A molecular model system of tetraphenyl porphyrins (TPP) adsorbed on metallic substrates is systematically investigated within a joint scanning tunnelling microscopy/molecular modelling approach. The molecular conformation of TPP molecules, their adsorption on a gold surface and the growth of highly ordered TPP islands are modelled with a combination of density functional theory and dynamic force field methods. The results indicate a subtle interplay between different contributions. The molecule-substrate interaction causes a bending of the porphyrin core which also determines the relative orientations of phenyl legs attached to the core. A major consequence of this is a characteristic (and energetically most favourable) arrangement of molecules within self-assembled molecular clusters; the phenyl legs of adjacent molecules are not aligned parallel to each other (often denoted as pi-pi stacking) but perpendicularly in a T-shaped arrangement. The results of the simulations are fully consistent with the scanning tunnelling microscopy observations, in terms of the symmetries of individual molecules, orientation and relative alignment of molecules in the self-assembled clusters.