Summary Practical Session 1: Step-by-Step Guide

Noa Van den Notelaer

Bioinformatics: Structure
Practical Session 1

Overview
Amino acids and non-covalent interactions.............................................................................. 2
UniProt .................................................................................................................................................. 3
1. How to find a name of a protein ....................................................................................... 3
2. How to find the subcellular location of a protein ....................................................... 3
3. How to find a FASTA sequence of a protein .................................................................. 3
4. How to see if a protein is an enzyme ............................................................................. 4
5. How to see if a given residue is in an active site/binding site ................................ 4
6. Determining what the PDB-ID is of the best available experimentally
determined structure for a protein .......................................................................................... 4
7. How to see if there is an AlphaFold structure & which coverage ......................... 5
8. Interpretating pLDDT score ............................................................................................... 6
Looking at structure ......................................................................................................................... 7
1. Looking at secondary structure of a residue ............................................................... 7
2. Checking the pLDDT score of a residue ......................................................................... 9
3. How to check if a residue is hydrophilic or hydrophobic.......................................... 9
4. Counting hydrogen bonds..................................................................................................10




1

,Noa Van den Notelaer


Amino acids and non-covalent interactions




Cα




- Amino acids substitutions are likely to be detrimental (harmful) if:
o Non-polar <=> polar
o + charged <=> - charged or vice versa
o Change involving a structurally unique residue
o Disruption of disulfide bonds
o Replacement with bulky side chain (large side chain)
- Types of interactions in UniProt:

Interaction type Involved regions Typical Example
interactions
Backbone  backbone (N, Backbone H-bonds in
Main – Main Cα, C, O) hydrogen bonds α-helix or β-
sheet
Main – Side Backbone  Side chain H-bonds, ionic, Backbone
polar contacts C=O ↔ Ser
side chain OH
Side-Side Side chain  Side chain H-bonds, ionic,
hydrophobic, π–
π, cation–π




2

, Noa Van den Notelaer


UniProt
UniProt
1. How to find a name of a protein
Go to site => copy paste protein ID

Protein
ID




2. How to find the subcellular location of a protein
Click on protein ID of interest => click on Subcellular Location




3. How to find a FASTA sequence of a protein
Go to Sequence & Isoform => choose the canonical sequence (or other if specified)
=> you can also download the sequence




3