ID code: '4K4S' 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' --------------------------------------------------------------------------------- 3714 C1' U B 595 beta 3709 3715 3712 3734 C1' C B 596 beta 3729 3735 3732 3754 C1' C B 597 beta 3749 3755 3752 3774 C1' A B 598 beta 3769 3775 3772 3796 C1' G B 599 beta 3791 3797 3794 3819 C1' G B 600 beta 3814 3820 3817 3842 C1' U B 601 beta 3837 3843 3840 3862 C1' C B 602 beta 3857 3863 3860 3882 C1' U B 603 beta 3877 3883 3880 3902 C1' C B 604 beta 3897 3903 3900 3922 C1' U B 605 beta 3917 3923 3920 3942 C1' C B 606 beta 3937 3943 3940 3962 C1' G B 607 beta 3957 3963 3960 3985 C1' C B 608 beta 3980 3986 3983 4005 C1' G B 609 beta 4000 4006 4003 4028 C1' A B 610 beta 4023 4029 4026 4050 C1' A B 611 beta 4045 4051 4048 4070 C1' U C 689 beta 4065 4071 4068 4090 C1' G C 690 beta 4085 4091 4088 4113 C1' U C 691 beta 4108 4114 4111 4133 C1' U C 692 beta 4128 4134 4131 4153 C1' C C 693 beta 4148 4154 4151 4173 C1' G C 694 beta 4168 4174 4171 4196 C1' C C 695 beta 4191 4197 4194 4216 C1' G C 696 beta 4211 4217 4214 4239 C1' A C 697 beta 4234 4240 4237 4261 C1' G C 698 beta 4256 4262 4259 4284 C1' A C 699 beta 4279 4285 4282 4306 C1' G C 700 beta 4301 4307 4304 4329 C1' A C 701 beta 4324 4330 4327 4352 C1' G D 1 beta 4347 4353 4350 4375 C1' G D 2 beta 4370 4376 4373 4398 C1' A D 3 beta 4393 4399 4396 4420 C1' G D 4 beta 4415 4421 4418 8146 C1' U F 595 beta 8141 8147 8144 8166 C1' C F 596 beta 8161 8167 8164 8186 C1' C F 597 beta 8181 8187 8184 8206 C1' A F 598 beta 8201 8207 8204 8228 C1' G F 599 beta 8223 8229 8226 8251 C1' G F 600 beta 8246 8252 8249 8274 C1' U F 601 beta 8269 8275 8272 8294 C1' C F 602 beta 8289 8295 8292 8314 C1' U F 603 beta 8309 8315 8312 8334 C1' C F 604 beta 8329 8335 8332 8354 C1' U F 605 beta 8349 8355 8352 8374 C1' C F 606 beta 8369 8375 8372 8394 C1' G F 607 beta 8389 8395 8392 8417 C1' C F 608 beta 8412 8418 8415 8437 C1' G F 609 beta 8432 8438 8435 8460 C1' A F 610 beta 8455 8461 8458 8482 C1' A F 611 beta 8477 8483 8480 8502 C1' U G 689 beta 8497 8503 8500 8522 C1' G G 690 beta 8517 8523 8520 8545 C1' U G 691 beta 8540 8546 8543 8565 C1' U G 692 beta 8560 8566 8563 8585 C1' C G 693 beta 8580 8586 8583 8605 C1' G G 694 beta 8600 8606 8603 8628 C1' C G 695 beta 8623 8629 8626 8648 C1' G G 696 beta 8643 8649 8646 8671 C1' A G 697 beta 8666 8672 8669 8693 C1' G G 698 beta 8688 8694 8691 8716 C1' A G 699 beta 8711 8717 8714 8738 C1' G G 700 beta 8733 8739 8736 8761 C1' A G 701 beta 8756 8762 8759 8784 C1' G H 1 beta 8779 8785 8782 8807 C1' G H 2 beta 8802 8808 8805 8830 C1' A H 3 beta 8825 8831 8828 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3712 C2' U B 595 OK 3714 3710 3713 3732 C2' C B 596 OK 3734 3730 3733 3752 C2' C B 597 OK 3754 3750 3753 3772 C2' A B 598 OK 3774 3770 3773 3794 C2' G B 599 OK 3796 3792 3795 3817 C2' G B 600 OK 3819 3815 3818 3840 C2' U B 601 OK 3842 3838 3841 3860 C2' C B 602 OK 3862 3858 3861 3880 C2' U B 603 OK 3882 3878 3881 3900 C2' C B 604 OK 3902 3898 3901 3920 C2' U B 605 OK 3922 3918 3921 3940 C2' C B 606 OK 3942 3938 3941 3960 C2' G B 607 OK 3962 3958 3961 3983 C2' C B 608 OK 3985 3981 3984 4003 C2' G B 609 OK 4005 4001 4004 4026 C2' A B 610 OK 4028 4024 4027 4048 C2' A B 611 OK 4050 4046 4049 4068 C2' U C 689 OK 4070 4066 4069 4088 C2' G C 690 OK 4090 4086 4089 4111 C2' U C 691 OK 4113 4109 4112 4131 C2' U C 692 OK 4133 4129 4132 4151 C2' C C 693 OK 4153 4149 4152 4171 C2' G C 694 OK 4173 4169 4172 4194 C2' C C 695 OK 4196 4192 4195 4214 C2' G C 696 OK 4216 4212 4215 4237 C2' A C 697 OK 4239 4235 4238 4259 C2' G C 698 OK 4261 4257 4260 4282 C2' A C 699 OK 4284 4280 4283 4304 C2' G C 700 OK 4306 4302 4305 4327 C2' A C 701 OK 4329 4325 4328 4350 C2' G D 1 OK 4352 4348 4351 4373 C2' G D 2 OK 4375 4371 4374 4396 C2' A D 3 OK 4398 4394 4397 4418 C2' G D 4 OK 4420 4416 4419 8144 C2' U F 595 OK 8146 8142 8145 8164 C2' C F 596 OK 8166 8162 8165 8184 C2' C F 597 OK 8186 8182 8185 8204 C2' A F 598 OK 8206 8202 8205 8226 C2' G F 599 OK 8228 8224 8227 8249 C2' G F 600 OK 8251 8247 8250 8272 C2' U F 601 OK 8274 8270 8273 8292 C2' C F 602 OK 8294 8290 8293 8312 C2' U F 603 OK 8314 8310 8313 8332 C2' C F 604 OK 8334 8330 8333 8352 C2' U F 605 OK 8354 8350 8353 8372 C2' C F 606 OK 8374 8370 8373 8392 C2' G F 607 OK 8394 8390 8393 8415 C2' C F 608 OK 8417 8413 8416 8435 C2' G F 609 OK 8437 8433 8436 8458 C2' A F 610 OK 8460 8456 8459 8480 C2' A F 611 OK 8482 8478 8481 8500 C2' U G 689 OK 8502 8498 8501 8520 C2' G G 690 OK 8522 8518 8521 8543 C2' U G 691 OK 8545 8541 8544 8563 C2' U G 692 OK 8565 8561 8564 8583 C2' C G 693 OK 8585 8581 8584 8603 C2' G G 694 OK 8605 8601 8604 8626 C2' C G 695 OK 8628 8624 8627 8646 C2' G G 696 OK 8648 8644 8647 8669 C2' A G 697 OK 8671 8667 8670 8691 C2' G G 698 OK 8693 8689 8692 8714 C2' A G 699 OK 8716 8712 8715 8736 C2' G G 700 OK 8738 8734 8737 8759 C2' A G 701 OK 8761 8757 8760 8782 C2' G H 1 OK 8784 8780 8783 8805 C2' G H 2 OK 8807 8803 8806 8828 C2' A H 3 OK 8830 8826 8829 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3710 C3' U B 595 OK 3708 3711 3712 3730 C3' C B 596 OK 3728 3731 3732 3750 C3' C B 597 OK 3748 3751 3752 3770 C3' A B 598 OK 3768 3771 3772 3792 C3' G B 599 OK 3790 3793 3794 3815 C3' G B 600 OK 3813 3816 3817 3838 C3' U B 601 OK 3836 3839 3840 3858 C3' C B 602 OK 3856 3859 3860 3878 C3' U B 603 OK 3876 3879 3880 3898 C3' C B 604 OK 3896 3899 3900 3918 C3' U B 605 OK 3916 3919 3920 3938 C3' C B 606 OK 3936 3939 3940 3958 C3' G B 607 OK 3956 3959 3960 3981 C3' C B 608 OK 3979 3982 3983 4001 C3' G B 609 OK 3999 4002 4003 4024 C3' A B 610 OK 4022 4025 4026 4046 C3' A B 611 OK 4044 4047 4048 4066 C3' U C 689 OK 4064 4067 4068 4086 C3' G C 690 OK 4084 4087 4088 4109 C3' U C 691 OK 4107 4110 4111 4129 C3' U C 692 OK 4127 4130 4131 4149 C3' C C 693 OK 4147 4150 4151 4169 C3' G C 694 OK 4167 4170 4171 4192 C3' C C 695 OK 4190 4193 4194 4212 C3' G C 696 OK 4210 4213 4214 4235 C3' A C 697 OK 4233 4236 4237 4257 C3' G C 698 OK 4255 4258 4259 4280 C3' A C 699 OK 4278 4281 4282 4302 C3' G C 700 OK 4300 4303 4304 4325 C3' A C 701 OK 4323 4326 4327 4348 C3' G D 1 OK 4346 4349 4350 4371 C3' G D 2 OK 4369 4372 4373 4394 C3' A D 3 OK 4392 4395 4396 4416 C3' G D 4 OK 4414 4417 4418 8142 C3' U F 595 OK 8140 8143 8144 8162 C3' C F 596 OK 8160 8163 8164 8182 C3' C F 597 OK 8180 8183 8184 8202 C3' A F 598 OK 8200 8203 8204 8224 C3' G F 599 OK 8222 8225 8226 8247 C3' G F 600 OK 8245 8248 8249 8270 C3' U F 601 OK 8268 8271 8272 8290 C3' C F 602 OK 8288 8291 8292 8310 C3' U F 603 OK 8308 8311 8312 8330 C3' C F 604 OK 8328 8331 8332 8350 C3' U F 605 OK 8348 8351 8352 8370 C3' C F 606 OK 8368 8371 8372 8390 C3' G F 607 OK 8388 8391 8392 8413 C3' C F 608 OK 8411 8414 8415 8433 C3' G F 609 OK 8431 8434 8435 8456 C3' A F 610 OK 8454 8457 8458 8478 C3' A F 611 OK 8476 8479 8480 8498 C3' U G 689 OK 8496 8499 8500 8518 C3' G G 690 OK 8516 8519 8520 8541 C3' U G 691 OK 8539 8542 8543 8561 C3' U G 692 OK 8559 8562 8563 8581 C3' C G 693 OK 8579 8582 8583 8601 C3' G G 694 OK 8599 8602 8603 8624 C3' C G 695 OK 8622 8625 8626 8644 C3' G G 696 OK 8642 8645 8646 8667 C3' A G 697 OK 8665 8668 8669 8689 C3' G G 698 OK 8687 8690 8691 8712 C3' A G 699 OK 8710 8713 8714 8734 C3' G G 700 OK 8732 8735 8736 8757 C3' A G 701 OK 8755 8758 8759 8780 C3' G H 1 OK 8778 8781 8782 8803 C3' G H 2 OK 8801 8804 8805 8826 C3' A H 3 OK 8824 8827 8828 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3708 C4' U B 595 OK 3710 3707 3709 3728 C4' C B 596 OK 3730 3727 3729 3748 C4' C B 597 OK 3750 3747 3749 3768 C4' A B 598 OK 3770 3767 3769 3790 C4' G B 599 OK 3792 3789 3791 3813 C4' G B 600 OK 3815 3812 3814 3836 C4' U B 601 OK 3838 3835 3837 3856 C4' C B 602 OK 3858 3855 3857 3876 C4' U B 603 OK 3878 3875 3877 3896 C4' C B 604 OK 3898 3895 3897 3916 C4' U B 605 OK 3918 3915 3917 3936 C4' C B 606 OK 3938 3935 3937 3956 C4' G B 607 OK 3958 3955 3957 3979 C4' C B 608 OK 3981 3978 3980 3999 C4' G B 609 OK 4001 3998 4000 4022 C4' A B 610 OK 4024 4021 4023 4044 C4' A B 611 OK 4046 4043 4045 4064 C4' U C 689 OK 4066 4063 4065 4084 C4' G C 690 OK 4086 4083 4085 4107 C4' U C 691 OK 4109 4106 4108 4127 C4' U C 692 OK 4129 4126 4128 4147 C4' C C 693 OK 4149 4146 4148 4167 C4' G C 694 OK 4169 4166 4168 4190 C4' C C 695 OK 4192 4189 4191 4210 C4' G C 696 OK 4212 4209 4211 4233 C4' A C 697 OK 4235 4232 4234 4255 C4' G C 698 OK 4257 4254 4256 4278 C4' A C 699 OK 4280 4277 4279 4300 C4' G C 700 OK 4302 4299 4301 4323 C4' A C 701 OK 4325 4322 4324 4346 C4' G D 1 OK 4348 4345 4347 4369 C4' G D 2 OK 4371 4368 4370 4392 C4' A D 3 OK 4394 4391 4393 4414 C4' G D 4 OK 4416 4413 4415 8140 C4' U F 595 OK 8142 8139 8141 8160 C4' C F 596 OK 8162 8159 8161 8180 C4' C F 597 OK 8182 8179 8181 8200 C4' A F 598 OK 8202 8199 8201 8222 C4' G F 599 OK 8224 8221 8223 8245 C4' G F 600 OK 8247 8244 8246 8268 C4' U F 601 OK 8270 8267 8269 8288 C4' C F 602 OK 8290 8287 8289 8308 C4' U F 603 OK 8310 8307 8309 8328 C4' C F 604 OK 8330 8327 8329 8348 C4' U F 605 OK 8350 8347 8349 8368 C4' C F 606 OK 8370 8367 8369 8388 C4' G F 607 OK 8390 8387 8389 8411 C4' C F 608 OK 8413 8410 8412 8431 C4' G F 609 OK 8433 8430 8432 8454 C4' A F 610 OK 8456 8453 8455 8476 C4' A F 611 OK 8478 8475 8477 8496 C4' U G 689 OK 8498 8495 8497 8516 C4' G G 690 OK 8518 8515 8517 8539 C4' U G 691 OK 8541 8538 8540 8559 C4' U G 692 OK 8561 8558 8560 8579 C4' C G 693 OK 8581 8578 8580 8599 C4' G G 694 OK 8601 8598 8600 8622 C4' C G 695 OK 8624 8621 8623 8642 C4' G G 696 OK 8644 8641 8643 8665 C4' A G 697 OK 8667 8664 8666 8687 C4' G G 698 OK 8689 8686 8688 8710 C4' A G 699 OK 8712 8709 8711 8732 C4' G G 700 OK 8734 8731 8733 8755 C4' A G 701 OK 8757 8754 8756 8778 C4' G H 1 OK 8780 8777 8779 8801 C4' G H 2 OK 8803 8800 8802 8824 C4' A H 3 OK 8826 8823 8825 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3707 C5' U B 595 3706 3708 3727 C5' C B 596 3726 3728 3747 C5' C B 597 3746 3748 3767 C5' A B 598 3766 3768 3789 C5' G B 599 3788 3790 3812 C5' G B 600 3811 3813 3835 C5' U B 601 3834 3836 3855 C5' C B 602 3854 3856 3875 C5' U B 603 3874 3876 3895 C5' C B 604 3894 3896 3915 C5' U B 605 3914 3916 3935 C5' C B 606 3934 3936 3955 C5' G B 607 3954 3956 3978 C5' C B 608 3977 3979 3998 C5' G B 609 3997 3999 4021 C5' A B 610 4020 4022 4043 C5' A B 611 4042 4044 4063 C5' U C 689 4062 4064 4083 C5' G C 690 4082 4084 4106 C5' U C 691 4105 4107 4126 C5' U C 692 4125 4127 4146 C5' C C 693 4145 4147 4166 C5' G C 694 4165 4167 4189 C5' C C 695 4188 4190 4209 C5' G C 696 4208 4210 4232 C5' A C 697 4231 4233 4254 C5' G C 698 4253 4255 4277 C5' A C 699 4276 4278 4299 C5' G C 700 4298 4300 4322 C5' A C 701 4321 4323 4345 C5' G D 1 4344 4346 4368 C5' G D 2 4367 4369 4391 C5' A D 3 4390 4392 4413 C5' G D 4 4412 4414 8139 C5' U F 595 8138 8140 8159 C5' C F 596 8158 8160 8179 C5' C F 597 8178 8180 8199 C5' A F 598 8198 8200 8221 C5' G F 599 8220 8222 8244 C5' G F 600 8243 8245 8267 C5' U F 601 8266 8268 8287 C5' C F 602 8286 8288 8307 C5' U F 603 8306 8308 8327 C5' C F 604 8326 8328 8347 C5' U F 605 8346 8348 8367 C5' C F 606 8366 8368 8387 C5' G F 607 8386 8388 8410 C5' C F 608 8409 8411 8430 C5' G F 609 8429 8431 8453 C5' A F 610 8452 8454 8475 C5' A F 611 8474 8476 8495 C5' U G 689 8494 8496 8515 C5' G G 690 8514 8516 8538 C5' U G 691 8537 8539 8558 C5' U G 692 8557 8559 8578 C5' C G 693 8577 8579 8598 C5' G G 694 8597 8599 8621 C5' C G 695 8620 8622 8641 C5' G G 696 8640 8642 8664 C5' A G 697 8663 8665 8686 C5' G G 698 8685 8687 8709 C5' A G 699 8708 8710 8731 C5' G G 700 8730 8732 8754 C5' A G 701 8753 8755 8777 C5' G H 1 8776 8778 8800 C5' G H 2 8799 8801 8823 C5' A H 3 8822 8824 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3703 P U B 595 distorted distorted 3704 3705 3706 3723 P C B 596 distorted distorted 3711 3724 3725 3726 3743 P C B 597 distorted distorted 3731 3744 3745 3746 3763 P A B 598 distorted distorted 3751 3764 3765 3766 3785 P G B 599 distorted distorted 3771 3786 3787 3788 3808 P G B 600 distorted distorted 3793 3809 3810 3811 3831 P U B 601 distorted distorted 3816 3832 3833 3834 3851 P C B 602 distorted distorted 3839 3852 3853 3854 3871 P U B 603 distorted distorted 3859 3872 3873 3874 3891 P C B 604 distorted distorted 3879 3892 3893 3894 3911 P U B 605 distorted distorted 3899 3912 3913 3914 3931 P C B 606 distorted distorted 3919 3932 3933 3934 3951 P G B 607 distorted distorted 3939 3952 3953 3954 3974 P C B 608 distorted distorted 3959 3975 3976 3977 3994 P G B 609 distorted distorted 3982 3995 3996 3997 4017 P A B 610 distorted distorted 4002 4018 4019 4020 4039 P A B 611 distorted distorted 4025 4040 4041 4042 4079 P G C 690 distorted distorted 4067 4080 4081 4082 4102 P U C 691 distorted distorted 4087 4103 4104 4105 4122 P U C 692 distorted distorted 4110 4123 4124 4125 4142 P C C 693 distorted distorted 4130 4143 4144 4145 4162 P G C 694 distorted distorted 4150 4163 4164 4165 4185 P C C 695 distorted distorted 4170 4186 4187 4188 4205 P G C 696 distorted distorted 4193 4206 4207 4208 4228 P A C 697 distorted distorted 4213 4229 4230 4231 4250 P G C 698 distorted distorted 4236 4251 4252 4253 4273 P A C 699 distorted distorted 4258 4274 4275 4276 4295 P G C 700 distorted distorted 4281 4296 4297 4298 4318 P A C 701 distorted distorted 4303 4319 4320 4321 4341 P G D 1 distorted distorted 4342 4343 4344 4364 P G D 2 distorted distorted 4349 4365 4366 4367 4387 P A D 3 distorted distorted 4372 4388 4389 4390 4409 P G D 4 distorted distorted 4395 4410 4411 4412 8135 P U F 595 distorted distorted 8136 8137 8138 8155 P C F 596 distorted distorted 8143 8156 8157 8158 8175 P C F 597 distorted distorted 8163 8176 8177 8178 8195 P A F 598 distorted distorted 8183 8196 8197 8198 8217 P G F 599 distorted distorted 8203 8218 8219 8220 8240 P G F 600 distorted distorted 8225 8241 8242 8243 8263 P U F 601 distorted distorted 8248 8264 8265 8266 8283 P C F 602 distorted distorted 8271 8284 8285 8286 8303 P U F 603 distorted distorted 8291 8304 8305 8306 8323 P C F 604 distorted distorted 8311 8324 8325 8326 8343 P U F 605 distorted distorted 8331 8344 8345 8346 8363 P C F 606 distorted distorted 8351 8364 8365 8366 8383 P G F 607 distorted distorted 8371 8384 8385 8386 8406 P C F 608 distorted distorted 8391 8407 8408 8409 8426 P G F 609 distorted distorted 8414 8427 8428 8429 8449 P A F 610 distorted distorted 8434 8450 8451 8452 8471 P A F 611 distorted distorted 8457 8472 8473 8474 8511 P G G 690 distorted distorted 8499 8512 8513 8514 8534 P U G 691 distorted distorted 8519 8535 8536 8537 8554 P U G 692 distorted distorted 8542 8555 8556 8557 8574 P C G 693 distorted distorted 8562 8575 8576 8577 8594 P G G 694 distorted distorted 8582 8595 8596 8597 8617 P C G 695 distorted distorted 8602 8618 8619 8620 8637 P G G 696 distorted distorted 8625 8638 8639 8640 8660 P A G 697 distorted distorted 8645 8661 8662 8663 8682 P G G 698 distorted distorted 8668 8683 8684 8685 8705 P A G 699 distorted distorted 8690 8706 8707 8708 8727 P G G 700 distorted distorted 8713 8728 8729 8730 8750 P A G 701 distorted distorted 8735 8751 8752 8753 8773 P G H 1 distorted distorted 8774 8775 8776 8796 P G H 2 distorted distorted 8781 8797 8798 8799 8819 P A H 3 distorted distorted 8804 8820 8821 8822 ---------------------------------------------------------------------------------