diff --git a/deeprank/domain/amino_acid.py b/deeprank/domain/amino_acid.py
index eff2b95..9112413 100644
--- a/deeprank/domain/amino_acid.py
+++ b/deeprank/domain/amino_acid.py
@@ -1,48 +1,332 @@
 from deeprank.models.amino_acid import AminoAcid
+from deeprank.models.polarity import Polarity
 
 
-alanine = AminoAcid("Alanine", "ALA", "A")
-arginine = AminoAcid("Arginine", "ARG", "R")
-asparagine = AminoAcid("Asparagine", "ASN", "N")
-aspartate = AminoAcid("Aspartate", "ASP", "D")
-protonated_aspartate = AminoAcid("Protonated Aspartate", "ASH", "D")
-cysteine = AminoAcid("Cysteine", "CYS", "C")
-cysteine_metal = AminoAcid("Cysteine Metal Ligand", "CYM", "C")
-cysteine_iron = AminoAcid("Cysteine Iron Ligand", "CFE", "C")
-cysteine_zinc = AminoAcid("Cysteine Zinc Ligand", "CYF", "C")
-cysteine_phosphate = AminoAcid("Cysteine Phosphate", "CSP", "C")
-glutamate = AminoAcid("Glutamate", "GLU", "E")
-protonated_glutamate = AminoAcid("Protonated Glutamate", "GLH", "E")
-glutamine = AminoAcid("Glutamine", "GLN", "Q")
-glycine = AminoAcid("Glycine", "GLY", "G")
-histidine = AminoAcid("Histidine", "HIS", "H")
-histidine_phophate = AminoAcid("Histidine Phosphate", "NEP", "H")
-isoleucine = AminoAcid("Isoleucine", "ILE", "I")
-leucine = AminoAcid("Leucine", "LEU", "L")
-lysine = AminoAcid("Lysine", "LYS", "K")
-methionine = AminoAcid("Methionine", "MET", "M")
-phenylalanine = AminoAcid("Phenylalanine", "PHE", "F")
-proline = AminoAcid("Proline", "PRO", "P")
-serine = AminoAcid("Serine", "SER", "S")
-threonine = AminoAcid("Threonine", "THR", "T")
-tryptophan = AminoAcid("Tryptophan", "TRP", "W")
-tyrosine = AminoAcid("Tyrosine", "TYR", "Y")
-valine = AminoAcid("Valine", "VAL", "V")
-selenocysteine = AminoAcid("Selenocysteine", "SEC", "U")
-pyrrolysine = AminoAcid("Pyrrolysine", "PYL", "O")
-alysine = AminoAcid("Alysine", "ALY", "K")
-methyllysine = AminoAcid("Methyllysine", "MLZ", "K")
-dimethyllysine = AminoAcid("Dimethyllysine", "MLY", "K")
-trimethyllysine = AminoAcid("Trimethyllysine", "3ML", "K")
-epsilon_mthionine = AminoAcid("Epsilon Methionine", "MSE", "M")
-hydroxy_proline = AminoAcid("Hydroxy Proline", "HYP", "P")
-serine_phosphate = AminoAcid("Serine Phosphate", "SEP", "S")
-threonine_phosphate = AminoAcid("Threonine Phosphate", "TOP", "T")
-tyrosine_phosphate = AminoAcid("Tyrosine Phosphate", "TYP", "Y")
-tyrosine_sulphate = AminoAcid("Tyrosine Sulphate", "TYS", "Y")
-tyrosine_phosphate = AminoAcid("Tyrosine Phosphate", "PTR", "Y")
-cyclohexane_alanine = AminoAcid("Cyclohexane Alanine", "CHX", "?")
-unknown_amino_acid = AminoAcid("Unknown", "XXX", "X")
+alanine = AminoAcid("Alanine", "ALA", "A",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=1,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+arginine = AminoAcid("Arginine", "ARG", "R",
+    charge=-1.65,
+    polarity=Polarity.POSITIVE_CHARGE,
+    size=7,
+    count_hydrogen_bond_donors=5,
+    count_hydrogen_bond_acceptors=0
+)
+
+asparagine = AminoAcid("Asparagine", "ASN", "N",
+    charge=-1.22,
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2
+)
+
+aspartate = AminoAcid("Aspartate", "ASP", "D",
+    charge=-1.37,
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+protonated_aspartate = AminoAcid("Protonated Aspartate", "ASH", "D",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=3
+)
+
+cysteine = AminoAcid("Cysteine", "CYS", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_metal = AminoAcid("Cysteine Metal Ligand", "CYM", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_iron = AminoAcid("Cysteine Iron Ligand", "CFE", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_zinc = AminoAcid("Cysteine Zinc Ligand", "CYF", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_phosphate = AminoAcid("Cysteine Phosphate", "CSP", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+glutamate = AminoAcid("Glutamate", "GLU", "E",
+    charge=-1.37,
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=5,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4,
+)
+protonated_glutamate = AminoAcid("Protonated Glutamate", "GLH", "E",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=3
+)
+
+glutamine = AminoAcid("Glutamine", "GLN", "Q",
+    charge=-1.22,
+    polarity=Polarity.POLAR,
+    size=5,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2,
+)
+
+glycine = AminoAcid("Glycine", "GLY", "G",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=0,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+histidine = AminoAcid("Histidine", "HIS", "H",
+    charge=-0.29,
+    polarity=Polarity.POLAR,
+    size=6,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2
+)
+
+histidine_phosphate = AminoAcid("Histidine Phosphate", "NEP", "H",
+    charge=-0.29,
+    polarity=Polarity.POLAR,
+    size=6,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2
+)
+
+isoleucine = AminoAcid("Isoleucine", "ILE", "I",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0,
+)
+
+leucine = AminoAcid("Leucine", "LEU", "L",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+lysine = AminoAcid("Lysine", "LYS", "K",
+    charge=-0.36,
+    polarity=Polarity.POSITIVE_CHARGE,
+    size=5,
+    count_hydrogen_bond_donors=3,
+    count_hydrogen_bond_acceptors=0
+)
+
+methionine = AminoAcid("Methionine", "MET", "M",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+phenylalanine = AminoAcid("Phenylalanine", "PHE", "F",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=7,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+proline = AminoAcid("Proline", "PRO", "P",
+    charge=0.0,
+    polarity=Polarity.APOLAR,
+    size=3,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+serine = AminoAcid("Serine", "SER", "S",
+    charge=-0.80,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2
+)
+
+threonine = AminoAcid("Threonine", "THR", "T",
+    charge=-0.80,
+    polarity=Polarity.POLAR,
+    size=3,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2
+)
+
+tryptophan = AminoAcid("Tryptophan", "TRP", "W",
+    charge=-0.79,
+    polarity=Polarity.POLAR,
+    size=10,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=0
+)
+
+tyrosine = AminoAcid("Tyrosine", "TYR", "Y",
+    charge=-0.80,
+    polarity=Polarity.POLAR,
+    size=8,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=1
+)
+
+valine = AminoAcid("Valine", "VAL", "V",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=3,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+selenocysteine = AminoAcid("Selenocysteine", "SEC", "U",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2,
+)
+
+pyrrolysine = AminoAcid("Pyrrolysine", "PYL", "O",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=13,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+alysine = AminoAcid("Alysine", "ALY", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=13,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+methyllysine = AminoAcid("Methyllysine", "MLZ", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=14,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+dimethyllysine = AminoAcid("Dimethyllysine", "MLY", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=15,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+trimethyllysine = AminoAcid("Trimethyllysine", "3ML", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=16,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+epsilon_methionine = AminoAcid("Epsilon Methionine", "MSE", "M",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+hydroxy_proline = AminoAcid("Hydroxy Proline", "HYP", "P",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2
+)
+
+serine_phosphate = AminoAcid("Serine Phosphate", "SEP", "S",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=7,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+threonine_phosphate = AminoAcid("Threonine Phosphate", "TOP", "T",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=8,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+tyrosine_phosphate = AminoAcid("Tyrosine Phosphate", "TYP", "Y",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=13,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+tyrosine_sulphate = AminoAcid("Tyrosine Sulphate", "TYS", "Y",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=13,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+cyclohexane_alanine = AminoAcid("Cyclohexane Alanine", "CHX", "?",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.APOLAR,
+    size=7,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+unknown_amino_acid = AminoAcid("Unknown", "XXX", "X",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.APOLAR,
+    size=0,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
 
 
 amino_acids = [alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine,
diff --git a/deeprank/features/amino_acid_swap.py b/deeprank/features/amino_acid_swap.py
new file mode 100644
index 0000000..36c5e0f
--- /dev/null
+++ b/deeprank/features/amino_acid_swap.py
@@ -0,0 +1,70 @@
+from typing import List, Union
+
+import h5py
+import numpy
+from pdb2sql import pdb2sql
+
+from deeprank.models.environment import Environment
+from deeprank.models.variant import PdbVariantSelection
+from deeprank.operate.pdb import get_pdb_path
+
+
+
+SIZE_DELTA_FEATURE_NAME = "size_delta"
+CHARGE_DELTA_FEATURE_NAME = "charge_delta"
+POLARITY_DELTA_FEATURE_NAME = "polarity_delta"
+HBACCEPTOR_DELTA_FEATURE_NAME = "hb_acceptor_delta"
+HBDONOR_DELTA_FEATURE_NAME = "hb_donor_delta"
+
+
+def _store_feature(feature_group_xyz: h5py.Group,
+                   atom_positions: numpy.array,
+                   feature_name: str,
+                   value: Union[float, int, numpy.array]):
+    """
+    atom_positions: [n_atom, 3] x,y,z per atom
+    value: one float or a vector
+    """
+
+    if type(value) == float or type(value) == int:
+        values = [value]
+    else:
+        values = list(value)
+
+    data = [list(position) + values for position in atom_positions]
+
+    feature_group_xyz.create_dataset(feature_name, data=data)
+
+
+def __compute_feature__(environment: Environment,
+                        distance_cutoff: float,
+                        feature_group: h5py.Group,
+                        variant: PdbVariantSelection):
+
+    "computes features that express the difference in physiochemical properties of the swapped amino acid"
+
+    # get the C-alpha position
+    pdb = pdb2sql(get_pdb_path(environment.pdb_root, variant.pdb_ac))
+    if variant.insertion_code is not None:
+        atom_positions = pdb.get("x,y,z", chainID=variant.chain_id, resSeq=variant.residue_number, iCode=variant.insertion_code)
+    else:
+        atom_positions = pdb.get("x,y,z", chainID=variant.chain_id, resSeq=variant.residue_number)
+
+    wildtype_amino_acid = variant.wildtype_amino_acid
+    variant_amino_acid = variant.variant_amino_acid
+
+    size_delta = variant_amino_acid.size - wildtype_amino_acid.size
+    _store_feature(feature_group, atom_positions, SIZE_DELTA_FEATURE_NAME, size_delta)
+
+    charge_delta = variant_amino_acid.charge - wildtype_amino_acid.charge
+    _store_feature(feature_group, atom_positions, CHARGE_DELTA_FEATURE_NAME, charge_delta)
+
+    polarity_delta = variant_amino_acid.polarity.onehot - wildtype_amino_acid.polarity.onehot
+    _store_feature(feature_group, atom_positions, POLARITY_DELTA_FEATURE_NAME, polarity_delta)
+
+    hb_acceptor_delta = variant_amino_acid.count_hydrogen_bond_acceptors - wildtype_amino_acid.count_hydrogen_bond_acceptors
+    _store_feature(feature_group, atom_positions, HBACCEPTOR_DELTA_FEATURE_NAME, hb_acceptor_delta)
+
+    hb_donor_delta = variant_amino_acid.count_hydrogen_bond_donors - wildtype_amino_acid.count_hydrogen_bond_donors
+    _store_feature(feature_group, atom_positions, HBDONOR_DELTA_FEATURE_NAME, hb_donor_delta)
+
diff --git a/deeprank/features/neighbour_profile.py b/deeprank/features/neighbour_profile.py
index 5fa14ce..c18aee8 100644
--- a/deeprank/features/neighbour_profile.py
+++ b/deeprank/features/neighbour_profile.py
@@ -43,7 +43,7 @@ def get_c_alpha_pos(environment, variant):
     db = pdb2sql(pdb_path)
     try:
         if variant.insertion_code is not None:
-            position = db.get("x,y,z", chainID=variant.chain_id, resSeq=variant.residue_number, iCode=variant, name="CA")[0]
+            position = db.get("x,y,z", chainID=variant.chain_id, resSeq=variant.residue_number, iCode=variant.insertion_code, name="CA")[0]
         else:
             position = db.get("x,y,z", chainID=variant.chain_id, resSeq=variant.residue_number, name="CA")[0]
 
diff --git a/deeprank/models/amino_acid.py b/deeprank/models/amino_acid.py
index d138440..cf0e086 100644
--- a/deeprank/models/amino_acid.py
+++ b/deeprank/models/amino_acid.py
@@ -1,11 +1,23 @@
+from deeprank.models.polarity import Polarity
 
 
 class AminoAcid:
-    def __init__(self, name, code, letter):
+    def __init__(self, name: str, code: str, letter: str,
+                 charge: float, polarity: Polarity, size: int,
+                 count_hydrogen_bond_donors: int,
+                 count_hydrogen_bond_acceptors: int):
+
         self.name = name
         self.code = code
         self.letter = letter
 
+        # these settings apply to the side chain
+        self._size = size
+        self._charge = charge
+        self._polarity = polarity
+        self._count_hydrogen_bond_donors = count_hydrogen_bond_donors
+        self._count_hydrogen_bond_acceptors = count_hydrogen_bond_acceptors
+
     def __repr__(self):
         return self.name
 
@@ -14,3 +26,24 @@ def __eq__(self, other):
 
     def __hash__(self):
         return hash(self.name)
+
+    @property
+    def count_hydrogen_bond_donors(self) -> int:
+        return self._count_hydrogen_bond_donors
+
+    @property
+    def count_hydrogen_bond_acceptors(self) -> int:
+        return self._count_hydrogen_bond_acceptors
+
+    @property
+    def charge(self) -> float:
+        return self._charge
+
+    @property
+    def polarity(self) -> Polarity:
+        return self._polarity
+
+    @property
+    def size(self) -> int:
+        return self._size
+
diff --git a/deeprank/models/polarity.py b/deeprank/models/polarity.py
new file mode 100644
index 0000000..505009b
--- /dev/null
+++ b/deeprank/models/polarity.py
@@ -0,0 +1,20 @@
+import numpy
+
+from enum import Enum
+
+
+class Polarity(Enum):
+    "a value to express a residue's polarity"
+
+    APOLAR = 0
+    POLAR = 1
+    NEGATIVE_CHARGE = 2
+    POSITIVE_CHARGE = 3
+
+    @property
+    def onehot(self):
+        t = numpy.zeros(4)
+        t[self.value] = 1.0
+
+        return t
+
diff --git a/scripts/preprocess_bioprodict.py b/scripts/preprocess_bioprodict.py
index c520fac..7e7821d 100755
--- a/scripts/preprocess_bioprodict.py
+++ b/scripts/preprocess_bioprodict.py
@@ -337,6 +337,7 @@ def get_subset(variants):
                               device=device)
 
     feature_modules = ["deeprank.features.atomic_contacts",
+                       "deeprank.features.amino_acid_swap",
                        "deeprank.features.accessibility"]
     target_modules = ["deeprank.targets.variant_class"]
 
diff --git a/test/features/test_amino_acid_swap.py b/test/features/test_amino_acid_swap.py
new file mode 100644
index 0000000..357a79c
--- /dev/null
+++ b/test/features/test_amino_acid_swap.py
@@ -0,0 +1,40 @@
+from tempfile import mkstemp
+import os
+import h5py
+
+from deeprank.features.amino_acid_swap import (
+    SIZE_DELTA_FEATURE_NAME,
+    CHARGE_DELTA_FEATURE_NAME,
+    POLARITY_DELTA_FEATURE_NAME,
+    HBACCEPTOR_DELTA_FEATURE_NAME,
+    HBDONOR_DELTA_FEATURE_NAME,
+    __compute_feature__
+)
+from deeprank.models.environment import Environment
+from deeprank.models.variant import PdbVariantSelection
+from deeprank.domain.amino_acid import glycine, tryptophan
+
+
+def test_compute_features():
+
+    environment = Environment(pdb_root="test/data/pdb", device="cpu")
+
+    variant = PdbVariantSelection("101M", "A", 25, glycine, tryptophan)
+
+    tmp_file, tmp_path = mkstemp(suffix=".h5py")
+    os.close(tmp_file)
+
+    try:
+        with h5py.File(tmp_path, 'w') as f5:
+
+            xyz_group = f5.require_group('xyz')
+
+            __compute_feature__(environment, 10.0, xyz_group, variant)
+
+            assert SIZE_DELTA_FEATURE_NAME in xyz_group
+            assert CHARGE_DELTA_FEATURE_NAME in xyz_group
+            assert POLARITY_DELTA_FEATURE_NAME in xyz_group
+            assert HBACCEPTOR_DELTA_FEATURE_NAME in xyz_group
+            assert HBDONOR_DELTA_FEATURE_NAME in xyz_group
+    finally:
+        os.remove(tmp_path)