Given　the　long　range　correlation　characteristics　of　information　about　protein　foldability　and　thermostability　the　multiple　sequence　alignment　of　a　SH3　domain　was　analyzed　using　the　modified　statistical　coupling　analysis　(SCA)　method.　Results　show　that　the　statistically　conserved　energy　from　the　SCA　method　could　be　used　to　evaluate　the　site　conservation　of　the　SH3　sequence　set　properly.　Sites　with　a　high　average　coupling　energy　correspond　to　structurally　and　functionally　important　positions.　Perturbing　analysis　on　several　sites　revealed　local　and　nonlocal　perturbing　modes　in　the　SH3　domain.　By　combining　the　SCA　and　the　clustering　reorder　method　the　structural　core　and　the　non-structural　core　sites　of　the　SH3　domain,　and　detailed　differences　between　several　functional　sites　could　be　distinguished.　Different　perturbing　modes　that　involve　different　sites　exist　in　the　SH3　domain.　By　sharing　the　common　perturbing　sites　and　the　responding　sites,　different　perturbing　modes　can　interact.　The　coupling　responding　mode　of　all　the　sites　in　the　structure　was　thus　determined.　Coupling　information　about　the　SH3　domain　can　improve　our　understanding　about　the　relationship　between　the　protein　sequence　and　its　structure　as　well　as　its　function.　It　is　also　valuable　in　new　protein　design.