NEW. This menu allows a very fast screening of basic structural elements (residues, base pairs, multiplets, dinucleotide steps, stems, and single stranded regions of loops (apical, bulge, internal, and n-way junctions).

Select appropriate tab to find requested 3D structural elements.

	Residue	Base pair	Multiplet	Dinucl. step	Stem	Loop
Residue See Help for RNA FRABASE notation Any A C G U a c g u ADE Experimental method Any X-Ray NMR Electron Microscopy Other Parameters Sugar pucker pseudorotation phase angle (P): Any North             <-45°, 45°> East              <45°, 135°> South             <135°, -135°> West              <-135°, -45°> C3'-endo/C2'-exo  <-9°, 9°> C3'-endo          <9°, 27°> C3'-endo/C4'-exo  <27°, 45°> C4'-exo           <45°, 63°> O4'-endo/C4'-exo  <63°, 81°> O4'-endo          <81°, 99°> O4'-endo/C1'-exo  <99°, 117°> C1'-exo           <117°, 135°> C2'-endo/C1'-exo  <135°, 153°> C2'-endo          <153°, 171°> C2'-endo/C3'-exo  <171°, -171°> C3'-exo           <-171°, -153°> C4'-endo/C3'-exo  <-153°, -135°> C4'-endo          <-135°, -117°> C4'-endo/O4'-exo  <-117°, -99°> O4'-exo           <-99°, -81°> C1'-endo/O4'-exo  <-81°, -63°> C1'-endo          <-63°, -45°> C1'-endo/C2'-exo  <-45°, -27°> C2'-exo           <-27°, -9°> Sugar pucker amplitude (Tm): Any <-90°, 15°> <15°, 30°> <30°, 50°> <50°, 90°> Glicosidic torsion angle (χ): Any Syn   <-90°, 90°> Anti  <90°, -90°> Exocyclic torsion angle around C4'-C5' (γ): Any gauche+  <-120°, 0°> gauche-  <0°, 120°> trans    <120°, -120°> Include all models of the structure: Associated residues See Help for RNA FRABASE notation Residue of the 1st strand: Any A C G U a c g u ADE Residue of the 2nd strand: Any A C G U a c g u ADE Experimental method Any X-Ray NMR Electron Microscopy Other Base pairs classification Westhof's notation: Any H/H cis H/H tran H/S cis H/S tran H/W cis H/W tran S/H cis S/H tran S/S cis S/S tran S/W cis S/W tran W/H cis W/H tran W/S cis W/S tran W/W cis W/W tran Unclassified Saenger's notation: Any XI XXIV XVII II XII,XIII V I XIX XXVIII XIV,XV XVIII III XXIII VII VIII XVI X IX XX XXV XXI IV XXII XXVI XXVII VI Base-base parameters Shear (Sx): Any <-180°, -0.52°> <-0.52°, -0.17°> <-0.17°, 0°> <0°, 0.16°> <0.16°, 0.56°> <0.56°, 180°> Stretch (Sy): Any <-180°, -0.51°> <-0.51°, -0.23°> <-0.23°, -0.15°> <-0.15°, -0.09°> <-0.09°, -0.01°> <-0.01°, 180°> Stagger (Sz): Any <-180°, -0.5°> <-0.5°, -0.22°> <-0.22°, -0.07°> <-0.07°, 0.06°> <0.06°, 0.31°> <0.31°, 180°> Buckle (κ): Any <-180°, -8.97°> <-8.97°, -3.08°> <-3.08°, 0.07°> <0.07°, 3.49°> <3.49°, 9.44°> <9.44°, 180°> Propeller (ω): Any <-180°, -15.03°> <-15.03°, -9.37°> <-9.37°, -4.62°> <-4.62°, -1.21°> <-1.21°, 2.49°> <2.49°, 180°> Opening (σ): Any <-180°, -5.64°> <-5.64°, -2°> <-2°, -0.11°> <-0.11°, 1.76°> <1.76°, 4.7°> <4.7°, 180°> Include all models of the structure: Associated residues See Help for RNA FRABASE notation Residue of the 1st strand: Any A C G U a c g u ADE Residue of the 2nd strand: Any A C G U a c g u ADE Residue of the 3rd strand: Any A C G U a c g u ADE Define another residue: Residue of the 4th strand: Any A C G U a c g u ADE Define another residue: Residue of the 5th strand: Any A C G U a c g u ADE Experimental method Any X-Ray NMR Electron Microscopy Other Include all models of the structure: First base pair See Help for RNA FRABASE notation Residue of the 1st strand: Any A C G U a c g u ADE Residue of the 2nd strand: Any A C G U a c g u ADE Second base pair See Help for RNA FRABASE notation Residue of the 1st strand: Any A C G U a c g u ADE Residue of the 2nd strand: Any A C G U a c g u ADE Experimental method Any X-Ray NMR Electron Microscopy Other Inter base pair parameters Shift (Dx): Any <-10Å, -0.73Å> <-0.73Å, -0.29Å> <-0.29Å, 0Å> <0Å, 0.3Å> <0.3Å, 0.73Å> <0.73Å, 10Å> Slide (Dy): Any <-10Å, -2.09Å> <-2.09Å, -1.74Å> <-1.74Å, -1.43Å> <-1.43Å, -1.07Å> <-1.07Å, -0.42Å> <-0.42Å, 10Å> Rise (Dz): Any <-10Å, 3Å> <3Å, 3.16Å> <3.16Å, 3.28Å> <3.28Å, 3.41Å> <3.41Å, 3.65Å> <3.65Å, 10Å> Tilt (τ): Any <-180°, -4.41°> <-4.41°, -1.74°> <-1.74°, 0°> <0°, 1.74°> <1.74°, 4.54°> <4.54°, 180°> Roll (ρ): Any <-180°, -0.46°> <-0.46°, 3.34°> <3.34°, 6.31°> <6.31°, 9.32°> <9.32°, 13.6°> <13.6°, 180°> Twist (Ω): Any <-180°, 26.83°> <26.83°, 30.5°> <30.5°, 33.07°> <33.07°, 36.25°> <36.25°, 42.68°> <42.68°, 180°> Include all models of the structure: Experimental method Any X-Ray NMR Electron Microscopy Other Case sensitive (modified residues sensitive search): Stem length Exact length Interval Length: Minimum length: Maximum length: Sequence See Help for RNA FRABASE notation First strand: Define second strand: Second strand: Include all models of the structure: Experimental method Any X-Ray NMR Electron Microscopy Other Parameters Case sensitive (modified residues sensitive search): Strand shift operation: Include all models of the structure: