Data Item _ndb_struct_na_base_pair.hbond_type_leontis_westhof

General

Item name
_ndb_struct_na_base_pair.hbond_type_leontis_westhof
Category name
ndb_struct_na_base_pair
Attribute name
hbond_type_leontis_westhof
Required in PDB entries
no
Used in currrent PDB entries
No

Item Description

Base pair classification of Leontis and Westhof. The Leontis-Westhof classification system annotates basepairs according to the interacting edge used by each base (Watson-Crick, Hoogsteen, or Sugar), and glycosidic bond orientation (cis, trans). For six of twelve classes, the correct Leontis-Westhof notation depends upon the order (i,j) of the identified nucleotides. Leontis NB and Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512. https://doi.org/10.1017/s1355838201002515 Replacement for category item _ndb_struct_na_base_pair.hbond_type_12. The older item encodes the 12 classes by a numerical index, without identifying the interacting edges used by each base in nucleotides i,j.

Data Type

Data type code
line
Data type detail
char item types / multi-word items ...
Primitive data type code
char
Regular expression
[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*

Controlled Vocabulary

Allowed Value Details
cHH LW#7 cis, Hoogsteen i/Hoogsteen j
cHS LW#9 cis, Hoogsteen i/Sugar j
cHW LW#3r cis, Hoogsteen i/Watson-Crick j
cSH LW#9r cis, Sugar i/Hoogsteen j
cSS LW#11 cis, Sugar i/Sugar j
cSW LW#5r cis, Sugar i/Watson-Crick j
cWH LW#3 cis, Watson-Crick i/Hoogsteen j
cWS LW#5 cis, Watson-Crick i/Sugar j
cWW LW#1 cis, Watson-Crick i/Watson-Crick j
tHH LW#8 trans, Hoogsteen i/Hoogsteen j
tHS LW#10 trans, Hoogsteen i/Sugar j
tHW LW#4r trans, Hoogsteen i/Watson-Crick j
tSH LW#10r trans, Sugar i/Hoogsteen j
tSS LW#12 trans, Sugar i/Sugar j
tSW LW#6r trans, Sugar i/Watson-Crick j
tWH LW#4 trans, Watson-Crick i/Hoogsteen j
tWS LW#6 trans, Watson-Crick i/Sugar j
tWW LW#2 trans, Watson-Crick i/Watson-Crick j

Controlled Vocabulary at Deposition

Allowed Value Details
cHH LW#7 cis, Hoogsteen i/Hoogsteen j
cHS LW#9 cis, Hoogsteen i/Sugar j
cHW LW#3r cis, Hoogsteen i/Watson-Crick j
cSH LW#9r cis, Sugar i/Hoogsteen j
cSS LW#11 cis, Sugar i/Sugar j
cSW LW#5r cis, Sugar i/Watson-Crick j
cWH LW#3 cis, Watson-Crick i/Hoogsteen j
cWS LW#5 cis, Watson-Crick i/Sugar j
cWW LW#1 cis, Watson-Crick i/Watson-Crick j
tHH LW#8 trans, Hoogsteen i/Hoogsteen j
tHS LW#10 trans, Hoogsteen i/Sugar j
tHW LW#4r trans, Hoogsteen i/Watson-Crick j
tSH LW#10r trans, Sugar i/Hoogsteen j
tSS LW#12 trans, Sugar i/Sugar j
tSW LW#6r trans, Sugar i/Watson-Crick j
tWH LW#4 trans, Watson-Crick i/Hoogsteen j
tWS LW#6 trans, Watson-Crick i/Sugar j
tWW LW#2 trans, Watson-Crick i/Watson-Crick j