! Chothia canonical definitions for KabatMan.
!
! V1.0  12.05.94 Original    By: ACRM
! V1.1  19.05.94 Modified L1 Class 7* & added 8*
! V1.2  20.02.95 Added H71=V for H2, class 2
! V1.3  16.05.95 Changed L1 8* to 9* adding requirements for L32 and L71
!                to match class numbering in AbM
!                Added new L1 Class 8* 
!                Modified L1 Class 7* by adding L32 and L71
!                Added L3 Classes 4* to 10*
! V1.4  09.05.96 Removed some additional classes as these are all treated
!                properly by chothia.dat.auto
!
! Each class is defined with the keyword LOOP followed by the loop ID,
! class name and length. This is then followed by the key residue numbers
! paired with the allowed amino acid types.
! Blank lines and lines starting with a ! or # are ignored
! The SOURCE keyword may follow the LOOP keyword, but is ignored by
! KabatMan.
!
! Class names contain a * if they are not defined by Chothia
!
! Note that the lengths of the loops are as defined by AbM since the
! Kabat numbering for H1 fails to place the inserted residues within
! the Chothia loop...
!
! MC 30/11/2012    Exemplar 2hfl of 3 has been superseded by 1yqv
!                  (occurs also in auto and strict)
!
! ACRM 05.09.18    Changed to Chothia numbering
CHOTHIANUMBERING

!!!!!!!!!!!!!!!!!!!!!!!!!!!!    CDR-L1   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
LOOP L1 1 10
SOURCE chothia:loops; Require L23, L35 (SMJS) [2fbj]
L2  I
L23 C
L25 A
L29 V
L33 LM
L35 W
L71 Y

LOOP L1 2 11
SOURCE chothia:loops; Require L23, L35 (SMJS) [1ikf]
L2  I
L23 C
L25 A
L29 IV
L33 L
L35 W
L71 YF

LOOP L1 3 17   
SOURCE chothia:loops; Require L23, L35 (SMJS) [1hil]
L2   I
L23  C
L25  S
L29  L
L33  L
L35  W
L71  YF

LOOP L1 4 16   
SOURCE chothia:loops; Require L23, L35 (SMJS) [1rmf]
L2   V
L23  C
L25  S
L29  L
L33  L
L35  W
L71  YF

LOOP L1 5L 13  
SOURCE SMJS [2fb4] This is a lambda Ab; later papers use class 5 for a 15-residue kappa
L2  S
L23 C
L25 G
L30 I
L33 V
L35 W
L71 A

LOOP L1 6L 14   
SOURCE  [7fab] This is a lambda Ab; later papers use class 6 for a 12-residue kappa
L25  G
L30  I
L33  V
L71  A

LOOP L1 7 14
SOURCE [1gig]
L25  S
L30  V
L33  A
L71  A

LOOP L1 8* 11  
SOURCE SMJS [8fab]
L3  E
L23 C
L25 SA
L29 P
L33 A
L35 W
L71 VSA

!!!!!!!!!!!!!!!!!!!!!!!!!!!!    CDR-L2   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
LOOP L2 1 7     
SOURCE chothia:loops [1lmk]
L48 IV
L64 G


!!!!!!!!!!!!!!!!!!!!!!!!!!!!    CDR-L3   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
LOOP L3 1 9     
SOURCE chothia:loops [1tet]
L88 C
L90 QNH
L95 P

LOOP L3 2 9     
SOURCE chothia:loops [2fbj]
L88 C
L90 Q
L94 P

LOOP L3 3 8     
!SOURCE chothia:loops [2hfl]
SOURCE chothia:loops [1yqv]
L88 C
L90 Q
L96 P



!!!!!!!!!!!!!!!!!!!!!!!!!!!!    CDR-H1   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
LOOP H1 1 10    
SOURCE chothia:human; Require H92, ignore H24, add RGHTK to H94 (SMJS) [2fbj]
! H24 AVGTS
H26 G
H27 GFY
H29 IFVL
H34 MILVTW
H92 C
H94 RTKHGL

! Note, AbM calls this Class 2
LOOP H1 1B 10   
SOURCE ACRM (Based on chothia:loops, chothia:human and SMJS) [7fab]
! H24 AVGTS
H26 G
H27 TD
H29 IF
H34 WS
H92 C
H94 RN

! Note, AbM calls this Class 3
LOOP H1 2 11    
SOURCE chothia:human; Require H92 (SMJS) [1baf]
! H24 FV
H26 G
H27 FYG
H29 LI
H34 CWV
H92 C
H94 HR

! Note, AbM calls this Class 4
LOOP H1 3 12    
SOURCE chothia:human; Require H92 SMJS [1ggi]
! H24  FVG
H26  G
H27  FGD
H29  LIV
H34  VW
H92  C
H94  RH

!!!!!!!!!!!!!!!!!!!!!!!!!!!!    CDR-H2   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
LOOP H2 1 9     
SOURCE chothia:human [1gig]
H55 DG
H71 KRVI

LOOP H2 2 10    
SOURCE chothia:human; Allow H71=V (ACRM) [1bbd]
H52A PTA
H55 GS
H71 ATLV

LOOP H2 3 10    
SOURCE chothia:human [1igc]
H54 GSND
H71 R

LOOP H2 4 12    
SOURCE chothia:human; Allow H54=G (SMJS) [1mcp]
H54 SKNG
H55 Y
H71 R