Anion–π contacts are common in the PDB
A PDB-wide search finds anion–π interactions in most protein structures, with Asp/Glu carboxylates packing on aromatics and frequent cation–π partners opposite.
Source
A thorough anion-π interaction study in biomolecules: on the importance of cooperativity effects
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Anion–π contacts are common in the PDB
These passages occur verbatim in the stored paper text. They support the points listed below; they do not verify every statement in the explanation.
Which residues supply most anions?
Due to their abundance, Asp and Glu are found in the vast majority of anion–π interactions
How do those carboxylates orient?
a preferred close-to-parallel orientation of their carboxylate with respect to the interacting aromatic system
What they did
Authors scanned the PDB for anion–π pairs among carboxylates, phosphates, and aromatic side chains/nucleobases, classified geometry, tested enrichment statistically, and looked for ternary anion–π–cation and anion–π–π contacts that could cooperate.
What they found
Thousands of anion–π contacts exist. 61.3% of 62 033 processed PDB structures contain them. Asp/Glu dominate with near-parallel carboxylates; His is the most common protein aromatic, but Tyr rises at interfaces. DNA vs RNA differ in Glu/Asp and base preferences. Opposite-face cation–π and stacking are common, implying cooperativity.
The limits
What it doesn't show
This is a structural census, not a measured binding free energy for a designed host; predicted cooperativity is inferred from geometry, not from a new titration series.
Key terms
- Anion–π interaction
- Contact between an anion (often carboxylate) and the face of an aromatic ring.
- Cooperativity
- A second interaction (cation–π or stacking) on the same ring that can strengthen a weak anion–π contact.
- Cation–π
- Attraction of a cation to an aromatic face, often opposite the anion here.
- PDB census
- Statistical search of deposited crystal/NMR structures for a contact type.
- Close-to-parallel carboxylate
- Preferred orientation of Asp/Glu relative to the aromatic plane.
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Quiz yourself
Fraction of processed PDB entries with anion–π contacts:
Common questions
How common are anion–π contacts in proteins?
In 61.3% of processed PDB structures.
Which anions dominate?
Asp and Glu carboxylates.
Which protein aromatic is most common?
His overall; Tyr at interfaces.
DNA vs RNA?
DNA shows no Glu/Asp selectivity; Glu is more present in RNA, with different base partners.
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