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: http://monkey.belozersky.msu.su/npidb/pdb/html_pfam/PF00178/hbond.html
Дата изменения: Wed Oct 1 16:33:00 2008 Дата индексирования: Tue Aug 18 04:42:35 2009 Кодировка: |
| General information | Species distribution | Numeration assumed | Sequence conservation | 3D conservation | Contacts with DNA |
Totally there have been found 9 conservative Hbonds with DNA backbone phosphates and two conservative bidentate Hbonds with major groove atoms. 7 of the aa residues bonded with the DNA backbone make contacts by their sidechain atoms, these residues are highly conservative and are seldom substituted. 2 AA residues make contacts by backbone atoms. One of them (leu53) shows conservation for unknown reason, possibly due to it's engagement in hydrophobic core, the other one (tyr353) is often substituted by quite different AA residues, though in proteins where it is not substituted it makes contact by its OH atom with DNA backbone.
The following table shows the details of Hbonds with
DNA backbone phosphates, i.e. contacting atoms of AA
residues and nucleotides, average distance between the interacting atoms in angstroms,
conservation of the contacting AA residues according to Pfam alignment and chains,
where the Hbond can be found.
| Bond ID | AA residue.atom | Nucleotide.atom | Average distance, Å | Chains | Proteins | Conservation |
|---|---|---|---|---|---|---|
| #1 | Leu53.o | 837.phosphate oxygen | 2,93 | All containing DNA, except W and X (18 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 99,25% |
| #2 | Trp257.ne1 | 838.phosphate oxygen | 2,95 | All containing DNA | All proteins, for which there are structures, containing DNA | 100% |
| #3 | Lys261.nz | 838.phosphate oxygen | 2,84 | All containing DNA, except W, X and M (17 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 99,96% |
| #4 | Tyr307.oh | 799.phosphate oxygen | 2,74 | A, B, C, D, E, I, J, K, N, O, P, Q, V, Y (14 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 99,01% |
| #5 | Lys309.nz | 839.phosphate oxygen | 2,76 | All containing DNA, except I (19 of 20) | All proteins, for which there are structures, containing DNA | 86,88% |
| #6 | Tyr317.oh | 837.phosphate oxygen | 2,57 | All containing DNA | All proteins, for which there are structures, containing DNA | 97,26% |
| #7 | Tyr318.oh | 800.phosphate oxygen | 2,70 | All containing DNA, except W, X, U, V (16 of 20) | ETS-1 & GABP alpha from mouse; Elk-1, SAP-1 & PDEF from human | 90,05% |
| #8 | Lys325.nz | 799.phosphate oxygen | 3.03 | All containing DNA, except W, X (18 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 91.54% |
| #9 | Tyr353.o; Leu353.o; Phe353.o | 799.phosphate oxygen | 2,85 | A, B, D, E, I, J, K, N, O, P, Q, U, V (13 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 39,24%; 37,22%; 21.01% |
Hbond was detected if an H donor atom was closer than 3.7 Å to an H acceptor atom.
On the left there shown the overall picture of conservative Hbonds with DNA backbone. The contacting residues are represented in wireframe model, while only backbone is displayed for superimposed DNA strands and an example of ETS domain. Helices are shown in pink, strands are colored yellow and turns are blue. DNA phosphorus atoms are shown as grey balls, contacting protein atoms are shown as coloured balls.
To see the picture of a particular Hbond click on the bond ID in the previous table.
There were found only two AA residues making Hbonds with the DNA
major groove atoms in 6 or more proteins. Both residues (arg312 and arg315)
are highly conserved and never substituted. The following table shows the
details of Hbonds with the DNA major groove.
| AA residue.atom | Nucleotide.atom | Average distance, Å | Chains | Proteins | Conservation |
|---|---|---|---|---|---|
| Arg312.ne | G801.n7 | 3,18 | All containing DNA except V, W, X (17 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 100% |
| Arg312.ne | G802.o6 | 2,93 | All containing DNA except V, W, X (17 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 100% |
| Arg312.nh | G802.n7 | 2,89 | All containing DNA except W, X (18 of 20) | ETS-1, GABP alpha & PU.1 from mouse; Elk-1, SAP-1 & PDEF from human | 100% |
| Arg315.ne | G801.n7 | 2,91 | A, C, D, E, L, M, N, O, P, Q, T, Y (12 of 20) | ETS-1 & GABP alpha from mouse; Elk-1, SAP-1 & PDEF from human | 100% |
| Arg315.nh | G801.o6 | 2,84 | A, B, C, D, E, I, J, L, M, N, O, P, Q, T, Y (15 of 20) | ETS-1 & GABP alpha from mouse; Elk-1, SAP-1 & PDEF from human | 100% |
| Arg315.nh | G801.n7 | 3,35 | B, C, I, J, K, L, M, N, P, T, U, V, X, Y (14 of 20) | ETS-1, GABP alpha & PU.1 from mouse; ETS-1, SAP-1 & PDEF from human | 100% |
According to the picture, both arginines are likely to make bidentate Hbonds with the corresponding guanine (arg312 contacts g802 and arg315 contacts g801), though there is also s possibility for arg312 to contact g801.
In the picture one can see the superimposed backbone models of recognition helix and wireframe models of both arginines, as well as wireframe models of two guanines (g801 is shown in red and g802 is shown in green respectively).
Download hbonds.xls