Contacts of the helix formed by residues 548 - 580 (chain B) in PDB entry 5Y41
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 ARG 548 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B VAL* 3.9 25.3 + - + +
540B THR* 4.8 1.0 + - - -
542B ASN* 6.0 3.8 - - - +
543B ASN* 3.5 41.0 + - + +
546B LEU 3.8 0.4 + - - -
547B ASN* 1.3 78.7 - - - +
549B PRO* 1.4 60.7 - - - +
550B ASN 3.3 2.7 - - - -
551B TYR* 3.1 56.5 + - + +
552B LEU* 2.8 28.7 + - - +
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Residues in contact with PRO 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ASN* 3.5 21.3 - - + +
548B ARG* 1.4 87.9 - - - +
550B ASN* 1.3 65.3 + - - +
552B LEU* 3.5 12.3 + - + +
553B SER* 3.0 27.0 + - - -
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Residues in contact with ASN 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ARG 3.3 0.4 - - - -
549B PRO* 1.3 81.1 - - + +
551B TYR* 1.3 61.3 + - - +
553B SER* 3.3 7.7 + - - -
554B LYS* 3.0 28.6 + - - +
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Residues in contact with TYR 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B MET* 3.0 45.8 + - + -
497B ASN 3.6 11.1 + - - -
498B ILE* 3.9 14.0 - - - +
502B ALA* 5.6 2.2 - - + +
539B VAL* 4.0 20.9 - - + -
548B ARG* 3.1 59.9 + - + +
550B ASN* 1.3 76.1 - - - +
552B LEU* 1.3 59.4 + - - +
554B LYS* 3.2 5.9 + - + +
555B LEU* 2.9 52.6 + - + +
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Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL* 5.3 1.3 - - + +
535B LEU* 3.8 36.3 - - + -
536B LYS* 3.7 47.8 - - + -
539B VAL* 4.5 12.6 - - + -
548B ARG 2.8 15.4 + - - +
549B PRO* 3.7 10.1 - - + +
551B TYR* 1.3 79.0 - - - +
553B SER* 1.3 57.4 + - - +
555B LEU* 3.3 8.1 + - + +
556B LEU* 2.9 45.1 + - + +
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Residues in contact with SER 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B PRO 3.0 18.0 + - - -
550B ASN* 3.5 9.2 - - - -
551B TYR 3.2 0.2 - - - -
552B LEU* 1.3 77.3 - - - +
554B LYS* 1.3 57.4 + - - +
556B LEU* 3.4 6.6 + - - +
557B GLY* 2.9 26.7 + - - -
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Residues in contact with LYS 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ASN 5.8 0.2 + - - -
496B MET* 3.7 24.9 - - + +
550B ASN 3.0 15.8 + - - +
551B TYR* 3.2 4.7 + - + +
553B SER* 1.3 75.2 - - - +
555B LEU* 1.3 62.8 + - - +
557B GLY* 3.3 11.2 + - - -
558B LYS* 3.4 38.4 + - - +
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B MET* 3.7 12.3 - - + +
498B ILE* 3.6 41.7 - - + -
502B ALA* 4.5 7.2 - - + -
506B ILE* 3.8 24.7 - - + +
535B LEU* 4.0 28.5 - - + -
539B VAL* 4.5 5.4 - - + -
551B TYR* 2.9 38.8 + - + +
552B LEU* 3.3 12.1 - - - +
554B LYS* 1.3 76.8 - - - +
556B LEU* 1.3 60.8 + - + +
558B LYS* 3.2 22.0 + - + +
559B LEU* 4.1 1.4 - - - +
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Residues in contact with LEU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ILE* 3.8 6.5 - - + -
509B LEU* 3.8 29.6 - - + -
532B VAL* 5.3 13.0 - - + -
535B LEU* 3.8 16.4 - - + -
536B LYS* 6.2 0.2 - - - -
552B LEU* 2.9 45.1 + - + +
553B SER* 4.1 4.9 - - - +
555B LEU* 1.3 73.1 - - - +
557B GLY* 1.3 57.7 + - - +
559B LEU* 3.1 38.0 + - + +
560B PRO* 3.3 4.7 - - - +
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Residues in contact with GLY 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B SER 2.9 15.9 + - - -
554B LYS* 3.5 7.6 - - - -
555B LEU 3.2 0.8 - - - -
556B LEU* 1.3 73.8 - - - +
558B LYS* 1.3 63.5 + - - +
559B LEU 3.2 0.2 - - - -
560B PRO* 3.2 18.6 - - - +
561B GLU* 3.6 19.4 - - - +
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Residues in contact with LYS 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 5.6 1.8 - - + -
489B PHE* 3.6 26.4 - - + -
492B ASN* 4.0 30.5 - - - +
493B LEU* 3.9 23.8 - - + +
496B MET* 3.4 30.2 - - - +
506B ILE* 5.8 1.8 - - + -
554B LYS* 3.4 29.1 + - - +
555B LEU* 3.2 16.2 + - + +
556B LEU 3.2 1.0 - - - -
557B GLY* 1.3 77.3 - - - +
559B LEU* 1.3 66.5 + - + +
561B GLU* 3.5 30.6 + - - +
562B LEU* 3.5 14.8 + - - +
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Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 4.3 4.7 - - - +
449B LEU* 5.6 0.9 - - + -
506B ILE* 3.4 37.5 - - + +
509B LEU* 3.9 33.7 - - + +
510B ALA* 4.8 11.0 - - + -
555B LEU 4.1 7.6 - - - +
556B LEU* 3.1 29.5 + - + +
558B LYS* 1.3 76.8 - - + +
560B PRO* 1.4 68.7 - - + +
562B LEU* 3.0 32.0 + - + +
563B ARG 3.9 1.4 + - - -
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Residues in contact with PRO 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B LEU 3.3 11.4 - - - +
557B GLY* 3.2 18.4 - - - +
559B LEU* 1.4 90.1 - - + +
561B GLU* 1.3 57.1 + - + +
563B ARG* 3.0 28.9 + - + +
564B THR* 4.1 3.6 + - - -
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Residues in contact with GLU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B PHE* 3.7 17.5 - - + -
492B ASN* 5.8 1.0 - - - +
557B GLY 3.6 19.0 - - - +
558B LYS* 3.5 35.6 + - - +
559B LEU 3.2 0.4 - - - -
560B PRO* 1.3 73.6 - - + +
562B LEU* 1.3 64.6 + - - +
563B ARG 3.3 0.5 + - - -
564B THR* 3.4 10.7 + - - -
565B LEU* 3.4 24.4 + - + +
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 3.6 38.1 - - + +
448B VAL* 4.1 9.9 - - + -
449B LEU* 3.9 32.3 - - + +
489B PHE* 3.8 28.7 - - + -
510B ALA* 4.1 22.9 - - + -
558B LYS 3.5 7.8 + - - +
559B LEU* 3.0 23.9 + - + +
561B GLU* 1.3 78.3 - - - +
563B ARG* 1.3 56.4 + - - +
565B LEU* 3.3 5.5 + - + +
566B CYS* 2.9 29.6 + - - +
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Residues in contact with ARG 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 3.8 20.1 - - - +
559B LEU 3.9 1.4 + - - +
560B PRO* 3.0 16.8 + - + +
562B LEU* 1.3 78.5 - - - +
564B THR* 1.3 58.1 + - - +
566B CYS* 3.1 5.4 + - - +
567B THR* 3.0 43.9 + - - +
597B PRO* 5.9 4.2 - - - +
601B RPG 3.6 33.3 + - + +
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Residues in contact with THR 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B PRO 4.5 4.5 + - - -
561B GLU* 3.7 11.1 + - - -
562B LEU 3.4 0.2 - - - -
563B ARG* 1.3 78.1 - - - +
565B LEU* 1.3 59.8 + - - +
567B THR* 3.2 9.8 + - - -
568B GLN* 3.0 48.3 + - + +
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Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B VAL* 3.8 23.1 - - + -
482B TRP* 2.8 28.6 + - - +
485B SER* 3.6 42.8 - - - +
486B ILE* 4.1 10.1 - - + +
489B PHE* 3.6 40.6 - - + -
561B GLU* 3.4 19.4 + - + +
562B LEU* 3.3 10.6 + - - +
563B ARG 3.3 0.4 - - - -
564B THR* 1.3 76.5 - - - +
566B CYS* 1.3 60.3 + - - +
568B GLN* 3.4 8.3 + - - +
569B GLY 3.1 5.7 + - - -
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Residues in contact with CYS 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU* 3.8 19.0 - - - +
445B GLU* 3.7 15.7 - - + +
448B VAL* 5.1 0.6 - - - +
562B LEU 2.9 13.2 + - - +
563B ARG 3.1 4.9 + - - +
565B LEU* 1.3 73.4 - - - +
567B THR* 1.3 60.4 + - - +
569B GLY* 3.0 4.0 + - - -
570B LEU* 2.9 25.7 + - - +
601B RPG 1.6 84.6 - - + -
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Residues in contact with THR 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B ARG* 3.0 27.0 + - - +
564B THR* 3.5 11.6 - - - -
566B CYS* 1.3 75.2 - - - +
568B GLN* 1.3 59.3 + - + +
570B LEU* 3.3 9.6 + - + +
571B GLN* 2.9 31.5 + - + +
601B RPG 3.8 17.1 + - - +
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Residues in contact with GLN 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B GLU 5.3 0.2 - - - -
482B TRP* 3.5 32.6 - - + +
485B SER* 2.8 39.6 + - - -
564B THR* 3.0 36.8 + - + +
565B LEU* 3.8 7.2 - - - +
566B CYS 3.2 0.2 - - - -
567B THR* 1.3 75.5 - - + +
569B GLY* 1.3 61.5 + - - +
571B GLN* 3.3 38.0 + - - +
572B ARG* 3.3 8.1 + - - +
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Residues in contact with GLY 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU* 4.2 7.2 - - - -
482B TRP* 3.4 37.4 - - - -
565B LEU 3.1 7.1 + - - -
566B CYS 3.0 7.5 + - - -
568B GLN* 1.3 75.2 - - - +
570B LEU* 1.3 64.1 + - - +
572B ARG* 3.2 5.4 + - - +
573B ILE* 3.2 25.7 + - - +
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU* 4.0 7.6 - - + +
566B CYS 2.9 12.5 + - - +
567B THR* 3.3 13.2 + - + +
569B GLY* 1.3 74.4 - - - +
571B GLN* 1.3 56.9 + - - +
573B ILE* 3.2 6.3 + - + +
574B PHE* 2.8 30.1 + - - +
592B PHE* 3.8 32.3 - - + +
595B THR* 5.2 3.6 - - - +
596B LEU* 4.2 20.9 - - + -
597B PRO* 5.4 2.0 - - + -
601B RPG 3.8 63.3 - - + +
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Residues in contact with GLN 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B TRP* 6.3 0.4 - - - +
567B THR* 2.9 16.2 + - + +
568B GLN* 3.3 28.8 + - - +
569B GLY 3.3 0.2 - - - -
570B LEU* 1.3 75.3 - - - +
572B ARG* 1.3 60.5 + - + +
574B PHE* 3.4 11.2 - - + +
575B TYR* 2.9 29.3 + - - +
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Residues in contact with ARG 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 4.2 6.1 - - - +
406B PHE* 4.0 19.7 - - + -
477B ARG 3.1 20.8 + - - -
478B GLY* 2.8 26.2 + - - -
479B PHE 3.5 23.4 - - - +
480B GLY* 4.1 11.4 - - - +
482B TRP* 4.7 3.1 - - + -
568B GLN 3.3 7.1 + - - +
569B GLY* 3.2 12.6 + - - +
571B GLN* 1.3 79.6 - - + +
573B ILE* 1.3 60.6 + - - +
575B TYR* 3.2 33.3 + - - +
576B LEU* 2.9 54.8 + - + +
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Residues in contact with ILE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PHE* 4.4 18.8 - - + -
407B TYR* 5.4 2.7 - - + -
410B LEU* 4.1 12.1 - - + -
444B LEU* 4.3 11.4 - - + -
482B TRP* 6.0 0.2 - - + -
569B GLY 3.2 14.6 + - - +
570B LEU* 3.2 8.0 + - + +
572B ARG* 1.3 75.6 - - - +
574B PHE* 1.3 52.4 + - - +
576B LEU* 3.3 8.1 + - - +
577B LYS* 2.8 35.5 + - + +
584B PRO* 5.1 9.7 - - + +
588B ILE* 4.0 21.1 - - + -
592B PHE* 3.7 23.6 - - + -
601B RPG 3.5 35.4 - - + -
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Residues in contact with PHE 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LEU 2.8 16.6 + - - +
571B GLN* 3.4 11.9 - - + +
573B ILE* 1.3 76.4 - - - +
575B TYR* 1.3 69.6 + - + +
577B LYS* 3.4 2.3 + - - +
578B LEU* 3.0 60.8 + - + +
592B PHE* 4.0 26.1 - + + -
596B LEU* 5.8 3.4 - - + -
598B PHE* 6.0 7.0 - + - -
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Residues in contact with TYR 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B GLN 2.9 17.8 + - - +
572B ARG* 3.2 30.3 + - - +
574B PHE* 1.3 81.4 - - + +
576B LEU* 1.3 57.8 + - + +
578B LEU* 3.2 5.2 + - + +
579B GLU* 2.7 77.0 + - + +
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Residues in contact with LEU 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 3.9 35.9 - - + -
406B PHE* 3.8 28.5 - - + -
407B TYR* 3.3 27.1 - - + +
478B GLY 4.4 0.2 - - - +
572B ARG* 2.9 51.9 + - - +
573B ILE* 3.8 4.0 - - - +
575B TYR* 1.3 76.6 - - + +
577B LYS* 1.3 57.2 - - - +
579B GLU* 3.4 16.5 + - - +
580B ASP* 2.9 26.7 + - - -
581B LEU 4.5 0.9 + - - -
582B VAL* 4.4 9.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ILE* 2.8 19.7 + - + +
574B PHE* 3.8 4.7 - - - +
576B LEU* 1.3 77.2 - - - +
578B LEU* 1.3 68.6 + - + +
580B ASP* 3.4 19.2 + - - +
583B PRO* 5.8 0.3 - - - +
584B PRO* 4.1 22.9 - - + +
589B ASP* 2.6 38.2 + - - +
592B PHE* 4.1 22.9 - - + -
593B LEU* 4.4 22.7 - - - +
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Residues in contact with LEU 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B PHE* 3.0 58.1 + - + +
575B TYR* 3.8 4.3 - - + +
577B LYS* 1.3 86.5 - - + +
579B GLU* 1.3 66.4 + - - +
580B ASP* 3.4 5.4 + - - +
592B PHE* 6.2 0.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 5.0 5.2 - - - +
575B TYR* 2.7 60.0 + - + +
576B LEU* 3.7 17.4 - - - +
578B LEU* 1.3 73.6 - - - +
580B ASP* 1.3 67.4 + - - +
581B LEU* 3.2 40.6 + - + +
582B VAL* 5.2 2.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LEU 2.9 13.3 + - - -
577B LYS 3.6 15.6 - - - +
578B LEU 3.2 5.6 - - - +
579B GLU* 1.3 78.8 - - - +
581B LEU* 1.3 64.1 + - - +
582B VAL 3.6 1.1 - - - +
583B PRO* 3.8 26.5 - - - +
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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).
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