Using electronegativity and atomic size to compare acidity of cysteine with serine In proteins, the alcohol group of serine is generally more difficult to deprotonate than the thiol group of cysteine. 

Serine and cysteine respectively:



In the literature, the explanation given is that the sulfur atom is larger than the oxygen atom, and therefore the resultant negative charge is stabilised over a larger surface. 

But I am confused. Oxygen is a more electronegative atom than sulfur and therefore can more stably carry a negative charge. How are these two assertions compatible?


oxygen can carry negative charge more easily because it is more electronegative, and 
sulfur can carry negative charge more easily because it is larger?


Clearly, they cannot both be true and in the case of these two amino acids, the size of the sulfur prevails over the electronegativity of the oxygen. Why is that? Why in some circumstances is it the other way around?
You are correct that Oxygen is more electronegative than Sulfur.  However, the relative size of the atoms affects more than their ability to carry charge.  In this case, the larger radius of the Sulfur atom actually causes the H-S bond in Cysteine to be longer than the H-O bond in Serine.  The longer bond is weaker and, thus, more easy to break, making Cysteine easier to deprotenate.