Contacts of the helix formed by residues 765 - 793 (chain A) in PDB entry 5CGD
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 PRO 765 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A ASN 3.3 8.0 - - - +
764A VAL* 1.3 86.9 - - + +
766A ALA* 1.3 67.3 + - - +
767A ASN 3.6 1.0 + - - -
768A PHE* 3.8 2.9 + - - -
769A ASN* 3.2 35.8 + - - +
1096A ARG* 4.2 26.0 - - - +
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Residues in contact with ALA 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A VAL* 3.4 17.2 + - + -
765A PRO* 1.3 80.0 - - - +
767A ASN* 1.3 74.2 + - - +
770A GLU* 3.0 21.4 + - - +
771A ALA* 4.4 1.9 + - - +
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Residues in contact with ASN 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A PRO 5.2 0.7 - - - -
609A VAL* 4.0 14.7 + - + +
612A SER* 2.5 56.0 + - - +
613A SER* 3.5 9.3 - - - +
765A PRO 3.6 0.6 + - - -
766A ALA* 1.3 79.6 - - - +
768A PHE* 1.3 81.3 + - + +
770A GLU* 3.1 39.3 + - + +
821A LYS* 6.0 2.8 - - + +
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Residues in contact with PHE 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A PRO* 5.4 5.4 - - + -
609A VAL* 4.5 33.9 - - + -
765A PRO 3.8 3.7 + - - -
766A ALA 3.5 0.2 - - - -
767A ASN* 1.3 82.1 - - - +
769A ASN* 1.3 70.7 + - - +
770A GLU 3.4 0.2 + - - -
773A TYR* 4.1 10.9 + - - -
824A ILE* 4.3 29.4 - - + -
831A ARG* 4.2 39.3 - - + -
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Residues in contact with ASN 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A ASN 5.8 1.3 + - - -
764A VAL 4.1 3.4 - - - +
765A PRO* 3.2 38.4 + - - +
766A ALA 3.8 3.4 - - - -
768A PHE* 1.3 78.1 - - - +
770A GLU* 1.3 64.2 + - - +
771A ALA 3.2 3.1 - - - -
772A LYS* 3.2 41.9 + - + +
773A TYR* 3.2 15.5 - - + -
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Residues in contact with GLU 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A SER* 3.5 6.1 + - - -
665A LYS* 2.5 38.9 + - - -
766A ALA* 3.0 10.8 + - - +
767A ASN* 3.1 44.5 + - + +
768A PHE 4.3 0.4 - - - -
769A ASN* 1.3 76.0 - - - +
771A ALA* 1.3 62.5 + - - +
773A TYR* 3.2 22.0 + - + +
774A ILE* 3.4 20.6 + - + +
821A LYS* 4.3 21.1 + - + -
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Residues in contact with ALA 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A ALA* 4.7 1.6 - - - +
761A THR* 3.1 34.3 - - - +
762A ARG* 4.1 5.4 - - - +
764A VAL* 3.6 21.0 + - + +
766A ALA 4.4 1.0 + - - +
769A ASN 3.2 1.2 - - - -
770A GLU* 1.3 76.8 - - - +
772A LYS* 1.3 63.5 + - - +
773A TYR 3.2 0.2 - - - -
774A ILE* 3.5 14.3 + - + +
775A ALA* 3.2 23.4 + - - +
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Residues in contact with LYS 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ARG* 3.8 18.4 + - + +
764A VAL 4.8 0.6 + - - +
769A ASN* 3.2 40.2 + - + +
770A GLU 3.2 1.0 - - - -
771A ALA* 1.3 78.5 - - - +
773A TYR* 1.3 76.0 + - + +
775A ALA* 3.8 5.0 + - - +
776A PHE* 3.5 20.3 + - - +
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Residues in contact with TYR 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A PHE 4.1 11.7 - - - -
769A ASN* 3.2 29.8 - - + -
770A GLU* 3.2 12.2 + - + +
772A LYS* 1.3 92.6 + - + +
774A ILE* 1.3 63.2 + - + +
776A PHE* 3.5 6.5 + - - +
777A THR* 3.0 28.1 + - - -
816A CYS* 3.3 27.4 - - + +
817A MET* 4.7 7.2 - - - +
820A PRO* 3.7 29.3 - - + +
824A ILE* 5.8 2.6 - - - +
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Residues in contact with ILE 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 3.9 32.3 - - + -
665A LYS* 3.8 31.2 - - + -
666A THR* 4.1 18.8 - - + -
758A ALA* 4.5 6.3 - - + -
770A GLU* 3.4 27.6 + - + +
771A ALA* 3.5 12.3 + - + +
773A TYR* 1.3 74.2 - - + +
775A ALA* 1.3 65.8 + - - +
777A THR* 3.4 6.3 + - - -
778A MET* 3.2 24.5 + - + +
817A MET* 4.4 15.9 - - + -
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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
----------------------------------------------------------
758A ALA* 4.0 28.9 - - - +
762A ARG* 4.3 9.6 - - + -
771A ALA 3.2 15.3 + - - +
772A LYS* 4.0 5.4 - - - +
773A TYR 3.3 0.2 - - - -
774A ILE* 1.3 80.4 - - - +
776A PHE* 1.3 60.9 + - - +
778A MET* 3.3 2.9 + - - +
779A TYR* 3.0 52.0 + - + +
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Residues in contact with PHE 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A LYS 3.5 15.1 + - - +
773A TYR* 3.8 6.1 - - - +
774A ILE 3.3 0.6 - - - -
775A ALA* 1.3 76.1 - - - +
777A THR* 1.3 66.5 + - - +
779A TYR* 3.3 19.5 + + + +
780A THR* 3.1 39.1 + - - -
816A CYS* 4.0 27.1 - - + -
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Residues in contact with THR 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 6.3 0.9 - - + -
773A TYR 3.0 15.1 + - - -
774A ILE 3.6 8.3 - - - -
775A ALA 3.3 0.4 - - - -
776A PHE* 1.3 80.3 - - - +
778A MET* 1.3 62.6 + - - +
780A THR* 3.2 4.5 + - - -
781A THR* 2.7 44.3 + - - +
812A VAL* 4.0 12.7 - - + +
813A ALA* 3.8 31.2 - - + -
816A CYS* 3.2 18.9 - - - +
817A MET* 3.5 18.1 - - + +
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Residues in contact with MET 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 4.7 7.4 - - + -
662A LEU* 3.8 25.6 - - + -
751A ILE* 3.6 34.5 - - + +
754A CYS* 3.5 25.6 - - + -
755A THR* 3.3 26.9 - - + +
758A ALA* 4.4 6.7 - - + -
774A ILE* 3.2 22.1 + - + +
775A ALA* 3.3 5.6 + - - +
777A THR* 1.3 78.6 - - - +
779A TYR* 1.3 64.5 + - - +
781A THR* 3.8 13.6 - - + -
782A CYS* 3.0 31.2 + - - -
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Residues in contact with TYR 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A THR* 4.3 19.7 - - + -
758A ALA* 6.4 0.4 - - + -
759A PHE* 3.2 36.8 - + + +
762A ARG* 4.2 9.2 - - - -
775A ALA* 3.0 42.8 + - + +
776A PHE* 3.5 23.1 - + + +
777A THR 3.2 0.2 - - - -
778A MET* 1.3 79.7 - - - +
780A THR* 1.3 62.2 + - - +
782A CYS* 3.5 5.1 + - - +
783A ILE* 3.2 29.5 + - + +
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Residues in contact with THR 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A PHE* 3.1 30.7 + - - -
777A THR 3.2 7.4 + - - -
779A TYR* 1.3 75.6 - - - +
781A THR* 1.3 54.7 + - - +
783A ILE* 3.0 13.0 + - + +
784A ILE* 2.7 59.0 + - + +
812A VAL* 4.1 18.1 - - + +
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Residues in contact with THR 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 3.2 37.1 + - + +
751A ILE* 4.0 15.0 - - + -
777A THR* 2.7 39.9 + - - +
778A MET* 3.9 11.9 - - + -
780A THR* 1.3 73.3 - - - +
782A CYS* 1.3 56.3 + - - +
784A ILE* 4.4 8.5 - - - -
785A TRP* 2.9 47.4 + - + +
809A SER* 4.8 4.9 + - - +
812A VAL* 4.5 5.7 - - - +
813A ALA* 5.6 0.9 + - - +
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Residues in contact with CYS 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A ILE* 3.7 9.9 - - - -
752A LEU* 5.4 3.6 - - - -
755A THR* 3.1 37.0 - - - -
778A MET 3.0 18.5 + - - +
779A TYR* 3.7 6.1 - - - +
781A THR* 1.3 76.6 - - - +
783A ILE* 1.3 58.1 + - + +
785A TRP 3.9 0.2 - - - -
786A LEU* 2.9 40.3 + - + +
4001A OLA 3.6 28.3 - - + +
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Residues in contact with ILE 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A TYR* 3.2 18.1 + - + +
780A THR* 3.0 13.9 + - + +
782A CYS* 1.3 75.6 - - + +
784A ILE* 1.3 63.1 + - + +
786A LEU* 3.3 6.2 + - + +
787A ALA* 2.9 35.2 + - + +
----------------------------------------------------------
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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 THR* 2.7 37.6 + - + +
781A THR* 3.8 6.5 - - - +
783A ILE* 1.3 74.9 - - + +
785A TRP* 1.3 63.9 + - + +
787A ALA* 3.5 4.6 + - - +
788A PHE* 3.0 27.1 + - + +
805A SER* 4.7 9.2 - - - +
808A LEU* 3.8 35.0 - - + +
809A SER* 4.7 6.1 - - - -
812A VAL* 3.7 31.2 - - + -
4005A 51E 4.0 16.8 - - + -
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Residues in contact with TRP 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A PRO* 3.8 13.2 - - + -
659A TYR* 3.4 20.2 + + - -
744A LEU* 3.5 36.1 - - + +
747A ASN* 3.6 35.2 - - + -
751A ILE* 3.4 15.9 - - + -
781A THR* 2.9 34.9 + - + +
784A ILE* 1.3 79.8 - - + +
786A LEU* 1.3 66.2 + - - +
788A PHE* 3.4 18.8 - - - +
789A VAL* 3.6 13.2 - - - +
809A SER* 3.0 20.7 + - - -
4001A OLA 3.7 26.9 - - + +
4005A 51E 3.4 45.9 - + + +
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Residues in contact with LEU 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A CYS* 2.9 28.9 + - + +
783A ILE* 3.8 6.3 - - + +
785A TRP* 1.3 74.6 - - - +
787A ALA* 1.3 63.4 + - - +
788A PHE 3.3 0.2 + - - -
789A VAL* 3.5 8.4 + - + +
790A PRO* 3.2 16.3 - - - +
4001A OLA 3.7 41.3 - - + -
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Residues in contact with ALA 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ILE* 2.9 24.0 + - + +
784A ILE* 3.9 4.7 - - - +
786A LEU* 1.3 74.6 - - - +
788A PHE* 1.3 64.3 + - - +
789A VAL 3.3 0.2 - - - -
790A PRO* 3.2 12.8 - - - +
791A ILE* 3.1 35.2 - - + +
----------------------------------------------------------
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Residues in contact with PHE 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A VAL* 5.2 1.1 - - + -
744A LEU* 4.1 19.3 - - + -
784A ILE* 3.0 19.5 + - + +
785A TRP* 3.4 10.1 - - - +
786A LEU 3.1 0.2 - - - -
787A ALA* 1.3 78.3 - - - +
789A VAL* 1.3 61.9 + - + +
791A ILE* 3.2 5.3 + - + -
792A TYR* 2.7 74.4 + + + +
793A PHE* 5.1 1.6 - + - -
801A THR* 4.9 2.0 - - + -
802A MET* 3.8 13.0 - - + -
805A SER* 3.4 31.6 - - - +
4005A 51E 3.7 51.6 - + + -
----------------------------------------------------------
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Residues in contact with VAL 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A LEU* 4.2 13.9 - - + -
785A TRP 3.6 15.9 - - - +
786A LEU* 3.8 6.3 - - + +
787A ALA 3.3 0.2 - - - -
788A PHE* 1.3 81.0 - - + +
790A PRO* 1.3 70.1 - - + +
793A PHE* 3.2 45.8 + - + +
4001A OLA 3.8 52.0 - - + -
----------------------------------------------------------
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Residues in contact with PRO 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A LEU 3.2 14.4 - - - +
787A ALA* 3.2 17.7 - - - +
789A VAL* 1.3 94.3 - - + +
791A ILE* 1.3 64.3 + - + +
793A PHE* 5.3 0.9 - - + -
794A GLY* 3.3 19.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A ALA* 3.1 31.2 - - + +
788A PHE* 3.2 6.8 + - + +
790A PRO* 1.3 81.0 - - + +
792A TYR* 1.3 65.9 + - - +
794A GLY 3.7 1.0 - - - -
795A SER* 3.2 25.3 + - - -
801A THR* 3.9 20.2 - - + -
----------------------------------------------------------
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Residues in contact with TYR 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A VAL* 4.3 23.6 - - + +
788A PHE* 2.7 54.8 + + + +
789A VAL 4.5 0.7 - - - +
791A ILE* 1.3 69.3 - - - +
793A PHE* 1.3 82.9 + + - +
794A GLY 3.0 4.3 - - - -
795A SER* 3.0 25.4 + - - -
798A LYS* 3.5 72.9 + - + +
801A THR* 4.3 9.6 - - + -
802A MET* 3.6 22.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A ASN* 3.7 22.2 - - + -
740A VAL* 4.2 17.9 - - + -
741A VAL* 3.7 24.0 - - + -
744A LEU* 4.4 13.5 - - + -
788A PHE* 5.1 1.1 - + - -
789A VAL* 3.2 37.0 + - + +
790A PRO* 5.0 0.9 - - + +
792A TYR* 1.3 98.6 - + - +
794A GLY* 1.3 56.9 - - - +
795A SER 3.4 0.8 - - - +
798A LYS* 4.3 13.5 + - - +
4001A OLA 3.4 55.6 - - + +
----------------------------------------------------------
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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