PREDICTION OF CONFORMATIONAL STATES OF AMINO-ACIDS USING A RAMACHANDRAN PLOT

(phi, psi) data from crystal structures of 221 proteins having high re solution and sequence similarity cut-off at the 25% level were analyse d by dividing the Ramachandran plot in three regions representing thre e conformational states: (i) conformational state 1: conformations in the (phi, psi range from (-140 degrees, -100 degrees) to (0 degrees, 0 degrees); (ii) conformational state 2: conformations with (phi, psi) from(-180 degrees, 80 degrees) to (0 degrees, 180 degrees); and (iii) conformational state 3: all the remaining conformations in the (phi, p si) plane which are not included in the above two conformational state s. Normalized probability values of the occurrence of single amino aci d residues in conformational regions 1-3 and similar values for dipept ides were calculated. Comparisons of single residue and dipeptide norm alized probability values have shown that short-range interactions, al though strong, destabilize conformational states of only 44 dipeptides out of the 400 x 9 possible states. However, dipeptide frequency valu es provide better resolving power than single-residue potentials when used to predict conformational states of residues in a protein from it s primary structure. The simple approach used in the present study to predict conformational states yields an accuracy of >70% for 14 protei ns and an accuracy in the range of 50-70% for 247 proteins. Thus these studies point out yet another use of the Ramachandran plot and the ro le of tertiary interactions in protein folding. (C) Munksgaard 1996.