Contacts of the helix formed by residues 623 - 650 (chain B) in PDB entry 6HBU
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 623 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B HIS* 4.6 5.8 - - - +
621B LEU 4.5 1.1 - - - +
622B SER* 1.3 83.8 - - - +
624B TRP* 1.3 61.4 + - - +
625B GLY 3.2 0.4 - - - -
626B LEU* 3.5 7.9 + - + +
627B TRP* 3.4 27.6 - - + -
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Residues in contact with TRP 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B ASP* 4.9 6.5 - - - -
622B SER* 3.1 11.7 + - - +
623B PRO* 1.3 79.0 - - - +
625B GLY* 1.3 58.9 + - - +
626B LEU 3.1 0.4 - - - -
627B TRP* 4.5 14.8 - - + -
628B LYS* 2.8 68.8 + - + +
631B VAL* 4.2 26.2 - - + -
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Residues in contact with GLY 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B THR* 4.9 0.2 - - - +
583B HIS* 4.4 10.7 - - - -
619B ILE* 4.6 6.9 - - - +
620B ASP* 3.7 28.9 - - - +
622B SER* 3.1 18.0 + - - -
624B TRP* 1.3 75.9 - - - +
626B LEU* 1.3 55.7 + - - +
628B LYS* 4.4 10.3 + - - +
629B ASN* 3.1 21.3 + - - -
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Residues in contact with LEU 626 (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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508B VAL* 3.9 24.0 - - + -
580B ALA* 3.3 35.2 - - + +
583B HIS* 3.4 29.4 - - + +
584B ASN* 4.2 8.1 - - - +
587B LEU* 6.4 0.7 - - + -
623B PRO* 3.5 10.2 + - + +
624B TRP 3.1 0.8 - - - -
625B GLY* 1.3 77.9 - - - +
627B TRP* 1.3 82.9 + - + +
628B LYS 3.3 0.4 - - - -
629B ASN* 3.2 24.2 + - - +
630B HIS* 3.3 20.3 + - + -
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Residues in contact with TRP 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B VAL* 4.1 28.0 - - + -
511B PHE* 3.6 35.9 - + + -
623B PRO* 3.4 21.7 - - + +
624B TRP* 3.3 18.0 + - + +
626B LEU* 1.3 91.7 - - + +
628B LYS* 1.3 63.3 + - - +
629B ASN 3.2 1.1 - - - -
630B HIS* 3.3 32.9 - + + +
631B VAL* 3.3 31.6 + - + +
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Residues in contact with LYS 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ARG* 5.5 11.2 - - - +
576B TYR* 4.8 3.9 - - + -
620B ASP* 3.3 26.8 + - - +
624B TRP* 2.8 43.1 + - + +
625B GLY* 4.7 9.9 - - - +
626B LEU 3.3 0.2 - - - -
627B TRP* 1.3 77.7 - - - +
629B ASN* 1.3 69.8 + - - +
631B VAL* 3.5 9.8 - - + +
632B ALA* 3.3 24.0 + - + +
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Residues in contact with ASN 629 (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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575B ARG* 4.4 5.4 + - - -
576B TYR* 3.3 47.2 - - - +
579B THR* 3.5 27.8 - - - +
580B ALA* 3.6 16.5 - - + +
625B GLY 3.1 25.6 + - - -
626B LEU 3.2 9.5 + - - +
627B TRP 3.2 0.4 - - - -
628B LYS* 1.3 87.8 - - - +
630B HIS* 1.3 58.4 + - - +
632B ALA 4.0 0.6 - - - -
633B LEU* 3.3 31.5 + - - +
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Residues in contact with HIS 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B VAL* 4.4 2.2 + - + -
511B PHE* 3.5 29.2 - + + -
512B THR* 2.7 40.5 + - + +
515B MET* 3.6 16.6 - - + +
580B ALA* 3.7 20.2 - - + -
626B LEU* 3.3 22.5 + - + -
627B TRP* 3.3 40.3 + + + +
628B LYS 3.4 0.2 - - - -
629B ASN* 1.3 77.6 - - - +
631B VAL* 1.3 61.2 + - + +
632B ALA 3.3 1.3 - - - -
633B LEU* 3.8 6.5 - - + +
634B ALA* 3.0 25.3 + - - +
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Residues in contact with VAL 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B TRP* 4.2 23.6 - - + -
627B TRP* 3.3 18.5 + - + +
628B LYS* 3.5 17.5 - - + +
630B HIS* 1.3 76.7 - - + +
632B ALA* 1.3 61.7 + - + +
633B LEU 3.4 0.2 - - - -
634B ALA* 3.8 7.5 - - + +
635B CYS* 3.2 34.1 + - - -
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Residues in contact with ALA 632 (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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576B TYR* 3.6 35.2 - - + +
628B LYS* 3.3 19.4 + - + +
629B ASN 4.2 0.4 - - - +
630B HIS 3.3 0.2 - - - -
631B VAL* 1.3 78.4 - - + +
633B LEU* 1.3 60.4 + - - +
635B CYS* 3.8 7.1 + - - +
636B MET* 3.2 30.7 + - - +
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Residues in contact with LEU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B THR* 4.9 2.9 - - + +
515B MET* 3.8 24.5 - - + +
516B VAL* 3.7 22.4 - - + -
519B SER* 3.0 34.7 + - - +
573B ILE* 3.8 32.5 - - + +
576B TYR* 3.9 25.1 - - + +
577B GLY* 4.5 3.8 - - - +
580B ALA* 6.3 0.2 - - + -
629B ASN 3.3 20.7 + - - +
630B HIS* 3.7 9.4 + - + +
632B ALA* 1.3 78.4 - - - +
634B ALA* 1.3 62.5 + - - +
635B CYS 3.3 0.7 - - - -
636B MET* 3.3 4.1 + - - +
637B ILE* 3.1 14.9 + - - +
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B MET* 3.6 16.1 - - + +
630B HIS 3.0 18.6 + - - +
631B VAL* 3.7 8.0 + - - +
632B ALA 3.4 0.2 - - - -
633B LEU* 1.3 76.0 - - - +
635B CYS* 1.3 63.2 + - - +
637B ILE* 3.4 7.4 + - + +
638B VAL* 3.2 29.7 + - + +
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Residues in contact with CYS 635 (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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631B VAL* 3.2 25.9 + - - +
632B ALA* 4.1 7.4 - - - +
633B LEU 3.3 0.2 - - - -
634B ALA* 1.3 77.0 - - - +
636B MET* 1.3 59.1 + - + +
637B ILE 3.3 0.2 - - - -
638B VAL* 4.0 5.3 - - - +
639B ILE* 3.2 41.6 + - + +
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Residues in contact with MET 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B SER* 4.5 8.7 - - - +
522B SER* 4.3 1.9 - - - -
548B MET* 4.9 1.6 - - + -
570B TYR 4.7 3.6 - - - +
571B PHE* 3.3 32.8 - - + +
573B ILE* 3.7 23.1 - - + -
576B TYR* 4.2 22.7 - - - -
632B ALA 3.2 17.2 + - - +
633B LEU* 3.3 14.3 + - - +
635B CYS* 1.3 77.2 - - + +
637B ILE* 1.3 59.2 + - - +
639B ILE* 4.7 5.4 - - + +
640B PHE* 3.1 58.2 - - + +
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Residues in contact with ILE 637 (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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515B MET* 3.8 24.2 - - + -
518B TYR* 3.7 26.5 - - + +
519B SER* 3.3 26.0 - - - +
522B SER* 3.8 14.8 - - - +
633B LEU 3.1 15.8 + - - +
634B ALA* 3.7 7.9 - - - +
635B CYS 3.3 0.4 - - - -
636B MET* 1.3 78.3 - - - +
638B VAL* 1.3 62.6 + - + +
641B LEU* 2.9 49.6 + - + +
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Residues in contact with VAL 638 (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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634B ALA* 3.2 17.1 + - + +
635B CYS* 3.8 5.8 + - - +
637B ILE* 1.3 79.8 - - + +
639B ILE* 1.3 60.1 + - + +
641B LEU* 3.9 2.4 - - - +
642B THR* 2.4 40.5 + - - +
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Residues in contact with ILE 639 (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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635B CYS* 3.2 28.8 + - + +
636B MET* 4.7 4.3 - - + -
638B VAL* 1.3 81.2 - - + +
640B PHE* 1.3 67.4 + - + +
642B THR* 3.2 5.7 + - - -
643B ILE* 3.0 45.3 + - + +
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Residues in contact with PHE 640 (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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519B SER 3.9 6.3 - - - -
522B SER* 3.3 20.8 - - - +
523B MET* 3.6 48.5 - - + -
526B ALA* 3.3 16.9 - - + +
548B MET* 5.7 0.4 - - + -
571B PHE* 6.4 1.1 - + - -
573B ILE* 4.6 0.9 - - + -
636B MET* 3.1 51.8 + - + +
637B ILE 3.6 1.6 + - - -
639B ILE* 1.3 87.3 - - + +
641B LEU* 1.3 56.8 + - - +
643B ILE* 4.0 16.2 - - + -
644B ALA* 3.2 24.3 + - - +
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Residues in contact with LEU 641 (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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470B PHE* 3.4 32.1 - - + -
474B LEU* 3.8 32.1 - - + -
478B LEU* 6.5 0.9 - - + -
522B SER* 3.4 21.1 - - - +
525B LEU* 3.8 16.2 - - + -
637B ILE* 2.9 38.7 + - + +
638B VAL* 3.9 2.7 - - - +
640B PHE* 1.3 76.5 - - - +
642B THR* 1.3 60.8 + - - +
644B ALA* 3.9 3.4 - - - -
645B TYR* 3.3 19.1 + - - +
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Residues in contact with THR 642 (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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638B VAL* 2.4 31.1 + - - +
639B ILE* 3.2 6.4 + - - -
641B LEU* 1.3 77.5 - - - +
643B ILE* 1.3 61.0 + - + +
644B ALA 3.3 0.2 - - - -
645B TYR* 3.3 7.1 + - + +
646B LEU* 3.0 47.1 + - + +
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Residues in contact with ILE 643 (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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526B ALA* 4.0 22.4 - - + +
639B ILE* 3.0 32.5 + - + +
640B PHE* 4.1 20.2 - - + +
642B THR* 1.3 77.5 - - - +
644B ALA* 1.3 56.5 + - - +
646B LEU* 3.4 7.2 + - + +
647B LYS* 3.0 38.8 + - + +
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Residues in contact with ALA 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B PHE* 4.0 14.1 - - + -
525B LEU* 3.5 41.7 - - + +
526B ALA* 4.1 2.0 - - - +
529B ALA* 3.4 21.7 - - + +
640B PHE 3.2 20.4 + - - +
641B LEU* 4.1 3.8 - - - -
642B THR 3.3 0.4 - - - -
643B ILE* 1.3 77.2 - - - +
645B TYR* 1.3 61.1 + - - +
647B LYS* 4.7 0.2 - - - -
648B LEU* 3.5 14.6 + - - +
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Residues in contact with TYR 645 (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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466B VAL* 3.6 13.9 - - + +
467B SER* 3.6 42.1 + - - -
470B PHE* 4.0 31.8 - + + -
641B LEU 3.3 19.7 + - - +
642B THR* 3.7 7.9 - - + +
643B ILE 3.3 0.6 - - - -
644B ALA* 1.3 78.8 - - - +
646B LEU* 1.3 72.7 + - + +
648B LEU* 3.1 6.7 + - - +
649B LEU* 2.9 57.1 + - + +
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Residues in contact with LEU 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B THR* 3.0 36.7 + - + +
643B ILE* 4.1 6.1 - - + +
645B TYR* 1.3 90.1 - - + +
647B LYS* 1.3 59.1 + - + +
649B LEU* 3.7 12.3 - - + -
650B PHE* 2.9 60.2 + - + +
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Residues in contact with LYS 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B ALA 2.9 24.1 + - - +
527B ILE* 2.9 30.1 + - - +
529B ALA* 3.3 30.1 + - + +
530B GLY* 4.2 7.6 - - - -
531B GLN* 5.1 0.6 + - - -
643B ILE* 3.0 29.8 + - + +
645B TYR 3.2 0.2 - - - -
646B LEU* 1.3 77.0 - - + +
648B LEU* 1.3 60.6 + - - +
650B PHE* 5.4 1.1 - - - -
651B LEU* 3.4 22.0 + - - +
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Residues in contact with LEU 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B PHE* 3.8 31.0 - - + +
455B PHE* 3.9 25.7 - - + -
466B VAL* 4.0 12.8 - - + -
469B TYR* 4.8 9.2 - - + -
470B PHE* 3.8 35.4 - - + -
529B ALA* 4.0 5.6 - - + -
530B GLY* 3.8 24.9 - - - +
644B ALA 3.5 10.7 + - - +
645B TYR 3.1 6.1 + - - +
647B LYS* 1.3 78.7 - - - +
649B LEU* 1.3 53.1 + - - +
651B LEU* 3.6 6.0 - - - +
653B LYS* 2.6 33.6 + - - -
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Residues in contact with LEU 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B TYR* 4.7 7.6 - - - +
466B VAL* 3.8 28.4 - - + +
645B TYR* 2.9 42.7 + - + +
646B LEU* 3.5 18.6 + - + +
647B LYS 3.5 0.2 - - - -
648B LEU* 1.3 78.3 - - - +
650B PHE* 1.3 75.9 + - + +
651B LEU 3.2 2.7 + - - +
653B LYS* 3.0 17.5 + - - +
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Residues in contact with PHE 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU* 2.9 61.5 + - + +
647B LYS* 4.4 1.8 - - - -
649B LEU* 1.3 86.2 - - + +
651B LEU* 1.3 64.2 + - - +
652B LYS* 3.7 6.4 + - - +
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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