text: user12686: I know how to traverse through structures, models, residues, and atoms in a protein chain using BioPython (which is very easy).
  How can I identify donor and acceptor atoms in a chain?
  
  user6322: A hydrogen bond donor heavy atom is one that is protonated, while the acceptor has a lone pair. If you talking about amino acids, then it's simple as they are fixed.
  
  
  
  
  atom name
  description
  role
  note
  
  
  
  
  N
  backbone nitrogen
  donor
  SS
  
  
  CA
  backbone Cα
  apolar
  
  
  
  C
  backbone carboxyl C
  sterically hindered and electrophilic
  nucleophilic attack
  
  
  O
  backbone carboxyl O
  acceptor
  SS
  
  
  CB etc.
  sidechain carbons
  apolar
  
  
  
  OXT
  C-terminal oxygen
  acceptor
  may be protonated especially if a membrane embedded C-terminus
  
  
  Serine's OG / Threonine's OG1
  sidechain hydroxyl
  donor
  SS: may form ST turns. Fairly uncommon: may be a donor
  
  
  Asp OD1/OD2/Asn OD1
  sidechain carboxyl/amide O
  acceptor
  SS: may form Asx turns
  
  
  Glu OG1/OG2/Gln OG1
  sidechain carboxyl/amide O
  acceptor
  
  
  
  Lysine NZ
  sidechain amine
  donor
  
  
  
  Asn ND2 / Gln NG2
  terminal admide N
  donor
  the direction of an Asn/Gln may be accidentally filled if manually assigned as N/O have the same density in X-ray crystals
  
  
  
  
  Water can be both a donor and an acceptor.
  Two charged residues form a salt bridge more so than a hydrogen bond, because the interaction is driven by the Coulomb electrostatic forces of the two heavy atoms.
  
original_text: 12686: <p>I know how to traverse through structures, models, residues, and atoms in a protein chain using BioPython (which is very easy).</p>
  <p>How can I identify donor and acceptor atoms in a chain?</p>
   6322: <p>A hydrogen bond donor heavy atom is one that is protonated, while the acceptor has a lone pair. If you talking about amino acids, then it's simple as they are fixed.</p>
  <div class="s-table-container">
  <table class="s-table">
  <thead>
  <tr>
  <th>atom name</th>
  <th>description</th>
  <th>role</th>
  <th>note</th>
  </tr>
  </thead>
  <tbody>
  <tr>
  <td><code>N</code></td>
  <td>backbone nitrogen</td>
  <td>donor</td>
  <td>SS</td>
  </tr>
  <tr>
  <td><code>CA</code></td>
  <td>backbone Cα</td>
  <td>apolar</td>
  <td></td>
  </tr>
  <tr>
  <td><code>C</code></td>
  <td>backbone carboxyl C</td>
  <td>sterically hindered and electrophilic</td>
  <td>nucleophilic attack</td>
  </tr>
  <tr>
  <td><code>O</code></td>
  <td>backbone carboxyl O</td>
  <td>acceptor</td>
  <td>SS</td>
  </tr>
  <tr>
  <td><code>CB</code> etc.</td>
  <td>sidechain carbons</td>
  <td>apolar</td>
  <td></td>
  </tr>
  <tr>
  <td><code>OXT</code></td>
  <td>C-terminal oxygen</td>
  <td>acceptor</td>
  <td>may be protonated especially if a membrane embedded C-terminus</td>
  </tr>
  <tr>
  <td>Serine's <code>OG</code> / Threonine's <code>OG1</code></td>
  <td>sidechain hydroxyl</td>
  <td>donor</td>
  <td>SS: may form ST turns. Fairly uncommon: may be a donor</td>
  </tr>
  <tr>
  <td>Asp <code>OD1</code>/<code>OD2</code>/Asn <code>OD1</code></td>
  <td>sidechain carboxyl/amide O</td>
  <td>acceptor</td>
  <td>SS: may form Asx turns</td>
  </tr>
  <tr>
  <td>Glu <code>OG1</code>/<code>OG2</code>/Gln <code>OG1</code></td>
  <td>sidechain carboxyl/amide O</td>
  <td>acceptor</td>
  <td></td>
  </tr>
  <tr>
  <td>Lysine <code>NZ</code></td>
  <td>sidechain amine</td>
  <td>donor</td>
  <td></td>
  </tr>
  <tr>
  <td>Asn <code>ND2</code> / Gln <code>NG2</code></td>
  <td>terminal admide N</td>
  <td>donor</td>
  <td>the direction of an Asn/Gln may be accidentally filled if manually assigned as N/O have the same density in X-ray crystals</td>
  </tr>
  </tbody>
  </table>
  </div>
  <p>Water can be both a donor and an acceptor.
  Two charged residues form a salt bridge more so than a hydrogen bond, because the interaction is driven by the Coulomb electrostatic forces of the two heavy atoms.</p>
  