This paper aims to investigate in what extent subject-centered clusters are different from one another in terms of message system, which is composed of curriculum, pedagogy and evaluation. For this, Bernstein's pedagogic transmission code(i.e., classification and framing) and school typology(i.e., open-type or close-type) have been explored, and then applied into Shimin Junior School, Japan, in order to find out substantial characteristics between subject-centered clusters. In this case study, VGA(visibility graph analysis), as one of syntactical methodologies in space syntax theory, has been used to measure to what degree they are actually different. Throughout in-depth investigation of spatial configurations, it can be said that the square of clusters is strongly connected and integrated very well, so that it acts as an anchor place for school life within a cluster. However, it works in different ways according to message systems. In the subjects like Japanese and Science whose message system are characterized by strong classification and strong framing, integration values are relatively low, and this means that it is hard to expect cross-referencing activities through the subject squares. On the contrary, the subject of Social Studies defined by weak classification and weak framing shows the highest mean integration values, and this can be expected that there are inter-changeable learning activities in the square.