Unusual sequence numbering: Difference between revisions
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===Insertion Codes=== | ===Insertion Codes=== | ||
[[Image:Sequence-insertion-codes-1igy.png|frame|Excerpt from PDB file 1igy showing insertion codes.]] | [[Image:Sequence-insertion-codes-1igy.png|frame|Excerpt from PDB file 1igy showing insertion codes.]] | ||
Sometimes the residues of a protein are numbered according to a different ''reference sequence''. When there are insertions relative to the reference sequence, the additional residues may all be given the same sequence number, but marked with alphabetic insertion codes. This is frequently done in antibodies, where the reference sequence is the germline sequence, but the antibody has been somatically mutated, especially in complementarity-determining region (CDR) 3. An example is [http://firstglance.jmol.org/fg.htm?mol=1igy 1igy] ([[1igy]]). Four residues in chain B all have sequence number 82. They are distinguished by insertion codes: 82, 82A, 82B, 82C. At right is this part of the PDB file. Below are residues 81-83 showing their sequence numbers in [[FirstGlance in Jmol]]. Insertion codes are given following a caret "^". (How? See note <ref name="how1"> | Sometimes the residues of a protein are numbered according to a different ''reference sequence''. When there are insertions relative to the reference sequence, the additional residues may all be given the same sequence number, but marked with alphabetic insertion codes. This is frequently done in antibodies, where the reference sequence is the germline sequence, but the antibody has been somatically mutated, especially in complementarity-determining region (CDR) 3. An example is [http://firstglance.jmol.org/fg.htm?mol=1igy 1igy] ([[1igy]]). Four residues in chain B all have sequence number 82. They are distinguished by insertion codes: 82, 82A, 82B, 82C. At right is this part of the PDB file. Below are residues 81-83 showing their sequence numbers in [[FirstGlance in Jmol]]. Insertion codes are given following a caret "^". (How? See note <ref name="how1">Click ''Find'' and enter ''chain=B and 81-83. Click ''Isolate'' and check ''Atoms with Halos''. Zoom in. In the left center after "Halos around:" click ''Change'', and then ''Clear Halos''. Check ''Sequence numbers'' (near the bottom of the upper left panel).</ref>) | ||
<center> | <center> | ||
<table width=200><tr><td>[[Image:1igy-chain-b-81-83.png|200px|center]]</td></tr><tr><td>1igy residues 81-83 displayed with sequence numbers in FirstGlance in Jmol.<ref name="how1" /></td></tr></table> | <table width=200><tr><td>[[Image:1igy-chain-b-81-83.png|200px|center]]</td></tr><tr><td>1igy residues 81-83 displayed with sequence numbers in FirstGlance in Jmol.<ref name="how1" /></td></tr></table> | ||
