While there has been much speculation on the role the lipid matrix plays in controlling and mediating the inter-molecular dynamics of proteins, there has been little direct evidence for how the lipid bilayer can mediate the supra-molecular organization of these proteins. With the technique of X-ray in-plane scattering, we can directly measure the correlation function of gramicidin channels in the plane of the bilayer. We have studied the simple case of gramicidin incorporated into model Dilauroyl and Dimyristoyl-Phosphocholine (DL-,DMPC) membranes, and have seen how changing the membrane thickness changes peptide-peptide correlation. In the fluid phase, DLPC and DMPC present an elastic medium that can perhaps match the hydrophobic length of the peptide. The resulting membrane deformation energy is expected to cause inter-peptide attraction. Indeed, the scattering data shows that the gramicidin-gramicidin correlation distance is smaller in DMPC than in DLPC. Thus we have obtained direct evidence of membrane mediated peptide-peptide interaction. As the temperature drops and DMPC approaches its main transition temperature, gramicidin exhibits close packing. This may indicate that the channels are being excluded from gel lipid regions and are packing closer together.