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Antibodies: numbering

The numbering schemes are rather confusing, particularly in CDR-1 where the equivalents change depending on the length of the CDR.

Anne Marie Honneger's pages show a useful comparison of numbering schemes. However, this comparison doesn't show the equivalent residues in different schemes.

CDR-L1

For CDR-L1, the lengths are expressed between residues L24 and L34 (the numbers for these residues do not change between Chothia and Kabat schemes).

Further confusion comes from the fact that Chothia (erroneously) changed his numbering scheme for some paper where the insertion occurred after L31 rather than after L30

Length 10

Kabat 24252627293031323334
Chothia24252627282930323334

Length 11

Kabat 2425262728293031323334
Chothia2425262728293031323334

Length 12

Kabat 2425262727a28293031323334
Chothia2425262728293030a31323334

Length 13

Kabat 2425262727a27b28293031323334
Chothia2425262728293030a30b31323334

Length 14

Kabat 2425262727a27b27c28293031323334
Chothia2425262728293030a30b30c31323334

Length 15

Kabat 2425262727a27b27c27d28293031323334
Chothia2425262728293030a30b30c30d31323334

Length 16

Kabat 2425262727a27b27c27d27e28293031323334
Chothia2425262728293030a30b30c30d30e31323334

Length 17

Kabat 2425262727a27b27c27d27e27f28293031323334
Chothia2425262728293030a30b30c30d30e30f31323334

CDR-L3

The numbering schemes for Kabat and Chothia CDR-L3 are identical. The Kabat CDR runs from L89 to L97.

However, in the Kabat data, there are discrepancies about where the deletion should occur for shorter loops (i.e. length 8). Looking in Kabat at the CDR-L3 loops where residue L97 is present (i.e. not truncated sequences), in 139 cases L95 is present and L96 is missing while in 140 cases L95 is missing and L96 is present. i.e. in the 8-residue loops, Kabat is completely unclear whether the residues should be numbered L89-L90-L91-L92-L93-L94-L96-L97, or whether they should be numbered L89-L90-L91-L92-L93-L94-L95-L97.

While a number of PDB files including 1yqv and 1a7o delete L96 from the numbering, it is clear on comparing the structures of 8 and 9 residue CDR-L3 loops, that it should be L95 that is removed.

The correct numbering is therefore:

Length 8

Kabat/Chothia8990919293949697

Length 9

Kabat/Chothia899091929394959697

Length 10

Kabat/Chothia8990919293949595A9697

Length 11

Kabat/Chothia8990919293949595A9B9697

...etc...

CDR-H1

For CDR-H1, the situation is even more confusing because, in the Kabat numbering scheme, the insertion is at the end of the loop. Again, the equivalences depend on the length of the loop, so the lengths shown below are for residues H31-H35B (Kabat numbering) or H31-H35 (Chothia numbering).

Length 5

Kabat 3132333435
Chothia3132333435

Length 6

Kabat 313233343535a
Chothia3131a32333435

Length 7

Kabat 313233343535a35b
Chothia3131a31b32333435