****************************************************************************************** Main chain conformational parameters: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) e-z: epsilon-zeta (BI/BII backbone classification) chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4 Range [170, -50(310)] is assigned to anti, and [50, 90] to syn phase-angle: the phase angle of pseudorotation and puckering sugar-type: ~C2'-endo for C2'-endo like conformation, or ~C3'-endo for C3'-endo like conformation Note the ONE column offset (for easy visual distinction) ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom (P) expressed in the standard reference frame of the 5' base; the value is POSITIVE when P lies on the +z-axis side (base in anti conformation); NEGATIVE if P is on the -z-axis side (base in syn conformation) Dp: perpendicular distance of the 3' P atom to the glycosidic bond [Ref: Chen et al. (2010): "MolProbity: all-atom structure validation for macromolecular crystallography." Acta Crystallogr D Biol Crystallogr, 66(1):12-21] nt alpha beta gamma delta epsilon zeta e-z chi phase-angle sugar-type ssZp Dp 1 1:A.G1 --- -157.6 75.5 83.9 -151.9 -76.5 -75(BI) -163.8(anti) 12.0(C3'-endo) ~C3'-endo 4.50 4.61 2 1:A.G2 -63.5 159.5 68.1 85.0 -150.3 -72.1 -78(BI) -164.0(anti) 12.9(C3'-endo) ~C3'-endo 4.30 4.56 3 1:A.C3 -101.3 179.3 83.7 84.7 -178.6 -79.5 -99(BI) -155.2(anti) 26.8(C3'-endo) ~C3'-endo 3.89 4.14 4 1:A.A4 -121.7 -150.5 91.8 87.6 -161.6 -56.2 -105(BI) -150.1(anti) 11.1(C3'-endo) ~C3'-endo 4.17 4.46 5 1:A.C5 -104.6 160.2 92.8 84.5 -125.6 -80.4 -45(..) -169.4(anti) 13.4(C3'-endo) ~C3'-endo 4.50 4.72 6 1:A.U6 -69.6 160.7 64.3 83.8 -157.8 -101.8 -56(BI) -161.8(anti) 20.1(C3'-endo) ~C3'-endo 4.40 4.48 7 1:A.U7 -170.0 154.3 62.1 133.7 -101.0 -60.5 -40(..) -131.3(anti) 150.3(C2'-endo) ~C2'-endo 1.46 1.54 8 1:A.C8 -103.4 -160.8 83.3 144.7 -102.5 91.0 166(..) -142.5(anti) 156.7(C2'-endo) ~C2'-endo 1.40 1.20 9 1:A.G9 64.2 -156.5 160.8 81.7 -148.6 -44.8 -104(BI) 63.2(syn) 33.1(C3'-endo) ~C3'-endo -2.19 4.36* 10 1:A.G10 -88.4 172.0 99.9 86.8 -156.3 -69.3 -87(BI) -155.8(anti) 0.3(C3'-endo) ~C3'-endo 4.35 4.66 11 1:A.U11 -70.1 178.3 60.5 86.0 -168.3 -65.5 -103(BI) -155.1(anti) 17.4(C3'-endo) ~C3'-endo 4.16 4.34 12 1:A.G12 -105.7 -176.0 88.0 86.7 -157.6 -66.1 -91(BI) -155.3(anti) 14.3(C3'-endo) ~C3'-endo 4.29 4.49 13 1:A.C13 -87.6 169.3 83.1 87.2 -165.2 -87.8 -77(BI) -160.0(anti) 31.0(C3'-endo) ~C3'-endo 4.05 4.19 14 1:A.C14 -145.0 -148.6 104.8 90.2 --- --- --- -146.1(anti) 30.7(C3'-endo) ~C3'-endo --- --- ****************************************************************************************** Virtual eta/theta torsion angles: eta: C4'(i-1)-P(i)-C4'(i)-P(i+1) theta: P(i)-C4'(i)-P(i+1)-C4'(i+1) [Ref: Olson (1980): "Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking." Macromolecules, 13(3):721-728] eta': C1'(i-1)-P(i)-C1'(i)-P(i+1) theta': P(i)-C1'(i)-P(i+1)-C1'(i+1) [Ref: Keating et al. (2011): "A new way to see RNA." Quarterly Reviews of Biophysics, 44(4):433-466] eta": base(i-1)-P(i)-base(i)-P(i+1) theta": P(i)-base(i)-P(i+1)-base(i+1) nt eta theta eta' theta' eta" theta" 1 1:A.G1 --- -145.6 --- -144.4 --- -114.6 2 1:A.G2 175.0 -140.3 -166.9 -144.8 -120.7 -135.4 3 1:A.C3 162.8 -159.2 -179.3 -158.6 -153.3 -134.8 4 1:A.A4 172.0 -130.2 -179.8 -137.0 -149.2 -107.2 5 1:A.C5 166.3 -136.3 -172.4 -138.2 -119.6 -103.3 6 1:A.U6 161.3 -172.3 -177.6 152.5 -123.0 105.8 7 1:A.U7 81.1 -40.5 92.3 -55.9 68.5 -31.8 8 1:A.C8 163.5 129.4 -140.5 73.9 -125.1 59.7 9 1:A.G9 109.0 -134.3 100.4 -127.3 122.8 -130.5 10 1:A.G10 -173.3 -146.6 -134.6 -151.6 -112.0 -141.3 11 1:A.U11 173.0 -144.0 -170.7 -144.9 -143.8 -115.4 12 1:A.G12 169.0 -139.0 -173.3 -143.1 -129.0 -117.6 13 1:A.C13 170.2 -144.7 -167.7 -149.9 -123.5 -135.5 14 1:A.C14 --- --- --- --- --- --- ****************************************************************************************** Sugar conformational parameters: v0: C4'-O4'-C1'-C2' v1: O4'-C1'-C2'-C3' v2: C1'-C2'-C3'-C4' v3: C2'-C3'-C4'-O4' v4: C3'-C4'-O4'-C1' tm: the amplitude of pucker P: the phase angle of pseudorotation [Ref: Altona & Sundaralingam (1972): "Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation." J Am Chem Soc, 94(23):8205-8212] nt v0 v1 v2 v3 v4 tm P Puckering 1 1:A.G1 4.7 -27.6 38.5 -37.0 20.5 39.4 12.0 C3'-endo 2 1:A.G2 3.8 -25.8 36.8 -35.5 20.0 37.7 12.9 C3'-endo 3 1:A.C3 -5.1 -17.1 31.3 -35.2 25.5 35.1 26.8 C3'-endo 4 1:A.A4 4.6 -25.1 34.8 -32.8 17.9 35.4 11.1 C3'-endo 5 1:A.C5 3.8 -27.6 39.7 -38.4 21.9 40.8 13.4 C3'-endo 6 1:A.U6 -1.1 -22.3 35.9 -37.4 24.3 38.3 20.1 C3'-endo 7 1:A.U7 -24.3 32.0 -27.4 14.3 6.1 31.6 150.3 C2'-endo 8 1:A.C8 -28.3 40.8 -37.7 22.5 3.5 41.1 156.7 C2'-endo 9 1:A.G9 -9.8 -14.9 32.3 -39.2 30.7 38.5 33.1 C3'-endo 10 1:A.G10 13.5 -34.9 42.1 -35.4 13.8 42.1 0.3 C3'-endo 11 1:A.U11 0.8 -22.2 34.0 -34.6 21.3 35.7 17.4 C3'-endo 12 1:A.G12 2.8 -24.3 35.4 -34.7 20.1 36.5 14.3 C3'-endo 13 1:A.C13 -7.4 -13.9 28.7 -33.7 25.9 33.5 31.0 C3'-endo 14 1:A.C14 -7.0 -13.6 27.7 -32.5 24.9 32.3 30.7 C3'-endo ****************************************************************************************** Assignment of sugar-phosphate backbone suites bin: name of the 12 bins based on [delta(i-1), delta, gamma], where delta(i-1) and delta can be either 3 (for C3'-endo sugar) or 2 (for C2'-endo) and gamma can be p/t/m (for gauche+/trans/gauche- conformations, respectively) (2x2x3=12 combinations: 33p, 33t, ... 22m); 'inc' refers to incomplete cases (i.e., with missing torsions), and 'trig' to triages (i.e., with torsion angle outliers) cluster: 2-char suite name, for one of 53 reported clusters (46 certain and 7 wannabes), '__' for incomplete cases, and '!!' for outliers suiteness: measure of conformer-match quality (low to high in range 0 to 1) [Ref: Richardson et al. (2008): "RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)." RNA, 14(3):465-481] nt bin cluster suiteness 1 1:A.G1 inc __ 0 2 1:A.G2 33p 1a 0.594 3 1:A.C3 33p !! 0 4 1:A.A4 33p !! 0 5 1:A.C5 33p !! 0 6 1:A.U6 33p 1a 0.570 7 1:A.U7 32p 1z 0.451 8 1:A.C8 22p !! 0 9 1:A.G9 23t 6n 0.518 10 1:A.G10 trig !! 0 11 1:A.U11 33p 1a 0.807 12 1:A.G12 33p !! 0 13 1:A.C13 33p 1a 0.027 14 1:A.C14 trig !! 0