Contacts of the helix formed by residues 763 - 788 (chain A) in PDB entry 4N78
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 ASP 763 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A GLN 3.8 0.7 - - - +
753A ARG* 3.2 50.7 + - - +
761A SER 3.9 3.0 + - - -
762A ILE* 1.3 72.6 - - - +
764A LEU* 1.3 63.5 + - - +
765A ASN 3.1 5.4 + - - -
766A ARG* 2.9 46.3 + - + +
767A LEU* 3.3 14.2 + - - +
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Residues in contact with LEU 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LEU* 4.7 6.3 - - + -
699A PHE* 4.4 17.0 - - + -
702A PHE* 4.1 22.7 - - + -
703A VAL* 4.5 12.3 - - + -
706A LEU* 4.0 19.1 - - + -
749A LEU* 3.7 30.3 - - + +
752A GLN* 3.2 23.9 + - + +
755A VAL* 4.2 8.7 - - + -
762A ILE* 3.3 9.0 + - + -
763A ASP* 1.3 73.4 - - - +
765A ASN* 1.3 62.5 + - - +
767A LEU* 3.3 4.8 + - + +
768A ILE* 3.0 46.2 + - + +
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Residues in contact with ASN 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A LEU 4.9 0.4 + - - -
750A LEU 2.6 29.8 + - - +
752A GLN 3.0 6.2 + - - +
753A ARG* 3.4 38.8 + - - +
763A ASP* 3.1 8.9 + - - +
764A LEU* 1.3 76.7 - - - +
766A ARG* 1.3 58.5 + - - +
768A ILE* 3.4 6.0 + - - +
769A THR* 2.7 40.9 + - - -
815A TYR 3.2 23.0 + - - -
816A LEU* 3.3 13.2 - - - +
817A THR 5.3 1.6 + - - -
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Residues in contact with ARG 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A ARG* 5.5 2.0 - - - +
763A ASP* 2.9 36.0 + - - +
765A ASN* 1.3 80.1 + - - +
767A LEU* 1.3 67.1 + - + +
769A THR* 3.4 6.8 + - - -
770A GLN* 3.2 52.1 + - + +
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Residues in contact with LEU 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A PHE* 3.9 18.6 - - + -
703A VAL* 4.0 17.3 - - + -
762A ILE* 3.7 29.8 - - + -
763A ASP 3.3 8.8 + - - +
764A LEU* 3.3 8.5 + - + +
766A ARG* 1.3 80.8 - - + +
768A ILE* 1.3 64.1 + - - +
770A GLN* 3.3 18.9 + - - +
771A ARG* 3.1 47.3 + - - +
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Residues in contact with ILE 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A VAL* 5.1 4.3 - - + -
706A LEU* 3.8 28.3 - - + -
707A ALA* 4.3 17.9 - - + +
710A ILE* 3.8 11.7 - - + -
749A LEU 4.6 5.8 - - - +
750A LEU* 3.8 34.8 - - + -
764A LEU* 3.0 37.8 + - + +
765A ASN* 3.9 3.8 - - - +
767A LEU* 1.3 73.0 - - + +
769A THR* 1.3 62.2 + - - +
771A ARG* 3.1 4.0 + - - +
772A VAL* 2.8 44.9 + - + +
816A LEU* 4.3 3.8 - - + -
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Residues in contact with THR 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ASN* 2.7 29.8 + - - -
766A ARG* 3.6 7.4 - - - -
768A ILE* 1.3 77.7 - - - +
770A GLN* 1.3 56.7 + - - +
772A VAL* 4.4 0.7 - - - -
773A SER* 2.8 37.2 + - - -
816A LEU* 3.4 26.0 - - + +
817A THR* 3.3 30.8 + - - +
818A LEU* 3.7 14.1 - - + -
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Residues in contact with GLN 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A ARG* 3.2 49.4 + - + +
767A LEU* 3.4 15.7 - - - +
768A ILE 3.2 0.4 - - - -
769A THR* 1.3 78.9 - - - +
771A ARG* 1.3 85.2 + - - +
773A SER* 3.9 4.3 - - - -
774A ALA* 3.3 20.8 + - - +
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Residues in contact with ARG 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A ASP* 5.5 8.1 + - - +
703A VAL* 3.7 26.6 - - + +
704A TYR* 5.3 11.9 - - + +
707A ALA* 3.4 27.8 - - + -
767A LEU* 3.1 30.1 + - - +
768A ILE 3.1 3.1 + - - +
770A GLN* 1.3 102.9 + - - +
772A VAL* 1.3 60.1 + - - +
774A ALA* 3.1 8.7 + - - +
775A ALA* 3.0 26.6 + - - +
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Residues in contact with VAL 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ALA* 4.3 16.8 - - + +
710A ILE* 4.6 9.4 - - + -
711A PHE* 4.1 9.6 - - + -
768A ILE* 2.8 41.8 + - + +
769A THR* 4.0 1.3 - - - +
771A ARG* 1.3 71.8 - - - +
773A SER* 1.3 63.1 + - - +
775A ALA* 3.1 8.9 + - - +
776A MET* 3.0 22.1 + - + +
812A LEU* 3.5 35.9 - - + -
816A LEU* 4.0 16.8 - - + -
818A LEU* 4.5 8.7 - - + -
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Residues in contact with SER 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A THR* 2.8 21.1 + - - -
770A GLN* 3.9 5.4 - - - -
772A VAL* 1.3 76.0 - - - +
774A ALA* 1.3 63.2 + - - +
776A MET* 3.2 6.8 + - - +
777A TYR* 3.1 45.8 + - - -
818A LEU* 4.0 19.0 - - - +
819A ASP* 4.8 4.7 + - - -
824A MET* 4.0 6.9 - - - +
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Residues in contact with ALA 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A GLN 3.3 11.9 + - - +
771A ARG* 3.1 12.2 + - - +
773A SER* 1.3 78.7 - - - +
775A ALA* 1.3 60.3 + - - +
777A TYR* 3.6 8.2 + - - +
778A LYS* 3.2 22.3 + - - +
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Residues in contact with ALA 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A PHE* 3.6 37.2 - - + -
771A ARG 3.0 12.6 + - - +
772A VAL* 3.1 10.3 + - - +
774A ALA* 1.3 76.0 - - - +
776A MET* 1.3 59.2 + - - +
778A LYS* 3.3 2.6 + - - +
779A SER* 3.0 32.6 + - - -
887A TYR* 4.0 17.6 - - + +
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Residues in contact with MET 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A PHE* 3.7 21.3 - - + -
772A VAL 3.0 15.4 + - - +
773A SER* 3.5 9.0 - - - +
775A ALA* 1.3 77.2 - - - +
777A TYR* 1.3 55.9 + - - +
779A SER* 3.3 3.6 + - - -
780A LEU* 3.0 37.4 + - + +
805A ASN* 3.6 32.1 - - + +
808A THR* 4.0 17.3 - - - -
809A HIS* 4.0 18.6 - - + -
812A LEU* 4.2 11.9 - - + -
818A LEU* 4.6 11.2 - - + -
821A PHE* 4.3 12.8 - - + -
824A MET* 3.8 21.3 - - + -
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Residues in contact with TYR 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A SER* 3.1 39.7 + - - +
774A ALA* 4.0 7.0 - - - +
775A ALA 3.3 0.2 - - - -
776A MET* 1.3 78.4 - - - +
778A LYS* 1.3 57.7 + - - +
780A LEU* 3.8 4.8 - - + +
781A GLU* 2.8 31.3 + - - +
819A ASP* 2.8 26.5 + - - +
823A ALA* 4.7 1.0 + - - +
824A MET* 3.5 48.9 + - + +
827A GLU* 3.1 40.0 + - + -
828A ALA* 4.8 7.4 - - + +
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Residues in contact with LYS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A ALA 3.2 17.6 + - - +
775A ALA 3.3 4.7 + - - +
777A TYR* 1.3 73.5 - - - +
779A SER* 1.3 61.0 + - - +
781A GLU* 3.7 7.7 - - + +
782A LEU* 2.9 30.7 + - + +
883A ALA* 4.6 13.6 - - - +
884A GLN* 5.6 1.6 + - - +
887A TYR* 3.6 47.6 + - + +
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Residues in contact with SER 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A PHE* 3.2 22.5 - - - -
715A LYS* 3.4 7.5 + - - -
775A ALA 3.0 14.0 + - - -
776A MET* 3.5 9.0 - - - -
778A LYS* 1.3 77.4 - - - +
780A LEU* 1.3 56.3 + - - +
782A LEU* 3.3 3.5 + - - +
783A ALA* 3.0 28.9 + - - +
801A LEU* 5.7 0.2 - - - +
805A ASN* 3.0 26.3 + - - +
887A TYR* 3.7 25.8 - - - +
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Residues in contact with LEU 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A MET* 3.0 26.9 + - + +
777A TYR* 3.8 5.6 - - - +
779A SER* 1.3 76.6 - - - +
781A GLU* 1.3 63.8 + - - +
783A ALA* 3.3 5.0 + - - +
784A ILE* 3.1 30.3 + - + +
802A LEU* 4.1 18.4 - - + -
805A ASN* 3.8 28.9 - - + +
821A PHE* 4.0 18.2 - - + -
824A MET* 3.6 44.4 - - + +
825A PHE* 3.8 9.2 - - + +
828A ALA* 3.8 14.4 - - + -
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Residues in contact with GLU 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A TYR 2.8 18.8 + - - +
778A LYS* 3.7 9.2 - - + +
780A LEU* 1.3 77.2 - - - +
782A LEU* 1.3 58.3 + - - +
784A ILE* 4.0 2.4 - - - +
785A GLY* 3.0 24.6 + - - -
828A ALA* 4.1 14.5 - - + +
830A HIS* 4.6 4.7 + - - -
838A ARG* 2.8 38.6 + - - -
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Residues in contact with LEU 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A LYS* 2.9 20.6 + - + +
779A SER 3.5 4.9 - - - +
780A LEU 3.2 0.2 - - - -
781A GLU* 1.3 76.0 - - - +
783A ALA* 1.3 59.8 + - - +
785A GLY* 3.0 1.8 + - - -
786A ARG* 2.8 42.1 + - + +
880A GLN* 3.8 30.3 - - + +
881A PRO 4.6 3.1 - - - +
882A ASN* 5.4 0.7 - - - -
883A ALA* 3.8 33.2 - - + +
887A TYR* 3.5 25.1 - - + +
888A LEU* 3.5 25.8 - - + -
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Residues in contact with ALA 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A SER 3.0 15.8 + - - +
780A LEU 3.3 4.7 + - - +
782A LEU* 1.3 77.7 - - - +
784A ILE* 1.3 62.0 + - - +
786A ARG* 3.4 5.9 + - - +
787A PHE 3.3 14.6 + - - -
798A LEU* 3.4 24.3 - - + +
801A LEU* 3.5 37.5 - - + +
802A LEU* 4.4 12.6 - - + -
805A ASN* 4.5 3.6 - - - +
888A LEU* 5.3 0.2 - - - +
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Residues in contact with ILE 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A LEU* 3.1 17.1 + - + +
781A GLU 4.1 2.7 - - - +
783A ALA* 1.3 74.3 - - - +
785A GLY* 1.3 66.2 + - - +
787A PHE* 3.2 6.2 + - + +
788A GLU* 3.1 24.3 + - + +
798A LEU* 4.2 9.4 - - + -
802A LEU* 4.9 3.4 - - + -
825A PHE* 4.4 15.0 - - + -
828A ALA* 3.8 10.1 - - + +
829A ASN* 3.6 42.6 - - + +
838A ARG* 3.8 38.1 - - + +
839A ILE* 4.5 17.7 - - + +
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Residues in contact with GLY 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A GLU* 3.0 18.3 + - - -
782A LEU 3.0 3.1 + - - -
784A ILE* 1.3 75.0 - - - +
786A ARG* 1.3 65.2 + - - +
788A GLU* 3.4 23.9 + - - +
789A SER* 3.5 12.0 + - - -
838A ARG* 4.1 4.0 - - - +
880A GLN* 3.5 20.4 - - - +
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Residues in contact with ARG 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A LEU* 2.8 39.9 + - + +
783A ALA* 3.5 9.6 - - - +
784A ILE 3.2 0.2 - - - -
785A GLY* 1.3 77.7 - - - +
787A PHE* 1.3 62.0 + - - +
789A SER* 2.8 23.2 + - - -
790A GLU* 3.4 16.3 - - + +
797A GLU* 3.9 21.3 + - - +
801A LEU* 5.1 4.1 - - + +
880A GLN* 4.1 20.4 + - + +
882A ASN* 3.7 34.6 - - - +
888A LEU* 4.1 28.2 - - + +
889A HIS* 5.7 2.8 - - - -
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Residues in contact with PHE 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ALA 3.3 6.1 + - - +
784A ILE* 3.2 11.3 + - + +
786A ARG* 1.3 78.7 - - - +
788A GLU* 1.3 55.8 + - + +
789A SER 3.0 1.3 + - - -
790A GLU* 3.1 10.3 + - - +
791A ASP 4.1 7.9 - - - -
792A LEU* 4.3 9.0 - - + -
794A SER* 3.4 21.8 - - - -
795A ILE* 3.5 48.5 - - + -
798A LEU* 3.6 28.5 - - + -
839A ILE* 3.8 34.5 - - + -
842A HIS* 2.7 57.7 + + + -
843A VAL* 4.0 8.3 - - + -
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Residues in contact with GLU 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A ILE* 3.1 15.5 + - + +
785A GLY* 3.7 10.7 - - - +
786A ARG 3.2 0.6 - - - -
787A PHE* 1.3 76.0 - - + +
789A SER* 1.3 56.8 + - - +
790A GLU 3.5 0.4 - - - -
838A ARG* 2.7 59.8 + - - +
842A HIS* 3.1 40.1 + - + +
877A ARG* 4.5 4.9 - - - +
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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