131. Internal coordinates for representation of the three-dimensional structure of a protein consists of:
1. bond lengths, bond angles and dihedral angles
2. Cartesian coordinates X, Y and Z for all the atoms
3. spherical polar coordinates R, θ, Φ for all atoms
4. all possible inter atomic distances

Question

Internal coordinates for representation of the three-dimensional structure of a protein consist of:

1. Bond lengths, bond angles and dihedral angles

2. Cartesian coordinates X, Y and Z for all the atoms

3. Spherical polar coordinates R, θ, Φ for all atoms

4. All possible inter-atomic distances

Detailed Explanation

In the context of protein structure representation, the three-dimensional (3D) shape of a protein is crucial for understanding its function. Internal coordinates help describe the positions and relationships between atoms in the protein in a way that is different from Cartesian coordinates (X, Y, Z), which specify exact atom positions in 3D space.

Types of Coordinates for Protein Representation

1. Internal Coordinates

   • Bond lengths: The distance between two connected atoms.

   • Bond angles: The angle formed between three connected atoms.

   • Dihedral angles: The angle between two planes defined by four atoms, which is especially important for the rotation around single bonds in proteins.

   These internal coordinates define the conformation of the protein without requiring the absolute positions of atoms in space. Instead, they define how atoms relate to each other internally.

2. Cartesian Coordinates (X, Y, Z for all atoms):
   These coordinates represent the absolute position of atoms in space. While this is a commonly used representation for protein structures, it’s not part of the internal coordinate system, which focuses on relative relationships.

3. Spherical Polar Coordinates (R, θ, Φ):
   These describe positions in a spherical system using radius (R), polar angle (θ), and azimuthal angle (Φ). Although this system is used in some contexts, it’s not the standard for protein internal coordinates.

4. Inter-atomic Distances:
   While inter-atomic distances (distances between every pair of atoms) are essential for structure determination, the complete set of distances isn’t typically used in internal coordinates, as it would result in a more complex and less efficient representation.

✅ Correct Answer: 1. Bond lengths, bond angles, and dihedral angles

Internal coordinates typically consist of bond lengths, bond angles, and dihedral angles, as they describe the relationships between atoms relative to each other in the structure. This method provides a compact and efficient way to represent protein conformation