This is an archive copy of the IUCr web site dating from 2008. For current content please visit
https://www.iucr.org.
![[IUCr Home Page]](/iucr-top/logos/iucrhome.gif)
![[CIF Home Page]](/iucr-top/logos/cifhome.gif)
![[mmCIF Home Page]](/iucr-top/logos/mmcifhome.gif)
Helix Classification
herbert_bernstein (yaya@aip.org)
Wed, 10 Jul 96 09:33:29 EDT
Could the PDB please consider adding the following additional HELIX
types to the HELIX class field (columns 39-40) of the HELIX record,
and creating a TURN class field in columns 39-40 of the TURN record.
This would allow a more detailed classification of secondary structure
and simplify transfer of data to and from mmCIF format:
Current classifications from PDB Contents Guide:
1. Right-handed alpha (default)
2. Right-handed omega
3. Right-handed pi
4. Right-handed gamma
5. Right-handed 3-10
6. Left-handed alpha
7. Left-handed omega
8. Left-handed gamma
9. 2-7 ribbon/helix
10. Polyproline
The PDB uses these classifications only for protein structures.
We assume classes 9 and 10 are for right-handed helices. We add
the left-handed variants and the nucleic acid helices in the
list below (derived from the mmCIF list).
Suggested additional classifications:
11. helix with handedness and type not specified (protein)
12. helix with handedness and type that do not
conform to an accepted category (protein)
13. right-handed helix with type not specified (protein)
14. right-handed helix with type that does not
conform to an accepted category (protein)
15. left-handed helix with type not specified (protein)
16. left-handed helix with type that does not
conform to an accepted category (protein)
17. left-handed pi helix (protein)
18. left-handed 2-7 helix (protein)
19. left-handed 3-10 helix (protein)
20. left-handed polyproline helix (protein)
21. helix with handedness and type not specified (nucleic acid)
22. helix with handedness and type that do not
conform to an accepted category (nucleic acid)
23. right-handed helix with type not specified (nucleic acid)
24. right-handed helix with type that does not
conform to an accepted category (nucleic acid)
25. right-handed A helix (nucleic acid)
26. right-handed B helix (nucleic acid)
27. right-handed Z helix (nucleic acid)
28. left-handed helix with type not specified (nucleic acid)
29. left-handed helix with type that does not
conform to an accepted category (nucleic acid)
30. left-handed A helix (nucleic acid)
31. left-handed B helix (nucleic acid)
32. left-handed Z helix (nucleic acid)
Suggested turn classifications:
1. turn with type not specified (protein)
2. turn with type that does not conform to an
accepted category (protein)
3. type I turn (protein)
4. type I prime turn (protein)
5. type II turn (protein)
6. type II prime turn (protein)
7. type III turn (protein)
8. type III prime turn (protein)
For reference the section of the current mmCIF dictionary on the
subject follows:
save__struct_conf_type.id
_item_description.description
; The descriptor that categorizes type of the conformation of the
backbone of the polymer (whether protein or nucleic acid).
Explicit values for the torsions angles that define each
conformation are not given here, but it is expected that the
author would provide such information in either the
_struct_conf_type.criteria or _struct_conf_type.reference data
items, or both.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_conf_type.id' struct_conf_type yes
'_struct_conf.conf_type_id' struct_conf yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_conf.conf_type_id' '_struct_conf_type.id'
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail HELX_P
; helix with handedness and type not specified
(protein)
;
HELX_OT_P
; helix with handedness and type that do not
conform to an accepted category (protein)
;
#
HELX_RH_P
; right-handed helix with type not specified
(protein)
;
HELX_RH_OT_P
; right-handed helix with type that does not
conform to an accepted category (protein)
;
HELX_RH_AL_P
'right-handed alpha helix (protein)'
HELX_RH_GA_P
'right-handed gamma helix (protein)'
HELX_RH_OM_P
'right-handed omega helix (protein)'
HELX_RH_PI_P
'right-handed pi helix (protein)'
HELX_RH_27_P
'right-handad 2-7 helix (protein)'
HELX_RH_3T_P
'right-handad 3-10 helix (protein)'
HELX_RH_PP_P
'right-handed polyproline helix (protein)'
#
HELX_LH_P
; left-handed helix with type not specified
(protein)
;
HELX_LH_OT_P
; left-handed helix with type that does not
conform to an accepted category (protein)
;
HELX_LH_AL_P
'left-handed alpha helix (protein)'
HELX_LH_GA_P
'left-handed gamma helix (protein)'
HELX_LH_OM_P
'left-handed omega helix (protein)'
HELX_LH_PI_P
'left-handed pi helix (protein)'
HELX_LH_27_P
'left-handed 2-7 helix (protein)'
HELX_LH_3T_P
'left-handed 3-10 helix (protein)'
HELX_LH_PP_P
'left-handed polyproline helix (protein)'
#
HELX_N
; helix with handedness and type not specified
(nucleic acid)
;
HELX_OT_N
; helix with handedness and type that do not
conform to an accepted category (nucleic
acid)
;
#
HELX_RH_N
; right-handed helix with type not specified
(nucleic acid)
;
HELX_RH_OT_N
; right-handed helix with type that does not
conform to an accepted category (nucleic
acid)
;
HELX_RH_A_N
'right-handed A helix (nucleic acid)'
HELX_RH_B_N
'right-handed B helix (nucleic acid)'
HELX_RH_Z_N
'right-handed Z helix (nucleic acid)'
#
HELX_LH_N
; left-handed helix with type not specified
(nucleic acid)
;
HELX_LH_OT_N
; left-handed helix with type that does not
conform to an accepted category (nucleic
acid)
;
HELX_LH_A_N
'left-handed A helix (nucleic acid)'
HELX_LH_B_N
'left-handed B helix (nucleic acid)'
HELX_LH_Z_N
'left-handed Z helix (nucleic acid)'
#
TURN_P
'turn with type not specified (protein)'
TURN_OT_P
; turn with type that does not conform to an
accepted category (protein)
;
TURN_TY1_P
'type I turn (protein)'
TURN_TY1P_P
'type 1 prime turn (protein)'
TURN_TY2_P
'type II turn (protein)'
TURN_TY2P_P
'type II prime turn (protein)'
TURN_TY3_P
'type III turn (protein)'
TURN_TY3P_P
'type III prime turn (protein)'
#
STRN
'beta strand (protein)'
save_