Both caps count as one amino acid I believe. That way when you mark the 2 cm lengths you end up with 140 amino acids, even though you have only 278 cm to work with.
The pre-build visualization site includes both end amino acids 421 and 560. therefore including 140 amino acids.
The tuber is 278 cm, and if each amino acid is 2 cm then it will represent 139 amino acids. Each endcap is appoximately 2 cm long and therefore will cover a total of 4 cm when placed on the model, leaving 274 cm to work with. That is enough to represent 137 amino acids and the 2 end amino acids, which is 139. Yet the online visualization site includes 140 amino acids. Which end amino do we leave off?
http://cbm.msoe.edu/scienceOlympiad/des ... build.html - here is the prebuild visualization. Once you restrict everything, type in "select 421-560" and then "color red" and it colors the whole protein red.