An Ig Proteomap is an explicit 2D projection of a 3D Ig-fold (β-sandwich) topology that preserves residue-residue contacts while making the sequential chain order visible. This document collects the rules that govern its construction. These rules apply to all Ig variants (IgV, IgC1, IgC2, IgI, FN3, …) and are encoded in the IgFold2D template format.
The Ig-fold has two β-sheets:
| Sheet | Strands |
|---|---|
| Sheet 1 | A · B · E · D |
| Sheet 2 | (A’) · G · F · C · C’ · C” |
A’ is present only in split A/A’ variants (IgV, IgI). When present, A is on sheet 1 and A’ on sheet 2; together they span both sheets at the N-terminus.
Strand presence varies by variant:
| Variant | Strands present | Example |
|---|---|---|
| IgV | A, A’, B, C, C’, C”, D, E, F, G | antibody V domain |
| IgC1 | A, B, C, D, E, F, G | antibody C domain |
| IgC2 | A, B, C, C’, D, E, F, G | CD2 |
| IgI | A, A’, B, C, C’, D, E, F, G | telokin |
| FN3 | A, B, C, C’, E, F, G | fibronectin type III |
These are the rules that govern how the dashed chain trace runs through the proteomap. They are non-negotiable for valid Ig proteomaps.
| Rule | Description |
|---|---|
| No crossing | The lace never visually crosses itself on colored cells (strand cells). On empty placeholder cells the trace may overlap. |
| Turns at strand ends | Right-angle turns happen above or below strands, never mid-loop. No “tourniquet” inside a loop. |
| Minimize bends | Each strand-to-strand transition uses the minimum number of right-angle turns. |
| Anchor alignment | All xx50 positions sit on one horizontal line — the anchor row. |
| Passes-behind | Where a 3D chain crosses behind another in space, the 2D trace either crosses visibly (dashed is OK) or breaks visually with a gap marker. |
| Placeholder traversal | Empty (white/gray) cells can be traversed as bridges; future residue insertions may land there. |
| n5xx → m5xx transitions | Loops start at the end of the exiting strand and end at the start of the entering strand. Loop residue numbering is variable across domains (may inherit from either flanking strand). |
Because some transitions admit multiple equally short routes, the template format supports explicit loop hints — waypoints the chain must pass through:
"loop_hints": {
"6546-6547": [
[7, 6], [7, 5], [7, 4], [8, 4], [9, 3], [10, 4]
]
}
Each entry is keyed "from_igstrand-to_igstrand" and lists intermediate [row, col] waypoints. Between consecutive waypoints the chain is drawn as a straight line; non-colinear pairs become L-shapes.
Loop hints can also include explicit gaps for “passes-behind”:
"loop_hints": {
"1852-2543": [
{"via": [10, 7]}, {"via": [10, 6]}, {"via": [10, 5]},
{"jump": [10, 2]} // pen-lift, trace gap from F11 to C11
]
}
(The widget supports both inline tuples and explicit {via}/{jump} objects.)
xx49, xx48, … or xx51, xx52, …… in cells that may receive inserted residues in other domain occurrences. Examples in the CD8 template: L12/M12 (top loop), D24/E24 (HV4), J34/K34 (CDR3 / FG loop)Every cell in the grid is addressable by any of:
"L10"(9, 11)2550This lets the widget interoperate with any external numbering scheme.
xx50 anchor concept adapted from GPCRs.)