ID code: '4E78' 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' --------------------------------------------------------------------------------- 9 C1' A T 2 4 7 21 C1' C T 3 beta 16 22 19 41 C1' C T 4 beta 36 42 39 61 C1' G T 5 beta 56 62 59 91 C1' GDO T 6 beta 87 92 89 107 C1' A P 2 beta 102 108 105 129 C1' C P 3 beta 124 130 127 149 C1' C P 4 beta 144 150 147 169 C1' G P 5 beta 164 170 167 199 C1' GDO P 6 beta 195 200 197 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A T 2 OK 9 5 8 19 C2' C T 3 OK 21 17 20 39 C2' C T 4 OK 41 37 40 59 C2' G T 5 OK 61 57 60 89 C2' GDO T 6 OK 91 88 90 105 C2' A P 2 OK 107 103 106 127 C2' C P 3 OK 129 125 128 147 C2' C P 4 OK 149 145 148 167 C2' G P 5 OK 169 165 168 197 C2' GDO P 6 OK 199 196 198 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A T 2 OK 3 6 7 17 C3' C T 3 OK 15 18 19 37 C3' C T 4 OK 35 38 39 57 C3' G T 5 OK 55 58 59 88 C3' GDO T 6 86 89 103 C3' A P 2 OK 101 104 105 125 C3' C P 3 OK 123 126 127 145 C3' C P 4 OK 143 146 147 165 C3' G P 5 OK 163 166 167 196 C3' GDO P 6 194 197 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A T 2 OK 5 2 4 15 C4' C T 3 OK 17 14 16 35 C4' C T 4 OK 37 34 36 55 C4' G T 5 OK 57 54 56 86 C4' GDO T 6 OK 88 85 87 101 C4' A P 2 OK 103 100 102 123 C4' C P 3 OK 125 122 124 143 C4' C P 4 OK 145 142 144 163 C4' G P 5 OK 165 162 164 194 C4' GDO P 6 OK 196 193 195 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A T 2 1 3 14 C5' C T 3 13 15 34 C5' C T 4 33 35 54 C5' G T 5 53 55 85 C5' GDO T 6 84 86 100 C5' A P 2 99 101 122 C5' C P 3 121 123 142 C5' C P 4 141 143 162 C5' G P 5 161 163 193 C5' GDO P 6 192 194 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 10 P C T 3 distorted distorted 6 11 12 13 30 P C T 4 distorted distorted 18 31 32 33 50 P G T 5 distorted distorted 38 51 52 53 81 P GDO T 6 distorted distorted 58 82 83 84 96 P A P 2 distorted distorted 97 98 99 118 P C P 3 distorted distorted 104 119 120 121 138 P C P 4 distorted distorted 126 139 140 141 158 P G P 5 distorted distorted 146 159 160 161 189 P GDO P 6 distorted distorted 166 190 191 192 ---------------------------------------------------------------------------------