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Re: Helix Classification
Sandeep Kumar Bansal (sandeep@mbu.iisc.ernet.in)
Wed, 10 Jul 1996 20:36:45 -0700 (PDT)
On Wed, 10 Jul 1996, herbert_bernstein wrote:
> 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_
>
Hi all,
let me add my support to Dr. Bernsteins' proposal. As a student who
does nothing but PDB database analysis, I believe this will make the job of
people like me much much simpler. I suggest Dr. Bernstein to forward this mail
to PDB listserver also so that it can reach a wider audience.
Sandeep
****************************************
* *
* SANDEEP KUMAR *
* M.B.U., IISC. *
* BANGALORE *
* 560012 *
* Phone 91-80-3092534 *
* sandeep@mbu.iisc.ernet.in *
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