ALQLNMQAKALL ooxoxoxoxooo ANQLLMQAAKLL oxxoooxooxoo |
o is hydrophobic; x is hydrophilic. Bottom one has better distribution of 0 and x. Also, N in middle helix is very bad. Perfect o-x distribution would, for example, be: ooxxooxooxxooxooxxoox or xxoxxooxxoxxooxxo etc. Repeats of seven.
ARAAEALLQAAE AEAAEALLQAAK |
Bottom one is better because negative E near (positive) N-terminus of helix and positive K near (negative) C-terminus.
ALLLAALLLAL AAEALAKALLR |
The top one is entirely hydrophobic. That cannot happen unless it is a membrane protein.