Human beings localize a sound source position by using interaural differences in time and sound pressure levels, along with spectral features such as spectral peaks and notches, which are involved in head-related transfer functions (HRTFs). The HRTFs represent acoustic transfer functions between a sound source and a listener's ears. Spectral peaks and notches produced because of a pinna reportedly provide cues for localization of elevation angles. The pinna shape varies markedly among individuals, thereby resulting in an interindividual variation of the HRTFs. Researchers have therefore proposed an estimation or individualization method of HRTFs using anthropometric features related to a pinna shape. However, because pinna effects on HRTFs' spectral features have not been clarified sufficiently, it remains unclear what anthropometric features should be considered when using such HRTF estimation methods. For investigating relevant physical phenomena in HRTFs, this paper reports a boundary element simulation of pinna-related transfer functions (PRTFs) and pinna surface pressures to observe resonance modes arising in a pinna cavity when the spectral notches occur for sound sources on the median plane. Numerical results show that, at frequencies below 12 kHz, nodal lines of the resonance mode exist as roughly perpendicular to the incident angle of the sound wave irrespective of the source elevation, suggesting that the pinna width in the direction of the incident angle dominantly characterizes how the resonance mode appears, which indicates that simple anthropometric measures, such as a pinna's vertical and horizontal widths, are insufficient for HRTF estimation for sound sources at an arbitrary elevation.