Contacts of the helix formed by residues 754 - 779 (chain F) in PDB entry 4OQB
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 ASN 754 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716F VAL* 5.1 0.2 - - - +
720F VAL* 4.0 10.9 - - - +
752F LEU 4.9 0.7 - - - -
753F ASN* 1.3 101.3 + - - +
755F ALA* 1.3 62.2 + - - +
756F ASP* 3.3 21.8 - - - +
757F SER* 3.0 25.8 + - - +
758F VAL* 3.5 10.2 - - - +
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Residues in contact with ALA 755 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717F GLN* 6.3 1.6 - - + -
720F VAL* 4.5 12.6 - - + +
754F ASN* 1.3 75.2 - - - +
756F ASP* 1.3 59.8 + - - +
758F VAL* 3.2 12.9 - - - +
759F GLN 3.8 1.2 + - - -
887F THR* 3.2 33.4 - - + +
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Residues in contact with ASP 756 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754F ASN* 3.3 18.7 - - - +
755F ALA* 1.3 74.2 + - - +
757F SER* 1.3 65.8 + - - +
758F VAL 3.4 0.7 - - - -
759F GLN* 3.5 20.0 - - + +
760F ALA* 2.8 28.4 + - - +
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Residues in contact with SER 757 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751F LEU 5.3 2.0 - - - -
752F LEU* 4.0 18.8 - - - +
753F ASN 3.9 6.1 + - - -
754F ASN* 3.0 40.6 + - - +
756F ASP* 1.3 80.6 + - - +
758F VAL* 1.3 65.1 + - - +
760F ALA* 3.3 7.2 + - - +
761F LYS* 3.0 35.2 + - - +
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Residues in contact with VAL 758 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713F LEU* 3.5 46.6 - - + +
716F VAL* 4.8 11.2 - - + -
717F GLN* 4.5 15.0 - - + +
752F LEU* 5.1 3.3 - - + +
754F ASN 3.5 14.4 - - - +
755F ALA* 3.2 24.0 - - - +
757F SER* 1.3 78.1 + - - +
759F GLN* 1.3 52.6 - - - +
761F LYS* 3.3 2.5 + - - +
762F VAL* 2.7 33.1 + - - +
885F PRO* 4.1 17.7 - - + -
887F THR* 4.3 11.4 - - - +
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Residues in contact with GLN 759 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755F ALA 4.0 5.6 - - - +
756F ASP* 3.4 26.3 + - - +
757F SER 3.3 0.2 - - - -
758F VAL* 1.3 82.3 - - - +
760F ALA* 1.3 57.6 + - - +
762F VAL* 3.5 7.5 - - + +
763F GLU* 2.9 32.5 + - + +
887F THR* 4.0 13.9 - - + +
888F GLY* 3.3 36.5 + - - -
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Residues in contact with ALA 760 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689F TYR* 3.8 12.7 - - + -
756F ASP 2.8 17.6 + - - +
757F SER* 3.5 9.0 - - - +
758F VAL 3.3 0.2 - - - -
759F GLN* 1.3 77.2 - - - +
761F LYS* 1.3 64.6 + - + +
763F GLU* 3.5 10.9 + - - +
764F MET* 3.1 24.9 + - - +
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Residues in contact with LYS 761 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689F TYR* 4.4 6.5 - - - +
690F GLU* 5.0 7.0 + - - -
713F LEU* 3.5 23.4 - - + +
736F PHE* 4.0 12.3 - - + -
737F TYR* 3.4 26.7 + - - -
742F HIS* 3.7 14.8 + - - +
744F PHE* 5.2 0.4 - - - -
750F PRO* 5.0 6.7 - - - +
752F LEU* 4.1 16.4 - - + +
757F SER* 3.0 21.4 + - - +
758F VAL 3.8 0.4 - - - +
760F ALA* 1.3 79.3 - - - +
762F VAL* 1.3 64.3 + - - +
764F MET* 3.5 32.2 - - + +
765F LEU* 3.3 29.5 + - - +
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Residues in contact with VAL 762 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F TYR* 4.2 4.8 - - + -
713F LEU* 3.5 8.5 - - + +
758F VAL 2.7 22.3 + - - +
759F GLN* 3.5 10.1 - - + +
761F LYS* 1.3 71.8 - - - +
763F GLU* 1.3 63.8 + - - +
765F LEU* 3.4 6.2 + - - +
766F ASP* 3.0 30.7 + - - +
884F ALA* 6.1 0.2 - - + -
885F PRO* 3.6 30.1 - - + +
887F THR 5.5 2.9 - - - +
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Residues in contact with GLU 763 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689F TYR* 3.2 24.4 + - - +
759F GLN* 2.9 20.5 + - + +
760F ALA* 3.6 8.9 - - - +
762F VAL* 1.3 72.5 - - - +
764F MET* 1.3 65.9 + - - +
766F ASP* 3.3 11.9 + - + +
767F ASN* 2.9 34.6 + - - +
865F ARG* 4.5 2.1 + - - +
909F HIS* 3.4 30.5 + - - -
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Residues in contact with MET 764 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686F MET* 4.5 2.0 - - - +
689F TYR* 3.1 58.9 - - + +
691F ILE* 3.6 35.2 - - + -
736F PHE* 4.7 0.7 - - - -
742F HIS* 3.4 26.5 - - - +
760F ALA 3.1 13.8 + - - +
761F LYS* 3.5 27.1 - - + +
763F GLU* 1.3 75.6 - - - +
765F LEU* 1.3 67.9 + - + +
767F ASN* 3.2 3.1 + - - +
768F LEU* 2.7 38.8 + - + +
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Residues in contact with LEU 765 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691F ILE* 5.8 0.4 - - + -
706F ILE* 4.2 10.0 - - + +
709F ALA* 3.9 13.0 - - + -
710F TYR* 3.4 60.8 + - + +
713F LEU* 4.1 9.2 - - + -
736F PHE* 3.9 9.6 - - + -
740F ILE* 3.5 25.4 - - + -
761F LYS 3.3 12.6 + - - +
762F VAL 3.8 5.6 - - - +
763F GLU 3.4 0.2 - - - -
764F MET* 1.3 89.8 - - + +
766F ASP* 1.3 57.2 + - - +
768F LEU* 3.8 11.4 - - + +
769F LEU* 2.9 33.3 + - - +
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Residues in contact with ASP 766 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F TYR* 2.7 25.6 + - - -
762F VAL* 3.0 23.5 + - - +
763F GLU* 3.5 11.0 - - + +
764F MET 3.3 0.2 - - - -
765F LEU* 1.3 76.2 - - - +
767F ASN* 1.3 61.9 + - - +
769F LEU* 3.6 3.0 + - - +
770F ASP* 3.0 30.9 + - - +
868F ASN* 5.0 1.8 - - - +
880F ALA* 5.5 2.8 - - - +
881F PRO* 4.8 9.5 - - - +
889F TYR* 4.9 8.3 + - - -
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Residues in contact with ASN 767 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686F MET* 3.5 22.4 - - + -
689F TYR* 3.1 21.6 + - + -
763F GLU* 2.9 29.3 + - - +
764F MET 3.7 1.6 - - - +
766F ASP* 1.3 76.1 - - - +
768F LEU* 1.3 66.3 + - - +
770F ASP* 3.1 13.3 + - - +
771F ILE* 3.2 18.0 + - - +
865F ARG* 3.6 28.1 + - - +
867F THR* 3.7 5.9 + - - +
868F ASN* 3.2 28.8 + - - +
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Residues in contact with LEU 768 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686F MET* 4.0 20.9 - - + -
691F ILE* 5.1 22.0 - - + -
696F MET* 5.7 9.9 - - + -
701F LEU* 5.3 9.0 - - + -
706F ILE* 4.2 28.3 - - + -
740F ILE* 6.3 2.0 - - + -
764F MET* 2.7 24.6 + - + +
765F LEU* 3.8 13.2 - - + +
767F ASN* 1.3 71.1 - - - +
769F LEU* 1.3 64.9 + - - +
771F ILE* 3.3 10.0 + - + +
772F GLU* 3.3 35.0 + - + +
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Residues in contact with LEU 769 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703F LYS* 3.8 35.0 - - + +
706F ILE* 3.7 41.5 - - + -
710F TYR* 5.1 6.5 - - + +
765F LEU 2.9 17.8 + - - +
766F ASP* 3.7 7.4 - - - +
768F LEU* 1.3 78.5 - - - +
770F ASP* 1.3 61.8 + - - +
772F GLU* 3.2 9.1 + - + +
773F VAL* 2.9 40.5 + - + -
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Residues in contact with ASP 770 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766F ASP 3.0 15.5 + - - +
767F ASN 3.1 6.9 + - - +
769F LEU* 1.3 83.9 - - - +
771F ILE* 1.3 56.9 - - + +
773F VAL* 3.5 11.0 + - - +
774F ALA* 2.8 27.4 + - - +
867F THR 4.4 7.1 - - - +
868F ASN* 3.0 48.1 - - - +
870F ALA* 5.1 1.4 - - - +
871F GLY* 5.3 5.4 + - - +
878F ARG* 3.4 27.7 + - - -
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Residues in contact with ILE 771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679F VAL* 4.1 14.5 - - + +
682F MET* 3.4 44.4 - - + +
683F LYS* 5.2 3.6 - - + +
686F MET* 3.4 33.7 - - + -
767F ASN 3.2 11.1 + - - +
768F LEU* 3.6 12.8 - - + +
769F LEU 3.2 0.2 - - - -
770F ASP* 1.3 75.0 - - - +
772F GLU* 1.3 61.8 + - + +
774F ALA* 3.2 7.7 + - - +
775F TYR* 2.9 47.7 + - + -
867F THR* 4.8 7.6 - - - -
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Residues in contact with GLU 772 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696F MET* 3.6 19.8 - - - +
697F PRO 4.6 2.4 - - - +
699F GLY 4.1 0.2 - - - +
700F LYS* 3.7 38.7 - - + +
701F LEU* 3.8 12.1 + - + +
706F ILE* 6.0 2.7 - - + -
768F LEU* 3.3 31.1 + - + +
769F LEU* 3.2 11.6 + - + +
771F ILE* 1.3 74.9 - - + +
773F VAL* 1.3 55.7 + - + +
775F TYR* 3.5 20.9 + - - +
776F SER* 2.7 35.1 + - - -
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Residues in contact with VAL 773 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703F LYS* 6.2 0.4 - - - -
769F LEU* 2.9 38.5 + - + +
770F ASP* 3.5 13.5 - - - +
772F GLU* 1.3 75.6 - - + +
774F ALA* 1.3 63.2 + - - +
776F SER* 3.1 9.2 + - - -
777F LEU* 3.0 44.3 + - + +
871F GLY* 4.4 18.2 - - - -
875F GLN* 3.7 28.7 - - - +
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Residues in contact with ALA 774 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677F PHE* 3.8 11.5 - - + -
679F VAL* 5.3 6.5 - - + +
682F MET* 4.0 21.8 - - + -
770F ASP 2.8 18.7 + - - +
771F ILE 3.2 6.5 + - - +
773F VAL* 1.3 75.6 - - - +
775F TYR* 1.3 56.9 + - - +
777F LEU* 3.7 5.1 + - - +
778F LEU* 3.1 28.8 + - - +
870F ALA* 3.9 26.9 - - + -
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Residues in contact with TYR 775 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679F VAL* 3.3 36.0 - - + +
683F LYS* 3.2 31.3 + - + +
697F PRO* 3.6 20.2 - - + +
700F LYS* 6.3 2.7 - - + -
771F ILE* 2.9 33.3 + - + -
772F GLU* 3.6 25.8 - - - +
774F ALA* 1.3 75.2 - - - +
776F SER* 1.3 56.6 + - - +
778F LEU* 3.2 8.9 + - + -
779F ARG* 2.7 81.6 + - + +
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Residues in contact with SER 776 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700F LYS* 5.7 4.7 - - - +
772F GLU 2.7 21.2 + - - -
773F VAL* 3.1 12.8 + - - -
775F TYR* 1.3 75.8 - - - +
777F LEU* 1.3 62.8 + - - +
779F ARG* 3.0 21.6 - - - +
780F GLY* 5.2 0.2 - - - -
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Residues in contact with LEU 777 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677F PHE* 4.1 19.5 - - + -
773F VAL* 3.0 43.4 + - + +
774F ALA* 3.9 8.7 - - - +
775F TYR 3.2 0.2 - - - -
776F SER* 1.3 80.6 - - - +
778F LEU* 1.3 64.2 + - - +
779F ARG 3.4 2.8 + - - -
780F GLY* 4.7 0.3 - - - -
796F LYS* 3.2 61.5 - - + +
797F LEU* 5.8 0.7 - - - -
798F LYS* 5.8 0.2 - - + -
870F ALA 5.0 4.3 - - - +
874F SER* 4.2 21.1 - - - +
875F GLN* 5.6 1.3 - - - +
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Residues in contact with LEU 778 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677F PHE* 4.2 19.2 - - + +
679F VAL* 4.1 25.8 - - + -
774F ALA 3.1 15.2 + - - +
775F TYR* 3.7 12.1 - - + +
777F LEU* 1.3 78.7 - - - +
779F ARG* 1.3 62.7 + - + +
780F GLY 3.3 1.6 + - - +
793F ASN* 3.4 30.7 - - - +
796F LYS* 2.8 21.1 + - - +
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Residues in contact with ARG 779 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697F PRO* 3.3 27.0 + - - +
698F LEU* 4.8 6.9 + - - +
700F LYS* 3.6 28.5 - - - +
775F TYR* 2.7 60.5 + - + +
776F SER* 3.0 19.9 - - - +
777F LEU 4.0 0.4 - - - -
778F LEU* 1.3 74.7 - - + +
780F GLY* 1.3 57.5 + - - +
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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