Contacts of the helix formed by residues 556 - 581 (chain C) in PDB entry 3K23
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 556 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C SER* 1.3 79.1 + - - +
557C TRP* 1.3 67.4 + - - +
558C ARG 3.1 1.9 + - - -
559C ILE* 3.2 3.8 + - - +
560C MET* 2.8 32.0 + - - +
637C PRO* 3.0 38.1 - - - -
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Residues in contact with TRP 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C SER* 3.9 4.1 + - - +
556C THR* 1.3 78.0 - - - +
558C ARG* 1.3 63.1 + - + +
560C MET* 4.7 3.8 - - - -
561C THR* 2.6 79.3 + - + -
747C ILE* 3.2 42.1 - - + +
748C GLU* 5.9 1.6 - - - -
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Residues in contact with ARG 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C TYR* 3.6 30.4 + - + +
549C ASP* 2.9 42.8 + - - +
552C VAL* 3.3 27.8 + - - +
553C PRO 3.1 28.1 + - - -
555C SER* 3.9 18.8 + - - +
556C THR 3.1 0.4 - - - -
557C TRP* 1.3 84.1 - - + +
559C ILE* 1.3 55.3 + - - +
561C THR* 4.9 1.1 - - - -
562C THR* 2.5 40.0 + - - +
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Residues in contact with ILE 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 5.3 5.8 - - - -
548C TYR* 3.3 34.5 - - + +
554C ASP* 5.0 2.2 - - + -
555C SER 3.2 24.0 - - - +
556C THR* 3.2 3.9 + - - +
558C ARG* 1.3 75.4 - - - +
560C MET* 1.3 59.6 + - - +
562C THR* 3.9 1.8 - - - -
563C LEU* 3.0 55.8 + - + +
627C LEU* 3.8 15.3 - - + -
629C ILE* 4.4 17.9 - - + -
633C ARG* 4.8 16.4 - - + +
639C MET* 5.9 6.3 - - + -
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Residues in contact with MET 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 3.2 57.7 - - + +
556C THR* 2.8 26.4 + - - +
557C TRP* 4.0 3.6 - - - +
559C ILE* 1.3 73.8 - - - +
561C THR* 1.3 63.3 + - - +
563C LEU* 3.4 1.6 + - - +
564C ASN* 2.9 31.9 + - - +
637C PRO* 5.7 4.5 - - + -
638C GLY* 4.3 15.9 - - - +
639C MET 5.1 0.4 - - - +
735C TYR* 3.9 16.6 - - - +
739C THR* 4.6 20.2 - - - -
747C ILE* 4.7 16.2 - - + -
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Residues in contact with THR 561 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C TRP* 2.6 74.8 + - + -
558C ARG* 4.4 1.6 - - - -
560C MET* 1.3 73.3 - - - +
562C THR* 1.3 59.8 + - - +
564C ASN* 3.8 5.5 + - - +
565C MET* 3.4 45.2 + - + +
747C ILE* 3.3 24.6 - - - +
748C GLU* 4.2 3.6 - - + +
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Residues in contact with THR 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C ALA* 3.5 42.5 - - + +
547C GLY 5.1 1.6 + - - -
548C TYR* 3.6 22.6 - - + +
558C ARG* 2.5 25.7 + - - +
559C ILE* 3.9 3.6 - - - -
560C MET 3.3 0.2 - - - -
561C THR* 1.3 76.2 - - - +
563C LEU* 1.3 60.6 + - - +
565C MET* 3.3 11.6 + - - +
566C LEU* 3.0 23.4 + - - +
627C LEU* 4.1 8.7 - - + -
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Residues in contact with LEU 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 2.5 49.2 + - + +
559C ILE* 3.0 44.2 + - + +
560C MET 3.4 1.1 + - - +
562C THR* 1.3 73.0 - - - +
564C ASN* 1.3 54.4 + - - +
566C LEU* 3.6 9.5 - - + +
567C GLY* 2.6 28.4 + - - -
623C PHE* 3.4 43.1 - - + -
627C LEU* 3.0 32.5 - - + -
629C ILE* 5.4 1.1 - - + -
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Residues in contact with ASN 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 2.9 45.2 - - - +
560C MET 2.9 15.9 + - - +
561C THR* 3.9 6.3 - - - +
562C THR 3.3 0.2 - - - -
563C LEU* 1.3 73.1 - - - +
565C MET* 1.3 55.9 + - + +
567C GLY 3.2 0.5 + - - -
568C GLY* 2.7 31.9 + - - -
747C ILE* 2.8 36.7 - - - +
748C GLU* 5.0 1.1 - - + -
749C PHE* 3.1 31.7 - - - +
750C PRO* 4.1 3.0 - - + +
753C LEU* 3.2 13.8 - - + +
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Residues in contact with MET 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C ALA 6.1 0.4 - - - +
561C THR* 3.4 38.6 - - + +
562C THR* 3.3 9.8 + - - +
564C ASN* 1.3 77.0 - - - +
566C LEU* 1.3 57.7 + - - +
568C GLY* 3.2 2.8 + - - -
569C ARG* 3.0 34.4 + - + +
748C GLU* 3.8 31.9 - - + +
750C PRO* 4.2 13.0 - - + +
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Residues in contact with LEU 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 3.3 23.1 - - + +
544C LEU* 4.0 24.9 - - + +
545C TYR 3.7 27.4 - - - +
546C ALA* 4.1 8.1 - - + +
562C THR 3.0 17.5 + - - +
563C LEU* 3.6 11.9 - - + +
565C MET* 1.3 72.1 - - - +
567C GLY* 1.3 65.4 + - - +
568C GLY 3.0 1.1 - - - -
569C ARG* 3.0 12.5 + - - +
570C GLN* 2.8 32.7 + - - +
623C PHE* 3.7 27.6 - - + +
624C ALA* 4.5 3.1 - - + -
627C LEU* 4.4 6.1 - - + -
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Residues in contact with GLY 567 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 3.7 27.8 - - - -
563C LEU 2.6 21.4 + - - -
564C ASN 3.6 1.3 - - - -
566C LEU* 1.3 72.5 - - - +
568C GLY* 1.3 61.5 + - - +
570C GLN* 3.2 0.8 + - - -
571C VAL* 3.0 22.2 + - - +
604C MET* 3.2 17.2 - - - +
753C LEU* 4.1 5.6 - - - -
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Residues in contact with GLY 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C ASN 2.7 19.0 + - - -
565C MET 3.4 5.4 - - - -
566C LEU 3.0 0.6 - - - -
567C GLY* 1.3 75.1 - - - +
569C ARG* 1.3 60.1 + - - +
571C VAL* 3.3 10.7 + - - +
572C ILE* 3.4 21.7 + - - +
750C PRO* 4.3 10.8 - - - -
752C MET* 3.8 6.8 - - - +
753C LEU* 3.9 17.4 - - - +
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Residues in contact with ARG 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B TYR* 4.0 14.6 - - - +
641B ASP* 3.0 33.5 + - - -
544C LEU* 3.6 25.0 - - + +
545C TYR 2.9 30.5 + - - +
546C ALA 5.3 1.2 + - - -
565C MET* 3.0 14.2 + - + +
566C LEU* 3.0 14.1 + - - +
568C GLY* 1.3 75.3 - - - +
570C GLN* 1.3 58.2 + - - +
571C VAL 3.3 0.2 - - - -
572C ILE* 3.7 17.6 + - + +
573C ALA* 3.2 19.9 + - - +
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Residues in contact with GLN 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 2.8 93.0 + - + +
542C GLU 4.8 0.2 - - - +
544C LEU* 3.8 27.8 + - + +
566C LEU* 2.8 24.6 + - - +
567C GLY 3.8 3.8 - - - +
569C ARG* 1.3 75.7 - - - +
571C VAL* 1.3 59.5 + - - +
573C ALA* 3.5 5.9 - - + +
574C ALA* 3.1 20.1 + - - +
604C MET* 4.0 5.8 - - + -
611C ARG* 3.6 23.4 + - - -
623C PHE 4.6 1.7 - - - +
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Residues in contact with VAL 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C GLY 3.0 11.9 + - - +
568C GLY 3.3 6.9 + - - +
570C GLN* 1.3 74.9 - - - +
572C ILE* 1.3 59.6 + - - +
573C ALA 3.1 1.1 - - - -
574C ALA* 2.7 28.7 + - + +
575C VAL* 2.9 22.7 + - + +
596C LEU* 6.3 1.8 - - + -
600C TRP* 3.8 27.4 - - + -
604C MET* 3.2 24.7 - - + -
752C MET* 3.7 15.5 - - + -
753C LEU* 4.0 10.3 - - + -
756C ILE* 3.5 27.1 - - + -
745F LEU* 6.3 0.2 - - + -
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Residues in contact with ILE 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C GLY 3.4 18.4 + - - +
569C ARG* 3.7 21.3 - - + +
571C VAL* 1.3 77.0 - - - +
573C ALA* 1.3 61.0 + - - +
575C VAL* 3.4 11.7 + - - +
576C LYS* 3.3 21.0 + - + +
752C MET* 3.4 31.2 - - + -
744F LEU* 5.7 2.9 - - + -
748F LEU* 3.7 22.6 - - + +
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Residues in contact with ALA 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 4.4 2.5 - - + -
541C PRO* 3.6 26.4 - - + +
542C GLU* 5.7 1.3 - - + +
544C LEU* 4.8 10.8 - - + -
569C ARG 3.2 12.2 + - - +
570C GLN* 3.5 13.5 - - + +
571C VAL 3.1 0.2 - - - -
572C ILE* 1.3 78.4 - - - +
574C ALA* 1.3 63.6 + - - +
576C LYS* 3.5 6.9 + - - +
577C TRP* 3.0 23.6 + - - +
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Residues in contact with ALA 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 4.1 18.2 - - + -
570C GLN 3.1 13.7 + - - +
571C VAL* 2.7 24.7 + - + +
573C ALA* 1.3 70.0 - - - +
575C VAL* 1.3 50.5 + - + +
577C TRP* 3.2 10.7 + - + +
578C ALA* 2.7 37.2 + - - +
596C LEU* 4.5 6.2 - - + +
600C TRP* 5.7 5.6 - - + -
603C LEU* 4.8 17.0 - - + -
604C MET* 6.2 0.4 - - + -
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Residues in contact with VAL 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C VAL* 2.9 28.2 + - + +
572C ILE* 3.7 10.8 - - - +
574C ALA* 1.3 74.3 - - + +
576C LYS* 1.3 59.7 + - - +
578C ALA* 3.8 0.5 - - - +
579C LYS* 3.0 30.5 + - - +
596C LEU* 4.2 16.4 - - + -
752C MET* 4.9 2.2 - - + -
745F LEU* 4.0 26.2 - - + -
748F LEU* 3.6 35.4 - - + +
749F LEU* 3.9 19.0 - - + +
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Residues in contact with LYS 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ILE 3.3 11.0 + - - +
573C ALA* 3.9 9.2 - - - +
574C ALA 3.3 0.2 - - - -
575C VAL* 1.3 75.6 - - - +
577C TRP* 1.3 68.0 + - - +
579C LYS* 3.5 20.6 - - - +
580C ALA* 3.5 8.7 + - - +
748F LEU* 5.3 1.3 - - - +
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Residues in contact with TRP 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 5.5 3.4 - + - -
536C LEU* 4.4 6.4 + - + +
539C ILE* 3.4 52.1 - - + +
540C GLU* 4.3 3.8 + - - -
541C PRO* 3.7 22.9 - - + -
573C ALA 3.0 14.6 + - - +
574C ALA* 3.3 24.2 - - + +
576C LYS* 1.3 73.6 - - - +
578C ALA* 1.3 75.2 + - + +
580C ALA* 2.8 21.3 + - - +
581C ILE* 3.5 18.6 + - + +
596C LEU* 6.2 0.2 - - + -
603C LEU* 3.9 37.2 - - + -
664C LEU 5.3 0.7 - - - -
667C LYS* 3.5 23.4 - - + +
668C THR* 3.6 25.4 - - - -
671C LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C ALA 2.7 19.5 + - - +
575C VAL 3.8 2.7 - - - +
577C TRP* 1.3 77.9 - - + +
579C LYS* 1.3 55.3 + - - +
581C ILE* 2.7 41.1 + - - +
584C PHE* 3.6 32.0 - - + +
596C LEU* 3.8 18.8 - - + -
671C LEU* 4.3 10.8 - - + -
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Residues in contact with LYS 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B THR* 4.9 16.4 + - - +
575C VAL 3.0 19.4 + - - +
576C LYS* 3.5 11.7 - - - +
578C ALA* 1.3 74.9 - - - +
580C ALA* 1.3 58.2 + - - +
581C ILE 3.6 1.9 + - - +
584C PHE* 4.0 8.8 - - - -
585C ARG* 3.9 36.7 + - + +
592C GLN* 5.3 0.7 - - - +
748F LEU 3.1 22.9 + - - +
749F LEU* 3.1 43.1 + - + +
750F ASP 4.6 6.9 + - - -
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Residues in contact with ALA 580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C LEU* 4.0 11.3 - - - +
539C ILE* 3.8 28.0 - - + -
576C LYS 3.5 7.6 + - - +
577C TRP 2.8 15.9 + - - +
579C LYS* 1.3 73.6 - - - +
581C ILE* 1.3 63.1 + - - +
582C PRO* 3.5 6.9 - - - +
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Residues in contact with ILE 581 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C LEU* 4.4 4.5 - - + -
539C ILE* 3.7 18.8 - - + -
577C TRP* 3.6 39.5 - - + +
578C ALA* 2.7 21.3 + - - +
579C LYS 4.2 1.4 - - - +
580C ALA* 1.3 71.7 - - - +
582C PRO* 1.3 74.1 - - + +
583C GLY 3.4 0.7 + - - -
584C PHE* 3.1 23.9 + - + +
585C ARG* 3.9 4.7 + - - +
668C THR* 4.0 18.6 - - + +
671C LEU* 4.3 11.7 - - + -
689C ILE* 5.6 2.2 - - + -
693C TYR* 3.1 34.1 - - + +
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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