ID code: '1RTD' 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' --------------------------------------------------------------------------------- 15990 C1' C E 6 beta 15986 15991 15989 16009 C1' C E 7 beta 16005 16010 16008 16028 C1' G E 8 beta 16024 16029 16027 16050 C1' G E 9 beta 16046 16051 16049 16072 C1' C E 10 beta 16068 16073 16071 16091 C1' G E 11 beta 16087 16092 16090 16113 C1' C E 12 beta 16109 16114 16112 16132 C1' T E 13 beta 16128 16133 16131 16152 C1' C E 14 beta 16148 16153 16151 16171 C1' G E 15 beta 16167 16172 16170 16193 C1' A E 16 beta 16189 16194 16192 16214 C1' A E 17 beta 16210 16215 16213 16235 C1' C E 18 beta 16231 16236 16234 16254 C1' A E 19 beta 16250 16255 16253 16275 C1' G E 20 beta 16271 16276 16274 16297 C1' G E 21 beta 16293 16298 16296 16319 C1' G E 22 beta 16315 16320 16318 16341 C1' A E 23 beta 16337 16342 16340 16362 C1' C E 24 beta 16358 16363 16361 16381 C1' T E 25 beta 16377 16382 16380 16401 C1' G E 26 beta 16397 16402 16400 16441 C1' C F 2 beta 16437 16442 16440 16460 C1' A F 3 beta 16456 16461 16459 16481 C1' G F 4 beta 16477 16482 16480 16503 C1' T F 5 beta 16499 16504 16502 16523 C1' C F 6 beta 16519 16524 16522 16542 C1' C F 7 beta 16538 16543 16541 16561 C1' C F 8 beta 16557 16562 16560 16580 C1' T F 9 beta 16576 16581 16579 16600 C1' G F 10 beta 16596 16601 16599 16622 C1' T F 11 beta 16618 16623 16621 16642 C1' T F 12 beta 16638 16643 16641 16662 C1' C F 13 beta 16658 16663 16661 16681 C1' G F 14 beta 16677 16682 16680 16703 C1' A F 15 beta 16699 16704 16702 16724 C1' G F 16 beta 16720 16725 16723 16746 C1' C F 17 beta 16742 16747 16745 16765 C1' G F 18 beta 16761 16766 16764 16787 C1' C F 19 beta 16783 16788 16786 16806 C1' C F 20 beta 16802 16807 16805 16825 C1' G F 21 beta 16821 16826 16824 16846 C1' G F 22 beta 16843 16847 16845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 15989 C2' C E 6 15990 15987 16008 C2' C E 7 16009 16006 16027 C2' G E 8 16028 16025 16049 C2' G E 9 16050 16047 16071 C2' C E 10 16072 16069 16090 C2' G E 11 16091 16088 16112 C2' C E 12 16113 16110 16131 C2' T E 13 16132 16129 16151 C2' C E 14 16152 16149 16170 C2' G E 15 16171 16168 16192 C2' A E 16 16193 16190 16213 C2' A E 17 16214 16211 16234 C2' C E 18 16235 16232 16253 C2' A E 19 16254 16251 16274 C2' G E 20 16275 16272 16296 C2' G E 21 16297 16294 16318 C2' G E 22 16319 16316 16340 C2' A E 23 16341 16338 16361 C2' C E 24 16362 16359 16380 C2' T E 25 16381 16378 16400 C2' G E 26 16401 16398 16440 C2' C F 2 16441 16438 16459 C2' A F 3 16460 16457 16480 C2' G F 4 16481 16478 16502 C2' T F 5 16503 16500 16522 C2' C F 6 16523 16520 16541 C2' C F 7 16542 16539 16560 C2' C F 8 16561 16558 16579 C2' T F 9 16580 16577 16599 C2' G F 10 16600 16597 16621 C2' T F 11 16622 16619 16641 C2' T F 12 16642 16639 16661 C2' C F 13 16662 16659 16680 C2' G F 14 16681 16678 16702 C2' A F 15 16703 16700 16723 C2' G F 16 16724 16721 16745 C2' C F 17 16746 16743 16764 C2' G F 18 16765 16762 16786 C2' C F 19 16787 16784 16805 C2' C F 20 16806 16803 16824 C2' G F 21 16825 16822 16845 C2' G F 22 16846 16844 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 15987 C3' C E 6 OK 15985 15988 15989 16006 C3' C E 7 OK 16004 16007 16008 16025 C3' G E 8 OK 16023 16026 16027 16047 C3' G E 9 OK 16045 16048 16049 16069 C3' C E 10 OK 16067 16070 16071 16088 C3' G E 11 OK 16086 16089 16090 16110 C3' C E 12 OK 16108 16111 16112 16129 C3' T E 13 OK 16127 16130 16131 16149 C3' C E 14 OK 16147 16150 16151 16168 C3' G E 15 OK 16166 16169 16170 16190 C3' A E 16 OK 16188 16191 16192 16211 C3' A E 17 OK 16209 16212 16213 16232 C3' C E 18 OK 16230 16233 16234 16251 C3' A E 19 OK 16249 16252 16253 16272 C3' G E 20 OK 16270 16273 16274 16294 C3' G E 21 OK 16292 16295 16296 16316 C3' G E 22 OK 16314 16317 16318 16338 C3' A E 23 OK 16336 16339 16340 16359 C3' C E 24 OK 16357 16360 16361 16378 C3' T E 25 OK 16376 16379 16380 16398 C3' G E 26 OK 16396 16399 16400 16438 C3' C F 2 OK 16436 16439 16440 16457 C3' A F 3 OK 16455 16458 16459 16478 C3' G F 4 OK 16476 16479 16480 16500 C3' T F 5 OK 16498 16501 16502 16520 C3' C F 6 OK 16518 16521 16522 16539 C3' C F 7 OK 16537 16540 16541 16558 C3' C F 8 OK 16556 16559 16560 16577 C3' T F 9 OK 16575 16578 16579 16597 C3' G F 10 OK 16595 16598 16599 16619 C3' T F 11 OK 16617 16620 16621 16639 C3' T F 12 OK 16637 16640 16641 16659 C3' C F 13 OK 16657 16660 16661 16678 C3' G F 14 OK 16676 16679 16680 16700 C3' A F 15 OK 16698 16701 16702 16721 C3' G F 16 OK 16719 16722 16723 16743 C3' C F 17 OK 16741 16744 16745 16762 C3' G F 18 OK 16760 16763 16764 16784 C3' C F 19 OK 16782 16785 16786 16803 C3' C F 20 OK 16801 16804 16805 16822 C3' G F 21 OK 16820 16823 16824 16844 C3' G F 22 16842 16845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 15985 C4' C E 6 OK 15987 15984 15986 16004 C4' C E 7 OK 16006 16003 16005 16023 C4' G E 8 OK 16025 16022 16024 16045 C4' G E 9 OK 16047 16044 16046 16067 C4' C E 10 OK 16069 16066 16068 16086 C4' G E 11 OK 16088 16085 16087 16108 C4' C E 12 OK 16110 16107 16109 16127 C4' T E 13 OK 16129 16126 16128 16147 C4' C E 14 OK 16149 16146 16148 16166 C4' G E 15 OK 16168 16165 16167 16188 C4' A E 16 OK 16190 16187 16189 16209 C4' A E 17 OK 16211 16208 16210 16230 C4' C E 18 OK 16232 16229 16231 16249 C4' A E 19 OK 16251 16248 16250 16270 C4' G E 20 OK 16272 16269 16271 16292 C4' G E 21 OK 16294 16291 16293 16314 C4' G E 22 OK 16316 16313 16315 16336 C4' A E 23 OK 16338 16335 16337 16357 C4' C E 24 OK 16359 16356 16358 16376 C4' T E 25 OK 16378 16375 16377 16396 C4' G E 26 OK 16398 16395 16397 16436 C4' C F 2 OK 16438 16435 16437 16455 C4' A F 3 OK 16457 16454 16456 16476 C4' G F 4 OK 16478 16475 16477 16498 C4' T F 5 OK 16500 16497 16499 16518 C4' C F 6 OK 16520 16517 16519 16537 C4' C F 7 OK 16539 16536 16538 16556 C4' C F 8 OK 16558 16555 16557 16575 C4' T F 9 OK 16577 16574 16576 16595 C4' G F 10 OK 16597 16594 16596 16617 C4' T F 11 OK 16619 16616 16618 16637 C4' T F 12 OK 16639 16636 16638 16657 C4' C F 13 OK 16659 16656 16658 16676 C4' G F 14 OK 16678 16675 16677 16698 C4' A F 15 OK 16700 16697 16699 16719 C4' G F 16 OK 16721 16718 16720 16741 C4' C F 17 OK 16743 16740 16742 16760 C4' G F 18 OK 16762 16759 16761 16782 C4' C F 19 OK 16784 16781 16783 16801 C4' C F 20 OK 16803 16800 16802 16820 C4' G F 21 OK 16822 16819 16821 16842 C4' G F 22 OK 16844 16841 16843 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 15984 C5' C E 6 15983 15985 16003 C5' C E 7 16002 16004 16022 C5' G E 8 16021 16023 16044 C5' G E 9 16043 16045 16066 C5' C E 10 16065 16067 16085 C5' G E 11 16084 16086 16107 C5' C E 12 16106 16108 16126 C5' T E 13 16125 16127 16146 C5' C E 14 16145 16147 16165 C5' G E 15 16164 16166 16187 C5' A E 16 16186 16188 16208 C5' A E 17 16207 16209 16229 C5' C E 18 16228 16230 16248 C5' A E 19 16247 16249 16269 C5' G E 20 16268 16270 16291 C5' G E 21 16290 16292 16313 C5' G E 22 16312 16314 16335 C5' A E 23 16334 16336 16356 C5' C E 24 16355 16357 16375 C5' T E 25 16374 16376 16395 C5' G E 26 16394 16396 16435 C5' C F 2 16434 16436 16454 C5' A F 3 16453 16455 16475 C5' G F 4 16474 16476 16497 C5' T F 5 16496 16498 16517 C5' C F 6 16516 16518 16536 C5' C F 7 16535 16537 16555 C5' C F 8 16554 16556 16574 C5' T F 9 16573 16575 16594 C5' G F 10 16593 16595 16616 C5' T F 11 16615 16617 16636 C5' T F 12 16635 16637 16656 C5' C F 13 16655 16657 16675 C5' G F 14 16674 16676 16697 C5' A F 15 16696 16698 16718 C5' G F 16 16717 16719 16740 C5' C F 17 16739 16741 16759 C5' G F 18 16758 16760 16781 C5' C F 19 16780 16782 16800 C5' C F 20 16799 16801 16819 C5' G F 21 16818 16820 16841 C5' G F 22 16840 16842 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 15999 P C E 7 OK OK 15988 16000 16001 16002 16018 P G E 8 OK OK 16007 16019 16020 16021 16040 P G E 9 OK OK 16026 16041 16042 16043 16062 P C E 10 OK OK 16048 16063 16064 16065 16081 P G E 11 OK OK 16070 16082 16083 16084 16103 P C E 12 OK OK 16089 16104 16105 16106 16122 P T E 13 OK OK 16111 16123 16124 16125 16142 P C E 14 OK OK 16130 16143 16144 16145 16161 P G E 15 OK OK 16150 16162 16163 16164 16183 P A E 16 OK OK 16169 16184 16185 16186 16204 P A E 17 OK OK 16191 16205 16206 16207 16225 P C E 18 OK OK 16212 16226 16227 16228 16244 P A E 19 OK OK 16233 16245 16246 16247 16265 P G E 20 OK OK 16252 16266 16267 16268 16287 P G E 21 OK OK 16273 16288 16289 16290 16309 P G E 22 OK OK 16295 16310 16311 16312 16331 P A E 23 OK OK 16317 16332 16333 16334 16352 P C E 24 OK OK 16339 16353 16354 16355 16371 P T E 25 OK OK 16360 16372 16373 16374 16391 P G E 26 OK OK 16379 16392 16393 16394 16450 P A F 3 OK OK 16439 16451 16452 16453 16471 P G F 4 OK OK 16458 16472 16473 16474 16493 P T F 5 OK OK 16479 16494 16495 16496 16513 P C F 6 OK OK 16501 16514 16515 16516 16532 P C F 7 OK OK 16521 16533 16534 16535 16551 P C F 8 OK OK 16540 16552 16553 16554 16570 P T F 9 OK OK 16559 16571 16572 16573 16590 P G F 10 OK OK 16578 16591 16592 16593 16612 P T F 11 OK OK 16598 16613 16614 16615 16632 P T F 12 OK OK 16620 16633 16634 16635 16652 P C F 13 OK OK 16640 16653 16654 16655 16671 P G F 14 OK OK 16660 16672 16673 16674 16693 P A F 15 OK OK 16679 16694 16695 16696 16714 P G F 16 OK OK 16701 16715 16716 16717 16736 P C F 17 OK OK 16722 16737 16738 16739 16755 P G F 18 OK OK 16744 16756 16757 16758 16777 P C F 19 OK OK 16763 16778 16779 16780 16796 P C F 20 OK OK 16785 16797 16798 16799 16815 P G F 21 OK OK 16804 16816 16817 16818 16837 P G F 22 OK OK 16823 16838 16839 16840 ---------------------------------------------------------------------------------