Contacts of the helix formed by residues 634 - 659 (chain A) in PDB entry 2IUK
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 TYR 634 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.4 31.9 - - + -
380A PRO 2.6 28.9 + - - -
383A ILE* 4.5 5.6 - - + -
611A LEU* 4.3 2.2 - - + -
614A ARG* 2.9 26.1 + - - -
616A LEU* 3.4 45.1 - - + -
629A LEU* 4.9 1.1 - - + -
631A ILE* 3.3 25.6 - - + +
632A GLU 3.3 4.4 + - - +
633A ASP* 1.3 74.9 - - - +
635A PRO* 1.3 67.6 - - - +
636A TYR* 3.7 18.6 - + + -
637A ALA* 3.1 30.7 + - + -
638A VAL* 3.2 13.6 + - - +
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Residues in contact with PRO 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.7 14.4 - - + +
376A ALA* 3.8 9.4 - - + -
633A ASP* 3.4 22.0 - - - +
634A TYR* 1.3 84.8 - - - +
636A TYR* 1.3 55.6 + - - +
638A VAL* 3.2 6.2 + - + +
639A ASP 2.9 24.1 + - - -
833A ASN* 3.8 23.1 - - + +
834A ARG* 3.7 29.4 - - + +
842A TYR* 3.6 28.4 - - + -
845A LEU* 4.0 3.1 - - - +
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Residues in contact with TYR 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE 3.5 17.5 + - - +
380A PRO* 3.8 22.2 - - + -
381A ASN* 4.0 23.8 + - + +
607A LEU* 3.6 27.0 - - + +
610A ASP* 4.4 1.9 + - - -
614A ARG* 4.5 1.6 - - - -
634A TYR* 3.4 21.4 - + + -
635A PRO* 1.3 75.9 - - - +
637A ALA* 1.3 62.2 + - + +
639A ASP* 3.2 8.5 + - - +
640A GLY* 2.8 28.1 + - - -
710A TRP* 3.5 27.4 + + - -
714A ALA 5.5 0.2 - - - -
715A LEU* 3.7 17.7 - - + +
718A ALA* 3.9 23.1 - - + -
719A VAL* 5.8 0.4 - - + -
842A TYR* 3.9 27.2 - - + +
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Residues in contact with ALA 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 4.7 1.3 - - - -
611A LEU* 3.7 27.4 - - + -
629A LEU* 4.2 12.3 - - + -
634A TYR* 3.1 34.8 + - + +
636A TYR* 1.3 84.9 - - - +
638A VAL* 1.3 57.8 + - - +
640A GLY* 4.5 1.8 - - - +
641A LEU* 3.0 35.8 + - - +
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Residues in contact with VAL 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A HIS* 5.8 4.0 - - - +
629A LEU* 3.8 20.4 - - + -
632A GLU 4.0 12.3 - - - +
633A ASP* 5.5 0.4 - - - -
634A TYR 3.2 17.0 - - - +
635A PRO* 3.2 7.8 + - + +
636A TYR 3.1 0.4 - - - -
637A ALA* 1.3 76.0 - - - +
639A ASP* 1.4 67.1 + - - +
641A LEU* 4.5 3.7 - - - +
642A GLU* 3.6 24.6 + - + +
825A ARG* 3.5 38.9 + - - +
834A ARG* 4.5 5.4 - - - +
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Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A PRO 2.9 13.1 + - - +
636A TYR* 3.3 17.0 - - - +
638A VAL* 1.4 72.2 - - - +
640A GLY* 1.3 70.4 - - - +
642A GLU* 3.0 7.8 + - - +
643A ILE* 3.0 42.1 - - - +
710A TRP* 5.1 3.6 - - - -
714A ALA* 4.7 5.8 - - - +
718A ALA* 4.1 14.7 - - - +
822A ILE* 4.8 2.2 - - - -
842A TYR* 3.8 11.8 + - + -
844A LEU 4.2 2.4 - - - +
845A LEU* 3.1 58.7 - - + +
858A ILE* 4.2 4.7 - - - +
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Residues in contact with GLY 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 3.9 12.1 - - - -
636A TYR* 2.8 12.6 + - - -
637A ALA 3.8 1.1 - - - -
639A ASP* 1.3 82.6 - - - +
641A LEU* 1.3 52.2 + - - -
642A GLU 3.2 0.3 + - - -
643A ILE 3.2 2.6 + - - -
644A TRP* 2.6 36.8 + - - +
710A TRP* 3.5 26.6 - - - -
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Residues in contact with LEU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 3.4 20.4 - - + -
608A PRO* 4.4 14.4 - - + -
611A LEU* 4.3 2.5 - - + -
625A HIS* 3.4 46.2 - - + +
627A LEU* 4.1 23.1 - - + +
629A LEU* 4.1 29.4 - - + -
637A ALA 3.0 20.3 + - - +
638A VAL* 3.8 3.6 + - - +
639A ASP 3.3 0.4 + - - -
640A GLY* 1.3 74.5 - - - +
642A GLU* 1.3 56.4 + - - +
644A TRP* 4.0 4.5 - - + -
645A ASP* 3.0 34.8 + - - +
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Residues in contact with GLU 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A HIS* 3.9 20.8 + - + +
638A VAL* 3.6 17.4 - - - +
639A ASP 3.0 6.7 + - - +
641A LEU* 1.3 75.8 - - - +
643A ILE* 1.3 55.8 + - - +
645A ASP* 4.2 3.2 - - - +
646A ALA* 3.2 20.4 + - - +
818A ILE* 3.3 41.9 - - + +
821A LYS* 3.7 25.3 + - - +
825A ARG* 2.8 38.0 + - - -
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Residues in contact with ILE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ASP* 3.0 44.9 - - - +
640A GLY 3.2 5.3 + - - +
642A GLU* 1.3 73.8 - - - +
644A TRP* 1.3 61.5 + - - +
646A ALA* 3.9 6.6 - - - +
647A ILE* 3.1 32.7 + - + +
710A TRP* 3.8 6.1 - - + -
714A ALA* 3.6 28.7 - - + -
790A LEU* 4.2 13.0 - - + -
815A LEU* 4.9 3.8 - - + -
818A ILE* 3.7 10.5 - - + -
845A LEU* 3.6 4.9 - - + +
847A ARG* 3.2 32.5 - - - +
858A ILE* 3.9 9.0 - - + -
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Residues in contact with TRP 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ALA* 3.6 31.0 - - + -
607A LEU* 4.0 8.3 - - + -
608A PRO* 3.3 33.4 - - + +
640A GLY 2.6 23.4 + - - +
641A LEU* 3.2 9.8 + - + +
643A ILE* 1.3 69.5 - - - +
645A ASP* 1.3 76.1 + - - +
647A ILE* 3.1 7.4 + - + +
648A LYS* 2.9 54.6 + - + +
703A GLN* 3.5 20.0 - - - -
706A SER* 3.6 36.1 - - - -
707A ILE* 4.1 5.2 - - + -
710A TRP* 3.7 33.6 - + + -
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Residues in contact with ASP 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A HIS* 3.3 34.5 + - - +
641A LEU 3.0 16.1 + - - +
642A GLU* 4.2 3.8 - - - +
644A TRP* 1.3 88.4 - - - +
646A ALA* 1.3 53.9 + - - +
648A LYS* 3.7 6.0 - - - +
649A THR* 2.8 41.7 + - - +
814A LYS* 5.6 0.2 - - - -
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Residues in contact with ALA 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A GLU 3.2 18.1 + - - +
643A ILE 3.9 2.5 - - - +
644A TRP 3.2 0.2 - - - -
645A ASP* 1.3 78.1 - - - +
647A ILE* 1.3 63.1 + - - +
650A TRP 3.1 16.8 + - - -
811A PHE* 3.4 10.6 - - + -
814A LYS* 3.5 31.1 - - + +
815A LEU* 3.7 29.2 - - + -
818A ILE* 4.0 5.8 - - + -
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Residues in contact with ILE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ILE* 3.1 35.8 + - + +
644A TRP* 3.1 6.5 + - + +
646A ALA* 1.3 77.9 - - - +
648A LYS* 1.3 57.3 + - - +
650A TRP* 3.2 6.9 + - + +
651A VAL* 2.9 30.0 + - + +
706A SER* 4.0 17.9 - - - +
709A VAL* 3.5 33.0 - - + +
710A TRP* 3.8 33.2 - - + +
713A SER* 3.8 13.9 - - - +
790A LEU* 4.2 14.4 - - + -
811A PHE* 3.8 10.7 - - + -
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Residues in contact with LYS 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A TRP* 2.9 41.4 + - + +
645A ASP* 3.8 7.2 - - - +
647A ILE* 1.3 73.2 - - - +
649A THR* 1.3 59.6 + - - +
651A VAL 4.4 0.2 - - - +
652A HIS* 2.9 32.1 + - + +
699A GLU* 4.0 16.0 + - - -
702A ILE* 4.2 10.9 - - + +
703A GLN* 3.0 42.7 - - - +
706A SER* 3.6 15.4 + - - +
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Residues in contact with THR 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ASP* 2.8 27.9 + - - +
646A ALA 4.0 3.4 - - - -
648A LYS* 1.3 72.2 - - - +
650A TRP* 1.3 64.2 + - - +
652A HIS* 3.2 5.5 + - - +
653A GLU* 3.0 45.1 + - - +
814A LYS* 4.0 23.4 - - + +
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Residues in contact with TRP 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LEU* 4.0 20.8 - - + +
557A HIS* 5.4 6.3 + - - -
646A ALA 3.1 14.0 + - - +
647A ILE* 3.4 15.7 - - + +
649A THR* 1.3 75.8 - - - +
651A VAL* 1.3 63.1 + - + +
653A GLU* 3.4 5.2 + - - +
654A TYR* 2.9 50.2 + + + +
709A VAL* 5.4 4.0 - - + +
793A ARG* 3.8 24.8 - - - +
798A TRP* 4.1 9.0 - + - -
804A ALA 3.9 5.8 - - - -
807A ALA* 3.3 26.5 - - + -
808A PHE* 3.6 39.0 - + + -
811A PHE* 3.7 42.7 - + + -
814A LYS* 4.3 3.2 - - - +
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Residues in contact with VAL 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LEU* 4.2 14.8 - - + -
647A ILE* 2.9 26.8 + - + +
648A LYS 4.2 1.1 - - - +
650A TRP* 1.3 81.5 - - + +
652A HIS* 1.3 66.5 + - - +
654A TYR* 4.4 4.0 - - - -
655A VAL* 2.9 36.8 + - + +
702A ILE* 3.3 31.6 - - - +
705A CYS* 3.7 26.5 - - + +
706A SER* 3.9 13.2 - - - +
709A VAL* 4.5 6.3 - - + -
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Residues in contact with HIS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A LYS* 2.9 21.0 + - + +
649A THR* 3.5 5.8 - - - +
651A VAL* 1.3 75.2 - - - +
653A GLU* 1.3 59.2 + - + +
656A SER* 2.7 51.2 + - - -
698A THR* 5.8 3.2 - - + +
699A GLU* 4.2 12.5 + - - -
702A ILE* 3.7 29.8 - - + +
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Residues in contact with GLU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A THR* 3.0 40.7 + - + +
650A TRP* 4.0 5.0 - - - +
652A HIS* 1.3 78.8 - - + +
654A TYR* 1.3 66.2 + - - +
656A SER* 3.7 6.6 + - - -
657A LEU* 3.2 29.4 + - + +
807A ALA* 4.0 17.0 - - + +
810A ARG* 3.0 36.3 + - - +
814A LYS* 5.2 2.4 + - - -
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Residues in contact with TYR 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 4.4 2.6 - - - +
549A PRO* 2.6 39.5 + - + +
550A ILE* 4.4 3.8 - - + -
552A LYS* 3.6 14.9 - - - +
553A LEU* 3.5 33.2 - - + -
650A TRP* 2.9 45.8 + + + +
651A VAL 3.8 2.2 - - - +
653A GLU* 1.3 74.3 - - - +
655A VAL* 1.3 69.6 + - - +
657A LEU* 3.1 15.6 + - + +
658A TYR* 3.2 49.2 + + - -
798A TRP* 3.8 24.6 - + - -
799A THR* 5.6 0.2 - - - -
804A ALA* 4.0 13.2 - - + -
807A ALA* 5.4 1.1 - - - +
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Residues in contact with VAL 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ILE* 4.0 21.3 - - + -
553A LEU* 5.0 1.8 - - + -
651A VAL* 2.9 35.7 + - + +
654A TYR* 1.3 73.6 - - - +
656A SER* 1.3 58.1 + - - +
658A TYR* 2.9 20.2 + - - -
659A TYR* 2.9 29.4 + - + +
698A THR* 4.5 9.6 - - + +
701A LEU* 3.7 25.4 - - + -
702A ILE* 3.6 33.9 - - + -
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Residues in contact with SER 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A HIS* 2.7 42.7 + - - -
653A GLU* 3.9 8.3 - - - -
654A TYR 3.2 0.2 - - - -
655A VAL* 1.3 76.3 - - - +
657A LEU* 1.3 59.9 + - - +
659A TYR 4.0 16.0 - - - +
660A PRO* 4.9 3.8 - - - +
698A THR* 5.0 5.3 - - - +
702A ILE* 4.6 4.3 - - - +
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A GLU* 3.2 20.2 + - + +
654A TYR* 3.1 12.3 + - - +
655A VAL 3.1 0.2 + - - -
656A SER* 1.3 78.6 - - - +
658A TYR* 1.4 87.1 + - + +
659A TYR 5.3 0.2 - - - -
660A PRO* 5.3 4.0 - - - +
801A ASP* 4.4 4.9 - - - +
803A LYS* 4.0 30.7 - - + +
804A ALA* 3.6 31.9 - - + +
807A ALA* 5.7 4.3 - - + -
810A ARG* 6.4 0.2 - - - +
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Residues in contact with TYR 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 3.5 30.9 - - + +
176A LEU* 3.8 22.0 - - + +
549A PRO* 3.9 23.6 - - + -
654A TYR* 3.2 50.1 + + - -
655A VAL* 2.9 5.3 + - - +
657A LEU* 1.4 97.3 - - + +
659A TYR* 1.3 70.3 + + + +
660A PRO* 3.4 11.0 - - - +
799A THR* 4.1 1.9 + - - -
801A ASP* 2.9 43.4 + - - +
804A ALA* 3.5 8.8 - - - +
----------------------------------------------------------
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Residues in contact with TYR 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 3.3 14.8 - - + +
548A HIS* 3.1 20.3 - - - -
549A PRO* 4.5 1.3 - - + +
550A ILE* 3.5 15.7 - - + +
655A VAL* 2.9 24.8 + - + +
656A SER* 4.0 11.7 - - - +
658A TYR* 1.3 90.5 - - + +
660A PRO* 1.3 64.8 - - - +
661A THR 3.2 2.6 + - - +
664A ALA* 3.3 35.2 - - + -
665A VAL* 3.7 22.9 - - + -
668A ASP* 2.7 29.2 + - - -
671A LEU* 3.4 18.7 - - + +
698A THR* 4.1 11.6 + - - +
701A LEU* 3.6 20.9 - - + -
----------------------------------------------------------
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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