Last modified on 10 August 2011.

NOTE: This section is under development.

About the Lee-Gutell (LG) System:

The Lee-Gutell (LG) system introduces the 10 basepair groups, rather than the all possible 16 basepair types used in the Leontis-Westhof (LW) system, and the six basic topological transformations of basepair conformations in defining a wide variety of basepair conformations involved in all three types of RNA-RNA interactions, intramolecular and intermolecular:

Ten Basepair Groups Six Topological Transformaitons Three Types of RNA-RNA Ineractions
C:G Wobbling (e.g., C:G Wb) Base-Base (BB) Interactions
U:A Slipping (e.g., U:A sWC) Base-Backbone (BK) Interactions
U:G Shearing (e.g., G:A S) Backbone-Backbone (KK) Interactions
G:A Reversing (e.g., U:A rWC)  
C:A Flipping (e.g., G:A fS)  
U:C Paralleling (e.g., U:C pS)  
A:A    
C:C    
G:G    
U:U    

In order to compare the basepair conformations defined by the LG system with those defined by the LW system fairly and objectively, all the basepair conformations originally proposed by the LW system were re-defined based on the 10 basepair groups first introduced in the LG system (see below).

Legend: "Identification of Basepairs and Their Conformations in Crystal Structures Containing RNA"

Column Heading Description
PDB PDB ID of crystal structure
#nt Number of the resolved nucleotides in RNA in crystal structure
#bp(LG) Number of basepairs identifed by the Lee-Gutell (LG) system
#bp(LW) Number of basepairs claimed to be identifed by the Leontis-Westhof (LW) system
Res Resolution of crystal structure
Release Release date of crystal structure
RNA (Main) type of RNA in crystal structure, if more than on RNAs are included
Source Source of RNA sequence in PDB. This information was manually corrected with publication.
Structure Description Brief structural description about crystal structure. This information was manually corrected with publication.
Reference Publication describing crystal structures and their PubMed links

Legend: "Identified Basepairs and Their Conformations and Conformational Parameters"

Column Heading Description
RNA Main type of RNA in crystal structure, if more than one RNAs are included
PDB PDB ID of crystal structure
Position Positions of nucleotides involved in BB, BK, or KK interactions in the format: position1!chain:position2:chain. If a basepair happens to be assigned two or more basepair conformations, it is declared as an ambiguous basepair and an asterisk is accompanied by its position.
bp Basepair types of BB, BK, or KK interactions, represented by one of the all possible 16 basepair types.
bpC; LG [LW][Sanger] Basepair conformations in the LG system, the LW system, and the Sanger notation, respectively. Note that the basepair conformations for the LW system presented here is slightly different from those originally proposed since they are re-defined based on the 10 basepair groups originally introduced in the LG system!
  • Any subtype of a basepair conformation Z is discriminated by adding:
    Discriminator Description
    Z_1 The first subtype of Z
    Z_2 The second subtype of Z
    Z_3 The third subtype of Z
    Z_4 The fourth subtype of Z
    Z_Mo The subtype of Z, with the major groove opened
    Z_mo The subtype of Z, with the minor groove opened
    Z_v The subtype of Z, with one base plane nearly vertical to the other base plane
  • A basepair conformation Z for a BK or KK interaction in a basepair group X:Y is accompanied by a parenthesis enclosing the descriptor for their primary hydrogen bond, Z(ij:I-J), where the lowercase letters i and j are for the sources of the primary hydrogen-bond formed between nucleotides X and Y, respectively, and the uppercase letters I and J separated by a dash are for the sites of the hydrogen-bond on nucleotides X and Y, respectively. Each letter in the two-letter hydrogen-bonding source stands for:
    Code Description
    b Base
    s Sugar ring
    p Phosphate group
  • Basepair conformations missing in the LW system or the Sanger notation are indicated by:
    Indicator Description
    [---] Conformations not described by the LW system
    [-] Conformations not described by the Sanger notation
dCC C1'-C1' distance for BB, BK, and KK interactions
<X Angle formed between the glycosidic bond of nucleotide X and the C1' of nucleotide Y
<Y Angle formed between the glycosidic bond of nucleotide Y and the C1' of nucleotide X
|<X - <Y| Difference between two angles <X and <Y
Torsion Torsion angle between the two glycosidic bonds of two interacting nucleotides
Z-diff Vertical distance between the two base plances of two interacting nucleotides
Buckle Buckle angle formed between the two base planes of two interacting nucleotides