Antibodies - General Information

This page summarises a lot of generally useful information about antibodies.

The Kabat Numbering Scheme

The Kabat numbering scheme is a widely adopted standard for numbering the residues in an antibody in a consistent manner. However the scheme does have its problems!

First, since the numbering scheme was developed from (fairly limited) sequence data, the position at which insertions occur in CDR-L1 and CDR-H1 does not match the structural insertion position. Thus topologically equivalent residues in these loops do not get the same number.

Second, the numbering adopts a rigid specification. For example 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). If there are more residues than that, there is no standard way of numbering them. Such situations occur at other positions too.

The numbering throughout the chains 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

The Chothia Numbering Scheme

The Chothia numbering scheme is identical to the Kabat scheme, but places the insertions in CDR-L1 and CDR-H1 at the structurally correct positions. This means that topologically equivalent residues in these loops do get the same label (unlike the Kabat scheme). There are two disadvantages: first, the Kabat scheme is so widely used that some confusion can arise; second, Chothia et al. changed their numbering scheme as of their 1989 Nature paper such that insertions in CDR-L1 are placed after residue L31 rather than L30. Examining the conformations of the loops shows that L30 is the correct position.

The pre-1989 Chothia numbering (the structurally correct version) throughout the chains follows.

Note That in their latest paper (Al-Lazikani et al., (1997) JMB 273,927-948), Chothia's group returns to using residue 30 as the insertion site in CDR-L1!

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    28    29
 30    
 30A   30B   30C   30D   30E   30F
       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    
 31A   31B
             32    33    34    35    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

Table of CDR Definitions

A number if definitions of the CDRs are commonly in use:

The Kabat definition is based on sequence variability and is the most commonly used.
The Chothia definition is based on the location of the structural loop regions.
The AbM definition is a compromise between the two used by Oxford Molecular's AbM antibody modelling software.
The contact definition has been recently introduced by us and is based on an analysis of the available complex crystal structures. This definition is likely to be the most useful for people wishing to perform mutagenesis to modify the afinity of an antibody since these are residues which take part in interactions with antigen.

Loop Kabat         AbM           Chothia         Contact
---- -----         ---           -------         -------
L1   L24 -- L34    L24 -- L34    L24 -- L34      L30 -- L36
L2   L50 -- L56    L50 -- L56    L50 -- L56      L46 -- L55
L3   L89 -- L97    L89 -- L97    L89 -- L97      L89 -- L96
H1   H31 -- H35B   H26 -- H35B   H26 -- H32..34  H30 -- H35B
     (Kabat Numbering)
H1   H31 -- H35    H26 -- H35    H26 -- H32      H30 -- H35 
     (Chothia Numbering)
H2   H50 -- H65    H50 -- H58    H52 -- H56      H47 -- H58
H3   H95 -- H102   H95 -- H102   H95 -- H102     H93 -- H101

Note that the end of the Chothia CDR-H1 loop when numbered using the Kabat numbering convention varies between H32 and H34 depending on the length of the loop. (This is because the Kabat numbering scheme places the insertions at H35A and H35B.)

If neither 35A nor 35B is present, the loop ends at 32
If only 35A is present, the loop ends at 33
If both 35A and 35B are present, the loop ends at 34

This diagram illustrates the alternative definitions for CDR-H1. The Kabat and Chothia numbering schemes are shown horizontally and the Kabat, Chothia, AbM and Contact definitions of the CDRs are shown with arrows above and below the two numbering schemes.

Table of mean contact data

Following an analysis of the contacts between antibody and antigen in the complex structures available in the Protein Databank, we have generated a set of mean contact data. The full method by which these results were obtained is described in the following paper: MacCallum, R. M., Martin, A. C. R. and Thornton, J. T. Antibody-antigen interactions: Contact analysis and binding site topography. J. Mol. Biol. 262, 732-745.

Briefly, we have analysed the number of contacts made at each position, defining contact as burial by > 1 square Angstrom change in solvent accessibility. These data give a simple measure of how likely a residue is to be involved in antigen contact.

Second, we have calculated the mean percentage burial over the accessible residues.

Click here for an image showing a composite combining site containing all CDR conformations coloured by contact propensity.

The table presents the chain name, residue number (N.B. This is pre-1989 Chothia Numbering), the number of contacts and the mean percent burial. The data are available by clicking here.

An alternative simplified view is presented as a list of CDR residues making contact in each antibody with summary data for each CDR.

How to identify the CDRs by looking at a sequence

CDR-L1

Start - Approx residue 24
Residue before is always a Cys
Residue after is always a Trp. Typically TRP-TYR-GLN, but also, TRP-LEU-GLN, TRP-PHE-GLN, TRP-TYR-LEU
Length 10 to 17 residues

CDR-L2

Start - always 16 residues after the end of L1
Residues before generally ILE-TYR, but also, VAL-TYR, ILE-LYS, ILE-PHE
Length always 7 residues (except 7FAB which has a deletion in this region)

CDR-L3

Start - always 33 residues after end of L2 (except 7FAB which has the deletion at the end of CDR-L2)
Residue before is always Cys
Residues after always PHE-GLY-XXX-GLY
Length 7 to 11 residues

CDR-H1

Start - Approx residue 26 (always 4 after a CYS) [Chothia / AbM defintion] Kabat definition starts 5 residues later
Residues before always CYS-XXX-XXX-XXX
Residues after always a TRP. Typically TRP-VAL, but also, TRP-ILE, TRP-ALA
Length 10 to 12 residues (AbM definition) Chothia definition excludes the last 4 residues

CDR-H2

Start - always 15 residues after the end of Kabat / AbM definition) of CDR-H1
Residues before typically LEU-GLU-TRP-ILE-GLY, but a number of variations
Residues after LYS/ARG-LEU/ILE/VAL/PHE/THR/ALA-THR/SER/ILE/ALA
Length Kabat definition 16 to 19 residues (AbM definition ends 7 residues earlier)

CDR-H3

Start - always 33 residues after end of CDR-H2 (always 2 after a CYS)
Residues before always CYS-XXX-XXX (typically CYS-ALA-ARG)
Residues after always TRP-GLY-XXX-GLY
Length 3 to 25(!) residues