仓库源文，站点原文

layout: post title: 糖及其GLYCAM力场中的命名约定 categories:

子曰：“必也正名乎！名不正，则言不顺；言不顺，则事不成。故君子名之必可言也，言之必可行也。” 　　　　　　　　　　　　　　　　——《论语·子路》

道可道非常道。名可名非常名。无名天地之始。有名万物之母。 　　　　　　　　　　　　　　　　——《老子·第一章》

【按】以下说明整理自维基百科 糖类, 并翻译自Amber 16手册以及GLYCAM网站说明.

糖

糖(碳水化合物): 多羟基醛或多羟基酮及其缩聚物和某些衍生物的总称

半缩醛异构化: 呋喃糖(5元环)与吡喃糖(6元环)

葡萄糖

葡萄糖的α-与β-(后者)端基异构物。

注意结合在碳5上的CH2OH基团与端基异构碳上的羟基(红色或绿色)之间的空间关系:

两者异面为(α)型, 同面则为(β)型

葡聚糖

<table id='tab-0'><caption>D-葡萄糖单体组成的多糖</caption> <tr> <td rowspan="1" colspan="3" style="text-align:center;">α-葡聚糖</td> <td rowspan="12" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="3" style="text-align:center;">β-葡聚糖</td> </tr> <tr> <th rowspan="1" colspan="1" style="text-align:center;">结合类型</th> <th rowspan="1" colspan="1" style="text-align:center;">名称</th> <th rowspan="1" colspan="1" style="text-align:center;">主要存在场所</th> <th rowspan="1" colspan="1" style="text-align:center;">结合类型</th> <th rowspan="1" colspan="1" style="text-align:center;">名称</th> <th rowspan="1" colspan="1" style="text-align:center;">主要存在场所</th> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">α-1,4</td> <td rowspan="1" colspan="1" style="text-align:center;">直链淀粉</td> <td rowspan="1" colspan="1" style="text-align:center;">大米</td> <td rowspan="1" colspan="1" style="text-align:center;">β-1,4</td> <td rowspan="1" colspan="1" style="text-align:center;">纤维素</td> <td rowspan="1" colspan="1" style="text-align:center;">树</td> </tr> <tr> <td rowspan="3" colspan="1" style="text-align:center;">α-1,6</td> <td rowspan="3" colspan="1" style="text-align:center;">右旋糖酐</td> <td rowspan="3" colspan="1" style="text-align:center;">乳酸菌</td> <td rowspan="3" colspan="1" style="text-align:center;">β-1,3</td> <td rowspan="1" colspan="1" style="text-align:center;">酵母多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">酵母</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">黑木耳多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">黑木耳</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">金藻昆布多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">金藻门</td> </tr> <tr> <td rowspan="4" colspan="1" style="text-align:center;">α-1,4/1,6</td> <td rowspan="1" colspan="1" style="text-align:center;">糖原</td> <td rowspan="1" colspan="1" style="text-align:center;">动物</td> <td rowspan="4" colspan="1" style="text-align:center;">β-1,3/1,6</td> <td rowspan="1" colspan="1" style="text-align:center;">海带多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">海草、蕈类</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">支链淀粉</td> <td rowspan="1" colspan="1" style="text-align:center;">糯米</td> <td rowspan="1" colspan="1" style="text-align:center;">热凝胶多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">细菌</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">普鲁兰多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">酵母</td> <td rowspan="1" colspan="1" style="text-align:center;">愈伤葡聚糖</td> <td rowspan="1" colspan="1" style="text-align:center;">植物</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">　</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;">平菇多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">平菇</td> </tr> <tr> <td rowspan="2" colspan="1" style="text-align:center;">　</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;">β-1,6:β-1,3</td> <td rowspan="1" colspan="1" style="text-align:center;">香菇多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">香菇, 严格钝化</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;">β-1,3/1,4</td> <td rowspan="1" colspan="1" style="text-align:center;">地衣多糖</td> <td rowspan="1" colspan="1" style="text-align:center;">地衣</td> </tr> </table>

纤维素

属于广义的糖类, D-葡萄糖以β-1,4-糖苷键组成的大分子多糖，分子量约50,000~2,500,000，相当于300~15,000个葡萄糖基

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Mol1.specs.proteins_residueColor=resType : Mol1.specs.proteins_residueColor='none';Mol1.repaint()}</script><br><span class="meta">视图: <input type="radio" name="group2" onclick="setProj1(true)">投影 <input type="radio" name="group2" onclick="setProj1(false)" checked="">正交<br>着色: <input type="checkbox" onclick="Mol1.specs.macro_colorByChain=this.checked;Mol1.repaint()">按链 <input type="checkbox" onclick="resColor1(this)">按残基<br>模式: <input type="checkbox" value="Ribbon" checked="" onclick="setDisp1(this)">飘带 <input type="checkbox" value="Backbone" onclick="setDisp1(this)">骨架 <input type="checkbox" value="PipePlank" onclick="setDisp1(this)">管板 <input type="checkbox" checked="" onclick="Mol1.specs.proteins_ribbonCartoonize=this.checked;Mol1.repaint()">卡通<br>显示: <input type="checkbox" onclick="Mol1.specs.macro_showWater=this.checked;Mol1.repaint()">水分子 <input type="checkbox" onclick="Mol1.specs.atoms_nonBondedAsStars_3D=this.checked;Mol1.repaint()">非键原子   <input type="checkbox" onclick="Mol1.specs.atoms_displayLabels_3D=this.checked;Mol1.repaint()">名称<br>颜色: <input type="radio" value="amino" name="radio2" onclick="setColor1(this)">氨基酸 <input type="radio" value="shapely" name="radio2" onclick="setColor1(this)">形状 <input type="radio" value="polarity" name="radio2" onclick="setColor1(this)">极性 <input type="radio" value="acidity" name="radio2" onclick="setColor1(this)">酸性 <input type="radio" value="rainbow" name="radio2" onclick="setColor1(this)">彩虹<br>左键: 转动   滚轮: 缩放   双击: 自动旋转开关   Alt+左键: 移动</span><br><figurecaption>Fig.1</figurecaption></figure>

3.3 碳水化合物

GLYCAM06力场

使用孤对电子(额外点)的GLYCAM06EP力场

3.3.7 GLYCAM中的碳水化合物命名约定

为了将碳水化合物以标准方式添加到建模程序中, 也为了提供用于X射线和NMR pdb文件的标准, 我们已经发展了一套三字符的编码命名方法. 使用三字符是基于RCSB PDB Advisory Committee (<www.rcsb.org/pdb/pdbac.html></www.rcsb.org>)pdb文件标准, 实用原因在于, 所有的建模和实验软件都可以读入三字符编码, 主要是用于蛋白和核酸.

作为单糖三字符PDB编码的基础, 我们为单糖引入了单字符编码(表3.5). 如果可能, 字符取自单糖名称的第一个字母(A=Ara, F=Fuc, G=Glc, I=Ido, M=Man, P=Psi, Q=Qui, R=Rib, T=Tal, X=Xyl), 但出于其他考虑, L被用于Gal, 尽管它比Lyz更不常用. 考虑到单糖衍生物存在无限多种变体, 26个字母的限制无法保证单字母(或三字母)编码能够不重复. 因此我们首先将单字符用于所有的戊糖和己糖, 非衍生的单糖. 接下来, 根据出现频率或生物重要性来分配字母.

使用三字符(表3.6到3.8), 目前的GLYCAM残基名称编码了下列内容: 碳水化合物残基名称(Glc, Gal等), 环类型(吡喃p或呋喃f), 端基异构(α或β), 异构体类型(D或L)和出现的连接位置(2-, 2,3-, 2,4,6-等). 连接位置信息非常重要, 且不能由单糖名称获知, 不像氨基酸那样. 进一步, 三字符编码选择时与氨基酸目前使用的编码不重合.

纤维二糖的GLYCAM命名约定

<table id='tab-1'><caption>表 3.4: GLYCAM目前支持的单糖. (a) 目前正在开发. (b) 只有一种对映体和环类型可用.</caption> <tr> <th rowspan="1" colspan="1" style="text-align:center;">Carbohydrate<br>碳水化合物</th> <th rowspan="1" colspan="1" style="text-align:center;">Pyranose 吡喃(己)糖<br>α/β, D/L</th> <th rowspan="1" colspan="1" style="text-align:center;">Furanose 呋喃(戊)糖<br>α/β, D/L</th> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Arabinose 树胶醛醣/阿拉伯糖/阿糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Lyxose 来苏糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Ribose 核糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Xylose 木糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Allose 阿洛糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Altrose 阿卓糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Galactose 半乳糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">a</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Glucose 葡萄糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">a</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Gulose 古罗糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Idose 艾杜糖</td> <td rowspan="1" colspan="1" style="text-align:center;">a</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Mannose 甘露糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Talose 塔洛糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Fructose 果糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Psicose 阿卢糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Sorbose 山梨糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Tagatose 塔格糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Fucose 海藻糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Quinovose 奎诺糖/异万年青糖/鸡纳糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Rhamnose 鼠李糖</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Galacturonic Acid 半乳糖醛酸</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Glucuronic Acid 葡(萄)糖醛酸</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Iduronic Acid 艾杜糖醛酸</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">N-Acetylgalactosamine N-乙酰半乳糖胺</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">N-Acetylglucosamine N-乙酰葡糖胺</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">N-Acetylmannosamine N-乙酰甘露糖胺</td> <td rowspan="1" colspan="1" style="text-align:center;">yes</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">Neu5Ac N-乙酰神经氨酸</td> <td rowspan="1" colspan="1" style="text-align:center;">yes, b</td> <td rowspan="1" colspan="1" style="text-align:center;">yes, b</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">KDN 2-keto-3-deoxy-nonulosonate</td> <td rowspan="1" colspan="1" style="text-align:center;">a,b</td> <td rowspan="1" colspan="1" style="text-align:center;">a,b</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">KDO 2-keto-3-deoxy-octulosonate</td> <td rowspan="1" colspan="1" style="text-align:center;">a,b</td> <td rowspan="1" colspan="1" style="text-align:center;">a,b</td> </tr> </table><table id='tab-2'><caption>表 3.5: 单糖GLYCAM残基名称的核心--单字母编码</caption> <tr> <th rowspan="1" colspan="1" style="text-align:center;">编号</th> <th rowspan="1" colspan="1" style="text-align:center;">碳水化合物<sup>a</sup></th> <th rowspan="1" colspan="1" style="text-align:center;">单字母编码<sup>b</sup></th> <th rowspan="1" colspan="1" style="text-align:center;">常用简写</th> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">1</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Arabinose</td> <td rowspan="1" colspan="1" style="text-align:center;">A</td> <td rowspan="1" colspan="1" style="text-align:center;">Ara</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Lyxose</td> <td rowspan="1" colspan="1" style="text-align:center;">D</td> <td rowspan="1" colspan="1" style="text-align:center;">Lyx</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">3</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Ribose</td> <td rowspan="1" colspan="1" style="text-align:center;">R</td> <td rowspan="1" colspan="1" style="text-align:center;">Rib</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">4</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Xylose</td> <td rowspan="1" colspan="1" style="text-align:center;">X</td> <td rowspan="1" colspan="1" style="text-align:center;">Xyl</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">5</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Allose</td> <td rowspan="1" colspan="1" style="text-align:center;">N</td> <td rowspan="1" colspan="1" style="text-align:center;">All</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">6</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Altrose</td> <td rowspan="1" colspan="1" style="text-align:center;">E</td> <td rowspan="1" colspan="1" style="text-align:center;">Alt</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">7</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Galactose</td> <td rowspan="1" colspan="1" style="text-align:center;">L</td> <td rowspan="1" colspan="1" style="text-align:center;">Gal</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">8</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Glucose</td> <td rowspan="1" colspan="1" style="text-align:center;">G</td> <td rowspan="1" colspan="1" style="text-align:center;">Glc</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">9</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Gulose</td> <td rowspan="1" colspan="1" style="text-align:center;">K</td> <td rowspan="1" colspan="1" style="text-align:center;">Gul</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">10</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Idose</td> <td rowspan="1" colspan="1" style="text-align:center;">I</td> <td rowspan="1" colspan="1" style="text-align:center;">Ido</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">11</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Mannose</td> <td rowspan="1" colspan="1" style="text-align:center;">M</td> <td rowspan="1" colspan="1" style="text-align:center;">Man</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">12</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Talose</td> <td rowspan="1" colspan="1" style="text-align:center;">T</td> <td rowspan="1" colspan="1" style="text-align:center;">Tal</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">13</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Fructose</td> <td rowspan="1" colspan="1" style="text-align:center;">C</td> <td rowspan="1" colspan="1" style="text-align:center;">Fru</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">14</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Psicose</td> <td rowspan="1" colspan="1" style="text-align:center;">P</td> <td rowspan="1" colspan="1" style="text-align:center;">Psi</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">15</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Sorbose</td> <td rowspan="1" colspan="1" style="text-align:center;">B<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">Sor</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">16</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Tagatose</td> <td rowspan="1" colspan="1" style="text-align:center;">J</td> <td rowspan="1" colspan="1" style="text-align:center;">Tag</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">17</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Fucose (6-deoxy D-galactose)</td> <td rowspan="1" colspan="1" style="text-align:center;">F</td> <td rowspan="1" colspan="1" style="text-align:center;">Fuc</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">18</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Quinovose (6-deoxy D-glucose)</td> <td rowspan="1" colspan="1" style="text-align:center;">Q</td> <td rowspan="1" colspan="1" style="text-align:center;">Qui</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">19</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Rhamnose (6-deoxy D-mannose)</td> <td rowspan="1" colspan="1" style="text-align:center;">H</td> <td rowspan="1" colspan="1" style="text-align:center;">Rha</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">20</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Galacturonic Acid</td> <td rowspan="1" colspan="1" style="text-align:center;">O<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">GalA</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">21</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Glucuronic Acid</td> <td rowspan="1" colspan="1" style="text-align:center;">Z<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">GlcA</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">22</td> <td rowspan="1" colspan="1" style="text-align:center;">D-Iduronic Acid</td> <td rowspan="1" colspan="1" style="text-align:center;">U<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">IdoA</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">23</td> <td rowspan="1" colspan="1" style="text-align:center;">D-N-Acetylgalactosamine</td> <td rowspan="1" colspan="1" style="text-align:center;">V<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">GalNac</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">24</td> <td rowspan="1" colspan="1" style="text-align:center;">D-N-Acetylglucosamine</td> <td rowspan="1" colspan="1" style="text-align:center;">Y<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">GlcNAc</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">25</td> <td rowspan="1" colspan="1" style="text-align:center;">D-N-Acetylmannosamine</td> <td rowspan="1" colspan="1" style="text-align:center;">W<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">ManNAc</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">26</td> <td rowspan="1" colspan="1" style="text-align:center;">N-Acetyl-neuraminic Acid</td> <td rowspan="1" colspan="1" style="text-align:center;">S<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">NeuNAc, Neu5Ac</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;">KDN</td> <td rowspan="1" colspan="1" style="text-align:center;">KN<sup>c,d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">KDN</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;">KDO</td> <td rowspan="1" colspan="1" style="text-align:center;">KO<sup>c,d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">KDO</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;">N-Glycolyl-neuraminic Acid</td> <td rowspan="1" colspan="1" style="text-align:center;">SG<sup>c,d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">NeuNGc, Neu5Gc</td> </tr> <tfoot><tr><td colspan="4" style="text-align:left"> <sup>a</sup> 残基对应的prep文件目前不可用, 可联系Woods课题组(<a href="">www.glycam.org</a>)获取结构和电荷参数.<br> <sup>b</sup> 小写字母表示L型糖, 因此L-Fucose应表示为<code>f</code>, 参见表3.8.<br> <sup>c</sup> 对于不能指定单字母编码的不常用残基, 其名称忽略了一些信息.<br> <sup>d</sup> 在将来, 这些残基的命名方法可能会改变. 请查看<a href="">www.glycam.org</a>网站的最新信息.<br> </td></tr></tfoot> </table><table id='tab-3'><caption>表 3.6: 基于GLYCAM单字母编码, D型吡喃戊糖和己糖的三字母编码中连接位置与端基异构构象的指定方法</caption> <tr> <th rowspan="1" colspan="1" style="text-align:center;"></th> <th rowspan="1" colspan="1" style="text-align:center;">α-D-Glcp</th> <th rowspan="1" colspan="1" style="text-align:center;">β-D-Galp</th> <th rowspan="1" colspan="1" style="text-align:center;">α-D-Arap</th> <th rowspan="1" colspan="1" style="text-align:center;">β-D-Xylp</th> </tr> <tr> <th rowspan="1" colspan="1" style="text-align:center;">连接位置</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">末端<sup>b</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">0GA<sup>b</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">0LB</td> <td rowspan="1" colspan="1" style="text-align:center;">0AA</td> <td rowspan="1" colspan="1" style="text-align:center;">0XB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">1-<sup>c</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">1GA<sup>c</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">1LB</td> <td rowspan="1" colspan="1" style="text-align:center;">1AA</td> <td rowspan="1" colspan="1" style="text-align:center;">1XB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2-</td> <td rowspan="1" colspan="1" style="text-align:center;">2GA</td> <td rowspan="1" colspan="1" style="text-align:center;">2LB</td> <td rowspan="1" colspan="1" style="text-align:center;">2AA</td> <td rowspan="1" colspan="1" style="text-align:center;">2XB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">3-</td> <td rowspan="1" colspan="1" style="text-align:center;">3GA</td> <td rowspan="1" colspan="1" style="text-align:center;">3LB</td> <td rowspan="1" colspan="1" style="text-align:center;">3AA</td> <td rowspan="1" colspan="1" style="text-align:center;">3XB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">4-</td> <td rowspan="1" colspan="1" style="text-align:center;">4GA</td> <td rowspan="1" colspan="1" style="text-align:center;">4LB</td> <td rowspan="1" colspan="1" style="text-align:center;">4AA</td> <td rowspan="1" colspan="1" style="text-align:center;">4XB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">6-</td> <td rowspan="1" colspan="1" style="text-align:center;">6GA</td> <td rowspan="1" colspan="1" style="text-align:center;">6LB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2,3-</td> <td rowspan="1" colspan="1" style="text-align:center;">ZGA<sup>d</sup></td> <td rowspan="1" colspan="1" style="text-align:center;">ZLB</td> <td rowspan="1" colspan="1" style="text-align:center;">ZAA</td> <td rowspan="1" colspan="1" style="text-align:center;">ZXB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2,4-</td> <td rowspan="1" colspan="1" style="text-align:center;">YGA</td> <td rowspan="1" colspan="1" style="text-align:center;">YLB</td> <td rowspan="1" colspan="1" style="text-align:center;">YAA</td> <td rowspan="1" colspan="1" style="text-align:center;">YXB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2,6-</td> <td rowspan="1" colspan="1" style="text-align:center;">XGA</td> <td rowspan="1" colspan="1" style="text-align:center;">XLB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">3,4-</td> <td rowspan="1" colspan="1" style="text-align:center;">WGA</td> <td rowspan="1" colspan="1" style="text-align:center;">WLB</td> <td rowspan="1" colspan="1" style="text-align:center;">WAA</td> <td rowspan="1" colspan="1" style="text-align:center;">WXB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">3,6-</td> <td rowspan="1" colspan="1" style="text-align:center;">VGA</td> <td rowspan="1" colspan="1" style="text-align:center;">VLB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">4,6-</td> <td rowspan="1" colspan="1" style="text-align:center;">UGA</td> <td rowspan="1" colspan="1" style="text-align:center;">ULB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2,3,4-</td> <td rowspan="1" colspan="1" style="text-align:center;">TGA</td> <td rowspan="1" colspan="1" style="text-align:center;">TLB</td> <td rowspan="1" colspan="1" style="text-align:center;">TAA</td> <td rowspan="1" colspan="1" style="text-align:center;">TXB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2,3,6-</td> <td rowspan="1" colspan="1" style="text-align:center;">SGA</td> <td rowspan="1" colspan="1" style="text-align:center;">SLB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2,4,6-</td> <td rowspan="1" colspan="1" style="text-align:center;">RGA</td> <td rowspan="1" colspan="1" style="text-align:center;">RLB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">3,4,6-</td> <td rowspan="1" colspan="1" style="text-align:center;">QGA</td> <td rowspan="1" colspan="1" style="text-align:center;">QLB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2,3,4,6-</td> <td rowspan="1" colspan="1" style="text-align:center;">PGA</td> <td rowspan="1" colspan="1" style="text-align:center;">PLB</td> <td rowspan="1" colspan="1" style="text-align:center;"></td> <td rowspan="1" colspan="1" style="text-align:center;"></td> </tr> <tfoot><tr><td colspan="5" style="text-align:left"> <sup>a</sup> 在吡喃糖中, <code>A</code>表示α构象, <code>B</code>表示β构象.<br> <sup>b</sup> 以前称为<code>GA</code>, 前缀<code>0</code>表示没有氧原子能够成键, 即, 残基位于链的结束处.<br> <sup>c</sup> 引入以便能形成 1-1' 连接, 如α-D-Glc-1-1'-α-D-Glc {1GA 0GA}.<br> <sup>d</sup> 涉及多于一个的连接位置时, 有必要避免使用前缀字母, 以免导致形成的三字母编码与氨基酸所用的重复, 如ALA<br> </td></tr></tfoot> </table><table id='tab-4'><caption>表 3.7: 基于GLYCAM单字母编码, D型呋喃戊糖和己糖的三字母编码中连接位置与端基异构构象的指定方法. 在呋喃糖中 D(down) 表示α; U(up)表示β.</caption> <tr> <th rowspan="1" colspan="1" style="text-align:center;"></th> <th rowspan="1" colspan="1" style="text-align:center;">α-D-Glcf</th> <th rowspan="1" colspan="1" style="text-align:center;">β-D-Manf</th> <th rowspan="1" colspan="1" style="text-align:center;">α-D-Araf</th> <th rowspan="1" colspan="1" style="text-align:center;">β-D-Xylf</th> </tr> <tr> <th rowspan="1" colspan="1" style="text-align:center;">连接位置</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">末端</td> <td rowspan="1" colspan="1" style="text-align:center;">0GD</td> <td rowspan="1" colspan="1" style="text-align:center;">0MU</td> <td rowspan="1" colspan="1" style="text-align:center;">0AD</td> <td rowspan="1" colspan="1" style="text-align:center;">0XU</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">1-</td> <td rowspan="1" colspan="1" style="text-align:center;">1GD</td> <td rowspan="1" colspan="1" style="text-align:center;">1MU</td> <td rowspan="1" colspan="1" style="text-align:center;">1AD</td> <td rowspan="1" colspan="1" style="text-align:center;">1XU</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2-</td> <td rowspan="1" colspan="1" style="text-align:center;">2GD</td> <td rowspan="1" colspan="1" style="text-align:center;">2MU</td> <td rowspan="1" colspan="1" style="text-align:center;">2AD</td> <td rowspan="1" colspan="1" style="text-align:center;">2XU</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">3-</td> <td rowspan="1" colspan="1" style="text-align:center;">3GD</td> <td rowspan="1" colspan="1" style="text-align:center;">3MU</td> <td rowspan="1" colspan="1" style="text-align:center;">3AD</td> <td rowspan="1" colspan="1" style="text-align:center;">3XU</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> </tr> </table><table id='tab-5'><caption>表 3.8: L型吡喃戊糖和己糖的三字母编码中连接位置与端基异构构象的指定方法.</caption> <tr> <th rowspan="1" colspan="1" style="text-align:center;"></th> <th rowspan="1" colspan="1" style="text-align:center;">α-L-Glcp</th> <th rowspan="1" colspan="1" style="text-align:center;">β-L-Manp</th> <th rowspan="1" colspan="1" style="text-align:center;">α-L-Arap</th> <th rowspan="1" colspan="1" style="text-align:center;">β-L-Xylp</th> </tr> <tr> <th rowspan="1" colspan="1" style="text-align:center;">连接位置</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> <th rowspan="1" colspan="1" style="text-align:center;">残基名称</th> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">末端</td> <td rowspan="1" colspan="1" style="text-align:center;">0gA</td> <td rowspan="1" colspan="1" style="text-align:center;">0mB</td> <td rowspan="1" colspan="1" style="text-align:center;">0aA</td> <td rowspan="1" colspan="1" style="text-align:center;">0xB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">1-</td> <td rowspan="1" colspan="1" style="text-align:center;">1gA</td> <td rowspan="1" colspan="1" style="text-align:center;">1mB</td> <td rowspan="1" colspan="1" style="text-align:center;">1aA</td> <td rowspan="1" colspan="1" style="text-align:center;">1xB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">2-</td> <td rowspan="1" colspan="1" style="text-align:center;">2gA</td> <td rowspan="1" colspan="1" style="text-align:center;">2mB</td> <td rowspan="1" colspan="1" style="text-align:center;">2aA</td> <td rowspan="1" colspan="1" style="text-align:center;">2xB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">3-</td> <td rowspan="1" colspan="1" style="text-align:center;">3gA</td> <td rowspan="1" colspan="1" style="text-align:center;">3mB</td> <td rowspan="1" colspan="1" style="text-align:center;">3aA</td> <td rowspan="1" colspan="1" style="text-align:center;">3xB</td> </tr> <tr> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> <td rowspan="1" colspan="1" style="text-align:center;">···</td> </tr> </table>