Contacts of the helix formed by residues 604 - 629 (chain D) in PDB entry 2QMR
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 604 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D ILE* 3.5 37.0 + - + +
563D GLN* 4.5 9.2 - - - +
566D MET* 3.6 35.1 - - + +
567D PRO* 4.5 13.7 - - + +
570D ILE* 3.2 32.0 - - + +
600D GLY 3.9 10.5 - - - -
601D PHE* 2.9 18.6 + - + +
603D PRO* 1.3 98.3 - - + +
605D CYS* 1.3 64.6 + - - +
606D GLU 3.4 2.5 - - - -
607D PRO* 3.3 17.9 - - - +
608D VAL* 3.3 13.7 - - - +
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Residues in contact with CYS 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D PHE* 3.4 21.8 + - + +
602D LEU* 3.2 26.2 + - - +
604D TYR* 1.3 78.2 - - - +
606D GLU* 1.3 72.0 + - - +
608D VAL* 3.0 1.7 + - - -
609D TYR* 2.7 26.7 + - - +
651D LEU* 4.2 8.5 - - + -
655D LEU* 3.8 30.1 - - + -
658D ASN 6.0 0.4 - - - -
659D ILE* 6.3 0.2 - - - -
662D LEU* 3.9 20.2 - - + -
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Residues in contact with GLU 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D LEU 5.0 0.2 + - - -
603D PRO 5.5 2.0 - - - +
605D CYS* 1.3 85.4 - - - +
607D PRO* 1.4 69.0 - - + +
609D TYR* 3.9 1.0 - - - +
610D GLN* 3.1 34.7 + - + +
661D GLN* 5.0 4.2 - - - +
662D LEU* 3.4 35.0 - - + +
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Residues in contact with PRO 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D ILE* 5.1 10.1 - - + -
573D TRP* 3.1 16.6 + - + -
574D ASN* 3.6 28.9 - - - +
603D PRO 5.7 0.7 - - - +
604D TYR* 3.3 18.4 - - - +
606D GLU* 1.4 96.8 - - + +
608D VAL* 1.3 64.0 + - + +
610D GLN* 4.3 4.7 - - + +
611D ARG* 3.2 19.4 + - - +
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Residues in contact with VAL 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D ILE* 4.8 6.7 - - + -
573D TRP* 3.5 24.7 - - + +
590D LEU* 4.6 14.1 - - + -
601D PHE* 3.8 26.2 - - + -
604D TYR 3.3 19.5 - - - +
605D CYS 3.0 6.2 + - - +
607D PRO* 1.3 76.1 - - + +
609D TYR* 1.3 65.7 + - - +
612D CYS* 3.2 28.6 + - - -
647D LEU* 3.7 37.0 - - + -
651D LEU* 4.4 3.8 - - + -
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Residues in contact with TYR 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D CYS 2.7 18.7 + - - +
606D GLU 3.9 2.2 - - - +
608D VAL* 1.3 74.8 - - - +
610D GLN* 1.3 76.4 + - + +
612D CYS* 3.1 5.1 + - - +
613D VAL* 3.1 38.7 + - + +
648D LEU* 3.4 28.7 - - + +
651D LEU* 3.9 15.7 - - + +
659D ILE* 4.1 29.6 - - + -
662D LEU* 3.2 42.4 + - + -
663D VAL* 3.3 10.8 - - + -
666D SER* 2.6 27.9 + - - -
668D ILE* 3.3 17.6 - - + +
694D LEU* 6.1 0.2 - - + -
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Residues in contact with GLN 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D GLU* 3.1 28.2 + - + +
607D PRO* 4.3 4.5 - - + +
609D TYR* 1.3 90.9 - - + +
611D ARG* 1.3 58.0 - - - +
613D VAL* 3.5 6.1 + - - +
614D ASN* 3.1 30.5 + - - +
662D LEU* 5.5 9.2 - - + +
665D ARG* 5.1 9.0 - - - +
666D SER* 5.8 2.1 - - - -
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Residues in contact with ARG 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D TRP* 3.5 45.7 + - + +
574D ASN* 4.3 8.3 + - - +
576D LEU 2.8 33.0 + - - -
577D LYS 3.8 2.0 + - - -
578D ASP* 3.1 39.2 + - - +
583D LEU* 4.1 19.6 - - - +
607D PRO 3.2 18.2 + - - +
610D GLN* 1.3 76.2 - - - +
612D CYS* 1.3 60.2 + - - +
614D ASN* 3.4 9.4 - - + +
615D LEU* 2.8 35.6 + - + +
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Residues in contact with CYS 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D TRP* 4.5 7.9 - - - -
587D LEU* 4.2 10.3 - - - -
608D VAL 3.2 17.9 + - - +
609D TYR 3.1 9.4 + - - +
611D ARG* 1.3 74.7 - - - +
613D VAL* 1.3 62.3 + - - +
615D LEU* 3.1 8.7 + - - +
616D VAL* 2.9 31.1 + - - +
644D ALA* 3.8 14.3 - - + +
647D LEU* 3.4 37.9 - - - -
648D LEU* 3.9 18.6 - - + -
651D LEU* 6.1 0.2 - - - -
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Residues in contact with VAL 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609D TYR* 3.1 43.3 + - + +
610D GLN* 3.7 9.6 - - - +
612D CYS* 1.3 74.8 - - - +
614D ASN* 1.3 64.7 + - - +
616D VAL* 3.1 10.9 + - - +
617D GLN* 3.0 26.7 + - - +
648D LEU* 4.4 3.1 - - + -
666D SER* 4.5 13.7 - - - -
667D ASN* 4.7 4.9 - - - +
668D ILE* 4.1 19.3 - - + +
671D LEU* 3.6 22.5 - - + +
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Residues in contact with ASN 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ASP* 6.0 0.2 + - - -
610D GLN 3.1 16.7 + - - +
611D ARG* 3.4 14.8 - - + +
613D VAL* 1.3 78.8 - - - +
615D LEU* 1.3 58.0 + - + +
617D GLN* 3.6 10.4 + - - +
618D LYS* 3.1 46.7 + - + +
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Residues in contact with LEU 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D TRP* 6.2 0.4 - - + -
578D ASP* 3.7 25.4 - - + +
583D LEU* 3.9 21.8 - - + -
587D LEU* 4.0 21.5 - - + -
611D ARG* 2.8 26.5 + - + +
612D CYS* 3.1 11.8 + - - +
614D ASN* 1.3 74.3 - - + +
616D VAL* 1.3 61.2 + - - +
618D LYS* 4.0 8.0 - - + +
619D THR* 2.4 37.2 + - - +
640D PHE* 3.4 42.2 - - + +
641D MET* 5.1 0.7 - - - -
644D ALA* 4.3 4.5 - - + -
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Residues in contact with VAL 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D CYS 2.9 18.8 - - - +
613D VAL* 3.4 8.7 - - - +
615D LEU* 1.3 73.6 - - - +
617D GLN* 1.3 68.7 + - - +
619D THR* 3.4 2.9 + - - -
620D LEU* 3.1 25.2 + - + +
641D MET* 3.9 15.4 - - + +
644D ALA* 4.1 13.5 - - + -
645D LEU* 4.0 23.3 - - + -
648D LEU* 4.3 5.8 - - + -
671D LEU* 4.3 15.3 - - + -
675D CYS* 3.6 30.7 - - - -
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Residues in contact with GLN 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D VAL* 3.0 16.5 + - - +
614D ASN* 3.7 12.1 + - - +
616D VAL* 1.3 77.8 - - - +
618D LYS* 1.3 65.9 + - + +
620D LEU* 2.9 18.2 + - - +
621D ALA* 3.0 14.9 + - + +
667D ASN* 3.4 29.8 + - - +
671D LEU* 3.7 35.6 - - + +
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Residues in contact with LYS 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ASP* 3.1 44.2 + - - +
579D GLU* 4.7 6.2 + - - -
614D ASN* 3.1 31.4 + - + +
615D LEU* 4.0 8.8 - - + +
617D GLN* 1.3 80.5 - - + +
619D THR* 1.3 57.6 + - - +
621D ALA* 3.3 7.4 + - - +
622D GLN* 2.8 48.9 + - + +
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Residues in contact with THR 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D LEU* 2.4 27.3 + - - +
618D LYS* 1.3 76.0 - - - +
620D LEU* 1.3 58.5 + - - +
622D GLN* 3.5 9.6 + - - +
623D ALA* 2.9 29.1 + - - +
636D PRO* 3.6 23.5 - - + +
637D ASP 4.0 16.6 - - - +
638D LYS* 4.3 3.6 - - + -
640D PHE* 4.7 7.8 - - + +
641D MET* 3.7 38.8 + - + +
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Residues in contact with LEU 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D VAL* 3.1 23.7 + - + +
617D GLN* 2.9 7.7 + - - +
619D THR* 1.3 72.9 - - - +
621D ALA* 1.3 65.8 + - - +
623D ALA* 3.0 8.8 + - + +
624D MET* 2.9 29.9 + - + +
641D MET* 4.0 20.2 - - + -
671D LEU* 4.0 20.4 - - + +
674D GLN* 3.9 46.4 - - + +
675D CYS* 4.1 14.8 - - - +
678D ASP* 4.3 15.3 - - - +
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Residues in contact with ALA 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D GLN* 3.0 12.3 + - + +
618D LYS* 3.6 10.5 - - - +
620D LEU* 1.3 74.1 - - - +
622D GLN* 1.3 57.9 + - + +
624D MET* 2.9 17.6 + - - +
625D LEU* 2.8 39.1 + - + +
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Residues in contact with GLN 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D LYS* 2.8 39.4 + - + +
619D THR* 3.7 9.6 + - - +
621D ALA* 1.3 74.1 - - + +
623D ALA* 1.3 57.5 + - - +
625D LEU* 3.5 15.5 + - + +
626D ASN* 3.0 28.9 + - - +
634D GLU 3.8 9.7 - - - +
636D PRO* 3.6 31.1 - - + +
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Residues in contact with ALA 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D THR 2.9 18.5 + - - +
620D LEU* 3.0 7.6 + - + +
622D GLN* 1.3 73.6 - - - +
624D MET* 1.3 65.1 + - + +
626D ASN* 3.6 5.4 + - - +
627D ASN* 3.1 22.7 + - - +
636D PRO* 3.5 18.1 - - + +
638D LYS* 4.2 24.2 - - - +
641D MET* 5.7 0.9 - - + -
678D ASP* 5.7 0.9 - - - +
679D LYS* 5.9 1.5 + - - +
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Residues in contact with MET 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D LEU* 2.9 20.4 + - + +
621D ALA* 3.2 15.3 - - - +
623D ALA* 1.3 74.3 - - + +
625D LEU* 1.3 58.3 + - + +
627D ASN* 2.8 27.0 + - - +
628D ALA* 3.0 13.4 + - - +
674D GLN* 4.4 17.0 - - - +
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Residues in contact with LEU 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D ALA* 2.8 25.4 + - + +
622D GLN* 3.6 17.7 - - + +
624D MET* 1.3 72.1 - - + +
626D ASN* 1.3 56.9 + - - +
628D ALA* 3.5 6.4 + - + +
629D GLN 3.0 24.1 + - - -
633D TYR* 3.4 53.2 - - + +
634D GLU 5.8 0.4 - - - +
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Residues in contact with ASN 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D GLN 3.0 18.3 + - - +
623D ALA* 3.8 6.9 + - - +
624D MET 3.1 0.2 - - - -
625D LEU* 1.3 73.5 - - - +
627D ASN* 1.3 66.3 + - - +
629D GLN 4.2 0.2 - - - -
630D PRO* 3.3 31.6 - - - +
633D TYR* 3.1 25.4 - - - +
634D GLU* 3.7 10.9 - - - +
635D ALA* 3.1 31.9 + - - +
636D PRO* 5.2 1.0 - - - +
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Residues in contact with ASN 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623D ALA 3.1 13.2 + - - +
624D MET* 2.8 16.0 + - - +
626D ASN* 1.3 74.8 - - - +
628D ALA* 1.3 66.7 + - - +
630D PRO* 4.1 8.4 - - - +
679D LYS* 5.0 17.2 - - - +
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Residues in contact with ALA 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624D MET 3.0 9.8 + - - +
625D LEU* 3.8 10.1 - - + +
627D ASN* 1.3 79.0 + - - +
629D GLN* 1.3 73.6 + - + +
630D PRO* 3.3 8.9 - - - +
633D TYR* 6.0 0.4 - - + -
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Residues in contact with GLN 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625D LEU 3.0 10.1 + - - +
626D ASN 3.6 2.9 - - - -
628D ALA* 1.3 90.6 - - + +
630D PRO* 1.4 61.7 - - - +
631D ASP* 3.1 10.9 - - - +
632D GLN* 4.2 24.9 + - + +
633D TYR* 2.9 49.4 + - + +
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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