8 8 A D >< - 0 0 57 -4,-2.9 3,-1.4 3,-0.1 -1,-0.2 -0.852 61.5-167.8-144.3 106.0 3.6 13.0 49.9]]>
</pre>
<p>Below is a brief description of the data columns. More details are described in the Kabsch and Sander paper.</p>
<p>Below is a brief description of the data columns. More details are described in the Kabsch and Sander
paper.</p>
<h3>RESIDUE</h3>
<p>Two columns of residue numbers. First column is DSSP's sequential residue number, starting at the first residue actually in the model set
and including chain breaks; this number is used to refer to residues throughout. The second column gives the numbering as is used in the
structure model 'residue number','insertion code' and 'chain identifier'; these are given for reference only.</p>
<p>Two columns of residue numbers. First column is DSSP's sequential residue number, starting at the first
residue actually in the model set
and including chain breaks; this number is used to refer to residues throughout. The second column gives
the numbering as is used in the
structure model 'residue number','insertion code' and 'chain identifier'; these are given for reference
only.</p>
<h3>AA</h3>
<p>One letter amino acid code, non standard residues are marked as <em>X</em>. CYS in an SS-bridge are marked by a lower case letter. So when cysteines
are bridged, then the first bridged cysteine in the sequence and its partner elsewhere in the sequence are marked <em>a</em>. The next bridged cysteine,
that is not yet marked, and its partner are both marked <em>b</em>, etcetera. Unbridged cysteines remain marked as <em>C</em>.</p>
<p>One letter amino acid code, non standard residues are marked as <em>X</em>. CYS in an SS-bridge are
marked by a lower case letter. So when cysteines
are bridged, then the first bridged cysteine in the sequence and its partner elsewhere in the sequence
are marked <em>a</em>. The next bridged cysteine,
that is not yet marked, and its partner are both marked <em>b</em>, etcetera. Unbridged cysteines remain
marked as <em>C</em>.</p>
<h3>S (first column in STRUCTURE block)</h3>
<p>The one-letter summary of secondary structure, intended to approximate crystallographers' intuition, based on columns 19-38, which are the principal
<p>The one-letter summary of secondary structure, intended to approximate crystallographers' intuition,
based on columns 19-38, which are the principal
result of DSSP analysis of the atomic coordinates. More details in the Kabsch and Sander paper.</p>
<h3>BP1 and BP2</h3>
<p>Residue numbers of the first and (if available) second beta bridge partner. The letter marked the B-sheet that contains the bridges.</p>
<p>Residue numbers of the first and (if available) second beta bridge partner. The letter marked the B-sheet
that contains the bridges.</p>
<h3>ACC</h3>
<p>Water exposed surface in Angstrom**2. <em>Note:</em>The values for solvent exposure may not mean what you think:
<p>Water exposed surface in Angstrom**2. <em>Note:</em>The values for solvent exposure may not mean what you
think:
<ul>
<li>Effects leading to larger than expected values: solvent exposure calculation ignores unusual residues, like ACE, or residues with incomplete backbone.
it also ignores HETATOMS, like a heme or metal ligands. Also, side chains may not have all atoms explicitly modeled.</li>
<li>Effects leading to smaller than expected values: in complexes, e.g. a dimer, solvent exposure is for the entire assembly, not for the monomer.
Also, atom OXT of c-terminal residues is treated like a side chain atom if it is listed as part of the last residue.</li>
<li>Unknown or non-standard residues are named X on output and are not checked for the expected number of sidechain atoms.</li>
<li>Effects leading to larger than expected values: solvent exposure calculation ignores unusual
residues, like ACE, or residues with incomplete backbone.
it also ignores HETATOMS, like a heme or metal ligands. Also, side chains may not have all atoms
explicitly modeled.</li>
<li>Effects leading to smaller than expected values: in complexes, e.g. a dimer, solvent exposure is for
the entire assembly, not for the monomer.
Also, atom OXT of c-terminal residues is treated like a side chain atom if it is listed as part of
the last residue.</li>
<li>Unknown or non-standard residues are named X on output and are not checked for the expected number
of sidechain atoms.</li>
<li>All explicit water molecules, like other hetatoms, are ignored.</li>
</ul>
</p>
<h3>N-H-->O etc.</h3>
<p>Hydrogen bonds; e.g. -3,-1.4 means that this residue (i) has its HN atom H-bonded to O of residue i-3 with an electrostatic H-bond energy of -1.4 kcal/mol.
There are two columns for each type of H-bond, to allow for bifurcated H-bonds. <em>Note:</em>The marked H-bonds are the best and second best candidate. The second best
<h3>N-H-->O etc.</h3>
<p>Hydrogen bonds; e.g. -3,-1.4 means that this residue (i) has its HN atom H-bonded to O of residue i-3
with an electrostatic H-bond energy of -1.4 kcal/mol.
There are two columns for each type of H-bond, to allow for bifurcated H-bonds. <em>Note:</em>The marked
H-bonds are the best and second best candidate. The second best
and even the best (in rare occasions) may be unrealistically por H-bonds.</p>
<h3>TCO</h3>
<p>The cosine of angle between C=O of residue i and C=O of residue i-1. For α-helices, TCO is near +1, for β-sheets TCO is near -1.
<p>The cosine of angle between C=O of residue i and C=O of residue i-1. For α-helices, TCO is near +1,
for β-sheets TCO is near -1.
These values are descriptive and not used for structure definition.</p>
<h3>KAPPA</h3>
<p>Virtual bond angle (bend angle) defined by the three Cα atoms of residues i-2, i, and i+2. Used to define bends (structure code <em>S</em>).</p>
<p>Virtual bond angle (bend angle) defined by the three Cα atoms of residues i-2, i, and i+2. Used to
define bends (structure code <em>S</em>).</p>
<h3>ALPHA</h3>
<p>Virtual torsion angle (dihedral angle) defined by the four Cα atoms of residues i-1, i, i+1, and i+2. Used to define chirality (structure code <em>+</em> or <em>-</em>).
<p>Virtual torsion angle (dihedral angle) defined by the four Cα atoms of residues i-1, i, i+1, and
i+2. Used to define chirality (structure code <em>+</em> or <em>-</em>).</p>
<h3>PHI and PSI</h3>
<p>The peptide backbone torsion angles as described in the IUPAC standard</p>
<p>The mmCIF-formatted DSSP output caries the same information as the DSSP format but in a more scalable way and with a formal description caputered in
an mmCIF dictionary. It is designed to be machine readable. Developers who create software to read these annotations can use our
<ahref="https://github.com/PDB-REDO/dssp/blob/trunk/mmcif_pdbx/dssp-extension.dic"target="_BLANK">extension to the mmCIF dictionary</a> on GitHub.
<em>Note:</em> For sake of speed the solvent accessibility is not calculated by default when using mmCIF output. The command-line switch
<p>The mmCIF-formatted DSSP output caries the same information as the DSSP format but in a more scalable way
and with a formal description caputered in
an mmCIF dictionary. It is designed to be machine readable. Developers who create software to read these
