Contacts of the helix formed by residues 722 - 749 (chain F) in PDB entry 4UJ3
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 GLU 722 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720F LEU 3.2 5.7 - - - +
721F MET* 1.3 77.9 - - - +
723F ALA* 1.3 61.1 + - - +
724F ILE 3.4 0.7 - - - -
725F GLN* 3.5 9.3 + - - +
726F LYS* 3.4 21.0 + - - +
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Residues in contact with ALA 723 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720F LEU* 3.6 18.3 - - - +
721F MET 3.2 0.4 - - - -
722F GLU* 1.3 80.0 - - - +
724F ILE* 1.3 57.8 + - - +
726F LYS* 3.5 4.2 + - - +
727F GLN* 3.1 30.8 + - - +
724I ILE* 3.9 19.0 - - + +
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Residues in contact with ILE 724 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720F LEU 4.4 4.9 - - - +
721F MET* 3.8 32.1 + - + +
722F GLU 3.4 0.2 - - - -
723F ALA* 1.3 74.5 - - - +
725F GLN* 1.3 63.3 + - - +
727F GLN* 4.1 3.8 - - - +
728F GLU* 3.3 24.6 + - + +
719I GLU 5.3 0.2 - - - +
720I LEU* 4.3 11.2 - - - +
723I ALA* 3.3 35.4 - - + +
724I ILE* 3.3 29.6 - - + -
727I GLN* 5.9 6.4 - - + +
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Residues in contact with GLN 725 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721F MET 4.0 7.0 + - - +
722F GLU* 3.5 14.2 + - - +
723F ALA 3.2 0.6 - - - -
724F ILE* 1.3 81.5 - - - +
726F LYS* 1.3 59.5 + - - +
728F GLU* 4.1 3.8 - - - +
729F GLU* 3.4 19.8 + - - +
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Residues in contact with LYS 726 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722F GLU 3.4 13.6 + - - +
723F ALA* 3.5 4.2 + - - +
724F ILE 3.4 0.2 - - - -
725F GLN* 1.3 78.0 - - - +
727F GLN* 1.3 59.1 + - - +
728F GLU 3.2 2.2 - - - -
729F GLU* 3.2 9.2 + - - +
730F ILE* 3.1 28.6 + - - +
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Residues in contact with GLN 727 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723F ALA 3.1 17.3 + - - +
724F ILE* 4.9 3.4 - - - +
726F LYS* 1.3 74.7 - - - +
728F GLU* 1.3 63.1 + - - +
729F GLU 3.2 0.4 - - - -
730F ILE* 3.4 16.1 + - + +
731F ASN* 3.3 16.6 + - - +
724I ILE* 4.2 15.4 - - + +
727I GLN* 4.2 11.9 - - + +
728I GLU* 3.0 43.0 - - - +
731I ASN* 3.3 28.9 + - - +
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Residues in contact with GLU 728 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724F ILE* 3.3 23.1 + - + +
725F GLN* 4.1 4.9 - - - +
726F LYS 3.2 0.4 - - - -
727F GLN* 1.3 76.9 - - - +
729F GLU* 1.3 60.7 + - - +
730F ILE 3.2 0.4 - - - -
731F ASN* 3.5 8.3 + - - +
732F PHE* 3.3 19.9 + - - +
727I GLN* 4.7 15.6 - - + +
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Residues in contact with GLU 729 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725F GLN 3.4 13.6 + - - +
726F LYS* 3.2 13.6 + - - +
727F GLN 3.2 0.4 - - - -
728F GLU* 1.3 78.1 - - - +
730F ILE* 1.3 58.6 + - - +
732F PHE* 3.5 10.8 - - - +
733F ARG* 3.1 24.1 + - - +
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Residues in contact with ILE 730 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726F LYS 3.1 18.3 + - - +
727F GLN* 3.6 20.2 - - + +
729F GLU* 1.3 76.4 - - + +
731F ASN* 1.3 54.6 + - - +
733F ARG* 3.0 7.1 + - + +
734F LEU* 2.7 45.8 + - + +
731I ASN* 2.9 22.9 - - - +
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Residues in contact with ASN 731 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727F GLN 3.3 3.5 + - - +
728F GLU* 3.7 9.2 - - - +
730F ILE* 1.3 77.6 - - - +
732F PHE* 1.3 64.3 + - - +
734F LEU* 4.0 3.3 - - - +
735F GLN* 2.9 34.7 + - - +
727I GLN* 2.7 29.6 + - - +
730I ILE* 3.3 22.7 - - - +
731I ASN* 2.3 45.8 + - - -
734I LEU* 4.2 8.7 - - + +
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Residues in contact with PHE 732 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728F GLU 3.3 10.4 + - - +
729F GLU* 3.5 13.2 - - - +
730F ILE 3.2 0.2 - - - -
731F ASN* 1.3 79.0 - - - +
733F ARG* 1.3 61.5 + - - +
735F GLN* 4.4 2.0 - - - +
736F ASP* 3.2 26.5 + - - +
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Residues in contact with ARG 733 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729F GLU 3.1 10.2 + - - +
730F ILE* 3.0 11.9 + - + +
732F PHE* 1.3 78.2 - - - +
734F LEU* 1.3 65.3 + - + +
736F ASP* 3.6 3.8 + - - +
737F TYR 3.2 16.1 + - - -
44G ILE* 3.5 21.8 - - + +
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Residues in contact with LEU 734 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730F ILE* 2.7 28.1 + - + +
731F ASN 4.0 2.7 - - - +
733F ARG* 1.3 72.9 - - - +
735F GLN* 1.3 62.6 + - - +
737F TYR* 3.3 5.7 - - - +
738F ILE* 3.1 27.4 + - - +
44G ILE* 3.6 29.4 - - + -
731I ASN* 3.4 28.9 - - + +
734I LEU* 3.9 30.1 - - + -
735I GLN* 3.7 24.9 - - - +
738I ILE* 3.5 23.9 - - + +
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Residues in contact with GLN 735 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 5.9 3.6 - - - +
731F ASN* 2.9 22.7 + - - +
732F PHE* 4.4 2.2 - - - +
734F LEU* 1.3 73.7 - - - +
736F ASP* 1.3 65.6 + - - +
737F TYR 3.0 1.6 - - - -
738F ILE* 3.2 11.6 + - + +
739F ASP* 3.0 42.3 + - - +
734I LEU* 4.1 21.9 - - + +
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Residues in contact with ASP 736 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732F PHE 3.2 20.0 + - - +
733F ARG* 4.0 4.7 - - - +
735F GLN* 1.3 77.3 - - - +
737F TYR* 1.3 61.8 + - - +
739F ASP* 3.7 9.3 + - - +
740F ARG* 3.3 22.0 + - - +
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Residues in contact with TYR 737 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733F ARG 3.2 13.9 + - - +
734F LEU 3.3 9.9 - - - +
735F GLN 3.0 0.4 - - - -
736F ASP* 1.3 76.0 - - - +
738F ILE* 1.3 64.2 + - - +
740F ARG* 3.2 6.5 + - + +
741F ILE* 3.0 47.8 + - + +
44G ILE* 3.7 33.8 + - + -
45G GLY* 3.5 20.1 - - - -
46G VAL 3.6 8.8 + - - -
47G GLU* 5.4 7.9 - - + +
738I ILE* 3.5 42.8 - - + -
741I ILE* 6.0 1.3 - - + -
742I ILE* 3.5 17.9 - - + +
753I LEU* 4.7 0.2 - - - +
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Residues in contact with ILE 738 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 5.6 2.2 - - + -
45D GLY* 4.4 10.8 - - - +
734F LEU 3.1 15.6 + - - +
735F GLN* 3.2 10.2 + - + +
737F TYR* 1.3 77.5 - - - +
739F ASP* 1.3 61.6 + - - +
741F ILE* 3.5 5.3 + - - +
742F ILE* 2.9 43.5 + - + +
734I LEU* 3.6 32.5 - - + +
737I TYR* 3.6 34.1 - - + -
738I ILE* 3.5 30.3 - - + -
741I ILE* 5.1 2.0 - - + -
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Residues in contact with ASP 739 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 2.9 43.1 - - + +
735F GLN* 3.0 37.5 + - - +
736F ASP* 3.8 8.6 - - - +
737F TYR 3.2 0.2 - - - -
738F ILE* 1.3 77.9 - - - +
740F ARG* 1.3 67.4 + - - +
742F ILE 3.1 1.0 + - - -
743F VAL* 3.0 13.9 + - - +
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Residues in contact with ARG 740 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736F ASP 3.3 14.1 + - - +
737F TYR* 3.2 9.2 + - + +
739F ASP* 1.3 80.1 - - - +
741F ILE* 1.3 63.0 + - + +
743F VAL* 3.3 9.6 + - - +
744F ALA* 3.3 19.8 + - - +
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Residues in contact with ILE 741 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737F TYR* 3.0 55.0 + - + +
738F ILE* 3.9 3.6 - - - +
740F ARG* 1.3 77.7 - - + +
742F ILE* 1.3 59.4 + - - +
744F ALA* 3.4 5.5 + - + +
745F ILE* 2.9 35.0 + - + +
741I ILE* 3.5 29.6 - - + -
742I ILE* 4.9 1.6 - - + -
745I ILE* 3.7 15.5 - - + -
752I ILE* 4.3 14.6 - - + +
753I LEU* 4.0 22.9 - - + -
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Residues in contact with ILE 742 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLY* 4.7 4.7 - - - -
46D VAL* 4.0 22.4 - - + +
76D ILE* 3.5 30.3 - - + -
738F ILE* 2.9 38.0 + - + +
739F ASP 3.1 0.2 + - - -
741F ILE* 1.3 78.1 - - + +
743F VAL* 1.3 62.2 + - - +
745F ILE* 3.2 10.3 + - + +
746F MET* 3.2 33.0 + - + +
753F LEU* 3.6 22.9 - - + -
737I TYR* 3.3 28.7 - - + +
741I ILE* 5.0 2.2 - - + -
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Residues in contact with VAL 743 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 3.3 35.9 - - + +
79D ALA* 5.2 8.8 - - + +
739F ASP* 3.0 16.5 + - + +
740F ARG* 3.5 10.5 - - - +
742F ILE* 1.3 77.5 - - - +
744F ALA* 1.3 63.0 + - - +
746F MET* 3.4 6.0 + - - +
747F GLU* 3.1 22.2 + - + +
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Residues in contact with ALA 744 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740F ARG 3.3 9.4 + - - +
741F ILE* 3.6 9.9 - - + +
742F ILE 3.3 0.2 - - - -
743F VAL* 1.3 77.1 - - - +
745F ILE* 1.3 66.6 + - - +
747F GLU* 3.0 18.9 + - - +
748F THR* 3.3 18.3 + - + +
752I ILE* 3.9 23.6 - - + +
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Residues in contact with ILE 745 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741F ILE* 2.9 29.7 + - + +
742F ILE* 3.2 10.1 + - + +
744F ALA* 1.3 76.6 - - - +
746F MET* 1.3 57.7 + - - +
749F ASN 3.1 43.4 + - - +
750F PRO* 4.4 0.4 - - + -
752F ILE* 3.8 17.3 - - + -
753F LEU* 3.7 37.2 - - + -
741I ILE* 4.5 9.2 - - + -
745I ILE* 3.5 35.4 - - + -
752I ILE* 4.3 12.6 - - + -
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Residues in contact with MET 746 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LYS* 5.9 0.2 - - - -
46D VAL* 3.5 27.8 - - + -
65D TRP* 3.1 36.3 - - + -
76D ILE* 4.4 7.0 - - + -
79D ALA* 3.6 38.4 - - + +
80D TYR* 4.4 8.5 - - - -
82D ARG* 5.8 3.3 + - - +
742F ILE* 3.2 15.7 + - + +
743F VAL 3.7 7.6 - - - +
744F ALA 3.1 0.6 - - - -
745F ILE* 1.3 75.2 - - - +
747F GLU* 1.3 62.6 + - - +
748F THR 3.1 3.1 + - - -
750F PRO* 3.3 25.3 - - + +
753F LEU* 3.6 15.7 - - + -
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Residues in contact with GLU 747 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ARG* 5.6 7.2 - - - +
743F VAL* 3.1 15.5 + - + +
744F ALA* 3.0 14.2 + - - +
746F MET* 1.3 76.4 - - - +
748F THR* 1.3 63.5 + - + +
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Residues in contact with THR 748 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744F ALA* 3.3 14.2 + - + +
745F ILE 3.9 3.3 + - - -
746F MET 3.1 1.8 - - - +
747F GLU* 1.3 87.8 - - + +
749F ASN* 1.3 79.8 + - - +
750F PRO* 3.5 9.8 - - - +
749I ASN* 4.8 5.7 - - - +
752I ILE* 4.2 22.1 - - + +
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Residues in contact with ASN 749 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745F ILE* 3.1 11.4 + - - +
748F THR* 1.3 89.4 + - - +
750F PRO* 1.3 58.8 - - - +
751F SER* 3.0 16.0 + - - +
752F ILE* 3.3 30.4 - - + +
748I THR* 5.0 3.4 - - - +
749I ASN* 4.9 12.6 - - + -
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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