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If set on 2 then 3DM will only show positions in the network for which at least two different mutations have been published that had an effect on specificity. This is to ensure no falls false positive are included. In protein families for which a lot of mutations are available it is usually smart to leave this at at least two. If there is not so much data available it might be better to set it on 1 to get reliable E-scores.

They have the same number using the class A numbering scheme: 3.25a. In the class B alignment this residue has number 3.39B29b. Obviously there are more structural conserved positions before this residue in the class B alignment compared to the class A alignment. When this common numbering scheme was designed they didn't realize that they could have made a numbering scheme that could be applied to all classes. As everyone uses this numbering scheme now, it is too late to synchronize the numbering schemes of the different families.