Contacts of the helix formed by residues 553 - 581 (chain B) in PDB entry 3H52
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 PRO 553 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B SER 3.9 6.3 - - - +
552B VAL* 1.3 93.8 - - + +
554B ASP* 1.3 59.7 + - - +
555B SER* 3.8 13.7 - - - +
556B THR* 3.3 22.5 + - + +
557B TRP* 3.0 23.9 + - - +
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Residues in contact with ASP 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B TYR* 5.2 2.9 + - - -
552B VAL 3.9 2.6 - - - +
553B PRO* 1.3 70.3 - - - +
555B SER* 1.3 65.9 + - - +
557B TRP* 3.6 8.0 - - - +
558B ARG* 3.0 29.1 + - - +
554C ASP* 3.8 24.6 - - + +
555C SER* 3.3 28.0 - - - -
558C ARG* 3.3 28.6 + - + +
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Residues in contact with SER 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PRO* 3.8 13.5 - - - +
554B ASP* 1.3 77.4 + - - +
556B THR* 1.3 63.9 + - - -
558B ARG* 3.8 1.7 - - - +
559B ILE* 3.3 21.2 + - - +
633B ARG* 3.2 26.8 + - - +
636B LEU* 6.4 0.7 - - - -
554C ASP* 3.4 25.1 + - - +
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Residues in contact with THR 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B VAL* 4.2 14.4 - - + -
553B PRO* 3.3 30.7 + - + +
555B SER* 1.3 77.1 + - - +
557B TRP* 1.3 64.5 + - - +
559B ILE* 4.1 2.1 - - - +
560B MET* 2.9 44.8 + - + +
633B ARG* 3.7 1.5 + - - +
638B ASP* 2.7 39.3 + - + +
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Residues in contact with TRP 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASP* 6.5 0.2 - - + -
552B VAL* 4.3 9.9 - - + -
553B PRO 3.0 16.4 + - - +
554B ASP 3.3 4.2 + - - +
556B THR* 1.3 76.1 - - - +
558B ARG* 1.3 69.5 + - + +
560B MET* 3.8 2.1 - - - +
561B THR* 2.7 66.6 + - + -
748B GLU* 2.7 40.6 + - - -
557C TRP* 3.9 17.9 - + - -
558C ARG* 3.2 69.0 - - + +
561C THR* 4.0 21.1 - - + -
562C THR* 3.8 23.1 - - + -
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Residues in contact with ARG 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B ASP 3.0 14.5 + - - +
555B SER 3.8 3.8 - - - +
557B TRP* 1.3 81.6 - - + +
559B ILE* 1.3 56.1 - - + +
561B THR* 3.6 2.7 - - - -
562B THR* 2.7 44.8 + - - +
548C TYR* 3.4 39.2 + - + +
549C ASP* 2.7 33.5 + - - +
552C VAL* 2.7 26.3 + - - +
553C PRO 3.7 2.4 - - - -
554C ASP* 3.5 33.2 + - - +
557C TRP* 3.1 60.4 - - + +
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Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B SER* 3.3 8.7 + - - +
556B THR* 4.1 2.9 - - - +
558B ARG* 1.3 81.8 - - + +
560B MET* 1.3 59.0 + - - +
562B THR* 3.6 4.5 - - - -
563B LEU* 2.8 53.1 + - + +
627B LEU* 5.2 10.1 - - + -
629B ILE* 4.0 28.3 - - + -
633B ARG* 3.0 45.5 - - + +
639B MET* 4.2 17.9 - - + -
548C TYR* 5.3 9.4 - - + +
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Residues in contact with MET 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 3.6 39.7 - - + +
556B THR* 2.9 35.2 + - + +
557B TRP* 4.0 2.9 - - - +
559B ILE* 1.3 80.7 - - - +
561B THR* 1.3 53.0 + - - +
563B LEU* 3.7 8.1 - - + +
564B ASN* 2.7 36.5 + - - +
638B ASP 5.0 0.9 - - - +
639B MET* 3.8 27.8 - - - -
642B GLN* 4.1 9.9 - - - +
735B TYR* 5.4 2.9 - - + +
743B LYS* 6.2 2.2 - - - +
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Residues in contact with THR 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B TRP* 2.7 66.5 + - + -
558B ARG* 3.7 4.7 - - - -
560B MET* 1.3 72.8 - - - +
562B THR* 1.3 61.5 + - - +
564B ASN* 3.4 7.8 + - - +
565B MET* 3.2 44.6 + - + +
748B GLU* 4.9 3.6 + - - +
557C TRP* 6.0 2.2 - - - +
561C THR* 5.9 2.7 - - + -
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Residues in contact with THR 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B ARG* 2.7 31.1 + - - +
559B ILE* 3.6 4.0 - - - -
561B THR* 1.3 70.9 - - - +
563B LEU* 1.3 62.8 + - - +
564B ASN 3.0 1.7 + - - -
565B MET* 3.1 8.7 + - + +
566B LEU* 2.7 30.8 + - + +
627B LEU* 3.6 26.5 - - + -
546C ALA* 3.9 27.5 - - + +
547C GLY 5.9 0.2 - - - +
548C TYR* 4.0 19.0 - - + -
557C TRP* 5.5 6.1 + - - -
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Residues in contact with LEU 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 3.0 68.0 - - + +
559B ILE* 2.8 41.9 + - + +
560B MET* 4.0 7.4 - - + +
562B THR* 1.3 73.2 - - - +
564B ASN* 1.3 57.9 + - - +
566B LEU* 4.1 6.1 - - + -
567B GLY* 2.7 22.9 + - - -
623B PHE* 3.4 50.5 - - + -
627B LEU* 4.1 9.4 - - + -
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Residues in contact with ASN 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 3.5 30.3 - - - +
560B MET 2.7 19.6 + - - +
561B THR* 3.5 9.4 + - - +
562B THR 3.0 0.2 - - - -
563B LEU* 1.3 81.1 - - - +
565B MET* 1.3 67.2 + - - +
568B GLY* 3.2 15.9 + - - -
750B PRO* 4.5 21.9 - - - +
752B MET* 4.8 16.4 - - - +
753B LEU* 4.8 2.6 + - - +
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Residues in contact with MET 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B THR* 3.2 38.3 + - + +
562B THR* 3.1 10.5 + - + +
564B ASN* 1.3 81.6 - - - +
566B LEU* 1.3 66.3 + - - +
568B GLY* 3.3 2.2 + - - -
569B ARG* 3.1 36.2 + - + +
752B MET* 5.5 11.1 - - + +
546C ALA 5.7 4.0 - - - +
561C THR* 6.4 2.0 - - + -
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Residues in contact with LEU 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 4.2 6.7 - - + -
562B THR 2.7 21.4 + - - +
563B LEU* 4.1 9.0 - - + +
565B MET* 1.3 74.1 - - - +
567B GLY* 1.3 55.2 + - - +
569B ARG* 3.4 27.9 + - - +
570B GLN* 2.8 47.2 + - + +
623B PHE* 3.7 40.8 - - + +
624B ALA* 4.0 7.2 - - + -
627B LEU* 5.0 1.6 - - + -
544C LEU* 4.1 17.3 - - + +
545C TYR 4.1 10.3 - - - +
546C ALA* 4.3 13.9 - - + +
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Residues in contact with GLY 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 3.6 36.3 - - - -
563B LEU 2.7 23.9 + - - -
566B LEU* 1.3 69.6 - - - +
568B GLY* 1.3 65.4 + - - +
570B GLN* 3.2 4.1 + - - +
571B VAL* 2.9 27.9 + - - +
604B MET* 4.0 0.9 - - - +
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Residues in contact with GLY 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 3.7 21.6 + - - -
564B ASN 3.2 12.2 + - - -
565B MET 3.3 2.6 + - - -
567B GLY* 1.3 74.2 - - - +
569B ARG* 1.3 62.7 + - - +
571B VAL* 3.3 4.4 + - - +
572B ILE* 3.1 29.2 + - - +
752B MET* 4.3 13.5 - - - -
2266M ILE* 5.2 5.9 - - - +
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Residues in contact with ARG 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B MET* 3.1 24.0 + - + +
566B LEU* 3.6 17.3 - - - +
568B GLY* 1.3 74.5 - - - +
570B GLN* 1.3 63.5 + - - +
572B ILE* 3.3 13.7 + - + +
573B ALA* 3.0 22.9 + - - +
544C LEU* 3.1 37.0 - - + +
545C TYR 2.4 33.1 + - - +
546C ALA* 4.2 8.3 + - - +
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Residues in contact with GLN 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 2.8 41.7 + - - +
566B LEU* 2.8 31.8 + - + +
567B GLY 3.2 4.7 + - - +
569B ARG* 1.3 72.5 - - - +
571B VAL* 1.3 54.9 + - - +
573B ALA* 3.1 5.1 + - + +
574B ALA* 2.7 35.0 + - - +
604B MET* 3.4 27.1 - - + +
607B ALA* 5.9 0.6 - - - +
611B ARG* 3.4 13.8 + - - +
623B PHE 3.3 16.1 - - - +
544C LEU* 3.5 24.2 - - + +
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Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 486 3.3 24.9 - - - -
567B GLY 2.9 19.7 + - - +
568B GLY* 3.4 8.1 - - - +
570B GLN* 1.3 75.3 - - - +
572B ILE* 1.3 64.2 + - - +
574B ALA* 3.0 5.0 + - - +
575B VAL* 2.9 24.4 + - + +
600B TRP* 3.7 11.0 - - + -
604B MET* 3.2 29.1 - - + +
756B ILE* 4.5 7.4 - - + -
2266M ILE* 4.9 7.4 - - + -
2267M ILE* 3.8 33.7 - - + +
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Residues in contact with ILE 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B GLY 3.1 18.1 + - - +
569B ARG* 3.6 14.6 - - + +
570B GLN 3.2 0.2 - - - -
571B VAL* 1.3 72.9 - - - +
573B ALA* 1.3 62.5 + - - +
575B VAL* 3.0 13.9 + - - +
576B LYS* 3.1 33.1 + - + +
2266M ILE* 4.2 24.5 - - + +
2269M LYS* 4.5 23.3 - - - +
2270M ALA* 3.9 21.5 - - + -
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Residues in contact with ALA 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B ARG 3.0 14.2 + - - +
570B GLN* 3.2 8.3 - - - +
572B ILE* 1.3 75.3 - - - +
574B ALA* 1.3 63.1 + - - +
576B LYS* 3.5 15.0 + - - +
577B TRP* 3.1 23.4 + - - +
541C PRO* 4.2 21.6 - - + +
544C LEU* 4.0 19.5 - - + -
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Residues in contact with ALA 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLN 2.7 15.6 + - - +
571B VAL* 3.0 16.8 + - + +
573B ALA* 1.3 72.9 - - - +
575B VAL* 1.3 60.5 + - - +
577B TRP* 3.4 13.7 - - + +
578B ALA* 3.1 22.7 + - - +
596B LEU* 4.3 6.3 - - + +
600B TRP* 5.4 2.5 - - + -
603B LEU* 4.4 21.7 - - + +
604B MET* 4.2 13.7 - - + -
541C PRO* 6.0 0.2 - - - -
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Residues in contact with VAL 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B VAL* 2.9 19.9 + - + +
572B ILE 3.0 7.1 + - - +
574B ALA* 1.3 76.3 - - - +
576B LYS* 1.3 59.8 + - - +
578B ALA* 3.3 5.4 + - - +
579B LYS* 3.0 29.9 + - + +
596B LEU* 3.7 32.5 - - + -
600B TRP* 6.4 0.2 - - + -
2267M ILE* 3.8 26.9 - - + -
2270M ALA* 3.6 17.3 - - + +
2271M LEU* 3.6 33.7 - - + +
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Residues in contact with LYS 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ILE* 3.1 34.3 + - + +
573B ALA* 3.9 14.6 - - - +
575B VAL* 1.3 73.3 - - + +
577B TRP* 1.3 67.3 + - - +
579B LYS* 3.0 28.5 + - - +
580B ALA* 3.2 10.2 + - - +
2270M ALA 5.1 9.9 - - - +
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Residues in contact with TRP 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ALA 3.1 12.1 + - - +
574B ALA* 3.4 18.2 - - - +
576B LYS* 1.3 76.6 - - - +
578B ALA* 1.3 66.4 + - + +
580B ALA* 2.7 30.4 + - - +
581B ILE* 3.2 39.2 + - + +
603B LEU* 3.7 24.0 - - + -
664B LEU 5.1 0.7 - - - -
667B LYS* 3.3 55.8 - - + +
668B THR* 3.9 13.7 - - - -
671B LEU* 3.6 14.4 - - + -
536C LEU* 5.1 4.4 + - + +
539C ILE* 3.5 33.8 - - + +
540C GLU* 3.6 5.3 + - - -
541C PRO* 3.9 21.2 - - + +
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Residues in contact with ALA 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B ALA 3.1 10.7 + - - +
575B VAL 3.4 9.4 - - - +
577B TRP* 1.3 80.4 - - + +
579B LYS* 1.3 61.8 + - - +
580B ALA 3.2 1.0 + - - -
581B ILE* 3.3 22.6 + - - +
584B PHE* 2.9 35.5 - - + -
596B LEU* 4.1 12.8 - - + -
671B LEU* 3.4 23.8 - - + -
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Residues in contact with LYS 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B VAL* 3.0 18.3 + - + +
576B LYS* 3.0 21.5 + - - +
578B ALA* 1.3 76.1 - - + +
580B ALA* 1.3 55.3 + - - +
581B ILE 3.5 0.4 - - - -
584B PHE* 4.7 5.8 - - + -
585B ARG* 3.3 33.3 + - - +
592B GLN* 4.8 9.6 - - - +
596B LEU* 5.6 0.7 - - + -
2270M ALA 3.4 13.1 + - - -
2271M LEU* 2.7 47.3 + - + +
2273M GLY* 4.3 7.5 - - - +
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Residues in contact with ALA 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LYS 3.2 6.9 + - - +
577B TRP* 2.7 19.2 + - - +
579B LYS* 1.3 74.1 - - - +
581B ILE* 1.3 60.5 + - - -
582B PRO* 3.3 7.3 - - - +
585B ARG* 4.6 8.5 + - - +
539C ILE* 3.1 38.9 - - + +
----------------------------------------------------------
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Residues in contact with ILE 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B TRP* 3.2 61.2 + - + +
578B ALA* 3.3 11.4 + - - +
580B ALA* 1.3 75.6 - - - +
582B PRO* 1.3 70.7 - - + +
584B PHE* 3.3 17.6 + - + -
585B ARG* 3.1 17.7 + - - +
668B THR* 4.0 12.3 - - + -
671B LEU* 3.5 16.4 - - + -
672B LEU* 6.0 1.1 - - + -
693B TYR* 3.1 29.4 - - + +
536C LEU* 4.4 7.2 - - + -
539C ILE* 3.8 9.0 - - + -
----------------------------------------------------------
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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