Contacts of the helix formed by residues 740 - 765 (chain B) in PDB entry 2BKU
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 THR 740 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B ASN* 2.7 36.0 + - + +
739B GLY* 1.3 83.7 - - - +
741B LEU* 1.3 82.9 + - + +
742B GLU* 4.1 2.3 + - - +
743B ALA* 3.3 24.0 + - - +
744B LEU* 3.6 8.1 - - - +
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Residues in contact with LEU 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B THR* 1.3 87.1 - - + +
742B GLU* 1.3 90.2 + - + +
744B LEU* 3.8 1.9 + - - +
745B ASP* 3.4 27.6 + - - +
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Residues in contact with GLU 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B ARG* 6.1 0.7 - - - -
740B THR* 5.0 0.9 - - - +
741B LEU* 1.3 96.9 - - + +
743B ALA* 1.3 69.1 + - - +
744B LEU 2.9 0.3 + - - -
745B ASP* 3.0 6.9 + - - -
746B TYR* 2.8 32.2 + - + +
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Residues in contact with ALA 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B PRO* 3.9 9.8 - - + +
737B GLU* 4.3 10.2 + - - +
738B ASN* 3.1 42.4 - - - +
740B THR* 3.3 27.3 + - - +
742B GLU* 1.3 79.7 - - - +
744B LEU* 1.3 59.3 + - + +
746B TYR* 4.0 6.4 - - - +
747B GLN* 3.3 21.7 + - - +
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Residues in contact with LEU 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B PRO* 3.7 28.5 - - + -
739B GLY* 4.0 21.3 - - - +
740B THR 3.6 14.9 + - - +
741B LEU 4.5 2.2 - - - +
742B GLU 3.1 0.6 - - - -
743B ALA* 1.3 76.3 - - + +
745B ASP* 1.3 62.1 + - - +
746B TYR 3.2 2.2 - - - -
747B GLN* 3.5 6.9 - - - +
748B ILE* 2.7 40.8 + - + +
791B GLN* 3.6 29.8 - - - +
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Residues in contact with ASP 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B LEU* 3.4 22.1 + - - +
742B GLU* 3.0 7.2 + - - +
744B LEU* 1.3 81.5 - - - +
746B TYR* 1.3 57.5 + - - +
748B ILE* 4.0 8.4 - - - +
749B LYS* 3.2 33.2 + - - +
791B GLN* 5.5 2.1 + - - -
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Residues in contact with TYR 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B ARG* 2.7 55.1 + - + +
697B GLU* 4.9 0.7 - - - -
699B LYS* 4.0 19.6 - - + +
700B PRO* 4.4 9.2 - - + -
737B GLU* 4.3 24.5 - - + +
742B GLU* 2.8 20.4 + - + +
743B ALA* 4.0 5.2 - - - +
745B ASP* 1.3 74.8 - - - +
747B GLN* 1.3 58.8 + - - +
748B ILE 3.2 0.2 - - - -
749B LYS* 2.9 32.2 + - + +
750B VAL* 2.8 51.7 + - + +
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Residues in contact with GLN 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ALA 5.3 0.4 + - - +
732B GLN 4.9 2.6 + - - -
734B THR* 2.9 32.8 + - + +
735B LYS* 4.1 6.7 - - - +
736B PRO* 4.0 26.1 - - + +
743B ALA 3.3 17.0 + - - +
744B LEU* 3.2 6.7 + - - +
746B TYR* 1.3 84.9 - - + +
748B ILE* 1.3 75.7 + - - +
750B VAL* 3.4 8.7 + - + +
751B LEU* 3.0 58.5 + - + +
785B GLN* 5.6 0.6 + - - -
789B ASP* 5.1 3.5 - - - +
791B GLN* 5.1 0.7 + - - -
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Residues in contact with ILE 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B LEU 2.7 23.2 + - - +
745B ASP* 4.0 10.1 - - - +
747B GLN* 1.3 87.1 - - - +
749B LYS* 1.3 55.6 + - + +
751B LEU* 3.0 11.9 + - + +
752B GLU* 2.8 58.0 + - + +
789B ASP* 4.9 3.8 - - - +
791B GLN* 3.1 56.1 - - + +
792B LEU* 4.5 9.9 - - + -
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Residues in contact with LYS 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B GLU* 5.7 8.5 - - - +
700B PRO* 3.9 20.1 - - + +
745B ASP* 3.2 24.3 + - - +
746B TYR* 2.9 36.2 + - + +
748B ILE* 1.3 76.8 - - + +
750B VAL* 1.3 62.4 + - - +
752B GLU* 3.5 14.5 + - - +
753B ALA* 3.2 22.5 + - - +
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Residues in contact with VAL 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B LYS* 4.5 13.9 - - + +
700B PRO* 4.4 16.6 - - + -
703B LEU* 4.0 7.9 - - + +
731B ALA* 3.9 38.8 - - + +
734B THR* 6.0 1.8 - - + -
746B TYR* 2.8 47.5 + - + +
747B GLN* 3.5 11.7 - - + +
749B LYS* 1.3 72.5 - - - +
751B LEU* 1.3 61.7 + - + +
753B ALA* 3.0 5.8 + - - +
754B VAL* 2.9 25.7 + - + +
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Residues in contact with LEU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ALA 4.5 4.3 - - - +
732B GLN* 3.8 31.6 - - - +
747B GLN* 3.0 50.5 + - - +
748B ILE* 3.0 11.4 + - + +
750B VAL* 1.3 76.1 - - + +
752B GLU* 1.3 61.6 + - - +
754B VAL* 3.4 4.3 + - + +
755B LEU* 3.1 17.7 + - - +
782B PHE* 3.2 24.4 - - + -
785B GLN* 3.8 15.0 - - - +
789B ASP* 5.3 3.8 - - - +
792B LEU* 3.9 34.3 - - + -
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Residues in contact with GLU 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748B ILE* 2.8 41.0 + - + +
749B LYS* 3.9 15.0 - - - +
750B VAL 3.2 0.2 - - - -
751B LEU* 1.3 73.1 - - - +
753B ALA* 1.3 56.9 + - - +
755B LEU* 3.4 11.9 - - + +
756B ASP* 3.0 31.2 + - - +
791B GLN 5.4 1.4 - - - +
792B LEU* 4.8 8.1 - - + -
795B GLU* 4.6 14.2 - - - +
798B THR* 3.6 24.5 + - + +
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Residues in contact with ALA 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B PRO* 3.3 33.0 - - + +
703B LEU* 3.5 23.5 - - + +
704B SER* 3.3 13.7 - - - +
749B LYS 3.2 13.0 + - - +
750B VAL 3.0 9.9 + - - +
752B GLU* 1.3 76.5 - - - +
754B VAL* 1.3 62.5 + - - +
756B ASP* 3.3 3.9 + - - +
757B ALA* 3.1 16.5 + - - +
838D GLN* 4.8 2.0 - - - +
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Residues in contact with VAL 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU* 4.0 4.9 - - + +
728B CYS* 3.6 23.6 - - + -
731B ALA* 3.9 20.2 - - + -
732B GLN* 3.8 12.8 - - + +
750B VAL* 2.9 19.2 + - + +
751B LEU* 3.4 9.8 + - - +
753B ALA* 1.3 72.7 - - - +
755B LEU* 1.3 61.3 + - - +
757B ALA* 2.9 22.3 + - - +
758B TYR* 3.0 45.3 + - + -
782B PHE* 3.7 17.3 - - + -
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Residues in contact with LEU 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B LEU 3.1 10.1 + - - +
752B GLU* 3.4 15.3 - - + +
754B VAL* 1.3 80.9 - - - +
756B ASP* 1.3 62.6 + - - +
758B TYR* 3.4 3.8 + - - +
759B VAL* 3.1 43.0 + - + +
782B PHE* 3.7 22.8 - - + -
786B VAL* 5.4 0.9 - - + -
798B THR* 3.6 44.2 - - + +
801B ALA* 3.7 16.6 - - + -
802B ALA* 4.5 5.2 - - + +
805B LEU* 4.1 16.4 - - + -
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Residues in contact with ASP 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B SER* 2.6 39.0 + - - +
707B GLY* 3.5 6.5 - - - -
752B GLU* 3.0 21.3 + - - +
753B ALA* 3.5 4.4 - - - +
754B VAL 3.2 0.4 - - - -
755B LEU* 1.3 75.4 - - - +
757B ALA* 1.3 62.5 + - - +
759B VAL* 4.6 1.1 - - - -
760B GLY 3.1 17.7 + - - -
838D GLN* 4.4 6.5 + - - +
841D SER* 3.2 18.6 - - - -
842D GLN* 2.9 42.9 + - + +
843D ALA 4.8 0.2 + - - -
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Residues in contact with ALA 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU* 3.4 21.1 + - - +
706B PHE* 4.5 7.9 - - + -
707B GLY* 3.8 15.1 - - - +
724B ILE* 5.2 0.2 - - + -
728B CYS* 4.1 21.8 - - - -
753B ALA 3.1 7.0 + - - +
754B VAL* 2.9 11.0 + - - +
756B ASP* 1.3 77.1 - - - +
758B TYR* 1.3 56.9 + - - +
760B GLY* 3.3 1.7 + - - -
761B ILE* 2.9 39.9 + - + +
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Residues in contact with TYR 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B MET* 3.5 33.7 - - + -
728B CYS* 2.5 36.6 + - - -
732B GLN* 2.7 16.5 + - - -
754B VAL* 3.0 36.3 + - + +
755B LEU* 4.1 2.9 - - - +
757B ALA* 1.3 71.9 - - - +
759B VAL* 1.3 61.7 + - - +
761B ILE* 3.3 9.2 + - + +
762B VAL* 2.9 34.7 + - - +
778B THR* 3.7 12.3 - - + +
779B ILE* 3.9 31.2 - - + -
782B PHE* 3.7 26.2 - + + -
805B LEU* 4.1 16.2 - - + -
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Residues in contact with VAL 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B LEU* 3.1 42.4 + - + +
756B ASP* 3.9 2.9 - - - +
758B TYR* 1.3 76.1 - - - +
760B GLY* 1.3 58.3 + - - +
762B VAL* 3.4 1.9 + - - +
763B ALA* 3.0 28.3 + - - +
801B ALA* 4.3 13.0 - - + +
805B LEU* 3.7 20.2 - - + -
842D GLN* 3.9 8.5 - - + -
843D ALA* 3.7 30.5 - - + +
846D ASP* 3.9 10.1 - - - +
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Residues in contact with GLY 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B GLY 3.4 24.5 - - - -
710B ALA* 3.9 0.2 - - - -
711B SER* 3.2 18.3 + - - -
756B ASP 3.1 11.1 + - - -
757B ALA 3.7 2.5 - - - -
759B VAL* 1.3 76.5 - - - +
761B ILE* 1.3 51.8 + - - +
763B ALA* 3.4 2.0 + - - +
764B GLY 2.8 28.9 + - - -
842D GLN* 3.6 13.2 - - - -
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Residues in contact with ILE 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B PHE* 5.1 1.6 - - + +
710B ALA* 3.8 20.0 - - + -
717B PHE* 4.2 9.0 - - + -
721B LEU* 3.9 17.7 - - + -
724B ILE* 4.1 25.8 - - + -
725B MET* 4.4 12.6 - - - -
757B ALA* 2.9 29.4 + - + +
758B TYR* 3.3 11.6 + - + +
760B GLY* 1.3 73.4 - - - +
762B VAL* 1.3 59.4 + - - +
764B GLY* 3.3 0.3 + - - -
765B LEU* 2.8 51.0 + - + +
772B LEU* 3.9 18.8 - - + -
779B ILE* 5.7 1.6 - - + -
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Residues in contact with VAL 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B TYR 2.9 22.8 + - - +
759B VAL 3.9 3.4 - - - +
761B ILE* 1.3 70.9 - - + +
763B ALA* 1.3 66.1 + - - +
765B LEU* 3.6 1.9 + - - -
766B HIS* 3.3 21.5 + - - +
772B LEU* 4.1 19.3 - - + -
779B ILE* 4.5 8.1 - - + -
805B LEU* 4.0 15.0 - - + -
808B ASP* 3.9 30.3 - - + +
809B ILE* 3.9 27.4 - - + -
812B MET* 4.1 16.4 - - - +
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Residues in contact with ALA 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B SER* 4.2 8.9 - - - +
759B VAL 3.0 13.7 + - - +
760B GLY 3.5 5.8 - - - +
762B VAL* 1.3 80.9 - - - +
764B GLY* 1.3 63.1 + - - +
765B LEU 3.3 0.9 + - - -
766B HIS* 3.4 15.8 + - - +
846D ASP* 3.3 30.3 - - - +
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Residues in contact with GLY 764 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B ALA* 3.3 26.2 - - - -
711B SER* 3.7 9.4 - - - +
714B GLY* 3.3 20.4 - - - -
715B ALA 4.5 0.2 + - - -
760B GLY 2.8 16.0 + - - -
761B ILE 3.3 2.0 + - - -
763B ALA* 1.3 74.9 - - - +
765B LEU* 1.3 59.7 + - - +
766B HIS* 3.4 2.3 + - - +
767B ASP* 4.9 2.4 + - - +
768B LYS* 5.6 1.0 - - - +
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Residues in contact with LEU 765 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B ALA* 6.3 1.3 - - + -
714B GLY 3.9 25.6 - - - +
715B ALA* 4.3 0.7 - - - -
717B PHE* 5.6 5.6 - - + -
718B ILE* 3.9 22.2 - - + +
721B LEU* 4.2 24.0 - - + -
761B ILE* 2.8 37.0 + - + +
762B VAL* 3.8 4.5 - - - +
763B ALA 3.3 0.2 - - - -
764B GLY* 1.3 76.9 - - - +
766B HIS* 1.3 64.7 + - - +
767B ASP 3.2 2.9 - - - +
768B LYS* 2.9 36.0 + - + +
771B ALA* 4.4 7.9 - - + -
772B LEU* 4.4 11.0 - - + -
812B MET* 3.1 18.6 - - + +
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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