Contributions to social security (including pension) will be automatically deducted from your salary. You contract states your gross salary before any deductions. This is if your job is an actual full-time position (i.e. with a monthly salary, not some sort of freelance position).
Holiday allowance ("Urlaubsgeld") is a matter of negotiations (but while it was once customary it's for the most part an obscure thing of the past now).
Travel expenses are usually handled on a case by case basis, but you should ask during job negotiations if there is a budget for travel and on which basis this is allocated.