Contacts of the helix formed by residues 550 - 580 (chain C) in PDB entry 5YD6
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 ASN 550 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PRO* 1.3 77.3 - - + +
551C TYR* 1.3 64.8 + - - +
552C LEU 3.2 0.7 - - - -
553C SER* 3.1 24.6 + - - -
554C LYS* 3.8 15.1 + - - +
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Residues in contact with TYR 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C MET* 3.1 47.8 + - + -
497C ASN 4.6 1.9 + - - -
498C ILE* 4.1 13.0 - - - +
539C VAL* 4.3 20.4 - - + -
549C PRO* 3.4 6.7 - - + -
550C ASN* 1.3 79.3 + - - +
552C LEU* 1.3 59.6 + - - +
554C LYS* 2.9 30.0 + - + +
555C LEU* 3.1 41.0 + - + +
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Residues in contact with LEU 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C VAL* 6.2 0.9 - - + -
535C LEU* 5.0 7.3 - - + +
536C LYS* 3.6 49.6 - - + +
539C VAL* 4.6 15.7 - - + -
540C THR* 5.9 0.7 - - - +
549C PRO* 3.4 26.9 + - + +
551C TYR* 1.3 82.7 - - - +
553C SER* 1.3 60.7 + - - +
555C LEU* 3.7 11.6 + - + +
556C LEU* 3.3 35.8 + - + +
388D GLN* 3.8 27.4 - - - +
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Residues in contact with SER 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PRO 4.2 1.7 + - - -
550C ASN* 3.1 19.9 + - - -
552C LEU* 1.3 80.1 - - - +
554C LYS* 1.3 53.1 + - - +
556C LEU* 3.5 6.4 + - - +
557C GLY* 2.8 30.8 + - - -
388D GLN* 6.2 0.7 - - - +
390D ASN* 4.2 17.5 + - - -
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Residues in contact with LYS 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C MET* 3.6 18.3 - - + +
550C ASN* 4.4 16.4 - - - +
551C TYR* 2.9 19.0 + - + +
553C SER* 1.3 74.0 - - - +
555C LEU* 1.3 65.3 + - - +
557C GLY* 3.2 3.5 + - - -
558C LYS* 3.2 25.6 + - - +
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Residues in contact with LEU 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C MET* 3.5 14.0 - - + +
498C ILE* 3.7 39.9 - - + -
502C ALA* 4.7 5.6 - - + -
506C ILE* 3.8 40.3 - - + +
535C LEU* 4.2 12.3 - - + -
539C VAL* 4.1 19.5 - - + -
551C TYR* 3.1 37.6 + - + +
552C LEU* 3.7 11.9 - - - +
554C LYS* 1.3 76.9 - - - +
556C LEU* 1.3 61.7 + - + +
558C LYS* 3.3 20.9 - - + +
559C LEU* 4.2 1.2 + - - +
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Residues in contact with LEU 556 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C ILE* 4.6 2.0 - - + -
509C LEU* 3.9 16.8 - - + -
532C VAL* 5.2 13.2 - - + -
535C LEU* 3.9 28.3 - - + -
552C LEU* 3.3 26.7 + - + +
553C SER* 3.9 5.8 - - - +
555C LEU* 1.3 77.1 - - - +
557C GLY* 1.3 58.2 + - - +
558C LYS 3.2 0.7 - - - -
559C LEU* 3.2 32.4 + - + +
560C PRO* 3.2 10.9 - - - +
388D GLN* 4.2 23.1 - - - +
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Residues in contact with GLY 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C SER 2.8 16.9 + - - -
554C LYS* 3.2 8.2 + - - -
556C LEU* 1.3 72.1 - - - +
558C LYS* 1.3 61.4 + - - +
559C LEU 3.2 2.4 + - - -
560C PRO* 3.5 16.4 - - - +
561C GLU* 3.6 18.2 + - - +
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Residues in contact with LYS 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C LEU* 6.0 1.1 - - + -
489C PHE* 3.8 18.2 - - + -
492C ASN* 3.5 35.2 - - - +
493C LEU* 3.8 27.6 - - + -
496C MET* 3.6 28.7 - - - -
498C ILE* 5.5 0.9 - - + -
506C ILE* 5.3 5.6 - - + -
554C LYS 3.2 16.6 + - - +
555C LEU* 3.3 12.8 - - + +
556C LEU 3.2 0.4 - - - -
557C GLY* 1.3 75.8 - - - +
559C LEU* 1.3 59.3 + - - +
561C GLU* 2.7 37.0 + - - +
562C LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C GLU* 4.0 5.8 - - - +
506C ILE* 3.6 37.9 - - + +
509C LEU* 3.8 29.4 - - + +
510C ALA* 3.7 22.9 - - + +
555C LEU 4.8 0.7 - - - +
556C LEU* 3.2 33.3 + - + +
558C LYS* 1.3 74.3 - - - +
560C PRO* 1.4 68.3 - - + +
562C LEU* 3.3 15.9 + - + +
563C ARG* 3.1 20.6 + - - +
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Residues in contact with PRO 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C LEU 3.2 17.9 - - - +
557C GLY* 3.5 13.5 - - - +
559C LEU* 1.4 83.3 - - + +
561C GLU* 1.3 64.3 + - - +
563C ARG* 3.2 11.2 + - + +
564C THR* 3.0 25.9 + - - -
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Residues in contact with GLU 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C PHE* 3.8 19.5 - - + -
492C ASN* 5.0 3.5 + - - +
557C GLY 3.6 15.1 + - - +
558C LYS* 2.7 41.6 + - - +
559C LEU 3.3 0.6 - - - -
560C PRO* 1.3 76.2 - - - +
562C LEU* 1.3 57.3 + - - +
564C THR* 3.2 8.5 + - - -
565C LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 562 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C GLU* 3.3 46.4 - - + +
448C VAL* 3.7 26.2 - - + -
449C LEU* 3.7 35.7 - - + +
489C PHE* 4.2 13.9 - - + -
510C ALA* 4.1 13.2 - - + -
558C LYS 3.0 13.5 + - - +
559C LEU* 3.4 16.4 - - + +
560C PRO 3.2 0.2 - - - -
561C GLU* 1.3 74.0 - - - +
563C ARG* 1.3 54.4 + - - +
565C LEU* 3.3 6.2 + - - +
566C CYS* 2.8 34.3 + - - +
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Residues in contact with ARG 563 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C GLU* 2.8 33.7 + - - -
510C ALA 5.1 1.2 + - - -
513C THR* 4.3 14.1 + - - +
514C GLU 5.5 1.8 + - - -
515C ARG* 3.4 35.1 - - - +
559C LEU 3.1 11.6 + - - +
560C PRO* 3.3 14.8 - - + +
562C LEU* 1.3 75.2 - - - +
564C THR* 1.3 62.1 + - - +
566C CYS* 3.2 4.3 - - - +
567C THR* 3.1 24.3 + - - +
601C 8SU 4.1 29.2 + - - +
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Residues in contact with THR 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C PRO 3.0 15.0 + - - -
561C GLU* 3.2 9.6 + - - -
563C ARG* 1.3 75.7 - - - +
565C LEU* 1.3 60.9 + - - +
567C THR* 3.2 27.6 - - + +
568C GLN* 3.4 7.8 + - - +
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Residues in contact with LEU 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C VAL* 3.3 32.8 - - + -
482C TRP* 2.7 36.7 + - - +
485C SER* 3.4 37.5 - - - +
486C ILE* 4.2 7.2 - - + -
489C PHE* 3.6 31.9 - - + -
561C GLU 2.9 14.6 + - - +
562C LEU* 3.3 9.4 + - + +
564C THR* 1.3 73.2 - - - +
566C CYS* 1.3 63.5 - - - +
568C GLN* 3.4 11.2 + - - +
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Residues in contact with CYS 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C LEU* 3.7 18.5 - - - +
445C GLU* 3.6 19.7 - - + +
448C VAL* 5.6 2.2 - - - +
482C TRP* 4.9 2.7 - - - -
562C LEU 2.8 13.4 + - - +
563C ARG 3.2 8.7 - - - +
565C LEU* 1.3 74.3 - - - +
567C THR* 1.3 55.3 + - - +
569C GLY* 2.8 23.4 + - - -
570C LEU* 2.9 12.5 + - - +
601C 8SU 1.6 68.2 - - + -
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Residues in contact with THR 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C ARG* 3.1 11.8 + - - +
564C THR* 3.2 22.1 - - + +
566C CYS* 1.3 77.8 - - - +
568C GLN* 1.3 61.5 + - - +
570C LEU* 3.5 7.4 + - - +
571C GLN* 3.2 22.3 + - - +
601C 8SU 4.2 15.9 + - - -
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Residues in contact with GLN 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C GLU* 4.3 10.9 - - - +
482C TRP* 3.3 38.8 - - + +
485C SER* 2.7 35.2 + - - -
564C THR 3.4 6.6 + - - +
565C LEU* 3.4 11.3 - - - +
566C CYS 3.2 0.6 - - - -
567C THR* 1.3 80.9 - - + +
569C GLY* 1.3 60.6 + - - +
571C GLN* 3.3 22.0 + - - +
572C ARG* 3.3 18.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C LEU* 3.8 6.5 - - - -
482C TRP* 3.4 42.5 - - - +
566C CYS 2.8 13.2 + - - -
568C GLN* 1.3 71.0 - - - +
570C LEU* 1.3 64.0 + - - -
572C ARG* 3.1 15.1 + - - +
573C ILE* 3.1 17.0 + - - +
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Residues in contact with LEU 570 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C LEU* 3.7 5.9 - - + +
566C CYS 2.9 11.4 + - - +
567C THR* 3.7 11.7 - - - +
569C GLY* 1.3 73.7 - - - +
571C GLN* 1.3 57.1 + - - +
573C ILE* 3.5 6.3 + - + +
574C PHE* 3.0 28.3 + - + +
592C PHE* 3.7 31.2 - - + -
595C THR* 5.0 4.3 - - + -
596C LEU* 4.3 18.4 - - + -
597C PRO* 5.0 7.9 - - + -
601C 8SU 4.0 60.1 - - + +
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Residues in contact with GLN 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C THR* 3.2 13.1 + - + +
568C GLN* 3.4 24.6 - - - +
569C GLY 3.2 0.2 - - - -
570C LEU* 1.3 74.3 - - - +
572C ARG* 1.3 55.5 + - - +
574C PHE* 3.4 12.6 + - + +
575C TYR* 2.8 33.9 + - + +
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Residues in contact with ARG 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE* 4.0 14.5 - - - +
406C PHE* 4.3 12.6 - - + -
477C ARG 2.8 28.7 + - - -
478C GLY* 2.9 19.8 + - - -
479C PHE 3.4 23.8 + - - +
480C GLY* 4.2 9.1 - - - +
482C TRP* 5.2 3.8 - - + -
568C GLN 3.3 7.4 + - - +
569C GLY* 3.1 13.1 + - - +
571C GLN* 1.3 78.6 - - - +
573C ILE* 1.3 59.7 + - - +
575C TYR* 3.3 26.3 + - - +
576C LEU* 3.0 59.7 + - + +
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Residues in contact with ILE 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C PHE* 4.3 20.0 - - + -
407C TYR* 5.3 4.0 - - + -
410C LEU* 4.2 14.4 - - + -
444C LEU* 4.4 8.5 - - + -
482C TRP* 5.8 0.2 - - + -
569C GLY 3.1 20.3 + - - +
570C LEU* 3.7 7.0 - - - +
572C ARG* 1.3 71.0 - - - +
574C PHE* 1.3 61.4 + - - +
576C LEU* 3.8 6.8 - - - +
577C LYS* 2.9 33.9 + - + +
584C PRO* 5.3 5.7 - - + +
588C ILE* 3.9 21.5 - - + -
592C PHE* 3.9 22.0 - - + -
601C 8SU 3.9 32.5 - - + -
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Residues in contact with PHE 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C LEU 3.0 15.4 + - - +
571C GLN* 3.4 15.5 - - + +
573C ILE* 1.3 75.7 - - - +
575C TYR* 1.3 69.3 + + + +
577C LYS* 3.8 3.5 - - + +
578C LEU* 3.0 60.0 + - + +
592C PHE* 4.0 28.2 - + + -
596C LEU* 6.1 3.1 - - + -
598C PHE* 6.6 0.2 - + - -
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Residues in contact with TYR 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C GLN* 2.8 18.8 + - + +
572C ARG* 3.5 30.7 - - - +
573C ILE 3.2 0.2 - - - -
574C PHE* 1.3 82.6 - + + +
576C LEU* 1.3 56.4 + - - +
578C LEU* 3.2 6.6 + - + +
579C GLU* 2.7 74.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE* 3.8 41.5 - - + -
406C PHE* 4.0 26.5 - - + -
407C TYR* 3.3 25.8 - - + +
572C ARG* 3.0 49.1 + - - +
573C ILE* 3.8 5.6 - - - +
575C TYR* 1.3 78.0 - - + +
577C LYS* 1.3 56.9 + - - +
579C GLU* 3.7 16.4 - - - +
580C ASP* 2.9 26.2 + - - -
581C LEU 4.4 1.7 + - - -
582C VAL* 4.4 9.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ILE* 2.9 19.6 + - + +
574C PHE* 3.8 4.5 - - + +
576C LEU* 1.3 78.4 - - - +
578C LEU* 1.3 61.0 + - - +
580C ASP* 3.5 20.4 - - - +
584C PRO* 4.1 22.9 - - + +
589C ASP* 2.8 37.5 + - - +
592C PHE* 4.4 21.3 - - + -
593C LEU* 4.5 25.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C PHE* 3.0 55.2 + - + +
575C TYR* 3.6 5.6 - - + +
577C LYS* 1.3 75.2 - - - +
579C GLU* 1.3 65.6 + - - +
580C ASP* 3.4 4.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 579 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE* 4.9 6.4 - - - +
575C TYR* 2.7 57.2 + - + +
576C LEU* 3.7 19.5 - - - +
578C LEU* 1.3 72.2 - - - +
580C ASP* 1.3 67.7 + - - +
581C LEU* 3.7 41.6 + - + +
582C VAL* 5.2 2.1 + - - +
----------------------------------------------------------
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Residues in contact with ASP 580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C LEU 2.9 15.6 + - - -
577C LYS* 3.5 15.5 - - - +
578C LEU 3.2 5.4 - - - +
579C GLU* 1.3 77.8 - - - +
581C LEU* 1.3 66.4 + - - +
582C VAL 3.7 0.7 - - - +
583C PRO* 3.4 30.5 - - - +
----------------------------------------------------------
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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