Created and last modified by Jung C. Lee on 21 February 2001.

Item Description
E. coli
E. coli numbering. Note that Phe-tRNA follows the yeast Phe-tRNA numbering.
lptl
lonepair triloop. 1186:1190 (H. maris) came from the crystal structure of E. coli L11-binding domain, and 125:129 (H. maris) approximately corresponds to the E. coli numbering of 131:148.
lp
lonepair
lpC
lonepair conformation:
  • WC/rWC: non-reversed/reversed Watson-Crick
  • H/rH: non-reversed/reversed Hoogsteen
  • Wb/rWb: non-reversed/reversed Wobble basepair
  • S: sheared G:A or A:A conformation
  • NC: noncanonical G:C basepair resembling sheared G:A conformation
  • UU rWb: U:U bp resembling the G:U Wobble basepair
  • TA rH: T is basically methylated U at its C5'-position
U/bS
U-turns/base stacking in lptl's when going from one nucleotide to another.
  • u: U-turns between the two nt's
  • s: direct base stacking onto the next base
  • ms: mediated base stacking onto the next base by the third intercalating nt through tertiary interactions
dCC
distance between two C1's of the lonepair
lpso
lonepair stacking onto its immediate 5'- or 3'-helix
dlc
directionality of local chains involved in the formation of lonepairs
  • a: antiparallel
  • p: parallel
sp/bf
sugar puckering/base facing
  • 3: C3'-endo sugar ring puckering
  • 2: C2'-endo sugar ring puckering
  • m: facing toward the minor groove
  • M: facing toward the major groove
  • b: M-m boundary and under the triloop backbone
  • u: M-m boundary but up the triloop backbone
trl
triloop containing three nt's
tert
tertiary interactions (short- or long-range)
lpp
lonepair triloop-protein interactions
  • m: minor groove
  • M: major groove
lptlT
loop type which a lonepair triloop belongs to
  • H: hairpin loop
  • I: internal loop
  • M: multi-stem loop
lptlC
lonepair triloop class
  • I: LPTLs with no intervening bp between lp and its immediate 5'-helix
  • II: LPTLs with intervening bp between lp and its immediate 5'-helix
  • III: LPTLs just occurring internal regions of helices
  • A: LPTLs involving base stacking of Z and B, mediated by the third intercalating base through tertiary interactions
  • B: LPTLs not involving base stacking of Z and B. Instead, the third base from tertiary interactions interact directly with one or more triloop bases without intercalating.
  • R1: LPTLs involving LPTL-RNA interactions through one or both of the first and second triloop bases
  • R2: LPTLs involving LPTL-RNA interactions through the second triloop base
  • R3: LPTLs involving LPTL-RNA interactions through the third triloop base
  • R4: LPTLs involving LPTL-RNA interactions through the second and third triloop bases
  • R5: LPTLs involving no LPTL-RNA interactions