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class="vector-toc-numb">2</span> <span>Contact map prediction</span> </div> </a> <ul id="toc-Contact_map_prediction-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-HB_Plot" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#HB_Plot"> <div class="vector-toc-text"> <span class="vector-toc-numb">3</span> <span>HB Plot</span> </div> </a> <button aria-controls="toc-HB_Plot-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle HB Plot subsection</span> </button> <ul id="toc-HB_Plot-sublist" class="vector-toc-list"> <li id="toc-Features" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Features"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.1</span> <span>Features</span> </div> </a> <ul id="toc-Features-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Secondary_structure_elements_in_HB_plot" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Secondary_structure_elements_in_HB_plot"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.2</span> <span>Secondary structure elements in HB plot</span> </div> </a> <ul id="toc-Secondary_structure_elements_in_HB_plot-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Examples_of_usage" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Examples_of_usage"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.3</span> <span>Examples of usage</span> </div> </a> <ul id="toc-Examples_of_usage-sublist" class="vector-toc-list"> <li id="toc-Cytochrome_P450s" class="vector-toc-list-item vector-toc-level-3"> <a class="vector-toc-link" href="#Cytochrome_P450s"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.3.1</span> <span>Cytochrome P450s</span> </div> </a> <ul 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class="mw-body-content"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><figure class="mw-default-size mw-halign-right" typeof="mw:File/Thumb"><a href="/wiki/File:Protein_Contact_Map,_2-Color,_2QIP-A.png" class="mw-file-description"><img alt="Protein contact map" src="//upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Protein_Contact_Map%2C_2-Color%2C_2QIP-A.png/220px-Protein_Contact_Map%2C_2-Color%2C_2QIP-A.png" decoding="async" width="220" height="220" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/8/8d/Protein_Contact_Map%2C_2-Color%2C_2QIP-A.png 1.5x" data-file-width="300" data-file-height="300" /></a><figcaption>Protein Contact Map of protein VPA0982 from <i>Vibrio parahaemolyticus</i></figcaption></figure> <p>A <b>protein contact map</b> represents the distance between all possible <a href="/wiki/Amino_acid" title="Amino acid">amino acid residue</a> pairs of a three-dimensional <a href="/wiki/Protein_structure" title="Protein structure">protein structure</a> using a binary two-dimensional <a href="/wiki/Matrix_(mathematics)" title="Matrix (mathematics)">matrix</a>. For two residues <span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle i}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <mi>i</mi> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle i}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/add78d8608ad86e54951b8c8bd6c8d8416533d20" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.338ex; width:0.802ex; height:2.176ex;" alt="{\displaystyle i}"></span> and <span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle j}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <mi>j</mi> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle j}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/2f461e54f5c093e92a55547b9764291390f0b5d0" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.671ex; margin-left: -0.027ex; width:0.985ex; height:2.509ex;" alt="{\displaystyle j}"></span>, the <span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle ij}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <mi>i</mi> <mi>j</mi> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle ij}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/53fcc7b57da64979c370eb150eb5a61a625a08e8" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.671ex; width:1.761ex; height:2.509ex;" alt="{\displaystyle ij}"></span> element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise. Various contact definitions have been proposed: The distance between the C<sub>α</sub>-C<sub>α</sub> atom with threshold 6-12 <a href="/wiki/%C3%85ngstr%C3%B6m" class="mw-redirect" title="Ångström">Å</a>; distance between C<sub>β</sub>-C<sub>β</sub> atoms with threshold 6-12 Å (C<sub>α</sub> is used for <a href="/wiki/Glycine" title="Glycine">Glycine</a>); and distance between the side-chain <a href="/wiki/Center_of_mass" title="Center of mass">centers of mass</a>. </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Overview">Overview</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=1" title="Edit section: Overview"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Contact maps provide a more reduced representation of a protein structure than its full 3D atomic coordinates. The advantage is that contact maps are invariant to rotations and translations. They are more easily predicted by <a href="/wiki/Machine_learning" title="Machine learning">machine learning</a> methods. It has also been shown that under certain circumstances (e.g. low content of erroneously predicted contacts) it is possible to reconstruct the 3D coordinates of a protein using its contact map.<sup id="cite_ref-Pietal2015_1-0" class="reference"><a href="#cite_note-Pietal2015-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Vassura2008_2-0" class="reference"><a href="#cite_note-Vassura2008-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> </p><p>Contact maps are also used for protein <a href="/wiki/Superimposition" title="Superimposition">superimposition</a> and to describe similarity between protein structures.<sup id="cite_ref-Holm1996_3-0" class="reference"><a href="#cite_note-Holm1996-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> They are either predicted from <a href="/wiki/Protein_sequence" class="mw-redirect" title="Protein sequence">protein sequence</a> or calculated from a given structure. </p> <div class="mw-heading mw-heading2"><h2 id="Contact_map_prediction">Contact map prediction</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=2" title="Edit section: Contact map prediction"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>With the availability of high numbers of genomic sequences it becomes feasible to analyze such sequences for <i>coevolving residues</i>. The effectiveness of this approach results from the fact that a mutation in position <i>i</i> of a protein is more likely to be associated with a mutation in position <i>j</i> than with a back-mutation in <i>i</i> if both positions are functionally coupled (e.g. by taking part in an enzymatic domain, or by being adjacent in a folded protein, or even by being adjacent in an oligomer of that protein).<sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p><p>Several statistical methods exist to extract from a <a href="/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment">multiple sequence alignment</a> such coupled residue pairs: observed versus expected frequencies of residue pairs (OMES);<sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> the McLachlan Based Substitution correlation (McBASC);<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> <a href="/wiki/Statistical_coupling_analysis" title="Statistical coupling analysis">statistical coupling analysis</a>; <a href="/wiki/Mutual_Information" class="mw-redirect" title="Mutual Information">Mutual Information</a> (MI) based methods;<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> and recently <a href="/wiki/Direct_coupling_analysis" title="Direct coupling analysis">direct coupling analysis</a> (DCA).<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> </p><p><a href="/wiki/Machine_learning" title="Machine learning">Machine learning</a> algorithms have been able to enhance MSA analysis methods, especially for non-homologous proteins (ie. shallow MSA's).<sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> </p><p>Predicted contact maps have been used in the prediction of <a href="/wiki/Membrane_proteins" class="mw-redirect" title="Membrane proteins">membrane proteins</a> where helix-helix interactions are targeted.<sup id="cite_ref-Lo2009_11-0" class="reference"><a href="#cite_note-Lo2009-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="HB_Plot">HB Plot</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=3" title="Edit section: HB Plot"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Knowledge of the relationship between a <a href="/wiki/Protein" title="Protein">protein</a>'s structure and its dynamic behavior is essential for understanding protein function. The description of a protein three dimensional structure as a network of <a href="/wiki/Hydrogen_bonding" class="mw-redirect" title="Hydrogen bonding">hydrogen bonding</a> interactions (<b>HB plot</b>)<sup id="cite_ref-hb_12-0" class="reference"><a href="#cite_note-hb-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> was introduced as a tool for exploring protein structure and function. By analyzing the network of tertiary interactions, the possible spread of information within a protein can be investigated. </p><p>HB plot offers a simple way of analyzing protein <a href="/wiki/Secondary_structure" class="mw-redirect" title="Secondary structure">secondary structure</a> and <a href="/wiki/Tertiary_structure" class="mw-redirect" title="Tertiary structure">tertiary structure</a>. <a href="/wiki/Hydrogen_bonds" class="mw-redirect" title="Hydrogen bonds">Hydrogen bonds</a> stabilizing secondary structural elements (<b><a href="/wiki/Secondary_hydrogen_bond" class="mw-redirect" title="Secondary hydrogen bond">secondary hydrogen bonds</a></b>) and those formed between distant <a href="/wiki/Amino_acid" title="Amino acid">amino acid</a> residues - defined as <b><a href="/wiki/Tertiary_hydrogen_bond" class="mw-redirect" title="Tertiary hydrogen bond">tertiary hydrogen bonds</a></b> - can be easily distinguished in HB plot, thus, amino acid residues involved in stabilizing <a href="/wiki/Protein_structure" title="Protein structure">protein structure</a> and function can be identified. </p> <div class="mw-heading mw-heading3"><h3 id="Features">Features</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=4" title="Edit section: Features"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The plot distinguishes between main chain-main chain, main chain-<a href="/wiki/Side_chain" title="Side chain">side chain</a> and side chain-side chain <a href="/wiki/Hydrogen_bonding" class="mw-redirect" title="Hydrogen bonding">hydrogen bonding</a> interactions. Bifurcated hydrogen bonds and multiple hydrogen bonds between <a href="/wiki/Amino_acid" title="Amino acid">amino acid</a> residues; and intra- and interchain <a href="/wiki/Hydrogen_bonds" class="mw-redirect" title="Hydrogen bonds">hydrogen bonds</a> are also indicated on the plots. Three classes of hydrogen bondings are distinguished by color-coding; short (distance smaller than 2.5 <a href="/wiki/%C3%85ngstr%C3%B6m" class="mw-redirect" title="Ångström">Å</a> between donor and acceptor), intermediate (between 2.5 Å and 3.2 Å) and long hydrogen bonds (greater than 3.2 Å). </p> <div class="mw-heading mw-heading3"><h3 id="Secondary_structure_elements_in_HB_plot">Secondary structure elements in HB plot</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=5" title="Edit section: Secondary structure elements in HB plot"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-halign-right" typeof="mw:File/Thumb"><a href="/wiki/File:Elements_hb2.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Elements_hb2.jpg/300px-Elements_hb2.jpg" decoding="async" width="300" height="225" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Elements_hb2.jpg/450px-Elements_hb2.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Elements_hb2.jpg/600px-Elements_hb2.jpg 2x" data-file-width="960" data-file-height="720" /></a><figcaption>Secondary structure elements in HB plot, there is swapped parallel and anti-parallel sheets</figcaption></figure> <p>In representations of the HB plot, characteristic patterns of <a href="/wiki/Secondary_structure" class="mw-redirect" title="Secondary structure">secondary structure</a> elements can be recognised easily, as follows: </p> <ol><li><a href="/wiki/Helices" class="mw-redirect" title="Helices">Helices</a> can be identified as strips directly adjacent to the diagonal.</li> <li>Antiparallel <a href="/wiki/Beta_sheet" title="Beta sheet">beta sheets</a> appear in HB plot as cross-diagonal.</li> <li>Parallel <a href="/wiki/Beta_sheet" title="Beta sheet">beta sheets</a> appears in the HB plot as parallel to the diagonal.</li> <li><a href="/wiki/Loop_(graph_theory)" title="Loop (graph theory)">Loops</a> appear as breaks in the diagonal between the cross-diagonal <a href="/wiki/Beta-sheet" class="mw-redirect" title="Beta-sheet">beta-sheet</a> motifs.</li></ol> <div class="mw-heading mw-heading3"><h3 id="Examples_of_usage">Examples of usage</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=6" title="Edit section: Examples of usage"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading4"><h4 id="Cytochrome_P450s">Cytochrome P450s</h4><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=7" title="Edit section: Cytochrome P450s"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><b>The <a href="/wiki/Cytochrome_P450" title="Cytochrome P450">cytochrome P450s</a> (P450s)</b> are <a href="/wiki/Xenobiotic" title="Xenobiotic">xenobiotic</a>-metabolizing <a href="/wiki/Membrane_(selective_barrier)" class="mw-redirect" title="Membrane (selective barrier)">membrane</a>-bound <a href="/wiki/Heme" title="Heme">heme</a>-containing enzymes that use molecular <a href="/wiki/Oxygen" title="Oxygen">oxygen</a> and electrons from <a href="/w/index.php?title=NADPH_cytochrome_P450_reductase&action=edit&redlink=1" class="new" title="NADPH cytochrome P450 reductase (page does not exist)">NADPH cytochrome P450 reductase</a> to oxidize their <a href="/wiki/Substrate_(biochemistry)" class="mw-redirect" title="Substrate (biochemistry)">substrates</a>. <a href="/w/index.php?title=CYP2B4&action=edit&redlink=1" class="new" title="CYP2B4 (page does not exist)">CYP2B4</a>, a member of the cytochrome P450 family is the only protein within this family, whose <a href="/wiki/X-ray_crystallography" title="X-ray crystallography">X-ray structure</a> in both open 11 and closed form 12 is published. The comparison of the open and closed structures of CYP2B4 structures reveals large-scale <a href="/wiki/Conformational_change" title="Conformational change">conformational</a> rearrangement between the two states, with the greatest conformational change around the residues 215-225, which is widely open in ligand-free state and shut after ligand binding; and the region around loop C near the heme. </p> <figure class="mw-halign-center" typeof="mw:File/Frame"><a href="/wiki/File:HB_Plot_and_structure_of_Cytochrome_P450_2B4_in_closed_form.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/b/b5/HB_Plot_and_structure_of_Cytochrome_P450_2B4_in_closed_form.jpg" decoding="async" width="700" height="281" class="mw-file-element" data-file-width="700" data-file-height="281" /></a><figcaption>HB Plot and structure of Cytochrome P450 2B4 in closed form</figcaption></figure> <p>Examining the HB plot of the closed and open state of CYP2B4 revealed that the rearrangement of tertiary hydrogen bonds was in excellent agreement with the current knowledge of the cytochrome P450 <a href="/wiki/Catalytic_cycle" title="Catalytic cycle">catalytic cycle</a>. </p><p>The first step in <a href="/wiki/P450" class="mw-redirect" title="P450">P450</a> catalytic cycle is identified as substrate binding. Preliminary binding of a ligand near to the entrance breaks hydrogen bonds S212-E474, S207-H172 in the open form of CYP2B4 and hydrogen bonds E218-A102, Q215-L51 are formed that fix the entrance in the closed form as the HB plot reveals. </p><p>The second step is the transfer of the first electron from <a href="/wiki/NADPH" class="mw-redirect" title="NADPH">NADPH</a> via an electron transfer chain. For the electron transfer a conformational change occurs that triggers interaction of the P450 with the NADPH cytochrome P450 reductase. Breaking of hydrogen bonds between S128-N287, S128-T291, L124-N287 and forming S96-R434, A116-R434, R125-I435, D82-R400 at the NADPH cytochrome P450 reductase <a href="/wiki/Binding_site" title="Binding site">binding site</a>—as seen in HB plot—transform CYP2B4 to a conformation state, where binding of NADPH cytochrome P450 reductase occurs. </p><p>In the third step, oxygen enters CYP2B4 in the closed state - the state where newly formed hydrogen bonds S176-T300, H172-S304, N167-R308 open a tunnel which is exactly the size and shape of an <a href="/wiki/Oxygen" title="Oxygen">oxygen</a> molecule. </p> <div class="mw-heading mw-heading4"><h4 id="Lipocalin_family">Lipocalin family</h4><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=8" title="Edit section: Lipocalin family"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-halign-right" typeof="mw:File/Thumb"><a href="/wiki/File:Lipo_label.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/en/thumb/3/37/Lipo_label.png/300px-Lipo_label.png" decoding="async" width="300" height="233" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/3/37/Lipo_label.png/450px-Lipo_label.png 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/3/37/Lipo_label.png/600px-Lipo_label.png 2x" data-file-width="804" data-file-height="624" /></a><figcaption>Beta-lactoglobulin in open (white) and ligand-bound (red) form</figcaption></figure> <p>The <b><a href="/wiki/Lipocalin" title="Lipocalin">lipocalin</a> family</b> is a large and diverse family of proteins with functions as small <a href="/wiki/Hydrophobic" class="mw-redirect" title="Hydrophobic">hydrophobic</a> molecule transporters. <a href="/wiki/Beta-lactoglobulin" class="mw-redirect" title="Beta-lactoglobulin">Beta-lactoglobulin</a> is a typical member of the lipocalin family. Beta-lactoglobulin was found to have a role in the transport of hydrophobic ligands such as <a href="/wiki/Retinol" title="Retinol">retinol</a> or <a href="/wiki/Fatty_acid" title="Fatty acid">fatty acids</a>.<sup id="cite_ref-13" class="reference"><a href="#cite_note-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> Its <a href="/wiki/Crystal_structure" title="Crystal structure">crystal structure</a> were determined [e.g. Qin, 1998] with different ligands and in ligand-free form as well. The crystal structures determined so far reveal that the typical lipocalin contains eight-stranded <a href="/wiki/Antiparallel_(biochemistry)" title="Antiparallel (biochemistry)">antiparallel</a>-barrel arranged to form a conical central cavity in which the hydrophobic ligand is bound. The structure of beta-lactoglobulin reveals that the barrel-form structure with the central cavity of the protein has an "entrance" surrounded by five <a href="/w/index.php?title=Beta-loop&action=edit&redlink=1" class="new" title="Beta-loop (page does not exist)">beta-loops</a> with centers around 26, 35, 63, 87, and 111, which undergo a conformational change during the ligand binding and close the cavity. </p><p>The overall shape of beta-lactoglobulin is characteristic of the lipocalin family.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (January 2009)">citation needed</span></a></i>]</sup> In the absence of <a href="/wiki/Alpha-helices" class="mw-redirect" title="Alpha-helices">alpha-helices</a>, the main diagonal almost disappears and the cross-diagonals representing the <a href="/wiki/Beta-sheet" class="mw-redirect" title="Beta-sheet">beta-sheets</a> dominate the plot. Relatively low number of tertiary hydrogen bonds can be found in the plot, with three high-density regions, one of which is connected to a loop at the residues around 63, a second is connected to the loop around 87, and a third region which is connected to the regions 26 and 35. The fifth loop around 111 is represented only one tertiary hydrogen bond in the HB plot. </p><p>In the three-dimensional structure, tertiary hydrogen bonds are formed (1) near to the entrance, directly involved in conformational rearrangement during ligand binding; and (2) at the bottom of the "barrel". HB plots of the open and closed forms of beta-lactoglobulin are very similar, all unique motifs can be recognized in both forms. Difference in HB plots of open and ligand-bound form show few important individual changes in tertiary hydrogen bonding pattern. Especially, the formation of hydrogen bonds between Y20-E157 and S21-H161 in closed form might be crucial in conformational rearrangement. These hydrogen bonds lie at the bottom of the cavity, which suggests that the closure of the entrance of a lipocalin starts when a ligand reached the bottom of the cavity and broke hydrogen bonds R123-Y99, R123-T18, and V41-Q120. Lipocalins are known to have very low sequence similarity with high structural similarity.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (January 2009)">citation needed</span></a></i>]</sup> The only conserved regions are exactly the region around 20 and 160 with an unknown role. </p> <figure class="mw-halign-center" typeof="mw:File/Thumb"><a href="/wiki/File:Lipohb.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/en/thumb/3/36/Lipohb.jpg/700px-Lipohb.jpg" decoding="async" width="700" height="279" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/3/36/Lipohb.jpg/1050px-Lipohb.jpg 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/3/36/Lipohb.jpg/1400px-Lipohb.jpg 2x" data-file-width="1615" data-file-height="643" /></a><figcaption>HB Plots of beta-lactoglobulin in open (2BLG) and ligand-bound (2AKQ) form</figcaption></figure> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=9" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a href="/wiki/Ramachandran_plot" title="Ramachandran plot">Ramachandran plot</a></li> <li><a href="/wiki/Circuit_topology" title="Circuit topology">Circuit topology</a></li> <li><a href="/wiki/Structural_classification_of_proteins" class="mw-redirect" title="Structural classification of proteins">Structural classification of proteins</a></li> <li><a href="/wiki/CATH" class="mw-redirect" title="CATH">CATH</a></li> <li><a href="/wiki/HB_plot" class="mw-redirect" title="HB plot">HB plot</a></li> <li><a href="/wiki/Dot_plot_(bioinformatics)" title="Dot plot (bioinformatics)">Dot plot (bioinformatics)</a></li> <li><a href="/wiki/Self-similarity_matrix" title="Self-similarity matrix">Self-similarity matrix</a></li></ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=10" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist reflist-columns references-column-width reflist-columns-2"> <ol class="references"> <li id="cite_note-Pietal2015-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-Pietal2015_1-0">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output 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D.; Calvo, M (1995). <a rel="nofollow" class="external text" href="https://doi.org/10.3168%2Fjds.S0022-0302%2895%2976713-3">"Interaction of beta-lactoglobulin with retinol and fatty acids and its role as a possible biological function for this protein: A review"</a>. <i>Journal of Dairy Science</i>. <b>78</b> (5): 978–88. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.3168%2Fjds.S0022-0302%2895%2976713-3">10.3168/jds.S0022-0302(95)76713-3</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/7622732">7622732</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Journal+of+Dairy+Science&rft.atitle=Interaction+of+beta-lactoglobulin+with+retinol+and+fatty+acids+and+its+role+as+a+possible+biological+function+for+this+protein%3A+A+review&rft.volume=78&rft.issue=5&rft.pages=978-88&rft.date=1995&rft_id=info%3Adoi%2F10.3168%2Fjds.S0022-0302%2895%2976713-3&rft_id=info%3Apmid%2F7622732&rft.aulast=P%C3%A9rez&rft.aufirst=M.+D.&rft.au=Calvo%2C+M&rft_id=https%3A%2F%2Fdoi.org%2F10.3168%252Fjds.S0022-0302%252895%252976713-3&rfr_id=info%3Asid%2Fen.wikipedia.org%3AProtein+contact+map" class="Z3988"></span></span> </li> </ol></div> <div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein_contact_map&action=edit&section=11" title="Edit section: External links"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20080503131233/http://distill.ucd.ie/distill/">DISTILL</a>— prediction of protein structural features (including protein residue contact maps)</li> <li><a rel="nofollow" class="external text" href="http://www.igb.uci.edu/?page=tools&subPage=psss">Structural Proteomics Tools</a> — includes amino acid contact maps</li> <li><a rel="nofollow" class="external text" href="http://rostlab.org/services/profcon/index.php">ProfCon</a> — prediction of inter-residue contacts</li> <li><a rel="nofollow" class="external text" href="https://webclu.bio.wzw.tum.de/tmhcon/">TMHcon</a> — prediction of helix-helix contacts specifically within the transmembrane parts of membrane proteins</li> <li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20100905110709/http://bio-cluster.iis.sinica.edu.tw/TMhit/">TMhit</a> — A new transmembrane helix-helix interaction prediction method based on residue contacts<sup class="noprint Inline-Template"><span style="white-space: nowrap;">[<i><a href="/wiki/Wikipedia:Link_rot" title="Wikipedia:Link rot"><span title=" Dead link tagged July 2017">dead link</span></a></i><span style="visibility:hidden; color:transparent; padding-left:2px">‍</span>]</span></sup></li> <li><a rel="nofollow" class="external text" href="http://www.ics.uci.edu/~baldig/index.html">CMAPpro</a> — A protein contact map prediction server</li> <li><a rel="nofollow" class="external autonumber" href="https://jerseysforcheapshop.com/how-to-check-protein-deficiency">[1]</a> —A Tool for Protein Contact-Map Visualization in jerseysforcheapshop</li></ul>    </div><noscript><img src="https://login.wikimedia.org/wiki/Special:CentralAutoLogin/start?type=1x1&useformat=desktop" alt="" width="1" height="1" style="border: none; position: absolute;"></noscript> <div class="printfooter" data-nosnippet="">Retrieved from "<a dir="ltr" href="https://en.wikipedia.org/w/index.php?title=Protein_contact_map&oldid=1174454765">https://en.wikipedia.org/w/index.php?title=Protein_contact_map&oldid=1174454765</a>"</div></div> <div id="catlinks" class="catlinks" data-mw="interface"><div id="mw-normal-catlinks" class="mw-normal-catlinks"><a href="/wiki/Help:Category" title="Help:Category">Categories</a>: <ul><li><a href="/wiki/Category:Proteomics" title="Category:Proteomics">Proteomics</a></li><li><a href="/wiki/Category:Protein_structure" title="Category:Protein structure">Protein structure</a></li></ul></div><div id="mw-hidden-catlinks" class="mw-hidden-catlinks mw-hidden-cats-hidden">Hidden categories: <ul><li><a href="/wiki/Category:All_articles_with_unsourced_statements" title="Category:All articles with unsourced statements">All articles with unsourced statements</a></li><li><a href="/wiki/Category:Articles_with_unsourced_statements_from_January_2009" title="Category:Articles with unsourced statements from January 2009">Articles with unsourced statements from January 2009</a></li><li><a href="/wiki/Category:All_articles_with_dead_external_links" title="Category:All articles with dead external links">All articles with dead external links</a></li><li><a href="/wiki/Category:Articles_with_dead_external_links_from_July_2017" title="Category:Articles with dead external links from July 2017">Articles with dead external links from July 2017</a></li></ul></div></div> </div> </main> </div> <div class="mw-footer-container"> <footer id="footer" class="mw-footer" > <ul id="footer-info"> <li id="footer-info-lastmod"> This page was last edited on 8 September 2023, at 15:06<span class="anonymous-show"> (UTC)</span>.</li> <li id="footer-info-copyright">Text is available under the <a href="/wiki/Wikipedia:Text_of_the_Creative_Commons_Attribution-ShareAlike_4.0_International_License" title="Wikipedia:Text of the Creative Commons Attribution-ShareAlike 4.0 International License">Creative Commons Attribution-ShareAlike 4.0 License</a>; 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