Introduction

Loop classification table

• Class - The class of loops defined by the loop clustering in the paper, e.g., aa{b}aa is a loop that links two alpha helices with residues of beta Ramachandran angle in the loop.
  
• CN - Class number, a numerical number for the definition of the class, e.g., 1.1.1 and so on
  
• NR - Number of residues in the loop. This number may vary in the same loop class.
  
• RMSD(Å) - Root Mean Square Deviation of the superposed loops and their bracing secondary structure. It is used to quantify agreement but not for clustering.
  
• Consensus - Sequence Consensus within the loop class. Capital letters for conserved residues, such as G - Glycine, D - Aspatic acid. p for polar residues [D, E, H, N, Q, R, S, T, Y]; h for non-polar residues [A, C, F, G, I, L, M, P, V, W, Y]. Tyr (Y) is assigned for both polar and non-polar residues. X denotes no sequence consensus.
  
• Nomenclature - Classical Nomenclature such as "Kinked helix", "Type II" beta-turn, etc.
  

Ramanchandran Angles

b b b p o M e e e b b b p o M M e e b b b p . l l s e a a a T . l l g N N a a a . U l g N N a a a . U g g N I a a a . G G G I e F F F o e e e e b b b p o e e e e +180 0 (psi) -180 -180 0 +180 phi

a: alpha helix l: left handed alpha helix b: beta strand p: parellel beta sheet g: gamma e: epsilon l/g: bridge region between left handed alpha helix and gamma b/p: bridge region between beta strand and parellel beta sheet l/g: bridge region between left handed alpha helix and gamma l/g: bridge region between left handed alpha helix and gamma l/g: bridge region between left handed alpha helix and gamma

Java Picture

Java pictures of all the loop class were generated by superimposing four loops in each class. Here is an example of the java picture. The table at the right side of the picture gives the PDB code and residue ID of these four loops. You may click the PDB code to check the PDB header lines of the protein.

PDB Code Residue ID 8acn 650-655 1ddt 310-315 2hsc 161-166 8acn 408-413 Mouse Buttons Left - Rotate Middle - Move Right - Zoom Up: Zoom Out (smaller) Down: Zoom In (bigger)

[ alpha-alpha | alpha-beta | beta-alpha | beta-beta links | beta-hairpins ]

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Last modified: Mon, 18-Aug-1997