Started interval training and now my knee hurts

Hello

I wanted to ask a questions about my knee.  I have started interval training.  This is my routine.  I warm up for 5 minutes, then walk 3 minutes at 3.2 mph and then I jog 1 minute at 4.2 mph...I do this for 30 minutes.  Then I finish with a brisk walk at 3.5 mph for 20 minutes, then a 5 minute cool down.  

I have been doing this for 4 days now.  I have a fairly new pair of New Balance cross trainers.  I am noticing a slight pain near my knee now.  It's actually on the left side of my knee toward the back of my knee.  When I do my stretching I can really feel it.  What I am afraid of is, injury of course.  I read some where to help prevent knee injury you should strengthen the muscles around the knee.  First is this accurate...second, what exercises would I do to strengthen the muscles around my knee???

Also, I am still over weight by about 60 lbs...I have a BMI of 35.  So am I jumping the gun here...am I still too heavy to be jogging?  I thought since it's at one minute spurts I could handle it.  I just don't want to injure myself.  What would you do if you were me???  One more thing I have been working out for almost 6 months now and feel like this is the next step in conditioning myself and building endurance. 

Thanks for any advice that you may have 

When I started StairMastering my knees hurt a lot.  My doctor suggested trying a Glucosamine supplement.  It worked wonders and I only take 1/2 a dose daily. It has really helped me with joint pain. 

Try a Patella Tendon Knee Strap they work wonders for me.