4 4 A L G >> S+ 0 0 23 31,-2.5 4,-2.9 -2,-0.7 3,-2.0 0.786 71.6 72.4 -65.6 -32.5 7.1 10.6 54.1
</pre>
5 5 A Y G 34 S+ 0 0 2 30,-0.8 -1,-0.3 1,-0.3 31,-0.1 0.709 101.0 46.1 -56.9 -26.7 7.0 8.7 50.7
6 6 A Y G <4 S+ 0 0 39 -3,-1.2 -1,-0.3 2,-0.1 -2,-0.2 0.439 115.4 47.1 -93.5 -4.1 3.5 7.4 51.7
<p>Below is a brief description of the data columns. More details are described in the Kabsch and Sander paper.</p>
7 7 A E T <4 S- 0 0 138 -3,-2.0 2,-0.3 1,-0.2 -2,-0.2 0.825 135.2 -0.3 -99.6 -48.8 2.4 10.9 52.8
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]]>
<h3>RESIDUE</h3>
</pre>
<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
<p>Below is a brief description of the data columns. More details are described in the Kabsch and Sander
structure model 'residue number','insertion code' and 'chain identifier'; these are given for reference only.</p>
paper.</p>
<h3>AA</h3>
<h3>RESIDUE</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
<p>Two columns of residue numbers. First column is DSSP's sequential residue number, starting at the first
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,
residue actually in the model set
that is not yet marked, and its partner are both marked <em>b</em>, etcetera. Unbridged cysteines remain marked as <em>C</em>.</p>
and including chain breaks; this number is used to refer to residues throughout. The second column gives
the numbering as is used in the
<h3>S (first column in STRUCTURE block)</h3>
structure model 'residue number','insertion code' and 'chain identifier'; these are given for reference
<p>The one-letter summary of secondary structure, intended to approximate crystallographers' intuition, based on columns 19-38, which are the principal
only.</p>
result of DSSP analysis of the atomic coordinates. More details in the Kabsch and Sander paper.</p>
<h3>AA</h3>
<h3>BP1 and BP2</h3>
<p>One letter amino acid code, non standard residues are marked as <em>X</em>. CYS in an SS-bridge are
<p>Residue numbers of the first and (if available) second beta bridge partner. The letter marked the B-sheet that contains the bridges.</p>
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
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>
<h3>ACC</h3>
<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
<ul>
think:
<li>Effects leading to larger than expected values: solvent exposure calculation ignores unusual residues, like ACE, or residues with incomplete backbone.
<ul>
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 larger than expected values: solvent exposure calculation ignores unusual
<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.
residues, like ACE, or residues with incomplete backbone.
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>
it also ignores HETATOMS, like a heme or metal ligands. Also, side chains may not have all atoms
<li>Unknown or non-standard residues are named X on output and are not checked for the expected number of sidechain atoms.</li>
explicitly modeled.</li>
<li>All explicit water molecules, like other hetatoms, are ignored.</li>
<li>Effects leading to smaller than expected values: in complexes, e.g. a dimer, solvent exposure is for
</ul>
the entire assembly, not for the monomer.
</p>
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>
<h3>N-H-->O etc.</h3>
<li>Unknown or non-standard residues are named X on output and are not checked for the expected number
<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.
of sidechain atoms.</li>
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
<li>All explicit water molecules, like other hetatoms, are ignored.</li>
and even the best (in rare occasions) may be unrealistically por H-bonds.</p>
</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
and even the best (in rare occasions) may be unrealistically por H-bonds.</p>
<h3>TCO</h3>
<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,
These values are descriptive and not used for structure definition.</p>
for β-sheets TCO is near -1.
These values are descriptive and not used for structure definition.</p>
<h3>KAPPA</h3>
<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>
<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>
<h3>PHI and PSI</h3>
<p>The peptide backbone torsion angles as described in the IUPAC standard</p>
<p>The peptide backbone torsion angles as described in the IUPAC standard</p>
<h3>X-CA, Y-CA, and Z-CA</h3>
<h3>X-CA, Y-CA, and Z-CA</h3>
<p>Just a copy of the Cα atom coordinates in the structure model</p>
<p>Just a copy of the Cα atom coordinates in the structure model</p>
</article>
</article>
<article>
<article>
<aid="mmCIF"></a>
<aid="mmCIF"></a>
<h2>DSSP data in mmCIF files</h2>
<h2>DSSP data in mmCIF files</h2>
<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
<p>The mmCIF-formatted DSSP output caries the same information as the DSSP format but in a more scalable way
an mmCIF dictionary. It is designed to be machine readable. Developers who create software to read these annotations can use our
and with a formal description caputered in
<ahref="https://github.com/PDB-REDO/dssp/blob/trunk/mmcif_pdbx/dssp-extension.dic"target="_BLANK">extension to the mmCIF dictionary</a> on GitHub.
an mmCIF dictionary. It is designed to be machine readable. Developers who create software to read these
<em>Note:</em> For sake of speed the solvent accessibility is not calculated by default when using mmCIF output. The command-line switch
annotations can use our
<code>--calculate-accessibility</code> can be used to switch this feature on.
