Contacts of the helix formed by residues 562 - 585 (chain B) in PDB entry 2BKU
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 562 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS* 5.5 6.2 - - - -
561B LEU* 1.3 79.5 - - - +
563B LEU* 1.3 72.0 + - - +
564B GLU* 3.2 17.2 + - + +
565B ASP* 3.1 37.5 + - - +
566B ALA* 3.0 20.3 + - - +
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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
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29A ARG 3.9 1.8 - - - +
30A HIS* 3.0 29.4 - - + +
31A LEU 4.1 5.2 - - - +
32A THR* 3.3 14.1 - - - +
33A GLY* 3.3 37.2 - - - +
52A PHE* 6.4 2.0 - - + -
157A PHE* 5.5 2.7 - - + -
561B LEU 3.8 0.8 + - - -
562B THR* 1.3 76.0 + - - +
564B GLU* 1.3 64.7 + - + +
566B ALA* 3.0 17.3 + - + +
567B GLN* 3.0 25.7 + - + +
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Residues in contact with GLU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 5.4 5.5 + - - +
157A PHE* 6.4 0.2 - - - -
158A GLU* 3.5 31.8 - - - +
176A PHE* 3.9 4.0 - - - +
177A VAL* 2.9 48.4 + - - +
562B THR* 3.2 14.6 + - + +
563B LEU* 1.3 83.7 - - + +
565B ASP* 1.3 68.4 + - - +
567B GLN* 3.3 6.1 + - - +
568B SER* 3.2 23.7 + - - -
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Residues in contact with ASP 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL 5.8 0.2 - - - +
561B LEU* 3.4 33.4 - - + +
562B THR* 3.1 22.6 + - + +
564B GLU* 1.3 83.0 - - - +
566B ALA* 1.3 62.5 + - - +
568B SER* 3.7 7.3 + - - -
569B LEU* 3.3 21.3 + - - +
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Residues in contact with ALA 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B GLU* 4.0 33.0 - - + +
561B LEU* 4.6 6.4 - - - +
562B THR 3.0 12.7 + - - +
563B LEU* 3.4 11.9 - - + +
565B ASP* 1.3 76.3 - - - +
567B GLN* 1.3 68.4 + - - +
569B LEU* 3.2 8.5 + - - +
570B GLN* 2.8 32.4 + - - +
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Residues in contact with GLN 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 2.9 45.7 + - - +
33A GLY* 3.5 24.5 - - - -
154A ASN* 3.1 23.2 + - - +
157A PHE* 3.9 23.1 - - + -
563B LEU* 3.0 25.6 + - + +
564B GLU* 3.3 5.6 + - - +
566B ALA* 1.3 82.9 - - - +
568B SER* 1.3 60.5 + - - +
570B GLN* 3.0 20.5 + - - +
571B GLU* 2.9 26.9 + - - +
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Residues in contact with SER 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B ASP* 6.0 1.0 - - - +
512B ASN* 5.6 3.1 + - - +
517B ARG* 4.0 18.7 + - - -
564B GLU* 3.2 15.6 + - - -
565B ASP* 3.8 8.3 - - - -
567B GLN* 1.3 78.8 - - - +
569B LEU* 1.3 60.3 + - - +
571B GLU* 3.5 13.6 + - - +
572B LEU* 3.2 19.2 + - - +
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Residues in contact with LEU 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ARG* 5.7 0.2 - - - +
553B THR* 4.0 40.2 - - + +
556B VAL* 4.0 15.0 - - + +
558B GLU* 5.0 15.9 - - + +
561B LEU* 5.2 6.7 - - + -
565B ASP 3.3 10.8 + - - +
566B ALA* 3.2 11.3 + - - +
568B SER* 1.3 77.6 - - - +
570B GLN* 1.3 63.8 + - + +
572B LEU* 3.0 15.1 + - + +
573B GLN* 2.9 37.9 + - - +
608B LYS* 5.6 2.7 - - - +
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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
----------------------------------------------------------
29A ARG* 2.7 38.4 + - - +
33A GLY 4.0 7.6 + - - +
154A ASN* 5.2 0.7 - - - -
558B GLU* 3.5 35.9 + - + +
566B ALA* 2.8 18.4 + - - +
567B GLN* 3.0 19.6 + - - +
569B LEU* 1.3 72.1 - - + +
571B GLU* 1.3 65.6 + - - +
573B GLN* 4.2 7.4 - - - +
574B SER* 2.9 28.2 + - - -
610B ASP* 4.0 15.6 + - - +
613B PHE* 3.4 35.3 - - + -
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Residues in contact with GLU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER 3.2 22.4 - - - +
154A ASN* 3.2 24.9 - - + +
155A TYR* 3.8 11.4 - - - -
156A ASN 4.5 0.9 + - - -
512B ASN* 2.7 39.0 + - - +
515B ASN* 4.0 5.0 - - - +
517B ARG* 5.5 0.2 + - - -
518B ALA* 4.3 5.0 - - - +
567B GLN 2.9 18.5 + - - +
568B SER* 3.5 12.6 + - - +
569B LEU 3.2 0.2 - - - -
570B GLN* 1.3 76.8 - - - +
572B LEU* 1.3 56.8 + - - +
574B SER* 3.3 2.7 + - - -
575B ASN* 2.9 45.5 + - - +
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Residues in contact with LEU 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ARG* 3.8 35.4 - - - +
521B PHE* 3.7 32.1 - - + -
549B LYS* 4.6 14.1 - - - -
553B THR* 3.4 29.2 - - + -
568B SER 3.2 9.9 + - - +
569B LEU* 3.0 17.8 + - + +
571B GLU* 1.3 79.8 - - - +
573B GLN* 1.3 57.1 + - - +
575B ASN* 3.2 10.5 + - - +
576B ILE* 2.9 37.8 + - + +
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Residues in contact with GLN 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B LEU* 4.4 8.5 - - + +
553B THR* 3.0 50.3 + - - +
554B MET* 3.8 7.5 - - - +
569B LEU* 2.9 22.1 + - - +
570B GLN* 3.3 11.8 + - - +
572B LEU* 1.3 73.2 - - - +
574B SER* 1.3 61.0 + - - +
576B ILE* 3.4 8.4 + - - +
577B LEU* 3.0 32.3 + - + +
605B LEU* 4.5 7.6 - - + +
608B LYS* 3.3 31.5 + - - +
613B PHE* 3.5 23.2 - - + -
614B ILE* 4.6 5.8 - - + -
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Residues in contact with SER 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LYS* 3.9 7.8 + - - +
153A SER* 4.1 23.7 - - - -
570B GLN 2.9 14.9 + - - -
571B GLU 3.5 7.9 - - - -
573B GLN* 1.3 73.4 - - - +
575B ASN* 1.3 64.6 + - - +
577B LEU* 3.2 3.9 + - - +
578B THR* 3.2 25.1 + - - -
613B PHE* 3.4 21.2 + - - -
614B ILE* 4.4 9.2 - - - +
617B ASP* 5.1 7.9 + - - +
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Residues in contact with ASN 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER* 4.6 7.4 - - - +
512B ASN* 5.0 2.2 - - - +
517B ARG* 4.8 2.4 - - - +
518B ALA* 3.6 37.8 - - - +
521B PHE* 3.8 36.6 - - + +
571B GLU* 2.9 36.9 + - - +
572B LEU* 3.4 14.2 - - - +
574B SER* 1.3 78.9 - - - +
576B ILE* 1.3 61.8 + - - +
578B THR* 3.4 17.1 + - - -
579B VAL 3.6 3.8 + - - -
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Residues in contact with ILE 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PHE* 3.7 26.2 - - + -
546B VAL* 3.5 29.8 - - + +
549B LYS* 3.6 30.5 - - + +
550B LEU* 3.7 33.2 - - + +
553B THR* 4.1 12.6 - - + -
572B LEU* 2.9 24.7 + - + +
573B GLN* 3.8 7.6 - - - +
574B SER 3.3 0.2 - - - -
575B ASN* 1.3 74.2 - - - +
577B LEU* 1.3 59.7 + - - +
579B VAL* 3.1 6.2 + - - +
580B LEU* 3.0 26.8 + - + +
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B LEU* 5.0 4.7 - - + -
573B GLN 3.0 17.4 + - - +
574B SER* 3.2 7.1 + - - +
576B ILE* 1.3 73.9 - - - +
578B THR* 1.3 66.2 + - - +
580B LEU* 4.2 8.7 - - + -
581B ALA* 2.8 28.6 + - + +
602B PHE* 4.3 15.9 - - + -
605B LEU* 3.8 16.6 - - + -
614B ILE* 3.5 26.9 - - + -
617B ASP* 4.0 36.6 - - + +
618B VAL* 3.7 16.8 - - + +
621B ALA* 4.3 15.0 - - + -
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Residues in contact with THR 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PHE 6.2 0.2 - - - -
522B SER* 5.7 4.3 - - - +
525B THR* 3.3 28.0 - - + +
574B SER 3.2 12.9 + - - -
575B ASN* 3.6 11.9 - - - -
577B LEU* 1.3 79.1 - - - +
579B VAL* 1.3 61.3 + - - +
581B ALA* 3.5 4.8 + - - +
582B ALA* 3.2 20.3 + - - +
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Residues in contact with VAL 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PHE* 3.3 44.6 - - + +
524B LEU* 4.0 9.2 - - + -
525B THR* 3.3 13.7 - - - +
528B VAL* 4.7 5.2 - - + -
542B ILE* 3.5 31.4 - - + -
546B VAL* 3.7 18.8 - - + -
575B ASN 3.6 2.9 + - - +
576B ILE 3.1 8.3 + - - +
578B THR* 1.3 76.9 - - - +
580B LEU* 1.3 58.5 + - - +
582B ALA* 3.2 7.1 + - - +
583B VAL* 3.0 30.6 + - + +
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B SER* 4.6 5.4 - - - +
546B VAL* 3.3 28.9 - - + -
547B MET* 4.0 12.6 - - + +
550B LEU* 3.6 31.2 - - + -
576B ILE* 3.0 18.4 + - + +
577B LEU* 3.3 11.2 + - + +
579B VAL* 1.3 77.8 - - - +
581B ALA* 1.3 61.5 + - - +
583B VAL* 3.6 7.3 + - + +
584B ILE* 3.2 30.6 + - + +
591B VAL* 5.5 1.8 - - + -
598B LEU* 3.6 34.1 - - + -
602B PHE* 3.8 15.5 - - + -
621B ALA* 5.6 0.2 - - - -
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Residues in contact with ALA 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B LEU* 2.8 20.9 + - + +
578B THR* 3.7 4.9 - - - +
580B LEU* 1.3 76.5 - - - +
582B ALA* 1.3 62.6 + - - +
584B ILE* 3.3 10.8 + - - +
585B ARG* 3.1 41.7 + - - +
617B ASP* 5.4 2.7 - - + +
620B TYR* 6.2 1.1 - - + -
621B ALA* 4.6 16.8 - - + +
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Residues in contact with ALA 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B THR* 3.9 21.1 - - + +
528B VAL* 3.5 21.8 - - + +
529B GLU* 4.2 19.1 - - - +
578B THR 3.2 10.7 + - - +
579B VAL 3.2 8.1 + - - +
581B ALA* 1.3 79.8 - - - +
583B VAL* 1.3 61.6 + - - +
585B ARG* 3.2 26.1 + - - +
586B LYS* 3.5 2.9 - - - +
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Residues in contact with VAL 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B VAL* 3.7 27.8 - - + -
539B SER* 4.9 4.7 - - - +
542B ILE* 4.4 3.1 - - + -
543B SER* 3.8 32.8 - - - +
579B VAL* 3.0 27.7 + - + +
580B LEU* 3.7 10.5 - - + +
581B ALA 3.3 0.2 - - - -
582B ALA* 1.3 75.6 - - - +
584B ILE* 1.3 61.0 + - + +
587B SER* 3.0 46.0 + - - +
590B SER* 4.1 5.2 - - - +
591B VAL* 4.1 13.2 - - + -
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Residues in contact with ILE 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B LEU* 3.2 18.6 + - + +
581B ALA* 3.3 7.7 + - - +
583B VAL* 1.3 77.9 - - + +
585B ARG* 1.3 57.6 + - - +
586B LYS 3.3 4.3 + - - -
588B PRO* 3.7 22.9 - - + +
591B VAL* 4.1 7.9 - - + -
598B LEU* 3.6 33.7 - - + -
602B PHE* 4.1 20.4 - - + -
621B ALA* 4.0 14.4 - - + +
624B ALA* 3.7 12.3 - - + +
625B LEU* 3.3 42.4 - - + +
628B SER* 4.5 2.9 + - - -
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Residues in contact with ARG 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B GLU* 5.6 2.2 - - - +
581B ALA* 3.1 33.4 + - - +
582B ALA* 3.2 8.7 + - - +
583B VAL 3.2 0.8 - - - -
584B ILE* 1.3 73.9 - - - +
586B LYS* 1.3 67.5 + - - +
620B TYR* 3.5 41.4 + - - +
621B ALA* 5.4 0.6 - - - +
623B SER* 5.9 0.2 - - - -
624B ALA* 3.9 24.4 - - + +
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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