Соседку беспокоил не сам укус, а то, что рука покраснела.

Because беспокоить works like to worry / to bother in a structure where:

• the cause of the worry is the grammatical subject, and
• the person affected is in the accusative.

So the sentence is structured more literally as:

Not the bite itself was bothering the neighbor, but the fact that the hand had turned red.

That is why соседку is accusative.

Yes. Соседку is the accusative singular of соседка, which means female neighbor.

If it were a male neighbor, you would expect соседа instead.

It agrees with укус, which is masculine singular.

So in the first part, the grammar is:

• укус = subject
• беспокоил = masculine singular verb matching укус
• соседку = object

Even though the second part is то, что рука покраснела, the verb here is aligned with the first contrasted item, укус.

If you said only the second idea by itself, you would normally get:

Соседку беспокоило то, что рука покраснела.

There the verb is беспокоило because то is neuter singular.

Because беспокоить here describes a state of concern, not a single completed action.

The idea is not something suddenly alarmed her once, but rather this was what was bothering her. Russian often uses the imperfective for that kind of ongoing or background state.

So беспокоил is very natural here.

It means not the bite itself.

The word сам adds emphasis. It tells you that the bite, by itself, was not the real issue. The real issue was something else: that the hand turned red.

Also note that сам agrees with укус, so it is masculine singular here.

No. Here сам is not a reflexive pronoun like myself.

In this sentence, сам is an emphatic adjective-like word meaning something like:

• itself
• the very
• in and of itself

So сам укус = the bite itself.

Because this is the standard Russian pattern:

не X, а Y = not X, but Y

Here а expresses a correction or contrast between two alternatives.
The sentence is essentially saying:

It wasn’t X; it was Y.

That is exactly the kind of contrast а is used for. Но would sound less precise here.

Here то, что means the fact that.

So:

то, что рука покраснела = the fact that the hand turned red

This is a very common Russian pattern for turning a whole clause into a noun-like idea.

You can think of то as a support word that lets the что-clause function as a single unit.

In standard Russian, that would not work well here.

After а, the sentence needs a noun-like element parallel to не сам укус.
That is why Russian uses то, что...

So the contrast is:

• не сам укус
• а то, что рука покраснела

That makes the structure balanced and grammatical.

Because the subject of that clause is рука, and рука is feminine singular.

So the verb in the past tense must also be feminine singular:

• рука покраснела

Also, покраснеть is perfective, so it means to turn red / to become red, with emphasis on the result.

If you used краснела, that would suggest a process like was reddening / was turning red, which is not the main idea here.

Yes, a little.

Starting with Соседку puts the affected person first, as the topic: as for the neighbor, what bothered her was...

A more straightforward order could be:

Не сам укус беспокоил соседку, а то, что рука покраснела.

Both are natural, but the original version gives slightly more focus to the neighbor’s reaction.

There are two different reasons:

1. ..., а ...
   A comma is needed before а because it joins two contrasted parts:
   не сам укус, а то...

2. то, что...
   A comma is needed before что because it introduces a subordinate clause:
   то, что рука покраснела

So both commas are required.