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4) Hydrogen bond A hydyogen bond plays a very important role in protein and enzyme models. It saves time if you known in advance the locations of hydrogen bonds in a model you are going to build. Hydrogen bonds occur mainly between N and O. Therefore, if you collect N-O distances less than 3.2A from protein coordinates calculation. it means that the hydrogen bonds are mostly known. Amino acid backbones Bio-101-1/5 in the peptide bond portions are for hydrogen bonds. Those Bio-102-1/5 are for non-hydrogen bond. The difference between them determines if the Hydrogen and Oxygen are for hydrogen bond or non-hydrogen bond. Bio-101 and Bio-102 can be easily changed into each other by substituting hydrogen and oxygen respectively. Two types of hydrogen for hydrogen bond are prepared in SET, a rigid type Bio-15 and a flexible type Bio-26. Actual hydyogen bonds are often fairly distorted, and the flexible tube Bio-26 will be effective in many cases for more precise modeling. |
 Fig. 6  Fig. 7 |
 Fig. 5 | |
|
Hydrogen bond list of Main chain (N-O bond distance less than 3.2A) |
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| 6 | GLU | N | ..... | 3 | SER | 0 | 2.922A |
| 7 | TRY | N | ..... | 3 | SER | 0 | 3.028A |
| 10 | VAL | N | ..... | 6 | GLU | 0 | 3.197A |
| 10 | VAL | N | ..... | 7 | TRY | 0 | 3.010A |
| 11 | LEU | N | ..... | 7 | TRY | 0 | 3.023A |
| 12 | HIS | N | ..... | 8 | GLN | 0 | 3.028A |
| 15 | ALA | N | ..... | 11 | LEU | 0 | 3.170A |
| 16 | LYS | N | ..... | 14 | TRY | 0 | 3.124A |
| 17 | VAL | N | ..... | 14 | TRY | 0 | 3.105A |
| 18 | GLU | N | ..... | 14 | TRY | 0 | 3.108A |
| 19 | ALA | N | ..... | 17 | VAL | 0 | |
| 20 | ASP | N | ..... | 17 | VAL | 0 | |
| 21 | VAL | N | ..... | 17 | VAL | ||
| 24 | HIS | N | ..... | 20 | ASP | ||
| 25 | GLY | N | ..... | ||||
| 26 | GLN | N | 2.187A | ||||
| 27 | ASP | N | 2.956A | ||||
| 28 | ILE | 0 | 3.164A | ||||
| 30 | ILE | 0 | 2.955A | ||||
| 63 | LYS | 0 | 3.108A | ||||
| ..... | 64 | THR | 0 | 3.002A | |||
| ..... | 65 | GLY | 0 | 3.192A | |||
| N | ..... | 66 | VAL | 0 | 2.891A | ||
| N | ..... | 67 | THR | 0 | 3.068A | ||
| 72 | LEU | N | ..... | 68 | VAL | 0 | 2.921A |
| 73 | GLY | N | ..... | 69 | LEU | 0 | 2.950A |
| 74 | ALA | N | ..... | 70 | THR | 0 | 3.033A |
| 74 | ALA | N | ..... | 74 | ALA | 0 | 3.176A |
| 75 | ILE | N | ..... | 72 | LEU | 0 | 2.818A |
| 76 | LEU | N | ..... | 72 | LEU | 0 | 2.843A |
| 72 | LEU | N | ..... | 68 | VAL | 0 | 2.921A |
| 73 | GLY | N | ..... | 69 | LEU | 0 | 2.950A |
| 74 | ALA | N | ..... | 70 | THR | 0 | 3.033A |
| 74 | ALA | N | ..... | 74 | ALA | 0 | 3.176A |
| 75 | ILE | N | ..... | 72 | LEU | 0 | 2.818A |
| 76 | LEU | N | ..... | 72 | LEU | 0 | 2.843A |
 HGS Molecular Structure Model HGS HINOMOTO PLASTICS CO., LTD. 1-10-24, Meguro-Honcho, Meguro-ku, Tokyo, Japan PHONE: +81-3-3714-7226 FAX: +81-3-3714-4657 E-MAIL(technical support): hgs@po.sphere.ne.jp E-MAIL(order support): t_kaneko@maruzen.co.jp |