Do not just send them a payment. Contact the IRS first, and you may want to elicit the help of a CPA in your hometown.
The notice should give you specific reasons as to where the change is coming from. It could be a decrease in your deductions, or an increase in your income (maybe you inadvertently left off income you didn't know about) etc...
Contact the IRS at the number listed on the notice and get them to explain any decrease in a deduction (or expense). Be ready to provide them with any documentation that they need. Just because the IRS says that they disagree with one of your deductions (or expenses) does not mean that you have to agree with their disagreement. Which is why it may be a good idea to get a local CPA involved.
If you did inadvertently forget to include any income, there may be little you can do. In this case, if you can show that you did not leave the income off in an attempt to skirt your responsibilities, then you should be able to get the IRS to abate any penalties. However, they will not forgive any interest due in a situation where you did not include all your income.
Also, the following website is an excellent tool in learning why the IRS sent you a letter to begin with. The letter you received should have a identifying number or type of notice (for example it could be a CP05). Use this number or "identifier" to search for more information.