Nomenclature

Atom names are given in the XPLOR nomenclature.

[ ]s represent RNA specific names, ()s represent DNA specific names

[r](d)ADE                      	    [r](d)GUA

P O3' O1P O2P				P O3' O1P O2P
C5' H5' H5''				C5' H5' H5''
C4' H4'					C4' H4'
C3' H3'					C3' H3'
C2' H2' [O2' HO2'] (H2'')		C2' H2' [O2' HO2'] (H2'')
C1' H1'					C1' H1'
N9					N9
C8 H8					C8 H8
N7					N7
C5					C5
C4					C4
N3					N3
C2 H2					C2 N2 H21 H22
N1					N1 H1
C6 N6 H61 H62				C6 O6


[rURI](dTHY)                        [r](d)CYT

P O3' O1P O2P				P O3' O1P O2P
C5' H5' H5''				C5' H5' H5''
C4' H4'					C4' H4'
C3' H3'					C3' H3'
C2' H2' [O2' HO2'] (H2'')		C2' H2' [O2' HO2'] (H2'')
C1' H1'					C1' H1'
N1					N1
C2 O2					C2 O2
N3 H3					N3
C4 O4					C4 N4 H41 H42
C5 [H5] (C5m H51 H52 H53) 		C5 H5
C6 H6					C6 H6

Structural parameters

Torsion angles: (Taken from 'cdih_measure define')

    Name = Definition
   alpha = O3'(n-1)-P-O5'-C5'            nu0 = C4'-O4'-C1'-C2'
    beta = P-O5'-C5'-C4'                 nu1 = O4'-C1'-C2'-C3'
   gamma = O5'-C5'-C4'-C3'               nu2 = C1'-C2'-C3'-C4'
 epsilon = C4'-C3'-O3'-P(n+1)            nu3 = C2'-C3'-C4'-O4'
    zeta = C3'-O3'-P(n+1)-O5'(n+1)       nu4 = C3'-C4'-O4'-C1'
chi(pur) = O4'-C1'-N9-C4
chi(pyr) = O4'-C1'-N1-C2

All angles are given as torsion angles from the heavy atoms, using the XPLOR nomenclature. Measurements of angles were done by making a standard structure from Insight95 and using cdih_measure to measure the angles.

from 'cdih_measure define'

Standard Values:
residue    alpha    beta   gamma     eps    zeta     chi     nu0     nu1     nu2     nu3     nu4
---  ---   ------ ------- ------- ------- ------- ------- ------- ------- ------- ------- -------
A-RNA      -62    -180      47    -152     -74     -166      3     -25      37     -36      21
B-DNA      -47    -146      36     155     -95     -98      -4      25     -35	    33	   -18
A-DNA      -84	  -152	    45	   179	   -49	   -154	     4	   -26      37     -36      20

Torsion angles from other structures:(Saenger,'Principles of Nucleic Acid Structure', Springer-Verlag 1984, pp230-232)

residue    alpha    beta   gamma     eps    zeta     chi     nu0     nu1     nu2     nu3     nu4
---  ---   ------ ------- ------- ------- ------- ------- ------- ------- ------- ------- -------
poly(dA.dT) -52	   -136	    39	    145	    -87	    -96

H-bonding distances: (Taken from Insight95)

(notice that Insight95 calls GUA H22 what XPLOR calls GUA H21 and Insight95 calls CYT H42 what XPLOR calls CYT H41!!)

A-form RNA:
A-U Watson Crick basepair:
N1-H3	1.93
N1-N3	2.95
N6-O4	2.83
H61-O4	1.82

G-C Watson Crick basepair:
H1-N3	1.89
N1-N3	2.91
H21-O2	2.08
N2-O2	3.08
O6-H41	1.71
O6-N4	2.72

B-form DNA:
A-T Watson Crick basepair:
N1-H3	1.92
N1-N3	2.95
N6-O4	2.81
H61-O4	1.78

G-C Watson Crick basepair:
H1-N3	1.89
N1-N3	2.91
H21-O2	1.98
N2-O2	3.01
O6-H41	1.67
O6-N4	2.70


A-form DNA:

marino@carb.nist.gov Last updated 1 December 1997