Contacts of the helix formed by residues 600 - 630 (chain A) in PDB entry 5M7T
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 ASP 600 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A VAL* 5.5 2.5 - - + +
594A VAL* 5.0 12.7 - - + +
599A LYS* 1.3 76.6 - - - +
601A SER* 1.3 64.5 + - - +
602A GLU* 3.4 16.1 + - - +
603A LYS* 3.5 33.6 + - + +
604A ILE* 3.2 37.1 + - + +
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Residues in contact with SER 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ASP* 1.3 71.3 + - - +
602A GLU* 1.3 67.5 + - - +
604A ILE* 4.7 1.3 - - - -
605A GLU* 2.9 49.8 + - - +
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Residues in contact with GLU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ASP* 3.4 10.5 + - - +
601A SER* 1.3 79.5 - - - +
603A LYS* 1.3 73.5 + - + +
605A GLU* 4.2 2.8 - - - +
606A GLU* 3.5 19.8 + - - +
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Residues in contact with LYS 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A TRP* 5.2 1.8 - - + -
591A VAL* 3.6 32.0 - - + +
600A ASP* 3.5 29.6 + - - +
601A SER 3.4 0.2 - - - -
602A GLU* 1.3 89.9 - - + +
604A ILE* 1.3 60.5 + - - +
606A GLU* 3.5 17.0 + - - +
607A TRP* 3.0 28.8 + - - +
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Residues in contact with ILE 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A VAL* 3.8 28.5 - - + +
592A VAL* 4.3 13.7 - - - +
594A VAL* 6.1 0.4 - - + -
599A LYS* 5.6 2.7 - - - +
600A ASP 3.2 32.4 + - - +
601A SER* 3.5 1.5 + - - -
603A LYS* 1.3 71.6 - - - +
605A GLU* 1.3 72.0 + - - +
606A GLU 3.0 1.6 - - - -
607A TRP* 2.8 5.2 + - - +
608A ARG* 2.7 59.3 + - + +
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Residues in contact with GLU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A SER* 2.9 42.1 + - - +
602A GLU* 4.2 3.4 - - - +
604A ILE* 1.3 83.6 - - - +
606A GLU* 1.3 52.5 + - - +
608A ARG* 4.3 4.6 - - - +
609A SER* 2.8 32.9 + - - -
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Residues in contact with GLU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A TRP* 3.7 23.5 + - + -
602A GLU 3.5 13.2 + - - +
603A LYS* 3.6 21.8 + - - +
604A ILE 3.0 0.8 - - - -
605A GLU* 1.3 77.0 - - - +
607A TRP* 1.3 65.0 + - - +
608A ARG 3.4 0.2 + - - -
609A SER* 3.5 2.8 + - - -
610A ARG* 3.0 61.5 + - + +
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Residues in contact with TRP 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A TRP* 3.6 30.2 - + + -
585A LEU* 3.0 40.7 + - + +
588A ASN* 3.5 23.8 + - + -
589A SER* 4.4 5.4 - - - -
591A VAL* 4.4 11.0 - - + -
592A VAL* 4.2 9.6 - - + -
603A LYS 3.0 16.4 + - - +
604A ILE* 2.8 9.9 + - - +
606A GLU* 1.3 73.1 - - - +
608A ARG* 1.3 83.7 + - + +
610A ARG* 3.9 0.3 - - - +
611A ALA* 2.9 40.9 + - + +
658A VAL* 3.9 14.8 - - + -
661A LEU* 3.8 32.1 - - + -
662A GLY* 4.0 8.7 - - - -
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Residues in contact with ARG 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A VAL* 4.0 23.8 + - - +
604A ILE* 2.7 43.6 + - + +
605A GLU* 4.3 5.4 - - - +
607A TRP* 1.3 90.1 - - + +
609A SER* 1.3 58.7 + - - +
611A ALA* 3.6 3.1 - - - +
612A ALA* 2.9 26.7 + - - +
662A GLY* 3.8 35.8 + - - -
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Residues in contact with SER 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLU 2.8 24.2 + - - -
606A GLU* 3.5 4.0 + - - -
608A ARG* 1.3 75.0 - - - +
610A ARG* 1.3 61.6 + - - +
612A ALA* 3.8 7.3 - - - +
613A LYS* 2.9 31.2 + - - +
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Residues in contact with ARG 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ARG* 5.3 1.6 + - - +
581A GLU* 2.6 48.6 + - - +
584A TRP* 3.4 51.9 - - + +
585A LEU* 4.2 11.3 - - + +
606A GLU* 3.0 51.3 + - + +
607A TRP 3.9 2.7 - - - +
609A SER* 1.3 78.5 + - - +
611A ALA* 1.3 56.0 + - - +
613A LYS* 3.4 6.8 + - - +
614A PHE* 3.0 27.2 + - - +
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Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A LEU* 3.8 17.4 - - + +
607A TRP* 2.9 43.2 + - + +
608A ARG* 3.6 4.5 - - - +
610A ARG* 1.3 74.0 - - - +
612A ALA* 1.3 59.7 + - - +
614A PHE* 3.2 2.9 + - - +
615A GLU* 2.9 35.1 + - - +
658A VAL* 3.9 13.8 - - + +
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Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ARG 2.9 17.9 + - - +
609A SER* 3.3 8.3 + - - +
611A ALA* 1.3 74.6 - - - +
613A LYS* 1.3 58.1 + - - +
615A GLU* 3.3 16.0 + - - +
616A GLU* 3.1 26.5 + - - +
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Residues in contact with LYS 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLN* 4.3 21.8 - - - +
581A GLU* 3.9 22.7 + - + +
609A SER 2.9 18.8 + - - +
610A ARG* 3.5 4.9 - - - +
612A ALA* 1.3 78.7 - - - +
614A PHE* 1.3 59.0 + - - +
616A GLU* 3.5 13.2 + - - +
617A MET* 3.3 37.2 + - + +
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Residues in contact with PHE 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A MET* 3.3 40.8 - - + -
581A GLU* 4.1 17.0 - - + +
582A PHE* 4.0 12.6 - + + -
585A LEU* 3.8 11.7 - - + -
610A ARG 3.0 13.9 + - - +
611A ALA 3.2 7.4 + - - +
613A LYS* 1.3 77.0 - - - +
615A GLU* 1.3 65.4 + - + +
616A GLU 3.2 0.4 - - - -
617A MET* 3.3 9.3 + - - +
618A CYS* 3.0 48.6 + - - -
651A MET* 5.3 0.4 - - - -
654A VAL* 3.6 30.7 - - + -
655A LYS* 4.7 1.6 - - - -
658A VAL* 4.0 28.3 - - + -
689B PHE* 4.3 4.9 - + - -
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Residues in contact with GLU 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ALA* 2.9 20.4 + - - +
612A ALA* 3.5 15.9 - - - +
614A PHE* 1.3 77.0 - - + +
616A GLU* 1.3 57.2 + - - +
618A CYS* 3.5 7.6 + - - +
619A GLY* 2.9 24.9 + - - -
655A LYS* 4.1 27.9 + - + +
658A VAL* 5.1 8.9 - - + +
659A GLN* 3.0 40.7 + - + +
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Residues in contact with GLU 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ALA 3.1 12.6 + - - +
613A LYS* 3.6 16.9 - - - +
614A PHE 3.2 0.2 - - - -
615A GLU* 1.3 78.5 - - - +
617A MET* 1.3 57.9 + - + +
619A GLY* 3.1 4.8 + - - -
620A LEU* 3.1 36.5 + - + +
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Residues in contact with MET 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LEU* 6.0 0.2 - - + -
574A LYS* 4.5 18.4 - - + +
577A GLN* 3.0 43.7 - - - +
578A MET* 3.6 45.4 - - + +
613A LYS* 3.3 28.7 + - + +
614A PHE* 3.7 12.6 - - + +
615A GLU 3.3 0.4 - - - -
616A GLU* 1.3 74.3 - - + +
618A CYS* 1.3 65.0 + - - +
619A GLY 3.1 1.3 - - - -
620A LEU* 3.1 27.4 + - + +
621A VAL* 3.3 9.2 + - - +
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Residues in contact with CYS 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A MET* 5.0 2.2 - - - -
614A PHE* 3.0 55.3 + - - +
615A GLU 3.7 4.5 - - - +
617A MET* 1.3 75.8 - - - +
619A GLY* 1.3 61.8 + - - +
621A VAL* 3.3 17.8 + - - +
622A MET* 3.3 21.6 + - + +
651A MET* 4.0 30.2 - - + +
654A VAL* 5.0 0.4 - - - -
655A LYS* 4.0 23.6 - - + -
----------------------------------------------------------
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Residues in contact with GLY 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A GLU 2.9 15.3 + - - -
616A GLU* 3.1 8.0 + - - -
617A MET 3.1 0.6 - - - -
618A CYS* 1.3 76.7 - - - +
620A LEU* 1.3 55.8 + - - +
622A MET* 3.2 8.5 + - - +
623A GLY* 3.0 24.9 + - - -
655A LYS* 4.5 12.0 - - - +
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASP* 4.8 0.7 - - - +
560A LEU* 3.6 17.6 - - + +
574A LYS* 6.4 1.6 - - + -
578A MET* 5.7 0.9 - - + -
616A GLU* 3.1 24.3 + - + +
617A MET* 3.1 20.6 + - + +
619A GLY* 1.3 72.1 - - - +
621A VAL* 1.3 59.0 + - - +
622A MET 3.4 0.2 - - - -
623A GLY* 4.5 2.5 - - - +
624A MET* 3.0 27.2 + - - +
627A ARG* 4.6 10.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LEU* 4.0 8.5 - - + -
564A LEU* 3.9 20.2 - - + -
578A MET* 3.9 20.2 - - + -
617A MET 3.3 12.3 + - - +
618A CYS* 3.7 7.0 - - - +
619A GLY 3.2 0.6 - - - -
620A LEU* 1.3 73.2 - - - +
622A MET* 1.3 65.6 + - - +
624A MET* 3.4 7.6 + - + +
625A PHE* 3.1 20.8 + - - +
647A ILE* 4.2 11.7 - - + +
648A LYS* 3.8 28.7 - - + +
651A MET* 4.0 24.5 - - + -
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Residues in contact with MET 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A CYS 3.3 22.0 + - - +
619A GLY* 3.2 9.4 + - - +
621A VAL* 1.3 75.5 - - - +
623A GLY* 1.3 59.4 + - - +
625A PHE* 3.1 7.6 + - + +
626A THR* 2.9 39.4 + - + +
648A LYS* 3.6 37.5 - - + +
651A MET* 4.8 2.7 - - - -
652A SER* 3.8 30.7 - - - +
655A LYS* 4.2 24.7 - - + +
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Residues in contact with GLY 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A GLY 3.0 14.6 + - - -
620A LEU* 3.6 2.7 + - - -
621A VAL 3.4 0.2 - - - -
622A MET* 1.3 75.1 - - - +
624A MET* 1.3 60.0 + - - +
626A THR* 3.4 6.3 + - - -
627A ARG* 3.1 54.5 + - - +
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Residues in contact with MET 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASP* 3.6 39.7 - - + +
560A LEU* 4.5 11.9 - - + -
561A LEU* 3.7 43.1 - - + -
564A LEU* 4.5 3.1 - - + -
620A LEU 3.0 18.6 + - - +
621A VAL* 3.4 12.8 - - + +
622A MET 3.2 0.2 - - - -
623A GLY* 1.3 71.6 - - - +
625A PHE* 1.3 71.9 + - + +
627A ARG* 3.4 3.1 + - - +
628A LEU* 2.9 32.6 + - + +
644A VAL* 3.6 30.5 - - + -
647A ILE* 4.6 14.4 - - + -
----------------------------------------------------------
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Residues in contact with PHE 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 6.0 0.7 - - - -
621A VAL 3.1 11.4 + - - +
622A MET* 3.5 6.7 - - + +
624A MET* 1.3 81.8 - - - +
626A THR* 1.3 71.9 + - + +
628A LEU* 3.2 3.4 + - + +
629A SER* 2.9 47.9 + - - -
637A LEU* 6.3 0.4 - - + -
641A TYR* 3.7 22.4 - + - -
644A VAL* 3.6 31.0 - - + -
645A TRP* 3.5 40.8 - + + -
648A LYS* 3.5 40.8 - - + -
69B TYR* 5.7 1.1 - + - -
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Residues in contact with THR 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 3.6 34.1 + - - +
622A MET* 2.9 30.9 + - + +
623A GLY* 3.4 6.8 + - - -
625A PHE* 1.3 90.1 - - + +
627A ARG* 1.3 66.8 + - - +
629A SER* 3.3 17.5 + - - -
630A ASN* 3.3 18.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLU* 3.4 52.5 + - + +
552A PRO* 3.4 25.6 - - - +
553A VAL* 3.5 12.7 + - - +
554A THR* 4.7 5.6 - - - +
557A ASP* 2.6 42.3 + - - +
620A LEU* 4.6 10.9 + - - +
623A GLY* 3.1 41.2 + - - +
624A MET 3.5 3.0 - - - +
626A THR* 1.3 79.0 + - - +
628A LEU* 1.3 65.6 + - - +
630A ASN* 3.3 13.3 + - - +
631A CYS* 3.4 8.1 + - - -
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Residues in contact with LEU 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE* 3.4 38.4 - - + -
553A VAL* 3.8 15.2 - - + +
557A ASP* 6.0 0.4 - - + -
558A LEU* 4.7 4.0 - - + -
561A LEU* 4.0 23.6 - - + -
624A MET* 2.9 28.4 + - + +
625A PHE* 3.5 8.3 - - + +
627A ARG* 1.3 74.6 - - - +
629A SER* 1.3 63.7 + - - +
630A ASN 3.0 1.4 + - - -
631A CYS* 3.0 24.9 + - - -
636A ILE* 5.8 0.7 - - + -
637A LEU* 3.5 21.0 - - + +
640A MET* 6.0 3.6 - - + -
644A VAL* 4.0 26.5 - - + -
----------------------------------------------------------
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Residues in contact with SER 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A PHE* 2.9 35.6 + - - -
626A THR* 3.4 16.8 - - - -
627A ARG 3.2 0.6 - - - -
628A LEU* 1.3 76.7 - - - +
630A ASN* 1.3 53.4 + - - +
634A ARG* 2.6 27.0 + - - -
637A LEU* 3.8 12.1 - - - +
641A TYR* 4.0 12.3 + - - -
99B ASP* 4.0 4.0 + - - +
104B ARG* 5.1 0.3 + - - -
105B MET* 3.5 30.8 - - - +
----------------------------------------------------------
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Residues in contact with ASN 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 3.3 29.8 - - - +
549A THR* 3.5 31.9 - - + +
551A GLU 5.1 4.6 - - - +
552A PRO* 6.5 0.2 - - + -
626A THR* 3.3 17.0 + - - +
627A ARG* 3.3 8.5 + - - +
628A LEU 3.1 0.8 - - - -
629A SER* 1.3 72.8 - - - +
631A CYS* 1.3 66.6 + - - +
632A ALA 3.7 0.5 + - - -
634A ARG* 3.9 3.1 - - - +
105B MET* 3.0 38.8 - - - +
106B PHE* 3.5 21.6 - - - -
----------------------------------------------------------
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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