Can i pay the tax dues on 1040x using https://www.irs.gov/payments ird direcpay or credit or debit card

[Opus 17]

Yes.  The IRS payment site has both bank debit and credit card options.   Be sure to select "2016 form 1040" or "2016 form 1040X" as the reason.

[arivamudhan]

will it be a issue if i mail just the 1040x form to IRS without check, since i am making online payment i will be covered and no question will arise right

[Opus 17]

It will be fine.  The amended returns take a long time to process, by the time they do, they will see the payment in the account.  To avoid late fees, pay by April 18.