 + - - +
858B LEU* 2.9 29.7 + - + +
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Residues in contact with ARG 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A GLU 3.7 7.5 + - - +
809A LEU* 3.9 22.0 - - + -
810A LYS* 2.9 75.7 - - - +
813A LEU* 3.8 19.3 - - + -
809B LEU* 4.8 10.1 - - + -
851B ALA 2.9 16.5 + - - +
852B GLU* 2.5 46.1 + - - +
854B ILE* 1.3 68.2 - - - +
856B GLU* 1.3 64.6 + - - +
857B ALA 2.8 4.5 + - - -
858B LEU* 2.8 7.6 + - - +
859B SER* 2.7 53.5 + - - -
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Residues in contact with GLU 856 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A LYS* 4.6 5.4 - - - +
774B ARG* 3.9 20.9 + - - -
789B ARG* 4.2 8.3 + - - -
852B GLU* 2.7 22.5 + - - +
853B ARG* 3.8 10.0 - - - +
855B ARG* 1.3 98.4 + - - +
857B ALA* 1.3 60.1 + - - +
859B SER* 3.4 4.7 - - - -
860B GLN* 3.1 44.8 + - - +
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Residues in contact with ALA 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B ALA 5.1 3.4 - - - +
780B VAL* 4.0 22.9 - - + -
801B TRP* 3.8 24.9 - - + -
853B ARG 2.9 19.5 + - - +
854B ILE* 3.3 8.1 - - - +
855B ARG 2.8 1.2 + - - -
856B GLU* 1.3 74.0 - - - +
858B LEU* 1.3 64.0 + - - +
859B SER 2.9 5.6 + - - -
860B GLN* 3.3 4.2 + - - +
861B ILE* 3.1 26.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A GLU* 3.7 6.8 - - - +
801B TRP* 3.3 34.1 - - + -
802B ARG* 4.0 23.0 + - + +
805B GLN* 3.6 19.3 - - + +
806B GLU* 3.4 45.3 - - + +
809B LEU* 5.0 8.3 - - + -
854B ILE* 2.9 20.0 + - + +
855B ARG* 2.8 8.7 + - - +
857B ALA* 1.3 73.0 - - - +
859B SER* 1.3 61.3 + - - +
861B ILE* 3.3 15.8 - - - +
----------------------------------------------------------
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Residues in contact with SER 859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A GLU* 3.4 32.3 + - - +
810A LYS* 3.5 18.1 + - - +
855B ARG* 2.7 33.3 + - - -
856B GLU* 3.4 8.5 - - - -
857B ALA 2.9 0.6 - - - -
858B LEU* 1.3 77.8 - - - +
860B GLN* 1.3 67.4 + - - -
861B ILE 3.2 6.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN 860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A LYS* 3.4 22.4 + - - +
776B ALA 5.5 6.5 - - - +
777B LYS* 6.0 7.8 - - + +
778B ALA 6.3 0.2 - - - +
856B GLU* 3.1 36.8 + - - +
857B ALA* 4.1 3.1 - - - +
859B SER* 1.3 80.6 + - - +
861B ILE* 1.3 68.2 + - + +
862B GLY 3.6 1.6 + - - -
----------------------------------------------------------
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Residues in contact with ILE 861 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A GLU* 5.1 0.9 - - - +
777B LYS* 5.2 2.7 - - + -
778B ALA 3.6 29.2 - - - +
779B LEU* 4.8 2.2 - - + -
792B LEU* 4.1 25.4 - - + -
798B VAL* 4.3 22.9 - - + -
801B TRP* 4.1 21.3 - - + -
802B ARG* 3.6 22.4 + - + +
857B ALA 3.1 18.0 + - - +
858B LEU 3.3 12.5 - - - +
859B SER 3.1 5.5 - - - +
860B GLN* 1.3 84.4 - - + +
862B GLY* 1.3 76.1 + - - +
----------------------------------------------------------
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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