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====== Cath Domall File (CDF) ======

===== Version 1.0 =====


The Cath Domall file describes domain boundaries for entries in the CATH database. 
Only PDB chains that have been split into domains have a CathDomall entry.
Domains that are composed of whole PDB chains are not found in this file.

  * Comment lines start with a '#' character
  * Segments are continuous sequence regions of domains
  * Fragments are small regions of the protein chain that are excluded from the domain definition



^ Column ^ Description ^
| 1  | Chain name (5 characters)  |
| 2  | Number of domains (formatted 'D%02d')  |
| 3  | Number of fragments (formatted 'F%02d')  |


The formatting of a Cath Domall file is best explained using examples.

===== Example Domall Entries =====

<code>
KEY:
N  = Number of segments
C  = Chain character
I  = Insert character/code ('-' indicates no insert character)
S  = Start PDB number
E  = End PDB number
NR = number of residues (fragment information only)
</code>

==== Example 1 ====


<code>
1chmA  D02 F00  1  A	2 - A  156 -  1  A  157 - A  402 -
		N |C	S I C	 E I| N |C    S I C    E I|
               |<----Domain One---->|<-----Domain Two---->|
                  |<--Segment One-->|   |<--Segment One-->|
</code>

This translates to:

^ Domain   ^ Chain  ^ Start/Stop  ^
| 1chmA01  | A      | 2-156     |
| 1chmA02  | A      | 157-402   |

==== Example 2 ====

<code>
1cnsA  D02 F00  2  A    1 - A   87 -  A  146 - A  243 -  1  A   88 - A  145 -

                N |C    S I C    E I| C    S I C    E I| N |C    S I C    E I|
               |<--------------Domain One------------->|<-----Domain Two---->|
                  |<--Segment One-->|<---Segment Two-->|   |<--Segment One-->|
</code>

This translates to:

^ Domain   ^ Chain  ^ Start/Stop  ^
| 1cnsA01  | A      | 1-87, 146-243  |
| 1cnsA02  | A      | 88-145        |


===== Fragment Information =====

Fragments are small regions of the protein chain that are not included
in the domain definition. These residue ranges are tagged on the end of the
segment information. The format is different from the segment range information.

==== Example 3 ====


<code>
1amg 0 D02 F01  1  0	1 - 0  360 -  1  0  362 - 0  417 -  0  361 - 0  361 - (1)
		N |C	S I C	 E I| N |C    S I C    E I| C	 S I C    E I  NR|
               |<----Domain One---->|<-----Domain Two---->|<---Fragment One----->|
                  |<--Segment One-->|   |<--Segment One-->|
</code>

This translates to:

^ Domain   ^ Chain  ^ Start/Stop  ^
| 1amg001   | A  | 1-360    |
| 1amg002   | A  | 362-417  |

Fragment = 361

==== Example 4 ====

<code>
1bcmA  D02 F02  1  A  257 - A  487 -  1  A  492 - A  559 -  A  488 - A  491 - (4)  A  560 - A  560 - (1)
		N |C	S I C	 E I| N |C    S I C    E I| C	 S I C    E I  NR| C	S I C	 E I  NR|
               |<----Domain One---->|<-----Domain Two---->|<---Fragment One----->|<---Fragment Two----->|
                  |<--Segment One-->|   |<--Segment One-->|
</code>

This translates to:

^ Domain   ^ Chain  ^ Start/Stop  ^
| 1bcmA01  | A  | 257-487  |
| 1bcmA02  | A  | 492-559  |

Fragments = 488-491, 560

Trace: • superfamily_naming_tutorial • greek_key • beta_sheet • welcome • 12web_services_in_java • cathdomall • eccb_t2_diverge • eccb_t2_fundi • browse_the_cath_hierarchy • test

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