iTechGuides is reader-supported. When you buy through links on our site, we may earn an affiliate commission. As an Amazon Associate I earn from qualifying purchases. Learn more
The overlooked interaction is the C5 hydrogen bond: a bond within one amino-acid residue, between its backbone amide proton and carbonyl oxygen. In a 2016 study, Robert W. Newberry and Ronald T. Raines argued that these individually weak interactions are common enough to make a cumulative contribution to protein stability.
What is a C5 hydrogen bond?
Proteins are chains of amino acids. Each residue in the chain contributes a repeating backbone that includes an amide N–H group and a carbonyl C=O group. In a C5 interaction, the amide proton acts as the hydrogen-bond donor and the carbonyl oxygen of that same residue acts as the acceptor. The name refers to the geometry of the resulting arrangement.
This differs from the familiar backbone hydrogen bonds in protein helices and sheets, which connect groups on different residues. A C5 bond is intraresidue: both participating groups belong to one residue. Newberry and Raines proposed that it arises from overlap between a lone pair on the carbonyl oxygen and the antibonding orbital of the N–H bond. Their 2016 paper describes the interaction and its evidence.
Quick wins for a faster PC:
Fix the driver behind crashes, sound loss and screen glitchesFind Drivers →Repair Windows errors before they cause bigger problemsFix Now →Scan for outdated or missing drivers - takes under a minuteDriver Scan →Why can a weak bond matter?
A single C5 interaction is weak, but protein stability reflects the combined effects of many interactions rather than one bond in isolation. If an interaction occurs repeatedly along a protein backbone, its small contributions may add up. That is the authors’ explanation for why a previously underappreciated interaction could matter despite being weak on its own.
#1 Best Overall
- Perfect for Visual Learners - This hands-on Biochemistry Model Kit is a tool that doesn’t just show you molecular structures; it lets you explore the magic of bonding, resonance, and chemical interactions like never before. It’s your key to understanding how molecular 3D structures influence chemical properties, such as in nucleotides and their base pairs, or in lipids and their hydrophobic behavior. You'll connect the dots between a compound's physical and chemical properties and its three-dimensional structure, deepening your understanding and making complex concepts intuitive.
- Versatile & Suitable for All Learning Levels - Whether you're a biochemistry student, an educator, or just passionate about molecular science, this model set will elevate your learning experience. It’s a powerful way to transform abstract molecular diagrams into tangible, interactive models you can touch, build, and explore. Get ready to turn curiosity into mastery—because biochemistry isn't just a subject, it's the science of life itself. With the Biochemistry Model Set, the possibilities are endless. Don’t just learn it—build it, see it, and truly understand it!
- High-Quality, Durable Components - Components are color-coded to international standards, with scaled bond lengths for accuracy. Rigid bonds allow easy single-bond rotation, while flexible bonds are ideal for double and triple bonds. Lost parts? No problem—Mega Molecules offers replacement atoms and bonds to keep your kit complete and long-lasting.
- Easy Assembly & Disassembly - Unlike many competitor kits that require special tools and make loud popping sounds during assembly or disassembly, Mega Molecules Model Sets offer a quiet, hassle-free experience. Atoms and bonds connect with a gentle push-and-twist motion and easily disconnect with a pull-and-twist—no noise, no tools needed. This thoughtful design minimizes distractions, making it perfect for classrooms, study sessions, and testing environments, ensuring a smooth, focused learning experience.
- Satisfaction Guarantee - Backed by a refund or replacement policy, this biochemistry building set offers a risk-free investment in chemistry education. Whether you're studying the protein structure, the base pairing in DNA, or the intricacies of a glycosidic linkage, this set brings your biochemistry lessons to life. Use it to model the relationships between carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur as they form covalent bonds. With every build, you’ll gain deeper insights into the connections between molecular structure and function.
Newberry and Raines estimated about 4.5 kcal/mol of stabilizing energy per 100 residues. This is the authors’ estimate, based on calculated energies assigned to structural bins; it is not a directly measured universal constant or a stability measurement for every protein.
What evidence did the 2016 study present?
The study combined several approaches rather than relying on a structural observation alone:
Rank #2
- [VIBRANT COLORS & SAFE DESIGN] The protein molecular model features bright and standardized atomic colors making it visually appealing and easy to identify. The high quality plastic construction ensures durability and safety for classroom use. The colorful balls and connecting are well made providing a tactile learning experience for students.
- [3D MOLECULAR VISUALIZATION] This model offers a comprehensive 3D representation of protein structures allowing students to study molecular and angles from all directions. The detailed design helps in understanding complex protein configurations making it an excellent tool for biochemistry and biology education.
- [HANDS ON LEARNING TOOL] Perfect for building both common and slightly complex protein structures this kit enhances interactive learning in classrooms and laboratories. The easy to assemble and disassemble design with included disconnect tool encourages student participation and engagement.
- [PORTABLE & USER FRIENDLY] Designed for convenience this molecular model is lightweight and easy to store or transport. The tightly held atoms and ensure stability during use while still allowing for effortless disassembly making it ideal for repeated classroom demonstrations.
- [EDUCATIONAL ENHANCEMENT] Specifically tailored for the QH3212 2 protein molecule this model aligns with textbook structures to boost student interest and comprehension. Teachers can leverage this visual aid to deliver more intuitive and effective lessons in molecular biology.
- Quantum calculations examined the proposed interaction and its energetics.
- Infrared and nuclear magnetic resonance spectroscopy provided experimental evidence for its chemical features.
- Modified synthetic β-sheets allowed the researchers to selectively alter the interaction and test resulting stability changes.
- High-resolution protein structures were analyzed to estimate how often the geometry appears.
Together, these lines of evidence supported the authors’ claim that C5 interactions share characteristic features of conventional hydrogen bonds and can affect the stability of synthetic β-sheets. The study’s structural prevalence and total-energy figures are analyses and estimates, not direct measurements of the contribution in every protein.
Recommended Free Tools
How common did the authors estimate it to be?
In their dataset, Newberry and Raines reported C5 interactions in approximately 5% of residues, and found that 94% of the proteins they examined contained at least one. The 94% figure describes that study’s protein set; it should not be generalized to every known protein.
Rank #3
- FOR BASIC TEACHING TO ADVANCED SCIENCE: 444 pieces molecular model kit, including 136 atoms, 158 bonds and 150 parts for Carbon-60(Fullerene), provides to students from Grade 7 to Graduate level.
- TWO CHEMICAL STRUCTURE MODELS: The ball-and-stick models use spheres to represent atoms and sticks to represent chemical bonds. In the space-filling model, the spheres are drawn to scale and are next to one another as atoms are in real molecules.
- CHEMISTRY EDUCATIONAL MOLECULE MODEL IN 3D: It can display chemical structure, molecular bond, and bond angle in all directions. Demonstrate fundamental molecular geometry, chemical molecular structure, stereochemistry with 3D modeling studies.
- EASY TO LEARN: The universal standard adopted for each atom's color makes it easier for you to use and learn. Atoms and chemical bonds combine tightly and firmly and can be easily disassembled by disconnecting tools.
- If you’re not in love with it for whatever reason, we’ll give you a full replacement or refund—no questions asked. If you have any doubt, please tell us. With nothing to worry about, or even to share with your friends, try it now.
These values are findings from the 2016 paper, not a settled field-wide consensus. The available evidence here does not establish whether later studies independently replicated or revised the prevalence and energy estimates.
What might this mean for protein structure and amyloid?
The authors suggested that accounting for C5 interactions could improve computational models of protein folding, function, and dysfunction. They also pointed to possible relevance in flat β-sheets, including those found in amyloid states. These are research implications, not evidence that the interaction causes Alzheimer’s disease or that it has a diagnostic or treatment use.
Rank #4
- Build common and slightly complex protein structures with this molecular model kit, perfect for teaching and lab use.
- Brightly colored balls and connectors follow standard color coding, making it easy to identify and use.
- Ideal for demonstrating protein molecular features from textbooks, boosting student interest and helping teachers explain clearly.
- 3D modeling shows basic molecular structure from all angles, helping visualize molecular and angles.
- Easy to learn, store, and carry; atoms and connectors fit tightly yet can be easily disassembled with a disconnect tool.
What to take away
C5 hydrogen bonding is a proposed, experimentally investigated interaction between the N–H and C=O groups of the same amino-acid residue. Newberry and Raines’s 2016 work made the case that it is common and may contribute collectively to protein stability. Its estimated prevalence and energetic contribution should be understood as results of that study, rather than universal values established for all proteins.
Sources: Newberry and Raines, Nature Chemical Biology (2016); full text at PubMed Central.
Quick Recap
Best Value
- Model the molecular mechanics of gene expression — from DNA to protein. The Protein Synthesis Molecular Model Set from Mega Molecules is a hands-on educational tool designed to guide students through the complete process of protein synthesis: transcription and translation. Using color-coded components, this set allows learners to construct and manipulate accurate physical models of DNA, mRNA, tRNA, and amino acids—making the molecular biology behind gene expression tangible and engaging.
- This model set supports an active learning experience in which students construct DNA nucleotides using phosphoric acid, deoxyribose, and the four nitrogenous bases: adenine, thymine, cytosine, and guanine.
- Users build a DNA strand from a gene sequence (e.g., T-A-C-C-T-G-C-A-G-A-C-T), physically connecting the nucleotides via gray bonding links to represent covalent bonds.
- Users transcribe mRNA by pairing RNA nucleotides (adenine, uracil, cytosine, guanine) to the DNA template, demonstrating base pairing rules (e.g., A–U, C–G).
- Users model tRNA molecules with built-in anticodons and specific amino acid attachments—highlighting how tRNA ensures accurate translation at the ribosome.
Product prices and availability are accurate as of the date/time indicated and are subject to change. Any price and availability information displayed on Amazon at the time of purchase will apply.
