Proteins will behave similarly to phospholipids in water; the polar groups will form favorable interactions on the surface with water, while the hydrophobic groups will be in the core and away from the water molecules. Usually, amino acids with non-polar residues will be found in the core of proteins. Tryptophan has a nonpolar side chain, and will thus be found in the core of a protein that is in a aqueous environment. 

In aqueous solutions, lipid molecules are surrounded by a lattice-like ring of water molecules known as a clathrate shell. This locks up previously free water molecules in this state, which is not entropically favored. Though it is unavoidable that some water molecules will have to be robbed of some of their freedom of motion by forming at least one clathrate shell, the ideal scenario thermodynamically is the one in which the fewest water molecules are stuck in the shell as possible. As a result, lipid bubbles in aqueous solutions tend to go from many to one, as this results in the  clathrate shell with the fewest number of water molecules. In the process, many smaller clathrate shells are broken, and many water molecules are freed, thus increasing the entropy of the system. 

Hydrophobic effects require water to occur. The reason that hydrophobic groups tend to group together is that by doing so, the network of water molecules around them stays intact. There are no other special forces at play between hydrophobic groups. It is precisely the non-polar nature of hydrophobic groups that gives them their character; water molecules are polar. Cell membranes have a phospholipid bilayer with internal hydrophobic regions (the lipid tails), holding together the membrane.

This is called the hydrophobic effect. Although initially the water molecules arrange themselves in clathrates and become more ordered, their exclusion of the hydrophobic/nonpolar solute is entropically driven and energetically favorable.

Phospholipids are amphipathic - in other words they are simultaneously hydrophobic and hydrophilic. They have hydrophobic carbon tails and hydrophilic head groups. Because the carbon chains are repulsed by water, phospholipids come together so that their carbon tails are touching and the polar heads face out in either direction. These hydrophobic interactions ultimately form a phospholipid bilayer.

Hydrogen bonds are the strongest of the intermolecular forces. However, that strength is little in comparison the strength of intramolecular forces, such as ionic and covalent bonds. The strongest of the listed forces is covalent bonds, followed by ionic bonds, hydrogen bonds, and then finally London dispersion forces.

Hydrogen bonds are important in biochemistry because of the incredible effect that they have on life due to their relative strength. But remember, this strength is not nearly as as strong as the covalent and ionic bonds, which actually hold atoms within the same molecule together. 

Note, hydrogen bonds can be either an intermolecular or an intramolecular force. A hydrogen bond is considered intramolecular if it is occurring between different molecules, and intermolecular if it is occurring within the same molecule.

Hydrophobic molecules are nonpolar molecules - from the Greek "hydro-" water and "phobic" fearing. Examples of hydrophobic molecules are lipids.