Contacts of the helix formed by residues 758 - 783 (chain C) in PDB entry 6VSB
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 SER 758 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961B THR* 3.3 19.9 + - - -
964B LYS* 5.5 12.9 - - - +
965B GLN* 2.9 21.8 + - - +
757C GLY* 1.3 70.5 - - - -
759C PHE* 1.3 64.4 + - - +
760C CYS* 3.2 5.6 - - - +
761C THR* 3.2 15.5 + - - +
762C GLN* 2.9 23.6 + - - +
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Residues in contact with PHE 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965B GLN* 3.2 23.3 - - - +
970B PHE* 4.2 11.4 - + - -
999B GLY 4.8 0.7 - - - -
1002B GLN* 3.6 17.9 - - + -
1003B SER* 3.9 25.8 - - - -
1006B THR* 3.8 14.4 - - + -
753C LEU* 6.1 1.6 - - + -
756C TYR* 3.0 31.2 - + + +
757C GLY 3.3 3.0 + - - +
758C SER* 1.3 76.9 - - - +
760C CYS* 1.3 64.3 + - - +
762C GLN* 3.0 15.6 + - - +
763C LEU* 2.8 39.9 + - + +
1001C LEU* 4.2 24.5 - - + -
1005C GLN* 3.6 28.5 - - - -
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Residues in contact with CYS 760 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738C CYS* 3.5 35.5 - - + +
739C THR* 4.8 11.4 - - + -
753C LEU* 4.7 23.4 - - + +
754C LEU* 6.4 1.6 - - - -
757C GLY 4.7 8.0 + - - -
758C SER* 4.7 5.4 - - - -
759C PHE* 1.3 78.6 - - - +
761C THR* 1.3 82.7 + - - +
763C LEU* 3.6 0.7 + - - +
764C ASN* 3.2 21.3 + - - +
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Residues in contact with THR 761 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758C SER* 3.2 14.3 + - - -
760C CYS* 1.3 88.8 - - - +
762C GLN* 1.3 60.0 + - - +
764C ASN* 3.1 7.4 + - + +
765C ARG* 2.8 50.7 + - + +
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Residues in contact with GLN 762 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B ALA* 5.8 0.4 - - - +
961B THR* 3.8 31.4 + - - +
965B GLN* 6.0 1.0 + - - -
1006B THR* 3.8 23.0 - - - +
1007B TYR* 5.8 3.2 - - - +
1010B GLN* 3.2 32.1 + - - +
758C SER* 2.9 19.7 + - - +
759C PHE* 3.6 16.4 - - - +
761C THR* 1.3 76.6 - - - +
763C LEU* 1.3 67.1 + - + +
765C ARG* 3.4 21.4 + - - +
766C ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 763 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006B THR* 6.2 4.0 - - + -
736C VAL* 6.2 1.3 - - + -
738C CYS* 3.8 16.4 - - + -
759C PHE* 2.8 24.8 + - + +
760C CYS 3.9 3.1 - - - +
762C GLN* 1.3 80.2 - - + +
764C ASN* 1.3 62.4 + - - +
766C ALA* 3.3 14.8 + - - +
767C LEU* 3.3 18.7 + - + +
1001C LEU* 4.7 18.6 - - + -
1004C LEU* 3.8 32.5 - - + -
1005C GLN* 4.2 30.5 - - + +
1008C VAL* 4.2 22.0 - - + +
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Residues in contact with ASN 764 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN* 4.1 22.5 + - - +
317B ASN* 5.5 5.1 - - - +
735C SER* 4.7 7.3 + - - -
736C VAL* 4.5 20.3 + - - +
737C ASP* 5.5 2.2 - - - +
738C CYS* 5.3 7.5 - - + +
760C CYS 3.2 10.8 + - - +
761C THR* 3.1 10.9 + - + +
763C LEU* 1.3 78.6 - - - +
765C ARG* 1.3 64.3 + - - +
767C LEU* 3.4 8.6 + - - +
768C THR* 3.0 30.6 + - - -
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Residues in contact with ARG 765 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957B GLN* 3.2 45.1 - - - +
961B THR* 5.3 7.9 + - - +
761C THR* 2.8 39.0 + - + +
762C GLN* 3.7 21.7 - - - +
763C LEU 3.2 0.2 - - - -
764C ASN* 1.3 73.2 - - - +
766C ALA* 1.3 65.4 + - - +
768C THR* 3.1 9.5 + - - -
769C GLY* 3.0 19.8 + - - -
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Residues in contact with ALA 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B GLN* 4.3 18.6 - - - +
762C GLN 3.1 14.2 + - - +
763C LEU* 3.3 7.4 + - - +
765C ARG* 1.3 78.9 - - - +
767C LEU* 1.3 62.6 + - - +
769C GLY* 3.1 10.8 + - - -
770C ILE* 3.2 19.3 + - - +
1008C VAL* 3.8 18.8 - - + -
1012C LEU* 4.4 14.3 - - + +
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Residues in contact with LEU 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734C THR* 4.4 15.8 - - + +
735C SER* 4.9 6.3 - - - +
736C VAL* 3.5 38.6 - - + +
763C LEU 3.3 8.3 + - - +
764C ASN* 3.9 8.1 - - - +
765C ARG 3.3 0.4 - - - -
766C ALA* 1.3 76.9 - - - +
768C THR* 1.3 57.2 + - - +
770C ILE* 3.1 26.0 - - + +
771C ALA* 3.0 31.1 + - - +
1007C TYR* 4.3 14.1 - - + -
1008C VAL* 3.6 36.1 - - + -
1011C GLN* 4.2 12.8 - - + -
1012C LEU* 6.5 0.2 - - + -
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Residues in contact with THR 768 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN* 4.5 15.3 + - + +
735C SER* 5.6 0.9 + - - -
764C ASN* 3.0 25.9 + - - -
765C ARG* 3.1 12.3 + - - +
767C LEU* 1.3 78.3 - - - +
769C GLY* 1.3 61.0 + - - +
771C ALA* 3.9 5.2 - - - +
772C VAL* 3.1 27.2 + - + +
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Residues in contact with GLY 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765C ARG 3.0 12.8 + - - -
766C ALA* 3.1 4.6 + - - -
768C THR* 1.3 75.4 - - - +
770C ILE* 1.3 58.8 + - - +
772C VAL* 3.1 12.1 - - - +
773C GLU* 2.8 28.9 + - - +
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Residues in contact with ILE 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C MET* 5.1 6.7 - - - -
734C THR* 5.1 4.7 - - + +
766C ALA 3.2 4.4 + - - +
767C LEU* 3.1 41.5 - - + +
769C GLY* 1.3 75.1 - - - +
771C ALA* 1.3 61.4 + - - +
773C GLU* 2.9 13.8 + - - +
774C GLN* 2.9 36.2 + - + +
1011C GLN* 4.1 27.1 - - + +
1012C LEU* 3.5 33.0 - - + +
1015C ALA* 4.0 23.3 - - + -
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Residues in contact with ALA 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733C LYS* 3.2 40.1 - - + +
734C THR 4.1 9.0 - - - +
767C LEU 3.0 19.5 + - - +
768C THR* 3.9 5.8 - - - +
770C ILE* 1.3 80.8 - - + +
772C VAL* 1.3 60.4 + - - +
774C GLN* 3.3 10.3 + - - +
775C ASP 3.7 1.6 + - - -
861C LEU* 4.0 27.1 - - + -
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Residues in contact with VAL 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733C LYS* 5.0 0.9 - - - +
768C THR* 3.1 18.1 + - + +
769C GLY* 3.1 19.7 - - - +
771C ALA* 1.3 73.9 - - - +
773C GLU* 1.3 64.1 + - - +
774C GLN 3.3 0.2 - - - -
775C ASP* 3.5 18.4 + - + +
776C LYS* 3.6 12.1 + - - +
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Residues in contact with GLU 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017B GLU* 4.2 2.8 - - - +
769C GLY 2.8 15.4 + - - +
770C ILE* 2.9 14.4 + - - +
772C VAL* 1.3 77.6 - - - +
774C GLN* 1.3 83.7 + - - +
776C LYS* 2.9 38.3 + - + +
777C ASN* 3.2 15.4 + - - +
1015C ALA* 4.1 16.0 - - - +
1019C ARG* 2.7 47.4 + - + +
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Residues in contact with GLN 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C VAL 4.6 1.0 - - - +
730C SER* 3.4 15.6 - - - +
731C MET* 3.4 46.4 + - + +
733C LYS* 4.0 14.4 - - + -
770C ILE* 2.9 23.2 + - + +
771C ALA* 3.6 11.4 - - - +
772C VAL 3.3 0.4 - - - -
773C GLU* 1.3 103.4 + - - +
775C ASP* 1.3 63.0 + - - +
777C ASN* 3.2 24.5 + - - +
778C THR* 3.3 17.4 + - - +
1015C ALA* 4.2 19.0 + - - +
1018C ILE* 4.2 5.3 - - - +
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Residues in contact with ASP 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B PRO* 6.1 0.3 - - - +
733C LYS* 2.3 39.1 + - - +
771C ALA 3.7 1.3 + - - +
772C VAL* 3.5 16.8 + - + +
773C GLU 3.2 0.6 - - - -
774C GLN* 1.3 78.0 - - - +
776C LYS* 1.3 59.7 + - - +
778C THR* 3.2 18.8 + - - -
779C GLN* 3.2 18.4 + - - +
863C PRO* 3.8 3.3 - - - +
864C LEU* 2.9 47.2 + - + +
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Residues in contact with LYS 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772C VAL 3.6 5.9 + - - +
773C GLU* 2.9 28.6 + - + +
775C ASP* 1.3 76.9 - - - +
777C ASN* 1.3 55.8 + - - +
779C GLN* 3.2 5.4 + - + +
780C GLU* 2.6 54.6 + - + +
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Residues in contact with ASN 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C VAL* 3.3 18.8 + - - +
773C GLU* 3.2 16.0 + - - +
774C GLN* 3.2 27.8 + - - +
776C LYS* 1.3 79.8 - - - +
778C THR* 1.3 55.3 + - - +
780C GLU* 4.4 11.6 - - - +
781C VAL* 2.7 40.3 + - - +
1018C ILE* 4.3 4.0 - - - +
1019C ARG* 4.1 25.7 - - - +
1022C ALA* 3.5 28.7 - - + +
1023C ASN* 4.9 1.0 - - - +
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Residues in contact with THR 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C VAL* 4.2 22.2 - - + +
730C SER* 4.2 15.3 - - - +
774C GLN 3.3 8.3 + - - +
775C ASP* 3.2 21.7 + - - -
777C ASN* 1.3 77.1 - - - +
779C GLN* 1.3 59.0 + - - +
781C VAL* 4.9 0.2 - - - -
782C PHE* 3.2 39.7 + - + +
863C PRO* 6.0 4.2 - - + +
864C LEU* 5.9 0.3 - - - +
865C LEU* 4.4 20.3 + - - +
870C ILE* 4.7 16.6 - - + -
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Residues in contact with GLN 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B CYS* 6.1 0.2 - - - +
697B MET* 4.5 15.8 - - - +
775C ASP 3.2 17.0 + - - +
776C LYS* 3.2 6.2 + - + +
777C ASN 3.2 0.4 - - - -
778C THR* 1.3 79.6 - - - +
780C GLU* 1.3 58.6 + - - +
783C ALA* 2.9 49.4 + - + +
864C LEU* 3.9 23.7 - - - +
865C LEU* 3.9 19.5 - - - +
873C TYR* 4.6 5.9 + - - -
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Residues in contact with GLU 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C LYS* 2.6 33.8 + - + +
777C ASN* 3.9 11.2 - - - +
779C GLN* 1.3 73.7 - - - +
781C VAL* 1.3 68.4 + - + +
783C ALA 4.6 2.2 - - - +
784C GLN* 3.7 19.4 + - - +
1022C ALA 5.7 0.7 - - - +
1023C ASN* 3.8 19.7 - - - +
1026C ALA* 4.5 16.2 - - + +
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Residues in contact with VAL 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C VAL* 4.0 21.3 - - + -
777C ASN* 2.7 25.0 + - - +
780C GLU* 1.3 76.4 - - + +
782C PHE* 1.3 70.3 + - + +
784C GLN* 3.3 10.0 - - - +
1022C ALA* 3.3 31.9 - - + +
1025C ALA* 4.3 9.6 - - + -
1026C ALA* 3.9 22.0 - - + +
1029C MET* 3.0 41.6 - - + +
1060C VAL* 4.7 5.2 - - + -
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Residues in contact with PHE 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C VAL* 4.2 21.1 - - + -
778C THR* 3.2 34.8 + - + +
781C VAL* 1.3 82.8 - - + +
783C ALA* 1.3 52.0 + - - +
784C GLN 2.6 19.2 + - - -
785C VAL* 4.5 1.4 + - - +
865C LEU* 5.3 1.1 - - + -
870C ILE* 3.6 29.4 - - + -
873C TYR* 3.7 27.3 - - + -
874C THR* 3.5 32.1 - - + -
877C LEU* 3.7 20.5 - - + +
1029C MET* 4.4 11.2 - - + -
1054C GLN 5.1 0.9 - - - -
1055C SER* 5.1 2.7 - - - -
1059C GLY 4.1 9.6 - - - -
1060C VAL* 4.0 31.9 - - + -
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Residues in contact with ALA 783 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779C GLN* 2.9 43.4 + - + +
780C GLU* 4.6 1.8 - - - +
782C PHE* 1.3 69.6 - - - +
784C GLN* 1.3 60.8 + - - +
785C VAL 3.4 8.5 - - - +
873C TYR* 3.8 31.4 - - + +
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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