In general, if a residue is important, it is conserved. So the more special residue will be conserved at the cost of the more common one.
1 LLLWASLLL LLLWASLLL right W/W LLLLWSLLL LLLWSLLLL |
why is W more important? It makes always very many contacts, so evolutionary speaking is not easy to mutate to or from a way (neither in evolution, nor in a test-tube).
2 LLLCANLLL LLLCANLLL right C/C LLLLCNLLL LLLCNLLLL |
C on C or N on N? Normally C on C but if it is a transmembrane part of a membrane protein then N on N because Asn is the most conserved amino acid in transmembrane regions in proteins
3 LLLRAGLLL LLLRAGLLL left G/G LLLLRGLLL LLLRGLLLL |
R on R or G on G? Normally G on G because of the mobility factor and the weird turns that G can make. But R is a very often seen (rather conserved) residue in nucleic acid binding proteins. So, if you know that your protein is nucleic acid binding, then R on R is better.
4 LLLHANLLL LLLHANLLL right H/H LLLLHNLLL LLLHNLLLL |
H aligns with H is more special (often in active sites)
5 LLLPAKLLL LLLPAKLLL right P/P LLLLPKLLL LLLPKLLLL |
P is (much) more conserved because it is needed in certain parts of molecules such as AT the beginnings of α-helices, or IN β-turns.