Contacts of the helix formed by residues 771 - 797 (chain A) in PDB entry 1TBF
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 771 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A SER* 3.7 35.0 - - - +
769A THR 4.6 1.1 - - - +
770A LYS* 1.3 89.6 - - + +
772A TRP* 1.3 67.2 + - - +
773A PRO* 3.3 9.2 - - + -
774A ILE* 2.9 37.5 + - + +
775A GLN 3.0 6.2 + - - -
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Residues in contact with TRP 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A LYS 3.3 1.8 + - - -
771A PRO* 1.3 69.8 - - - +
773A PRO* 1.3 75.5 - - + +
775A GLN* 4.3 4.7 - - + -
776A GLN* 2.9 51.7 + - + +
849A ASN* 3.5 22.9 + - - +
852A LYS* 3.5 58.4 - - + +
853A TRP* 3.5 57.2 - + - -
856A LEU* 3.8 19.7 - - + -
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Residues in contact with PRO 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A PRO* 3.4 11.0 - - + -
772A TRP* 1.3 101.4 - - + +
774A ILE* 1.3 62.0 + - + +
776A GLN* 3.7 7.9 + - + +
777A ARG* 3.3 35.5 + - - +
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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
----------------------------------------------------------
560A SER 3.7 9.6 - - - +
561A PHE 4.8 0.4 - - - +
562A SER* 3.5 34.8 - - - +
564A PHE* 4.1 17.3 - - + -
770A LYS* 3.6 20.2 - - + -
771A PRO* 2.9 37.0 + - + +
773A PRO* 1.3 76.0 - - + +
775A GLN* 1.3 65.7 + - - +
777A ARG* 3.2 3.3 + - - +
778A ILE* 2.9 42.0 + - + +
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Residues in contact with GLN 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VIA 4.7 3.2 + - - -
767A ALA* 2.9 38.6 + - - +
768A ILE* 3.5 19.4 - - - +
770A LYS* 3.8 5.8 - - - +
771A PRO 3.0 5.5 + - - -
772A TRP* 3.8 7.9 - - + +
774A ILE* 1.3 75.7 - - - +
776A GLN* 1.3 58.9 + - - +
778A ILE* 4.5 2.0 - - - +
779A ALA* 2.8 31.2 + - - +
817A GLN* 3.0 20.3 + - - +
849A ASN* 3.5 35.2 - - - +
853A TRP* 2.9 30.9 + - - +
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Residues in contact with GLN 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A TRP* 2.9 51.9 + - + +
773A PRO* 4.0 7.4 - - + +
775A GLN* 1.3 77.5 - - - +
777A ARG* 1.3 64.5 + - + +
779A ALA* 3.8 2.1 - - - +
780A GLU* 3.1 22.0 + - - +
853A TRP* 4.2 22.9 - - + -
856A LEU* 5.3 4.4 - - - +
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Residues in contact with ARG 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A PHE* 3.4 44.7 - - + +
565A GLU* 5.1 6.3 + - - -
773A PRO* 3.3 20.9 + - - +
774A ILE 3.2 4.8 + - - +
776A GLN* 1.3 80.4 - - + +
778A ILE* 1.3 60.3 + - - +
780A GLU* 3.3 9.8 + - - +
781A LEU* 3.2 23.6 + - - +
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Residues in contact with ILE 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A VIA 5.1 0.7 - - - -
563A ASP* 5.6 0.4 - - - +
564A PHE* 3.8 20.4 - - + -
612A TYR* 3.5 32.5 - - + -
620A ASN* 5.1 12.8 - - - +
767A ALA* 3.6 31.9 - - + +
770A LYS* 5.0 2.2 - - + -
774A ILE* 2.9 39.8 + - + +
775A GLN* 4.1 4.0 - - - +
777A ARG* 1.3 72.3 - - - +
779A ALA* 1.3 67.7 + - - +
781A LEU* 3.0 13.9 + - + +
782A VAL* 3.0 23.5 + - + +
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Residues in contact with ALA 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A VIA 3.6 8.9 - - + +
775A GLN* 2.8 28.2 + - - +
776A GLN 3.8 2.2 - - - +
778A ILE* 1.3 76.5 - - - +
780A GLU* 1.3 57.0 + - - +
782A VAL* 3.3 8.4 + - - -
783A ALA* 2.9 30.9 + - - +
813A ILE* 5.0 3.4 - - + -
817A GLN* 3.7 15.0 - - + +
853A TRP* 3.5 28.5 - - + -
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Residues in contact with GLU 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776A GLN 3.1 13.0 + - - +
777A ARG* 3.5 11.9 - - - +
778A ILE 3.2 0.2 - - - -
779A ALA* 1.3 77.2 - - - +
781A LEU* 1.3 58.3 + - + +
783A ALA* 3.5 6.5 + - - +
784A THR* 2.8 39.8 + - - +
810A LYS* 3.5 33.2 + - - -
813A ILE* 4.7 9.1 - - - +
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Residues in contact with LEU 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A PHE* 5.2 9.0 - - + -
611A ALA* 3.7 35.6 - - + +
612A TYR* 3.9 15.0 - - + +
614A ASN* 5.6 1.6 - - - +
777A ARG 3.2 14.9 + - - +
778A ILE* 3.0 22.0 + - + +
780A GLU* 1.3 76.6 - - + +
782A VAL* 1.3 65.7 + - - +
784A THR* 3.2 8.9 + - + +
785A GLU* 3.0 20.8 + - - +
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Residues in contact with VAL 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VIA 3.8 42.4 - - + +
612A TYR* 3.7 41.3 - - + -
778A ILE* 3.0 19.3 + - + +
779A ALA* 3.6 6.5 - - - +
781A LEU* 1.3 76.1 - - - +
783A ALA* 1.3 63.0 + - - +
785A GLU* 3.1 5.6 + - - +
786A PHE* 2.9 55.3 + - + -
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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
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501A VIA 3.9 10.7 - - + +
779A ALA 2.9 17.5 + - - +
780A GLU* 3.7 7.4 - - - +
782A VAL* 1.3 77.2 - - - +
784A THR* 1.3 55.0 + - - +
786A PHE* 3.7 7.7 - - - +
787A PHE* 2.8 49.4 + - + -
813A ILE* 3.6 30.7 - - + -
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Residues in contact with THR 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ALA* 3.6 19.5 - - + -
780A GLU* 2.8 33.5 + - - +
781A LEU* 3.2 10.1 + - + +
783A ALA* 1.3 75.9 - - - +
785A GLU* 1.3 60.9 + - - +
787A PHE* 3.9 7.5 - - - +
788A ASP* 3.0 25.1 + - + +
807A ARG* 4.9 12.1 + - - +
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Residues in contact with GLU 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A VAL* 3.3 14.0 - - + +
611A ALA* 4.3 9.6 - - + +
612A TYR* 2.9 12.3 + - + +
613A HIS* 2.7 54.1 + - - -
657A HIS* 3.4 4.3 + - - -
659A GLY* 3.3 32.2 - - - +
660A VAL 5.6 0.2 - - - -
781A LEU 3.0 12.4 + - - +
782A VAL* 3.5 8.1 - - - +
784A THR* 1.3 78.6 - - - +
786A PHE* 1.3 69.3 + - + +
788A ASP* 3.3 7.1 + - - +
789A GLN* 3.0 21.8 + - - +
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Residues in contact with PHE 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VIA 3.7 64.2 - + + -
613A HIS* 5.5 6.3 - + - -
782A VAL* 2.9 42.5 + - + -
783A ALA* 3.7 7.4 - - - +
785A GLU* 1.3 83.7 - - + +
787A PHE* 1.3 63.8 + - - +
789A GLN* 3.2 11.9 + - - +
790A GLY 3.0 18.4 + - - -
804A LEU* 3.5 39.9 - - + +
805A MET* 3.6 25.4 - - + +
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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
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783A ALA* 2.8 39.3 + - + +
784A THR* 4.0 2.0 - - - +
786A PHE* 1.3 72.9 - - - +
788A ASP* 1.3 56.8 + - - +
790A GLY* 3.2 1.6 + - - -
791A ASP* 2.9 32.6 + - - +
803A ASP 4.3 3.4 - - - -
804A LEU 3.6 17.5 - - - -
805A MET 3.6 11.4 - - - +
806A ASN 3.4 18.6 - - - -
807A ARG* 3.5 59.5 - - + +
809A LYS 4.7 1.3 - - - -
810A LYS* 3.9 40.4 - - + -
813A ILE* 4.2 10.8 - - + -
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Residues in contact with ASP 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A GLY* 5.0 5.0 - - - +
660A VAL* 5.8 0.3 - - - +
784A THR* 3.0 20.1 + - + +
785A GLU* 3.6 7.4 - - + +
786A PHE 3.2 0.2 - - - -
787A PHE* 1.3 74.3 - - - +
789A GLN* 1.3 65.3 + - - +
791A ASP* 3.2 15.9 + - - +
792A ARG* 3.1 35.9 + - - +
807A ARG* 4.0 3.5 - - - +
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Residues in contact with GLN 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GOL 3.5 6.8 + - - -
659A GLY 4.3 2.3 + - - +
660A VAL* 3.4 20.4 - - + +
661A SER* 3.0 47.7 + - - +
664A PHE* 3.6 18.2 - - + +
785A GLU 3.0 13.2 + - - +
786A PHE* 3.5 12.4 - - - +
788A ASP* 1.3 77.4 + - - +
790A GLY* 1.3 57.3 + - - +
792A ARG* 3.0 7.8 + - - +
793A GLU* 2.8 49.9 + - - +
805A MET* 3.7 19.1 - - + +
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Residues in contact with GLY 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786A PHE 3.0 11.5 + - - -
787A PHE 3.2 0.6 + - - -
789A GLN* 1.3 76.4 - - - +
791A ASP* 1.4 63.1 + - - +
793A GLU* 3.2 17.7 + - - +
794A ARG* 3.0 26.3 + - - +
801A PRO* 3.6 9.4 - - - +
805A MET* 3.2 24.4 - - - +
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Residues in contact with ASP 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A PHE 2.9 16.4 + - - +
788A ASP* 3.4 15.0 - - - +
789A GLN 3.2 0.2 - - - -
790A GLY* 1.4 75.5 - - - +
792A ARG* 1.3 63.2 + - + +
794A ARG* 2.8 35.1 + - - +
795A LYS* 3.2 29.2 + - + +
805A MET 5.3 0.2 - - - +
807A ARG* 2.8 36.1 + - - +
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Residues in contact with ARG 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A PRO* 4.9 8.1 + - - +
660A VAL* 3.6 32.1 - - - +
664A PHE* 3.8 23.6 - - + -
788A ASP* 3.1 27.9 + - - +
789A GLN 3.0 8.4 + - - +
791A ASP* 1.3 75.4 - - + +
793A GLU* 1.3 60.1 + - - +
795A LYS* 3.2 2.4 + - - -
796A GLU* 2.8 78.9 + - - +
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Residues in contact with GLU 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GOL 2.6 50.4 + - - +
664A PHE* 3.8 14.8 - - + -
789A GLN* 2.8 34.3 + - - +
790A GLY* 3.5 9.6 - - - +
792A ARG* 1.3 76.1 - - - +
794A ARG* 1.4 62.7 + - - +
797A LEU* 3.1 31.7 + - + +
798A ASN 3.2 5.9 + - - -
799A ILE* 3.6 19.1 + - + +
801A PRO* 3.7 26.4 - - + +
802A THR 4.9 0.2 + - - -
805A MET* 4.0 5.2 - - - +
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Residues in contact with ARG 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A GLY 3.0 15.2 + - - +
791A ASP* 2.8 45.4 + - - +
792A ARG 3.3 0.4 - - - -
793A GLU* 1.4 76.6 - - - +
795A LYS* 1.3 59.2 + - + +
798A ASN* 3.4 22.5 + - - +
799A ILE 3.4 18.5 + - - +
800A GLU* 5.7 0.2 - - - -
801A PRO* 3.7 25.4 - - + +
806A ASN* 3.4 29.3 + - - +
807A ARG* 4.6 2.8 - - - +
808A GLU* 4.7 9.8 + - - +
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Residues in contact with LYS 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A ASP* 3.2 16.9 + - + +
792A ARG* 3.2 4.5 + - - +
793A GLU 3.2 0.4 - - - -
794A ARG* 1.3 81.6 - - + +
796A GLU* 1.3 66.5 + - + +
797A LEU 3.6 0.2 - - - -
798A ASN* 4.6 8.7 + - - -
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Residues in contact with GLU 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A PHE* 3.9 8.8 - - + -
668A THR* 5.1 4.6 - - + +
792A ARG* 2.8 71.4 + - - +
795A LYS* 1.3 79.9 - - + +
797A LEU* 1.3 69.1 + - + +
798A ASN* 6.0 0.2 - - - -
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Residues in contact with LEU 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GOL 4.4 0.9 - - - +
664A PHE* 4.3 14.8 - - + -
667A ASN* 3.6 48.2 - - - +
668A THR* 3.7 27.6 - - + -
793A GLU* 3.1 16.3 + - + +
796A GLU* 1.3 84.2 - - + +
798A ASN* 1.3 72.3 + - - +
799A ILE* 3.7 23.3 - - + +
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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