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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="">
<meta name="author" content="">
<link rel="icon" href="imgs/favicon.ico">
<title>GetContacts - Interaction types</title>
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<style>
.interaction-fig{
width: 200px;
}
strong{
font-weight: bold;
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</head>
<body>
<!-- Jumbotron and menu -->
<header>
<div class="jumbotron">
<div class="container">
<h1 class="display-3"><a href="index.html">Getcontacts</a></h1>
<p>Interaction analysis for protein structures and dynamics</p>
</div>
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<div class="container">
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<li class="nav-item"><a class="nav-link" href="index.html">Home</a></li>
<li class="nav-item"><a class="nav-link" href="getting_started.html">Installation</a></li>
<li class="nav-item"><a class="nav-link" href="interactions.html">Interaction types</a></li>
<li class="nav-item">
<a class="nav-link" href="https://github.com/getcontacts/getcontacts">
Github <i class="fab fa-github"></i>
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<div class="container">
<p>
The following table defines criteria for interactions that are recognized by GetContacts. All numerical values can
be changed from the command-line if needed.
</p>
<table class="table">
<col>
<col>
<col>
<col style="width:40%">
<thead>
<tr>
<th scope="col">Interaction type</th>
<th scope="col">Illustration</th>
<th scope="col">Geometric criteria</th>
<th scope="col">Chemical criteria</th>
</tr>
</thead>
<tbody>
<tr>
<td>
Hydrogen bond
<ul>
<li>hbbb - backbone to backbone</li>
<li>hbsb - side-chain to backbone</li>
<li>hbss - side-chain to side-chain</li>
<li>lbs - ligand to side-chain</li>
<li>lbb - ligand to backbone</li>
</ul>
</td>
<td><img src="resources/interactions/fig_hb.png" class="interaction-fig"></td>
<td>
|AD| < 3.5Å<br>
180° - ∠AHD < 70°
</td>
<td>
<p>
A (acceptor) and D (donor) are any atom except hydrogen, carbon or sulphur
</p>
<p>
Ligands supported
</p>
</td>
</tr>
<tr>
<td>Salt bridge (sb)</td>
<td><img src="resources/interactions/fig_sb.png" class="interaction-fig"></td>
<td>|AC| < 4.0Å</td>
<td>
<p>
A (anion): ASP/OD1+OD2, GLU/OE1+OE2<br>
C (cation): LYS/NZ, ARG/NH1+NH2 <!--, HIS+HSD+HSE+HSP+HIE+HIP+HID/ND1+NE2-->
</p>
<p>
Ligands <strong>not</strong> supported
</p>
</td>
</tr>
<tr>
<td>Pi-cation (pc)</td>
<td><img src="resources/interactions/fig_pc.png" class="interaction-fig"></td>
<td>
|AC| < 6.0Å<br>
∠CAn < 60°
</td>
<td>
<p>
A (aromatic): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2)<br>
C (cation): LYS/NZ, ARG/NH1+NH2<!--, HIS/ND1+NE2--><br>
</p>
<p>
Ligands <strong>not</strong> supported
</p>
</td>
</tr>
<tr>
<td>Pi-stacking (ps)</td>
<td><img src="resources/interactions/fig_ps.png" class="interaction-fig"></td>
<td>
|A1A2| < 7.0Å<br>
∠(n1, n2) < 30°<br>
∠(n1, A1A2) < 45°<br>
∠(n2, A1A2) < 45°<br>
</td>
<td>
<p>
A1, A2 (aromatic rings): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2)<br>
</p>
<p>
Ligands <strong>not</strong> supported
</p>
</td>
</tr>
<tr>
<td>T-stacking (ts)</td>
<td><img src="resources/interactions/fig_ts.png" class="interaction-fig"></td>
<td>
|A1A2| < 5.0Å<br>
60° < ∠(n1, n2) < 90°<br>
∠(n1, A1A2) < 45°<br>
∠(n2, A1A2) < 45°<br>
</td>
<td>
<p>
A1, A2 (aromatic rings): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2)<br>
</p>
<p>
Ligands <strong>not</strong> supported
</p>
</td>
</tr>
<tr>
<td>Hydrophobic (hp)</td>
<td><img src="resources/interactions/fig_hp.png" class="interaction-fig"></td>
<td>
|AB| < R<sub>vdw</sub>(A) + R<sub>vdw</sub>(B) + 0.5
</td>
<td>
<p>
A, B: ALA+CYS+PHE+GLY+ILE+LEU+MET+PRO+VAL+TRP and element C or S
</p>
<p>
Ligands supported
</p>
</td>
</tr>
<tr>
<td>van der Waals (vdw)</td>
<td><img src="resources/interactions/fig_vdw.png" class="interaction-fig"></td>
<td>
|AB| < R<sub>vdw</sub>(A) + R<sub>vdw</sub>(B) + 0.5
</td>
<td>
<p>
A and B are any non-hydrogen atoms
</p>
<p>
Ligands supported
</p>
</td>
</tr>
</tbody>
</table>
</div>
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<i class="far fa-copyright"></i> Stanford and authors 2016-2018
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