ID code: '1K1G' 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' --------------------------------------------------------------------------------- 1969 C1' U B 501 alpha beta 1964 1984 1970 1967 2000 C1' A B 502 alpha beta 1995 2017 2001 1998 2033 C1' U B 503 alpha beta 2028 2048 2034 2031 2063 C1' A B 504 alpha beta 2058 2080 2064 2061 2096 C1' C B 505 alpha beta 2091 2111 2097 2094 2127 C1' U B 506 alpha beta 2122 2142 2128 2125 2157 C1' A B 507 alpha beta 2152 2174 2158 2155 2190 C1' A B 508 alpha beta 2185 2207 2191 2188 2223 C1' C B 509 alpha beta 2218 2238 2224 2221 2254 C1' A B 510 alpha beta 2249 2271 2255 2252 2287 C1' A B 511 alpha beta 2282 2305 2288 2285 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1967 C2' U B 501 OK OK 1969 1965 1982 1968 1998 C2' A B 502 OK OK 2000 1996 2015 1999 2031 C2' U B 503 OK OK 2033 2029 2046 2032 2061 C2' A B 504 OK OK 2063 2059 2078 2062 2094 C2' C B 505 OK OK 2096 2092 2109 2095 2125 C2' U B 506 OK OK 2127 2123 2140 2126 2155 C2' A B 507 OK OK 2157 2153 2172 2156 2188 C2' A B 508 OK OK 2190 2186 2205 2189 2221 C2' C B 509 OK OK 2223 2219 2236 2222 2252 C2' A B 510 OK OK 2254 2250 2269 2253 2285 C2' A B 511 OK OK 2287 2283 2303 2286 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1965 C3' U B 501 OK OK 1963 1981 1966 1967 1996 C3' A B 502 OK OK 1994 2014 1997 1998 2029 C3' U B 503 OK OK 2027 2045 2030 2031 2059 C3' A B 504 OK OK 2057 2077 2060 2061 2092 C3' C B 505 OK OK 2090 2108 2093 2094 2123 C3' U B 506 OK OK 2121 2139 2124 2125 2153 C3' A B 507 OK OK 2151 2171 2154 2155 2186 C3' A B 508 OK OK 2184 2204 2187 2188 2219 C3' C B 509 OK OK 2217 2235 2220 2221 2250 C3' A B 510 OK OK 2248 2268 2251 2252 2283 C3' A B 511 OK OK 2281 2301 2284 2285 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1963 C4' U B 501 OK OK 1965 1980 1962 1964 1994 C4' A B 502 OK OK 1996 2013 1993 1995 2027 C4' U B 503 OK OK 2029 2044 2026 2028 2057 C4' A B 504 OK OK 2059 2076 2056 2058 2090 C4' C B 505 OK OK 2092 2107 2089 2091 2121 C4' U B 506 OK OK 2123 2138 2120 2122 2151 C4' A B 507 OK OK 2153 2170 2150 2152 2184 C4' A B 508 OK OK 2186 2203 2183 2185 2217 C4' C B 509 OK OK 2219 2234 2216 2218 2248 C4' A B 510 OK OK 2250 2267 2247 2249 2281 C4' A B 511 OK OK 2283 2300 2280 2282 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1962 C5' U B 501 OK OK 1961 1978 1979 1963 1993 C5' A B 502 OK OK 1992 2011 2012 1994 2026 C5' U B 503 OK OK 2025 2042 2043 2027 2056 C5' A B 504 OK OK 2055 2074 2075 2057 2089 C5' C B 505 OK OK 2088 2105 2106 2090 2120 C5' U B 506 OK OK 2119 2136 2137 2121 2150 C5' A B 507 OK OK 2149 2168 2169 2151 2183 C5' A B 508 OK OK 2182 2201 2202 2184 2216 C5' C B 509 OK OK 2215 2232 2233 2217 2247 C5' A B 510 OK OK 2246 2265 2266 2248 2280 C5' A B 511 OK OK 2279 2298 2299 2281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1989 P A B 502 distorted distorted 1966 1990 1991 1992 2022 P U B 503 distorted distorted 1997 2023 2024 2025 2052 P A B 504 distorted distorted 2030 2053 2054 2055 2085 P C B 505 distorted distorted 2060 2086 2087 2088 2116 P U B 506 distorted distorted 2093 2117 2118 2119 2146 P A B 507 distorted distorted 2124 2147 2148 2149 2179 P A B 508 distorted distorted 2154 2180 2181 2182 2212 P C B 509 distorted distorted 2187 2213 2214 2215 2243 P A B 510 distorted distorted 2220 2244 2245 2246 2276 P A B 511 distorted distorted 2251 2277 2278 2279 ---------------------------------------------------------------------------------