ID code: '4F02' 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' --------------------------------------------------------------------------------- 1386 C1' A B 1 beta 1381 1387 1384 1408 C1' A B 2 beta 1403 1409 1406 1430 C1' A B 3 beta 1425 1431 1428 1452 C1' A B 4 beta 1447 1453 1450 1474 C1' A B 5 beta 1469 1475 1472 1496 C1' A B 6 beta 1491 1497 1494 1518 C1' A B 7 beta 1513 1519 1516 1540 C1' A B 8 beta 1535 1541 1538 1562 C1' A B 9 beta 1557 1563 1560 3128 C1' A E 1 beta 3123 3129 3126 3150 C1' A E 2 beta 3145 3151 3148 3172 C1' A E 3 beta 3167 3173 3170 3194 C1' A E 4 beta 3189 3195 3192 3216 C1' A E 5 beta 3211 3217 3214 3238 C1' A E 6 beta 3233 3239 3236 3260 C1' A E 7 beta 3255 3261 3258 3282 C1' A E 8 beta 3277 3283 3280 3304 C1' A E 9 beta 3299 3305 3302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1384 C2' A B 1 OK 1386 1382 1385 1406 C2' A B 2 OK 1408 1404 1407 1428 C2' A B 3 OK 1430 1426 1429 1450 C2' A B 4 OK 1452 1448 1451 1472 C2' A B 5 OK 1474 1470 1473 1494 C2' A B 6 OK 1496 1492 1495 1516 C2' A B 7 OK 1518 1514 1517 1538 C2' A B 8 OK 1540 1536 1539 1560 C2' A B 9 OK 1562 1558 1561 3126 C2' A E 1 OK 3128 3124 3127 3148 C2' A E 2 OK 3150 3146 3149 3170 C2' A E 3 OK 3172 3168 3171 3192 C2' A E 4 OK 3194 3190 3193 3214 C2' A E 5 OK 3216 3212 3215 3236 C2' A E 6 OK 3238 3234 3237 3258 C2' A E 7 OK 3260 3256 3259 3280 C2' A E 8 OK 3282 3278 3281 3302 C2' A E 9 OK 3304 3300 3303 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1382 C3' A B 1 OK 1380 1383 1384 1404 C3' A B 2 OK 1402 1405 1406 1426 C3' A B 3 OK 1424 1427 1428 1448 C3' A B 4 OK 1446 1449 1450 1470 C3' A B 5 OK 1468 1471 1472 1492 C3' A B 6 OK 1490 1493 1494 1514 C3' A B 7 OK 1512 1515 1516 1536 C3' A B 8 OK 1534 1537 1538 1558 C3' A B 9 OK 1556 1559 1560 3124 C3' A E 1 OK 3122 3125 3126 3146 C3' A E 2 OK 3144 3147 3148 3168 C3' A E 3 OK 3166 3169 3170 3190 C3' A E 4 OK 3188 3191 3192 3212 C3' A E 5 OK 3210 3213 3214 3234 C3' A E 6 OK 3232 3235 3236 3256 C3' A E 7 OK 3254 3257 3258 3278 C3' A E 8 OK 3276 3279 3280 3300 C3' A E 9 OK 3298 3301 3302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1380 C4' A B 1 OK 1382 1379 1381 1402 C4' A B 2 OK 1404 1401 1403 1424 C4' A B 3 OK 1426 1423 1425 1446 C4' A B 4 OK 1448 1445 1447 1468 C4' A B 5 OK 1470 1467 1469 1490 C4' A B 6 OK 1492 1489 1491 1512 C4' A B 7 OK 1514 1511 1513 1534 C4' A B 8 OK 1536 1533 1535 1556 C4' A B 9 OK 1558 1555 1557 3122 C4' A E 1 OK 3124 3121 3123 3144 C4' A E 2 OK 3146 3143 3145 3166 C4' A E 3 OK 3168 3165 3167 3188 C4' A E 4 OK 3190 3187 3189 3210 C4' A E 5 OK 3212 3209 3211 3232 C4' A E 6 OK 3234 3231 3233 3254 C4' A E 7 OK 3256 3253 3255 3276 C4' A E 8 OK 3278 3275 3277 3298 C4' A E 9 OK 3300 3297 3299 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1379 C5' A B 1 1378 1380 1401 C5' A B 2 1400 1402 1423 C5' A B 3 1422 1424 1445 C5' A B 4 1444 1446 1467 C5' A B 5 1466 1468 1489 C5' A B 6 1488 1490 1511 C5' A B 7 1510 1512 1533 C5' A B 8 1532 1534 1555 C5' A B 9 1554 1556 3121 C5' A E 1 3120 3122 3143 C5' A E 2 3142 3144 3165 C5' A E 3 3164 3166 3187 C5' A E 4 3186 3188 3209 C5' A E 5 3208 3210 3231 C5' A E 6 3230 3232 3253 C5' A E 7 3252 3254 3275 C5' A E 8 3274 3276 3297 C5' A E 9 3296 3298 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1397 P A B 2 distorted distorted 1383 1398 1399 1400 1419 P A B 3 distorted distorted 1405 1420 1421 1422 1441 P A B 4 distorted distorted 1427 1442 1443 1444 1463 P A B 5 distorted distorted 1449 1464 1465 1466 1485 P A B 6 distorted distorted 1471 1486 1487 1488 1507 P A B 7 distorted distorted 1493 1508 1509 1510 1529 P A B 8 distorted distorted 1515 1530 1531 1532 1551 P A B 9 distorted distorted 1537 1552 1553 1554 3117 P A E 1 OK OK 3118 3119 3120 3139 P A E 2 distorted distorted 3125 3140 3141 3142 3161 P A E 3 distorted distorted 3147 3162 3163 3164 3183 P A E 4 distorted distorted 3169 3184 3185 3186 3205 P A E 5 distorted distorted 3191 3206 3207 3208 3227 P A E 6 distorted distorted 3213 3228 3229 3230 3249 P A E 7 distorted distorted 3235 3250 3251 3252 3271 P A E 8 distorted distorted 3257 3272 3273 3274 3293 P A E 9 distorted distorted 3279 3294 3295 3296 ---------------------------------------------------------------------------------