Clustering molecular conformations into ''families'' is a common proce
dure in conformational analysis of molecular systems. An implicit assu
mption which often underlies this clustering approach is that the resu
lting geometric families reflect the energetic structure of the system
's potential energy surface. In a broader context we address the quest
ion whether structural similarity is correlated with energy basins, i.
e., whether conformations that belong to the same energy basin are als
o geometrically similar. 'Topological mapping' and principal coordinat
e projections are used here to address this question and to assess the
quality of the 'family clustering' procedure, Applying the analysis t
o a small tetrapeptide it was found that the general correlation that
exists between energy basins and structural similarity is not absolute
. Clusters generated by the geometric 'family clustering' procedure do
not always reflect the underlying energy basins. In particular it was
found that the 'family tree' that is generated by the 'family cluster
ing' procedure is completely inconsistent with its real topological co
unterpart, the 'disconnectivity' graph of this system. It is also demo
nstrated that principal coordinate analysis is a powerful visualizatio
n technique which, at least for this system, works better when distanc
es are measured in dihedral angle space rather than in cartesian space
. (C) 1997 Wiley-Liss, Inc.