ID code: '4E7A' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 12 C1' U T 3 7 10 24 C1' G T 4 beta 19 25 22 47 C1' G T 5 beta 42 48 45 70 C1' C T 6 beta 65 71 68 87 C1' DOC T 7 beta 91 79 88 106 C1' U P 3 beta 101 107 104 126 C1' G P 4 beta 121 127 124 149 C1' G P 5 beta 144 150 147 172 C1' C P 6 beta 167 173 170 189 C1' DOC P 7 beta 193 181 190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U T 3 OK 12 8 11 22 C2' G T 4 OK 24 20 23 45 C2' G T 5 OK 47 43 46 68 C2' C T 6 OK 70 66 69 88 C2' DOC T 7 87 89 104 C2' U P 3 OK 106 102 105 124 C2' G P 4 OK 126 122 125 147 C2' G P 5 OK 149 145 148 170 C2' C P 6 OK 172 168 171 190 C2' DOC P 7 189 191 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U T 3 OK 6 9 10 20 C3' G T 4 OK 18 21 22 43 C3' G T 5 OK 41 44 45 66 C3' C T 6 OK 64 67 68 89 C3' DOC T 7 90 88 102 C3' U P 3 OK 100 103 104 122 C3' G P 4 OK 120 123 124 145 C3' G P 5 OK 143 146 147 168 C3' C P 6 OK 166 169 170 191 C3' DOC P 7 192 190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U T 3 OK 8 5 7 18 C4' G T 4 OK 20 17 19 41 C4' G T 5 OK 43 40 42 64 C4' C T 6 OK 66 63 65 90 C4' DOC T 7 OK 89 92 91 100 C4' U P 3 OK 102 99 101 120 C4' G P 4 OK 122 119 121 143 C4' G P 5 OK 145 142 144 166 C4' C P 6 OK 168 165 167 192 C4' DOC P 7 OK 191 194 193 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U T 3 4 6 17 C5' G T 4 16 18 40 C5' G T 5 39 41 63 C5' C T 6 62 64 92 C5' DOC T 7 93 90 99 C5' U P 3 98 100 119 C5' G P 4 118 120 142 C5' G P 5 141 143 165 C5' C P 6 164 166 194 C5' DOC P 7 195 192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U T 3 OK OK 2 3 4 13 P G T 4 distorted distorted 9 14 15 16 36 P G T 5 distorted distorted 21 37 38 39 59 P C T 6 distorted distorted 44 60 61 62 94 P DOC T 7 distorted distorted 67 95 96 93 115 P G P 4 distorted distorted 103 116 117 118 138 P G P 5 distorted distorted 123 139 140 141 161 P C P 6 distorted distorted 146 162 163 164 196 P DOC P 7 distorted distorted 169 197 198 195 ---------------------------------------------------------------------------------