Contacts of the helix formed by residues 601 - 630 (chain B) 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 SER 601 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 1.3 72.5 + - - +
602B GLU* 1.3 67.4 + - - +
604B ILE* 4.7 1.3 - - - -
605B GLU* 2.9 48.5 + - - +
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Residues in contact with GLU 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 3.4 9.9 + - - +
601B SER* 1.3 80.3 - - - +
603B LYS* 1.3 65.6 + - + +
605B GLU* 4.3 2.6 - - - +
606B GLU* 3.5 19.8 + - - +
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Residues in contact with LYS 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B TRP* 5.3 1.4 - - - -
588B ASN* 5.8 1.8 + - - -
591B VAL* 3.8 33.8 - - + +
600B ASP* 3.5 26.8 + - - +
602B GLU* 1.3 81.1 - - + +
604B ILE* 1.3 61.8 + - - +
606B GLU* 3.5 13.8 + - - +
607B TRP* 3.0 29.1 + - - +
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Residues in contact with ILE 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B VAL* 4.0 24.9 - - + +
592B VAL* 5.3 2.7 - - + -
600B ASP* 3.2 32.5 + - + +
601B SER* 4.7 0.9 - - - -
603B LYS* 1.3 71.7 - - - +
605B GLU* 1.3 70.0 + - - +
606B GLU 3.0 1.1 - - - -
607B TRP* 2.8 5.1 + - - -
608B ARG* 2.7 69.4 + - + +
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Residues in contact with GLU 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B SER* 2.9 41.7 + - - +
602B GLU* 4.3 3.4 - - - +
604B ILE* 1.3 83.3 - - - +
606B GLU* 1.3 52.6 + - - +
608B ARG* 4.4 4.4 - - - +
609B SER* 2.7 33.4 + - - -
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Residues in contact with GLU 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B TRP* 3.7 22.4 + - + -
602B GLU 3.5 13.9 + - - +
603B LYS* 3.6 16.1 + - - +
604B ILE 3.0 0.6 - - - -
605B GLU* 1.3 77.6 - - - +
607B TRP* 1.3 60.5 + - - +
609B SER* 3.5 2.4 + - - -
610B ARG* 3.0 67.0 + - + +
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Residues in contact with TRP 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B TRP* 3.6 29.3 - + + -
585B LEU* 2.9 43.1 + - + +
588B ASN* 3.5 23.7 + - + -
589B SER* 4.4 6.5 - - - -
591B VAL* 5.1 6.5 - - + -
592B VAL* 4.3 11.7 - - + -
603B LYS 3.0 16.5 + - - +
604B ILE* 2.8 11.4 + - - +
606B GLU* 1.3 73.1 - - - +
608B ARG* 1.3 86.1 + - - +
610B ARG* 3.9 0.3 - - - +
611B ALA* 2.9 49.0 + - + +
658B VAL* 3.9 13.9 - - + -
661B LEU* 3.8 34.8 - - + -
662B GLY* 4.0 9.2 - - - -
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Residues in contact with ARG 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B VAL* 3.6 37.0 - - - +
604B ILE* 2.7 54.3 + - + +
605B GLU* 4.4 5.2 - - - +
607B TRP* 1.3 89.5 - - - +
609B SER* 1.3 57.0 + - - +
611B ALA* 3.5 3.4 + - - +
612B ALA* 3.0 27.2 + - - +
662B GLY* 3.8 32.5 + - - -
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Residues in contact with SER 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B GLU 2.7 23.0 + - - -
606B GLU* 3.5 4.2 + - - -
608B ARG* 1.3 76.3 - - - +
610B ARG* 1.3 62.8 + - - +
612B ALA* 3.8 6.5 - - - +
613B LYS* 2.9 36.0 + - - +
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Residues in contact with ARG 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B ARG 5.9 0.2 - - - -
581B GLU* 2.5 48.1 + - - +
584B TRP* 3.4 51.8 - - + +
585B LEU* 4.2 10.9 - - + +
606B GLU* 3.0 49.6 + - + +
607B TRP 3.9 3.1 - - - +
609B SER* 1.3 77.1 + - - +
611B ALA* 1.3 56.0 + - - +
613B LYS* 3.4 10.8 + - - +
614B PHE* 3.0 27.2 + - - +
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Residues in contact with ALA 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B LEU* 3.8 14.7 - - + +
607B TRP* 2.9 42.3 + - + +
608B ARG* 3.6 4.7 - - - +
610B ARG* 1.3 74.1 - - - +
612B ALA* 1.3 58.5 + - - +
614B PHE* 3.2 3.5 + - - +
615B GLU* 2.9 33.2 + - + +
658B VAL* 3.9 17.3 - - + +
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Residues in contact with ALA 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ARG 3.0 17.5 + - - +
609B SER* 3.3 8.5 + - - +
611B ALA* 1.3 75.2 - - - +
613B LYS* 1.3 56.1 + - - +
615B GLU* 3.3 15.1 + - - +
616B GLU* 3.1 28.7 + - - +
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Residues in contact with LYS 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B GLU* 5.2 6.5 + - - +
609B SER* 2.9 20.2 + - - +
610B ARG* 3.5 10.8 - - - +
612B ALA* 1.3 78.2 - - - +
614B PHE* 1.3 60.2 + - - +
616B GLU* 3.4 16.6 + - + +
617B MET* 3.3 32.2 + - + +
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Residues in contact with PHE 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A PHE* 4.3 4.5 - + - -
578B MET* 3.3 37.5 - - + -
581B GLU* 4.1 21.5 + - + +
582B PHE* 3.9 12.6 - - + -
585B LEU* 3.8 11.7 - - + -
610B ARG 3.0 14.3 + - - +
611B ALA 3.2 7.6 + - - +
613B LYS* 1.3 75.4 - - - +
615B GLU* 1.3 65.9 + - + +
616B GLU 3.2 0.2 - - - -
617B MET* 3.3 9.8 + - + +
618B CYS* 3.0 49.8 + - - -
651B MET* 5.3 0.2 - - - -
654B VAL* 3.6 32.8 - - + -
655B LYS* 4.7 1.8 - - - -
658B VAL* 4.0 26.7 - - + -
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Residues in contact with GLU 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B ALA 2.9 17.9 + - - +
612B ALA* 3.3 15.2 + - - +
614B PHE* 1.3 77.8 - - + +
616B GLU* 1.3 57.2 + - - +
618B CYS* 3.5 7.1 + - - +
619B GLY* 2.9 25.1 + - - -
655B LYS* 3.4 30.3 + - + +
658B VAL* 5.3 8.1 - - + -
659B GLN* 3.0 40.5 + - + +
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Residues in contact with GLU 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ALA 3.1 12.8 + - - +
613B LYS* 3.6 19.7 - - + +
614B PHE 3.2 0.4 - - - -
615B GLU* 1.3 78.0 - - - +
617B MET* 1.3 57.2 + - + +
619B GLY* 3.1 4.8 + - - -
620B LEU* 3.1 29.8 + - + +
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Residues in contact with MET 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LYS* 4.6 12.6 - - + +
577B GLN* 3.0 44.9 - - - +
578B MET* 3.6 45.0 - - + +
581B GLU* 5.8 0.9 - - - -
613B LYS* 3.3 20.6 + - + +
614B PHE* 3.7 14.1 - - + +
615B GLU 3.3 0.2 - - - -
616B GLU* 1.3 74.0 - - + +
618B CYS* 1.3 64.1 + - - +
619B GLY 3.1 1.6 - - - -
620B LEU* 3.1 30.6 + - + +
621B VAL 3.3 8.8 + - - -
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Residues in contact with CYS 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B MET* 5.1 2.5 - - - -
614B PHE* 3.0 56.0 + - - +
615B GLU 3.7 4.5 - - - +
617B MET* 1.3 75.8 - - - +
619B GLY* 1.3 61.4 + - - +
621B VAL* 3.3 17.8 + - - +
622B MET* 3.3 22.0 + - + +
651B MET* 4.0 31.3 - - + +
655B LYS* 4.1 22.7 - - + -
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Residues in contact with GLY 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B GLU 2.9 15.3 + - - -
616B GLU* 3.3 7.0 - - - -
617B MET 3.1 0.6 - - - -
618B CYS* 1.3 76.5 - - - +
620B LEU* 1.3 55.4 + - - +
622B MET* 3.2 9.5 + - - +
623B GLY* 3.0 25.3 + - - -
655B LYS* 4.7 9.8 - - - +
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ASP* 4.8 0.7 - - - +
560B LEU* 3.6 19.9 - - + +
574B LYS* 6.5 1.3 - - + -
578B MET* 5.5 1.3 - - + -
616B GLU* 3.1 18.9 + - + +
617B MET* 3.1 25.3 + - + +
619B GLY* 1.3 71.9 - - - +
621B VAL* 1.3 60.7 + - - +
623B GLY* 4.0 2.2 - - - +
624B MET* 3.0 26.9 + - - +
627B ARG* 4.6 9.1 + - - +
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Residues in contact with VAL 621 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B LEU* 4.0 8.1 - - + -
564B LEU* 4.0 20.6 - - + -
578B MET* 3.9 27.6 - - + -
617B MET 3.3 3.5 + - - +
618B CYS* 3.3 9.0 + - - +
619B GLY 3.2 0.8 - - - -
620B LEU* 1.3 73.2 - - - +
622B MET* 1.3 65.6 + - - +
624B MET* 3.4 8.0 + - + +
625B PHE* 3.1 20.6 + - - +
647B ILE* 4.2 12.1 - - + +
648B LYS* 3.8 28.5 - - + +
651B MET* 4.0 23.3 - - + -
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Residues in contact with MET 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B CYS 3.3 21.8 + - - +
619B GLY* 3.2 9.2 + - - +
621B VAL* 1.3 77.2 - - - +
623B GLY* 1.3 58.9 + - - +
625B PHE* 3.1 9.3 + - + +
626B THR* 2.9 35.0 + - - +
648B LYS* 3.6 37.2 - - + +
651B MET 4.8 2.0 - - - -
652B SER* 3.8 28.9 - - - +
655B LYS* 4.3 24.2 - - + +
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Residues in contact with GLY 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B GLY 3.0 14.1 + - - -
620B LEU* 3.6 2.2 + - - -
622B MET* 1.3 76.0 - - - +
624B MET* 1.3 60.3 + - - +
626B THR* 3.4 5.6 + - - -
627B ARG* 3.1 54.2 + - - +
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Residues in contact with MET 624 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ASP* 3.6 39.3 - - + +
560B LEU* 4.4 12.3 - - + -
561B LEU* 3.7 48.0 - - + -
564B LEU* 4.7 3.1 - - + -
620B LEU 3.0 19.0 + - - +
621B VAL* 3.5 17.0 - - + +
623B GLY* 1.3 72.1 - - - +
625B PHE* 1.3 78.0 + - + +
626B THR 3.3 0.2 + - - -
627B ARG* 3.3 2.2 + - - +
628B LEU* 2.9 35.8 + - + +
644B VAL* 4.7 5.8 - - + +
647B ILE* 4.5 18.6 - - + -
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Residues in contact with PHE 625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 5.6 1.3 - + - -
548B TYR* 5.7 3.1 - - - -
621B VAL 3.1 10.7 + - - +
622B MET* 3.5 8.7 - - + +
624B MET* 1.3 87.6 - - + +
626B THR* 1.3 67.7 + - - +
628B LEU* 3.2 6.5 + - - +
629B SER* 2.9 49.9 + - - -
637B LEU* 6.3 0.4 - - + -
641B TYR* 3.7 15.5 - + - -
644B VAL* 3.9 28.3 - - + +
645B TRP* 3.5 36.1 - + - -
648B LYS* 3.5 41.3 - - + -
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Residues in contact with THR 626 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B TYR* 3.7 43.2 + - + +
622B MET* 2.9 20.8 + - - +
623B GLY* 3.9 7.0 - - - -
625B PHE* 1.3 88.2 - - - +
627B ARG* 1.3 61.0 + - + +
629B SER* 3.3 8.6 + - - -
630B ASN* 2.4 38.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B GLU* 3.4 50.7 + - + +
552B PRO* 3.4 23.9 - - - +
553B VAL* 3.5 16.5 + - + +
554B THR* 4.7 4.3 - - - +
557B ASP* 2.6 42.4 + - - +
620B LEU* 4.6 9.3 + - - +
623B GLY* 3.1 39.3 + - - +
624B MET 3.5 3.0 - - - +
626B THR* 1.3 79.3 - - + +
628B LEU* 1.3 66.4 + - - +
630B ASN* 3.3 13.0 + - - +
631B CYS* 3.4 8.0 + - - +
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Residues in contact with LEU 628 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B PHE* 3.4 37.9 - - + -
553B VAL* 3.8 15.8 - - + +
557B ASP* 6.0 0.4 - - + -
558B LEU* 4.7 4.0 - - + -
561B LEU* 4.0 25.6 - - + -
624B MET* 2.9 32.2 + - + +
625B PHE* 3.5 8.1 - - - +
627B ARG* 1.3 75.5 - - - +
629B SER* 1.3 64.7 + - - +
630B ASN 3.0 1.6 + - - -
631B CYS* 3.0 25.3 + - - -
637B LEU* 3.5 21.8 - - + +
640B MET* 5.9 4.5 - - + -
644B VAL* 4.0 22.0 - - + -
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Residues in contact with SER 629 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP* 4.0 9.4 + - - +
104A ARG* 5.1 0.2 + - - -
105A MET* 3.5 29.9 - - - +
548B TYR* 5.8 0.4 - - - -
625B PHE* 2.9 38.5 + - - -
626B THR* 3.4 15.7 - - - -
627B ARG 3.2 0.2 - - - -
628B LEU* 1.3 75.3 - - - +
630B ASN* 1.3 56.8 + - - +
634B ARG* 2.9 25.3 + - - -
637B LEU* 3.8 11.3 - - - +
641B TYR* 4.1 5.7 + - - -
----------------------------------------------------------
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Residues in contact with ASN 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A MET* 3.6 19.6 - - - +
106A PHE* 3.4 23.7 - - - -
548B TYR* 3.7 24.9 + - - -
549B THR* 2.9 41.8 + - - +
551B GLU 5.2 3.6 - - - +
626B THR* 2.4 35.2 + - - +
627B ARG* 3.3 9.1 + - - +
628B LEU 3.1 1.0 - - - -
629B SER* 1.3 81.8 - - - +
631B CYS* 1.3 64.4 + - - +
632B ALA 3.7 0.3 + - - -
634B ARG* 3.8 2.5 - - - +
----------------------------------------------------------
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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