Contacts of the helix formed by residues 819 - 852 (chain N) in PDB entry 5L4K
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 VAL 819 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817N LEU* 3.8 2.8 - - - +
818N GLU* 1.3 103.4 - - - +
820N PRO* 1.3 65.9 - - - +
821N LYS* 3.4 3.1 - - - +
822N GLU* 3.7 29.8 - - + +
823N LYS* 3.1 26.9 + - + +
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Residues in contact with PRO 820 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817N LEU* 3.6 33.0 - - + -
818N GLU 3.4 9.6 - - - +
819N VAL* 1.3 87.6 - - - +
821N LYS* 1.3 66.0 + - + +
823N LYS* 3.4 11.3 + - + +
824N GLU* 3.0 34.0 + - - +
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Residues in contact with LYS 821 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817N LEU* 6.3 0.4 - - + -
819N VAL* 5.6 0.7 - - - -
820N PRO* 1.3 86.1 - - + +
822N GLU* 1.3 56.7 + - - +
824N GLU* 3.2 9.5 + - - +
825N LYS* 3.0 56.0 + - + +
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Residues in contact with GLU 822 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819N VAL* 3.7 32.4 + - + +
820N PRO 3.3 0.4 - - - -
821N LYS* 1.3 75.3 - - - +
823N LYS* 1.3 69.2 + - - +
825N LYS* 3.0 28.2 + - + +
826N GLU* 3.0 27.8 + - - +
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Residues in contact with LYS 823 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818N GLU* 4.0 27.5 + - - +
819N VAL* 3.1 19.2 + - + +
820N PRO* 3.5 13.0 - - + +
821N LYS 3.3 0.2 - - - -
822N GLU* 1.3 80.1 - - - +
824N GLU* 1.3 57.4 + - + +
826N GLU* 2.9 24.2 + - - +
827N LYS* 3.0 32.9 + - - +
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Residues in contact with GLU 824 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820N PRO 3.0 19.5 + - - +
821N LYS* 3.6 10.8 - - - +
823N LYS* 1.3 75.4 - - - +
825N LYS* 1.3 56.9 + - - +
827N LYS* 3.3 36.3 + - - +
828N VAL* 2.9 43.0 + - + +
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Residues in contact with LYS 825 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821N LYS* 3.0 55.4 + - + +
822N GLU* 3.0 26.6 + - + +
824N GLU* 1.3 77.9 - - - +
826N GLU* 1.3 56.8 + - - +
828N VAL* 3.9 5.1 - - - +
829N SER* 2.9 30.3 + - - -
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Residues in contact with GLU 826 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822N GLU* 3.0 19.2 + - - +
823N LYS* 2.9 13.2 + - - +
825N LYS* 1.3 78.3 - - - +
827N LYS* 1.3 59.4 + - + +
829N SER* 2.7 27.1 + - - -
830N THR* 2.8 27.7 + - - +
833N LEU* 6.0 0.9 - - - +
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Residues in contact with LYS 827 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823N LYS* 3.0 27.2 + - - +
824N GLU* 3.3 34.3 + - - +
825N LYS 3.4 0.2 - - - -
826N GLU* 1.3 75.2 - - + +
828N VAL* 1.3 64.5 + - + +
830N THR* 3.2 11.0 + - - -
831N ALA* 3.0 21.0 + - - +
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Residues in contact with VAL 828 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824N GLU* 2.9 30.6 + - + +
825N LYS* 4.0 6.1 - - - +
827N LYS* 1.3 76.4 - - + +
829N SER* 1.3 57.8 + - - +
831N ALA* 3.2 7.6 + - + +
832N VAL* 2.9 39.6 + - + +
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Residues in contact with SER 829 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825N LYS 2.9 17.0 + - - -
826N GLU* 2.7 34.7 + - - -
828N VAL* 1.3 74.8 - - - +
830N THR* 1.3 64.2 + - - +
832N VAL* 3.3 8.8 + - - +
833N LEU* 3.0 38.5 + - - +
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Residues in contact with THR 830 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826N GLU* 2.8 27.6 + - - +
827N LYS* 3.2 10.4 + - - -
829N SER* 1.3 77.8 + - - +
831N ALA* 1.3 60.7 + - - +
833N LEU* 3.6 17.2 + - + +
834N SER* 3.8 9.2 + - - -
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Residues in contact with ALA 831 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827N LYS 3.0 12.8 + - - +
828N VAL* 3.2 10.5 + - + +
830N THR* 1.3 76.2 - - - +
832N VAL* 1.3 62.9 + - + +
834N SER* 2.7 25.9 + - - -
835N ILE* 3.7 9.8 + - - +
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Residues in contact with VAL 832 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828N VAL* 2.9 34.6 + - + +
829N SER* 3.7 8.7 - - - +
831N ALA* 1.3 76.1 - - + +
833N LEU* 1.3 61.9 + - + +
835N ILE* 3.1 20.4 + - + +
836N THR* 3.0 30.0 + - - +
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Residues in contact with LEU 833 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826N GLU* 6.0 1.1 - - - +
829N SER* 3.0 32.9 + - - +
830N THR* 4.0 10.1 - - - +
831N ALA 3.2 0.8 - - - -
832N VAL* 1.3 80.4 - - + +
834N SER* 1.3 56.2 + - - +
836N THR* 3.5 19.3 + - + +
837N ALA* 2.9 24.6 + - - +
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Residues in contact with SER 834 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830N THR 3.8 7.7 + - - -
831N ALA* 2.7 23.7 + - - -
833N LEU* 1.3 73.5 - - - +
835N ILE* 1.3 63.9 + - - +
837N ALA* 3.3 10.5 + - - +
838N LYS* 3.0 24.1 + - - +
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Residues in contact with ILE 835 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831N ALA 3.7 14.4 - - - +
832N VAL* 3.1 18.3 + - + +
834N SER* 1.3 76.6 - - - +
836N THR* 1.3 62.7 + - - +
838N LYS* 3.0 13.0 + - + +
839N ALA* 2.9 19.8 + - - +
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Residues in contact with THR 836 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832N VAL* 3.0 20.9 + - - +
833N LEU* 3.5 25.2 - - + +
835N ILE* 1.3 76.0 - - - +
837N ALA* 1.3 58.3 + - - +
839N ALA* 2.8 27.7 + - + +
840N LYS* 3.1 10.4 + - - +
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Residues in contact with ALA 837 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833N LEU 2.9 15.0 + - - +
834N SER* 3.3 14.3 + - - +
836N THR* 1.3 74.4 - - - +
838N LYS* 1.3 62.3 + - - +
840N LYS* 3.1 11.4 + - - +
841N LYS* 3.0 41.1 + - - +
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Residues in contact with LYS 838 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834N SER 3.0 12.7 + - - +
835N ILE* 3.0 17.0 + - + +
837N ALA* 1.3 75.5 - - - +
839N ALA* 1.3 56.1 + - - +
841N LYS* 3.2 33.0 + - - +
842N LYS* 2.9 28.2 + - + +
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Residues in contact with ALA 839 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835N ILE 2.9 10.3 + - - +
836N THR* 2.8 18.9 + - + +
838N LYS* 1.3 74.8 - - - +
840N LYS* 1.3 62.8 + - - +
842N LYS* 3.6 10.9 + - - +
843N GLU* 3.6 21.3 - - - +
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Residues in contact with LYS 840 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836N THR 3.1 7.6 + - - +
837N ALA* 3.1 11.6 + - - +
839N ALA* 1.3 76.6 - - - +
841N LYS* 1.3 80.1 + - + +
843N GLU* 3.1 21.0 + - + +
844N LYS* 3.1 43.4 + - - +
610Z GLN* 4.7 7.3 + - - +
613Z LEU* 3.6 33.0 - - + +
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Residues in contact with LYS 841 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837N ALA* 3.0 28.3 + - - +
838N LYS* 3.2 35.9 + - - +
840N LYS* 1.3 90.3 - - + +
842N LYS* 1.3 65.2 + - - +
844N LYS* 3.1 16.6 - - + +
845N GLU* 3.0 28.6 + - + +
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Residues in contact with LYS 842 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838N LYS* 2.9 13.1 + - + +
839N ALA* 3.6 14.1 - - - +
841N LYS* 1.3 76.6 - - - +
843N GLU* 1.3 64.7 + - - +
845N GLU* 3.5 6.6 + - + +
846N LYS* 2.9 42.9 + - - +
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Residues in contact with GLU 843 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839N ALA 3.6 18.4 - - - +
840N LYS* 3.1 10.3 + - + +
842N LYS* 1.3 78.5 - - - +
844N LYS* 1.3 68.9 + - - +
846N LYS* 2.8 51.5 + - - +
847N GLU* 3.2 19.6 + - - +
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Residues in contact with LYS 844 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840N LYS* 3.1 34.4 + - - +
841N LYS* 3.1 24.2 - - + +
843N GLU* 1.3 76.2 - - - +
845N GLU* 1.3 83.7 + - - +
847N GLU* 3.1 33.0 + - - +
848N LYS* 3.9 15.4 - - + +
610Z GLN* 3.4 42.5 + - + +
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Residues in contact with GLU 845 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841N LYS* 3.0 17.4 + - + +
842N LYS* 4.2 5.4 - - + +
844N LYS* 1.3 98.2 + - - +
846N LYS* 1.3 58.8 + - - +
847N GLU 3.1 2.5 - - - -
848N LYS* 3.0 23.5 + - - +
849N LYS* 2.9 27.1 + - - +
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Residues in contact with LYS 846 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842N LYS* 2.9 28.1 + - - +
843N GLU* 2.8 48.4 + - - +
845N GLU* 1.3 75.9 - - - +
847N GLU* 1.3 59.7 + - - +
849N LYS* 3.6 18.7 + - + +
850N GLU* 4.2 8.7 + - - +
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Residues in contact with GLU 847 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843N GLU* 3.2 16.1 + - - +
844N LYS* 3.1 26.5 + - - +
845N GLU 3.1 0.8 - - - -
846N LYS* 1.3 77.9 - - + +
848N LYS* 1.3 66.3 + - + +
849N LYS 3.1 0.4 - - - -
850N GLU* 3.1 10.4 + - - +
851N GLU* 3.1 40.4 + - - +
609Z VAL* 4.9 16.0 - - - +
610Z GLN* 5.4 1.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 848 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844N LYS* 3.9 16.8 - - - +
845N GLU* 3.0 27.0 + - - +
847N GLU* 1.3 82.8 + - + +
849N LYS* 1.3 59.8 + - - +
850N GLU 3.2 1.1 - - - -
851N GLU* 3.2 39.8 + - + +
852N GLU* 3.0 39.2 + - + +
853N LYS* 3.2 8.3 + - - -
605Z ASN 3.3 22.8 + - - -
606Z VAL* 3.7 21.0 - - - +
610Z GLN* 6.1 2.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 849 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845N GLU 2.9 10.3 + - - +
846N LYS* 3.7 17.5 - - + +
847N GLU 3.1 0.6 - - - -
848N LYS* 1.3 77.8 - - - +
850N GLU* 1.3 75.8 + - - +
852N GLU 3.3 11.4 - - - +
853N LYS* 4.0 20.7 - - + +
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Residues in contact with GLU 850 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846N LYS 4.3 10.3 - - - +
847N GLU* 3.1 7.0 + - - +
849N LYS* 1.3 100.2 + - - +
851N GLU* 1.3 66.9 + - + +
852N GLU 4.0 2.1 - - - +
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Residues in contact with GLU 851 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847N GLU* 3.1 27.7 + - - +
848N LYS* 3.2 34.5 + - + -
850N GLU* 1.3 80.4 - - + +
852N GLU* 1.3 75.5 + - + +
603Z SER 4.5 8.6 - - - +
604Z GLY* 3.9 20.3 - - - +
605Z ASN 4.7 0.2 - - - +
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Residues in contact with GLU 852 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848N LYS* 3.0 20.3 + - + +
849N LYS 3.3 9.7 - - - +
850N GLU 4.0 2.6 - - - +
851N GLU* 1.3 91.5 - - + +
853N LYS* 1.3 74.6 + - - +
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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