Bwl., in press
- G. N. Ramachandran, S. K. Mazumdar, K. Venkatesan, A. V. Lakshiminarayanan, J . Mol
- Biophysics Research Division University of…
The conformation of a pair of peptide units in a polypeptide chain can be denoted in terms of a pair of dihedral angles 4, +'.I [The two angles should be denoted by + and $ ($ = 180" + $'), according to the latest conventions2 agreed to by the workers in this field a t the 1965 Gordon Conference on Proteins (New Hampton, June 27th to July 2nd, 1965) and the IOPAB symposium on Some Biological Systems a t the Molecular Level held in Naples from September 8-11, 1965. As these angles are not specifically discussed in this paper, the new conventions are not discussed further here.] All the conformations allowed by the exclusion of short contacts have been plotted on the (+,+') diagram when the alpha carbon atom a t which the peptide units are linked belongs to a glycyl or an alanyl residue.3 The restrictions of the allowed regions for some of the other amino acids have also been discussed r e ~ e n t l y , ~ making use of certain assumptions about the orientation of the CY and other atoms with respect to the backbone of the chain. We have for some time been making a survey of the known facts (contained in the published x-ray structure determinations) regarding the conformation of the side groups in various examples. A detailed report is in preparation and this note is a short r6sum6 of the main results. 1. The length of the bond C@Cy is not sensibly different from the standard value of 1.54 A. for a single bond. However, the angle CaC@Cy is significantly larger than the tetrahedral value and was found to have a mean value of 114" in 27 cases. (The authors are grateful to Professor Shneior Lifson of the Weizman Institute of Science for pointing out this possibility from a similar behavior in hydrocarbon chains, which led to their looking for the actual value of this angle. The earlier authors (e.g., Ref. 4) used avalue of 110" for this angle. The larger value has been used in examining the effect on the theoretically possible conformations of the type studied in ref. 4 (C. M. Venkatachalam and G. N. Ramachandran, in preparation).) The angles a t the alpha carbon atom (such as NC*C@, C'CaC@, and NCaC') were however found to be not significantly different from 109.5" in a systematic way. 2. The CY atom was found to occur close to one of three possible positions, one trans and two gauche about the C"C@ bond, with respect to the amino nitrogen. We may define an angle XI, by which CY has to be rotated about the C"C@ direction from its position when it is cis to N, in a clockwise sense looking from C" to C@. (This follows the st,andard conventions, mentioned above.) The three positions are then close to XI = 60, 180, and 300°, which may be denoted by I, 11, and I11 (Fig. 1). 3. The three positions were found to be fairly well represented in different side groups. Neglecting examples in which the gamma position in the side chain is occupied by an oxygen or sulfur atom, the position I was found to occur in ten cases, position I1 in 11 cases, and position I11 in 17 cases. However, oxygen and sulfur were found to occur mostly in position I (6 cases) as against zero for position 11 and 4 for position 111. Taking into account all the atoms, the mean values of x1 for the three positions were 66' for I, 184' for 11, and 294" for 111. The deviations from 60, 180, and 300", respectively, seem to be significant, although the data are not large enough to attach a standard deviation to these values. Thus, for position I, only three examples had x1 less than 60", while 13 had XI greater than 60".