Kabat Antibody Numbering

The Kabat numbering scheme is the most widely adopted standard for numbering residues in an antibody in a consistent manner. However the scheme is now known to have limitations:

Numbering adopts a rigid specification.

  • In the potentially very long CDR-H3, insertions are numbered between residue H100 and H101 with letters up to K (i.e. H100, H100A ... H100K, H101).
  • We now know it is possible to have more residues than that, but there is no standard way of numbering them. Such situations occur at other positions too.

The Kabat numbering scheme was developed from sequence data (a fairly limited set), without the knowledge of structure.

  • We now know that the position at which insertions occur in CDR-L1 and CDR-H1 does not actually match the structural insertion position.
  • Thus topologically equivalent residues in these loops do not get the same number.

Numbering throughout the chains is as follows:

Light chain

       0     1     2     3     4     5     6     7     8     9
      10    11    12    13    14    15    16    17    18    19
      20    21    22    23    24    25    26    27
      27A   27B   27C   27D   27E   27F               28    29
      30    31    32    33    34    35    36    37    38    39
      40    41    42    43    44    45    46    47    48    49
      50    51    52    53    54    55    56    57    58    59
      60    61    62    63    64    65    66    67    68    69
      70    71    72    73    74    75    76    77    78    79
      80    81    82    83    84    85    86    87    88    89
      90    91    92    93    94    95
      95A   95B   95C   95D   95E   95F   96    97    98    99
     100   101   102   103   104   105   106
     106A                                      107   108   109

Heavy chain

       0     1     2     3     4     5     6     7     8     9
      10    11    12    13    14    15    16    17    18    19
      20    21    22    23    24    25    26    27    28    29
      30    31    32    33    34    35
      35A  35B                            36    37    38    39
      40    41    42    43    44    45    46    47    48    49
      50    51    52
      52A   52B   52C   53    54    55    56    57    58    59
      60    61    62    63    64    65    66    67    68    69
      70    71    72    73    74    75    76    77    78    79
      80    81    82
      82A   82B   82C   83    84    85    86    87    88    89
      90    91    92    93    94    95    96    97    98    99
     100
     100A  100B  100C  100D  100E  100F  100G  100H  100I  100J
     100K  101   102   103   104   105   106   107   108   109
     110   111   112   113

For more information, visit the web site of our collaborator Professor Andrew Martin, from which the information here was adapted: www.bioinf.org.uk/abs