Contacts of the helix formed by residues 835 - 869 (chain A) in PDB entry 3HRO
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 SER 835 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL* 1.3 75.8 - - - +
836A TYR* 1.3 63.9 + - - +
837A GLU* 3.9 11.8 + - - +
838A GLU* 2.8 33.7 + - - +
839A PHE* 3.1 22.5 + - - +
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Residues in contact with TYR 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL 4.1 0.2 + - - -
835A SER* 1.3 73.2 - - - +
837A GLU* 1.3 72.5 + - + +
839A PHE* 3.2 8.9 + + - +
840A GLN* 2.8 71.6 + - + +
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Residues in contact with GLU 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A SER* 3.3 10.7 + - - +
836A TYR* 1.3 94.1 - - + +
838A GLU* 1.3 63.8 + - - +
840A GLN* 3.3 4.2 + - - +
841A VAL* 3.2 25.4 + - - +
844A ARG* 4.5 1.7 + - - -
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Residues in contact with GLU 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL* 3.2 24.9 - - + +
835A SER* 2.8 39.7 + - - +
837A GLU* 1.3 79.3 - - - +
839A PHE* 1.3 65.0 + - - +
841A VAL* 3.2 23.7 + - - +
842A LEU* 3.4 6.4 + - - +
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Residues in contact with PHE 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL* 4.3 12.6 - - + -
835A SER 3.1 14.2 + - - +
836A TYR* 3.2 9.4 + + - +
838A GLU* 1.3 82.8 - - - +
840A GLN* 1.3 73.6 + - - +
842A LEU* 3.0 26.0 + - + +
843A VAL* 3.0 38.8 + - + +
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Residues in contact with GLN 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A TYR* 2.8 64.3 + - + +
837A GLU* 3.8 4.9 - - - +
839A PHE* 1.3 82.4 - - - +
841A VAL* 1.3 67.3 + - - +
843A VAL* 3.7 24.8 - - - +
844A ARG* 2.9 41.6 + - - +
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Residues in contact with VAL 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A GLU 3.2 16.3 + - - +
838A GLU* 3.2 13.7 + - - +
840A GLN* 1.3 76.5 - - - +
842A LEU* 1.3 65.1 + - + +
844A ARG* 3.5 32.1 + - - +
845A ARG* 3.1 22.6 + - + +
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Residues in contact with LEU 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A GLU 3.4 5.9 + - - +
839A PHE* 3.0 20.4 + - + +
841A VAL* 1.3 81.1 - - + +
843A VAL* 1.3 64.6 + - + +
845A ARG* 3.2 13.1 + - + +
846A VAL* 3.0 33.6 + - + +
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Residues in contact with VAL 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A PHE* 3.0 47.9 + - + +
840A GLN* 3.3 24.4 + - - +
842A LEU* 1.3 75.0 - - - +
844A ARG* 1.3 64.5 + - + +
846A VAL* 3.4 7.2 + - + +
847A ASP* 3.0 25.9 + - + +
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Residues in contact with ARG 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A GLU 4.5 2.4 + - - -
840A GLN* 2.9 25.5 + - - +
841A VAL* 3.5 49.0 + - - +
843A VAL* 1.3 77.8 - - + +
845A ARG* 1.3 56.2 + - - +
847A ASP* 3.4 7.5 + - - +
848A ARG* 3.0 26.3 + - - +
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Residues in contact with ARG 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A VAL* 3.1 14.3 + - + +
842A LEU* 3.2 20.1 + - + +
844A ARG* 1.3 77.3 - - - +
846A VAL* 1.3 59.8 + - + +
848A ARG* 2.9 54.4 + - - +
849A MET* 2.9 45.4 + - - +
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Residues in contact with VAL 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A LEU* 3.0 30.4 + - + +
843A VAL* 3.7 6.7 - - - +
845A ARG* 1.3 71.8 - - + +
847A ASP* 1.3 69.6 + - - +
849A MET* 3.1 15.5 + - - +
850A GLU* 2.9 40.9 + - + +
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Residues in contact with ASP 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A VAL* 3.0 19.0 + - + +
844A ARG* 3.7 7.2 - - - +
845A ARG 3.3 0.2 - - - -
846A VAL* 1.3 76.8 - - - +
848A ARG* 1.3 65.4 + - - +
850A GLU* 3.2 29.9 + - - +
851A HIS* 3.3 47.3 + - - -
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Residues in contact with ARG 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A ARG 3.0 14.4 + - - +
845A ARG* 2.9 59.6 + - - +
847A ASP* 1.3 78.2 + - - +
849A MET* 1.3 61.7 + - - +
851A HIS* 3.0 28.3 + - + +
852A SER* 3.0 23.5 + - - +
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Residues in contact with MET 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A ARG* 2.9 43.5 + - - +
846A VAL* 3.1 13.2 + - - +
848A ARG* 1.3 78.8 - - - +
850A GLU* 1.3 60.5 + - + +
852A SER* 3.5 10.4 - - - +
853A ILE* 2.8 43.3 + - + +
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Residues in contact with GLU 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A VAL* 2.9 32.3 + - + +
847A ASP* 3.2 27.2 + - - +
849A MET* 1.3 75.9 - - + +
851A HIS* 1.3 64.2 + - + +
853A ILE* 3.4 11.8 + - + +
854A GLY* 3.0 24.3 + - - -
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Residues in contact with HIS 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ASP* 3.3 44.7 + - - -
848A ARG* 3.0 13.5 + - + +
850A GLU* 1.3 81.4 - - + +
852A SER* 1.3 64.5 + - - +
854A GLY* 3.2 2.6 + - - -
855A SER* 3.0 27.5 + - - -
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Residues in contact with SER 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A ARG* 3.0 23.8 + - - +
849A MET* 3.2 14.0 + - - +
851A HIS* 1.3 77.2 - - - +
853A ILE* 1.3 63.1 + - - +
855A SER* 3.3 7.7 + - - -
856A ILE* 3.1 33.5 + - - +
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Residues in contact with ILE 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A MET* 2.8 33.1 + - + +
850A GLU* 3.7 9.0 - - + +
851A HIS 3.2 0.2 - - - -
852A SER* 1.3 75.7 - - - +
854A GLY* 1.3 65.4 + - - +
856A ILE* 3.3 12.8 + - + +
857A VAL* 2.9 41.0 + - + +
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Residues in contact with GLY 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A GLU 3.0 14.7 + - - -
851A HIS* 3.2 3.8 + - - -
853A ILE* 1.3 77.3 - - - +
855A SER* 1.3 62.5 + - - +
857A VAL* 3.2 8.5 + - - +
858A SER* 3.0 26.5 + - - -
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Residues in contact with SER 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A HIS 3.0 14.1 + - - -
852A SER* 3.7 9.2 - - - -
853A ILE 3.2 0.4 - - - -
854A GLY* 1.3 78.0 - - - +
856A ILE* 1.3 56.4 + - - +
858A SER* 3.2 8.1 + - - -
859A LYS* 3.0 37.8 + - - +
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Residues in contact with ILE 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A SER* 3.1 25.6 + - - +
853A ILE* 3.6 15.5 - - + +
855A SER* 1.3 74.1 - - - +
857A VAL* 1.3 63.9 + - + +
859A LYS* 3.3 12.6 + - + +
860A ILE* 2.9 34.3 + - + +
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Residues in contact with VAL 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A ILE* 2.9 35.3 + - + +
854A GLY* 3.6 8.1 - - - +
856A ILE* 1.3 78.3 - - + +
858A SER* 1.3 58.5 + - - +
860A ILE* 3.1 12.4 - - + +
861A ASP* 3.0 46.4 + - - +
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Residues in contact with SER 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A GLY 3.0 14.5 + - - -
855A SER* 3.5 11.1 - - - -
857A VAL* 1.3 78.8 - - - +
859A LYS* 1.3 60.7 + - - +
861A ASP* 3.5 5.3 + - - +
862A ALA* 3.1 23.4 + - - +
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Residues in contact with LYS 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A SER* 3.0 23.2 + - - +
856A ILE* 3.7 14.1 - - + +
858A SER* 1.3 75.7 - - - +
860A ILE* 1.3 64.4 + - - +
862A ALA* 3.2 7.2 + - - +
863A VAL* 3.0 27.0 + - + +
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Residues in contact with ILE 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A ILE* 2.9 22.7 + - + +
857A VAL* 3.1 24.5 - - + +
859A LYS* 1.3 76.9 - - - +
861A ASP* 1.3 63.8 + - - +
863A VAL* 3.3 18.1 + - + -
864A ILE* 2.9 45.1 + - + +
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Residues in contact with ASP 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A VAL* 3.0 37.5 + - - +
858A SER* 3.9 6.1 - - - +
859A LYS 3.2 0.2 - - - -
860A ILE* 1.3 83.7 - - - +
862A ALA* 1.3 62.8 + - - +
864A ILE* 3.4 17.6 + - - +
865A VAL* 3.1 27.2 + - - +
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Residues in contact with ALA 862 (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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858A SER 3.1 15.2 + - - +
859A LYS* 3.5 11.0 - - - +
860A ILE 3.2 0.2 - - - -
861A ASP* 1.3 75.4 - - - +
863A VAL* 1.3 64.9 + - + +
865A VAL* 3.2 8.4 + - - +
866A LYS* 3.1 38.8 + - - +
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Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A LYS* 3.0 16.8 + - + +
860A ILE* 3.6 21.3 - - + +
862A ALA* 1.3 74.5 - - + +
864A ILE* 1.3 67.1 + - + +
866A LYS* 3.1 24.5 + - + +
867A LEU* 3.1 38.3 + - + +
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Residues in contact with ILE 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A ILE* 2.9 36.9 + - + +
861A ASP* 3.6 20.2 - - - +
863A VAL* 1.3 78.9 - - + +
865A VAL* 1.3 64.3 + - + +
867A LEU* 3.3 9.9 + - + +
868A GLU* 3.1 47.1 + - + +
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Residues in contact with VAL 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A ASP 3.1 15.3 + - - +
862A ALA* 3.7 8.7 - - - +
863A VAL 3.2 0.4 - - - -
864A ILE* 1.3 78.7 - - + +
866A LYS* 1.3 62.9 + - + +
868A GLU* 3.2 17.2 + - - +
869A ILE* 3.1 44.4 + - + +
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Residues in contact with LYS 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A ALA* 3.1 28.2 + - - +
863A VAL* 3.1 22.1 + - + +
865A VAL* 1.3 75.6 - - + +
867A LEU* 1.3 64.0 + - + +
869A ILE* 3.5 13.2 + - + +
870A MET* 3.1 27.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A VAL* 3.1 29.6 + - + +
864A ILE* 3.7 10.8 - - + +
865A VAL 3.2 0.2 - - - -
866A LYS* 1.3 77.6 - - + +
868A GLU* 1.3 64.5 + - + +
870A MET* 3.3 39.3 + - + +
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Residues in contact with GLU 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A ILE* 3.1 28.8 + - + +
865A VAL* 3.2 25.0 + - - +
867A LEU* 1.3 77.8 - - + +
869A ILE* 1.3 63.5 + - + +
870A MET 3.7 2.4 + - - +
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Residues in contact with ILE 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A VAL* 3.2 33.9 - - + +
866A LYS* 3.5 14.8 - - + +
868A GLU* 1.3 80.2 - - + +
870A MET* 1.3 65.8 + - - +
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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
------------------------------------------------------------
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