Contacts of the helix formed by residues 566 - 585 (chain B) in PDB entry 6NYY
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 GLU 566 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564B GLN* 3.1 6.5 - - + +
565B PRO* 1.3 78.9 - - - +
567B GLU* 1.3 63.1 + - + +
568B LYS 3.3 0.7 - - - -
569B LYS* 3.2 35.9 + - - +
570B THR* 3.0 39.1 + - - +
639B PHE* 4.5 4.2 - - - -
641B ARG* 3.8 21.3 + - - +
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Residues in contact with GLU 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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563B LEU* 4.1 23.3 - - + +
564B GLN* 3.0 28.8 + - + +
566B GLU* 1.3 79.6 - - + +
568B LYS* 1.3 62.4 + - - +
570B THR* 4.0 7.9 - - - +
571B VAL* 3.3 27.0 + - - +
612C GLU 5.1 1.6 - - - +
613C GLN* 3.4 37.9 + - - +
614C TYR* 3.8 16.9 + - - +
615C LEU* 4.2 22.7 + - + +
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Residues in contact with LYS 568 (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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559B LYS* 6.0 1.6 - - - +
561B GLN 5.7 2.6 + - - -
563B LEU* 3.7 47.7 + - + +
564B GLN 3.1 12.6 + - - +
565B PRO* 4.9 5.8 - - + +
567B GLU* 1.3 75.8 - - - +
569B LYS* 1.3 60.7 + - - +
570B THR 3.2 0.4 - - - -
571B VAL* 3.3 4.7 + - - +
572B ALA* 2.9 31.5 + - - +
596B ILE* 4.8 15.8 - - + +
731B LEU* 4.3 12.6 - - + -
734B GLU* 3.8 20.4 + - - +
762C GLY 5.6 2.2 + - - -
763C THR* 5.2 11.7 - - - +
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Residues in contact with LYS 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PRO 3.7 13.7 + - - +
566B GLU* 3.2 42.1 + - - +
568B LYS* 1.3 78.7 - - - +
570B THR* 1.3 61.9 + - - +
572B ALA* 4.0 0.9 - - - -
573B TYR* 3.2 49.7 + - + +
639B PHE* 3.7 13.7 - - + -
731B LEU* 4.2 24.8 - - + +
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Residues in contact with THR 570 (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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566B GLU* 3.0 23.7 + - - +
567B GLU* 4.3 4.2 - - - +
568B LYS 3.2 0.4 - - - -
569B LYS* 1.3 76.3 - - - +
571B VAL* 1.3 60.5 + - - +
573B TYR* 3.5 2.3 + - - +
574B HIS* 2.9 26.7 + - - +
635B GLU* 4.2 11.2 - - - +
639B PHE* 3.5 26.5 - - + -
641B ARG* 5.8 0.3 + - - -
643B THR* 3.8 27.8 - - + -
615C LEU* 3.8 20.2 - - + -
617C THR* 6.2 0.2 - - + -
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Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B LEU* 5.8 2.7 - - + -
567B GLU 3.3 19.7 + - - +
568B LYS* 3.3 6.6 + - - +
570B THR* 1.3 73.7 - - - +
572B ALA* 1.3 60.1 + - - +
574B HIS* 3.1 6.5 + - - +
575B GLN* 3.0 35.7 + - - +
596B ILE* 3.9 24.6 - - + +
603B LEU* 4.3 21.8 - - + -
604B GLY* 4.4 19.5 - - - +
615C LEU* 3.8 20.9 - - + -
7H ALA* 4.9 7.6 - - + -
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Residues in contact with ALA 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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568B LYS 2.9 18.3 + - - +
569B LYS 4.2 2.5 - - - +
571B VAL* 1.3 78.1 - - - +
573B TYR* 1.3 63.2 + - + +
575B GLN 4.2 0.5 - - - -
576B ALA* 3.3 17.8 + - - +
596B ILE* 4.3 15.4 - - + +
727B ALA* 3.4 33.5 - - + +
730B LEU* 4.4 12.9 - - + +
731B LEU* 4.0 16.2 - - + -
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Residues in contact with TYR 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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569B LYS* 3.2 33.3 + - + +
570B THR 4.1 2.7 - - - +
572B ALA* 1.3 76.0 - - + +
574B HIS* 1.3 64.1 + - - +
576B ALA* 4.2 1.8 - - - +
577B GLY 3.8 3.3 + - - -
634B SER* 2.7 30.6 + - - +
635B GLU* 5.0 2.2 - - - -
638B PHE* 3.5 36.6 - + + -
639B PHE* 3.4 39.0 - + + -
724B GLU* 3.3 29.1 + - - -
727B ALA* 3.4 25.1 - - + -
728B LEU* 4.1 18.7 - - + +
731B LEU* 5.8 1.6 - - + -
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Residues in contact with HIS 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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570B THR 2.9 18.6 + - - +
571B VAL* 3.1 9.8 + - - +
573B TYR* 1.3 77.9 - - - +
575B GLN* 1.3 71.9 + - + +
576B ALA 3.2 0.7 - - - -
577B GLY* 2.9 18.2 + - - -
578B HIS* 3.1 2.5 + - - -
631B GLY* 3.1 52.9 + - - -
632B ARG 3.7 0.2 - - - -
635B GLU* 2.7 26.1 + - - +
645B GLY* 6.3 0.2 - - - -
646B ALA* 3.5 26.9 + - + +
649B ASP* 3.5 1.8 - - - -
803B ZN 2.2 35.8 - - - -
7H ALA* 4.1 12.3 - - + -
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Residues in contact with GLN 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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571B VAL* 3.0 16.6 + - + +
572B ALA 4.2 0.7 - - - -
574B HIS* 1.3 87.3 - - + +
576B ALA* 1.3 62.1 + - - +
577B GLY 3.3 0.2 - - - -
578B HIS* 3.9 17.5 - - + +
579B ALA* 3.5 18.5 + - - +
594B VAL* 3.7 19.6 - - + +
595B SER 3.0 14.9 - - - +
596B ILE* 4.4 1.9 - - + +
604B GLY* 3.1 15.0 + - - -
605B TYR* 2.9 45.4 - - - +
606B ALA* 4.5 2.0 - - + -
730B LEU* 4.7 4.5 - - + -
5H ALA 4.0 2.9 + - - -
6H ALA 4.0 2.6 - - - -
7H ALA* 3.6 21.6 - - + +
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Residues in contact with ALA 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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572B ALA 3.3 19.1 + - - +
573B TYR 4.4 1.6 - - - +
574B HIS 3.2 1.4 - - - -
575B GLN* 1.3 77.4 - - - +
577B GLY* 1.3 58.6 + - - +
578B HIS 3.3 0.4 - - - -
579B ALA* 4.2 5.4 - - - -
580B VAL* 3.0 34.5 + - - +
723B VAL* 3.7 20.2 - - + +
726B VAL* 4.0 10.8 - - + -
727B ALA* 3.7 26.5 - - + +
730B LEU* 4.7 1.7 - - + +
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Residues in contact with GLY 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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573B TYR 3.8 2.6 + - - -
574B HIS 2.9 12.0 + - - -
576B ALA* 1.3 78.6 - - - +
578B HIS* 1.3 58.6 + - - +
581B ALA* 3.3 23.9 + - - +
630B GLY* 3.4 26.6 - - - +
634B SER* 3.7 13.0 - - - -
716B LEU* 3.8 8.8 - - - +
723B VAL* 4.0 3.7 - - - +
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Residues in contact with HIS 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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574B HIS* 3.1 21.2 + + - -
575B GLN* 3.8 15.9 + - + +
576B ALA 3.3 0.2 - - - -
577B GLY* 1.3 77.0 - - - +
579B ALA* 1.3 61.8 + - - +
581B ALA 4.1 0.2 - - - -
582B GLY* 3.3 17.2 + - - -
606B ALA* 4.8 7.6 - - + -
608B TYR* 3.1 28.1 + + - +
627B MET* 3.1 26.8 + - - +
628B THR* 3.1 29.1 - - + -
631B GLY* 3.4 14.3 + - - -
649B ASP* 3.0 14.9 + - - -
803B ZN 2.7 29.1 - - - -
5H ALA* 5.2 8.4 - - + +
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Residues in contact with ALA 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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575B GLN 3.5 15.1 + - - +
576B ALA* 3.2 9.7 + - - +
578B HIS* 1.3 79.1 - - - +
580B VAL* 1.3 65.2 + - - +
582B GLY 3.9 1.2 - - - -
583B TRP* 3.2 21.8 + - - +
591B LEU* 3.8 36.4 - - + +
594B VAL* 4.2 9.2 - - + -
726B VAL* 4.2 6.7 - - + -
741B MET* 4.0 12.9 - - + +
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Residues in contact with VAL 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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576B ALA 3.0 16.4 + - - +
579B ALA* 1.3 73.7 - - - +
581B ALA* 1.3 64.8 + - - +
583B TRP* 3.1 16.4 + - - +
584B TYR* 3.2 40.6 + - + +
716B LEU* 3.8 11.4 - - + -
719B LYS* 4.4 6.1 - - + +
722B ASP* 3.8 19.5 - - + +
723B VAL* 3.7 32.5 - - + -
726B VAL* 4.1 14.8 - - + -
745B LEU* 4.8 6.1 - - + -
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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 GLY 3.3 20.9 + - - +
578B HIS 4.3 1.3 - - - +
579B ALA 3.3 0.6 - - - -
580B VAL* 1.3 79.2 - - - +
582B GLY* 1.3 60.5 + - - +
583B TRP 3.3 0.7 + - - -
584B TYR 3.4 1.2 + - - -
585B LEU* 3.3 31.4 + - + +
626B CYS 4.1 8.3 - - - +
627B MET* 4.0 24.7 - - - +
630B GLY* 4.5 3.4 - - - -
712B THR* 4.9 0.9 - - + -
715B LEU* 4.1 17.7 - - + -
716B LEU* 4.1 7.7 - - + +
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Residues in contact with GLY 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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578B HIS 3.3 12.2 + - - -
579B ALA 3.9 1.6 - - - -
581B ALA* 1.3 77.6 - - - +
583B TRP* 1.3 59.9 + - - +
584B TYR 3.4 0.4 + - - -
585B LEU 4.1 0.4 - - - +
588B ALA* 3.9 16.2 - - - +
589B ASP 4.0 9.7 - - - +
590B PRO* 5.3 0.5 - - - +
591B LEU* 5.4 5.2 + - - -
608B TYR* 5.3 4.7 - - - -
627B MET* 3.7 17.1 - - - +
748B ARG* 3.5 23.7 + - - -
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Residues in contact with TRP 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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579B ALA 3.2 13.0 + - - +
580B VAL* 3.1 15.3 + - - +
582B GLY* 1.3 77.4 - - - +
584B TYR* 1.3 85.5 + + + +
585B LEU 3.7 0.4 - - - -
591B LEU* 4.6 15.9 - - + -
738B LYS* 4.4 19.7 - - + -
741B MET* 3.6 40.2 - - + -
742B VAL* 3.8 19.5 - - + -
745B LEU* 3.8 29.0 + - + +
746B GLY 3.3 22.2 - - - -
747B PRO 4.2 4.2 + - - -
748B ARG* 3.5 56.8 + - + +
749B PRO* 4.0 2.7 - - + +
750B PHE* 4.6 0.7 - - - -
752B GLU* 6.1 0.2 - - - -
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Residues in contact with TYR 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 VAL* 3.2 34.7 + - + +
581B ALA 3.4 0.2 + - - -
582B GLY 3.4 0.2 - - - -
583B TRP* 1.3 105.3 - + - +
585B LEU* 1.3 64.8 + - - +
715B LEU* 4.0 22.7 - - + +
719B LYS* 3.6 49.8 + - + +
722B ASP* 3.2 22.0 + - + -
745B LEU* 4.4 13.0 + - + +
749B PRO* 4.3 21.3 - - + -
750B PHE* 3.3 19.7 - + - -
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Residues in contact with LEU 585 (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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581B ALA 3.3 20.3 + - - +
582B GLY 4.3 0.6 + - - -
583B TRP 3.7 0.2 - - - -
584B TYR* 1.3 83.8 - - - +
586B GLU* 1.3 61.4 + - - +
587B HIS 3.6 0.2 + - - -
588B ALA* 3.7 11.1 + - + +
623B ASP* 3.3 36.6 - - - +
626B CYS* 3.7 20.6 - - + +
627B MET* 4.1 7.0 - - + +
711B ARG* 3.5 35.2 - - + +
715B LEU* 4.1 17.7 - - + -
748B ARG* 2.9 25.5 + - - -
750B PHE* 3.4 4.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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