J. Kendrew, G. Bodo, H. Dintzis, R. Parrish, H. Wyckoff et al., A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis, Nature, vol.178, issue.4610, pp.662-668, 1958.
DOI : 10.1002/hlca.19490320118

D. Eisenberg, The discovery of the ??-helix and ??-sheet, the principal structural features of proteins, Proceedings of the National Academy of Sciences, vol.47, issue.4, pp.11207-11217, 2003.
DOI : 10.1016/S0022-2836(63)80023-6

L. Pauling, R. Corey, and H. Branson, The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain, Proceedings of the National Academy of Sciences, vol.203, issue.4, pp.205-216, 1951.
DOI : 10.1021/cr60102a002

L. Pauling and R. Corey, The Pleated Sheet, A New Layer Configuration of Polypeptide Chains, Proceedings of the National Academy of Sciences, vol.37, issue.5, pp.251-257, 1951.
DOI : 10.1073/pnas.37.5.251

S. Miller, A. Watkins, N. Kallenbach, and P. Arora, Effects of side chains in helix nucleation differ from helix propagation, Proceedings of the National Academy of Sciences, vol.112, issue.30, pp.6636-6677, 2014.
DOI : 10.1021/jp8001614

A. Chakrabartty, T. Kortemme, and R. Baldwin, Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions, Protein Science, vol.32, issue.5, pp.843-52, 1994.
DOI : 10.1002/pro.5560030514

S. Kumar and M. Bansal, Geometrical and Sequence Characteristics of ??-Helices in Globular Proteins, Biophysical Journal, vol.75, issue.4, pp.1935-1979, 1998.
DOI : 10.1016/S0006-3495(98)77634-9

S. Malkov, M. Zivkovic, M. Beljanski, S. Stojanovic, and S. Zaric, A Reexamination of Correlations of Amino Acids with Particular Secondary Structures, The Protein Journal, vol.34, issue.45, pp.74-86, 2009.
DOI : 10.1002/(SICI)1097-0134(1999)37:3+<194::AID-PROT24>3.0.CO;2-F

J. Richardson and D. Richardson, Amino acid preferences for specific locations at the ends of alpha helices, Science, vol.240, issue.4859, pp.1648-52, 1988.
DOI : 10.1126/science.3381086

L. Pal, P. Chakrabarti, and G. Basu, Sequence and Structure Patterns in Proteins from an Analysis of the Shortest Helices: Implications for Helix Nucleation, Journal of Molecular Biology, vol.326, issue.1, pp.273-91, 2003.
DOI : 10.1016/S0022-2836(02)01338-4

L. Presta and G. Rose, Helix signals in proteins, Science, vol.240, issue.4859, pp.1632-1673, 1988.
DOI : 10.1126/science.2837824

R. Aurora, R. Srinivasan, and G. Rose, Rules for alpha-helix termination by glycine, Science, vol.264, issue.5162, pp.1126-1156, 1994.
DOI : 10.1126/science.8178170

R. Aurora and G. Rose, Helix capping, Protein Science, vol.31, issue.1, pp.21-38, 1998.
DOI : 10.1063/1.1730390

URL : http://onlinelibrary.wiley.com/doi/10.1002/pro.5560070103/pdf

M. Levitt, Conformational preferences of amino acids in globular proteins, Biochemistry, vol.17, issue.20, pp.4277-85, 1978.
DOI : 10.1021/bi00613a026

K. Imai and S. Mitaku, Mechanisms of secondary structure breakers in soluble proteins, BIOPHYSICS, vol.1, pp.55-65, 2005.
DOI : 10.2142/biophysics.1.55

B. Ho, A. Thomas, and R. Brasseur, Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the ??-helix, Protein Science, vol.285, issue.11, pp.2508-2530, 2003.
DOI : 10.1002/pro.5560070103

D. Ermolenko, S. Thomas, A. R. Gronenborn, A. Makhatadze, and G. , Hydrophobic Interactions at the Ccap Position of the C-capping Motif of ??-Helices, Journal of Molecular Biology, vol.322, issue.1, pp.123-158, 2002.
DOI : 10.1016/S0022-2836(02)00734-9

J. Prieto and L. Serrano, C-capping and helix stability: the pro C-capping motif, Journal of Molecular Biology, vol.274, issue.2, pp.276-88, 1997.
DOI : 10.1006/jmbi.1997.1322

H. Dirr, T. Little, D. Kuhnert, and Y. Sayed, -Transferases, Journal of Biological Chemistry, vol.213, issue.20, pp.19480-19487, 2005.
DOI : 10.1016/j.sbi.2004.08.001

URL : https://hal.archives-ouvertes.fr/pasteur-01302307

D. Kuhnert, Y. Sayed, S. Mosebi, M. Sayed, T. Sewell et al., Tertiary Interactions Stabilise the C-terminal Region of Human Glutathione Transferase A1-1: a Crystallographic and Calorimetric Study, Journal of Molecular Biology, vol.349, issue.4, pp.825-863, 2005.
DOI : 10.1016/j.jmb.2005.04.025

J. Donohue, Hydrogen Bonded Helical Configurations of the Polypeptide Chain, Proceedings of the National Academy of Sciences, vol.39, issue.6, pp.470-478, 1953.
DOI : 10.1073/pnas.39.6.470

L. Pal and G. Basu, Novel protein structural motifs containing two-turn and longer 310-helices, Protein Engineering, Design and Selection, vol.12, issue.10, pp.811-815, 1999.
DOI : 10.1093/protein/12.10.811

L. Pal, G. Basu, and P. Chakrabarti, Variants of 310-helices in proteins, Proteins: Structure, Function, and Genetics, vol.32, issue.3, pp.571-580, 2002.
DOI : 10.1002/prot.10184

E. Baker and R. Hubbard, Hydrogen bonding in globular proteins, Progress in Biophysics and Molecular Biology, vol.44, issue.2, pp.97-179, 1984.
DOI : 10.1016/0079-6107(84)90007-5

D. Barlow and J. Thornton, Helix geometry in proteins, Journal of Molecular Biology, vol.201, issue.3, pp.601-620, 1988.
DOI : 10.1016/0022-2836(88)90641-9

L. Pal, B. Dasgupta, and P. Chakrabarti, 310-Helix adjoining ??-helix and ??-strand: Sequence and structural features and their conservation, Biopolymers, vol.12, issue.3, pp.147-62, 2005.
DOI : 10.1002/pro.5560070103

M. Karpen, P. De-haseth, and K. Neet, -helices, Protein Science, vol.58, issue.10, pp.1333-1375, 1992.
DOI : 10.1007/978-1-4613-1571-1_1

URL : https://hal.archives-ouvertes.fr/jpa-00253188

V. Khrustalev, E. Barkovsky, and T. Khrustaleva, The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices, International Journal of Proteomics, vol.1, issue.2, p.360230, 2014.
DOI : 10.1371/journal.pone.0053785

B. Low and R. Baybutt, THE ?? HELIX???A HYDROGEN BONDED CONFIGURATION OF THE POLYPEPTIDE CHAIN, Journal of the American Chemical Society, vol.74, issue.22, p.5806, 1952.
DOI : 10.1021/ja01142a539

B. Low and H. Greenville-wells, Generalized Mathematical Relationships for Polypeptide Chain Helices: The Coordinates of the II Helix, Proceedings of the National Academy of Sciences, vol.39, issue.8, pp.785-801, 1953.
DOI : 10.1073/pnas.39.8.785

G. Ramachandran and V. Sasisekharan, Conformation of Polypeptides and Proteins, Advan Protein Chem, vol.23, pp.283-438, 1968.
DOI : 10.1016/S0065-3233(08)60402-7

C. Rohl and A. Doig, -helix/coil transitions in isolated peptides, Protein Science, vol.31, issue.8, pp.1687-96, 1996.
DOI : 10.1021/bk-1993-0526.ch013

URL : https://hal.archives-ouvertes.fr/jpa-00227842

T. Weaver, The ??-helix translates structure into function, Protein Science, vol.21, issue.1, pp.201-207, 2000.
DOI : 10.1110/ps.9.1.201

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144447

P. Kumar and M. Bansal, Dissecting ??-helices: sequence, structure and function, FEBS Journal, vol.175, issue.22, pp.4415-4447, 2015.
DOI : 10.1016/0022-2836(84)90446-7

M. Fodje and S. Karadaghi, Occurrence, conformational features and amino acid propensities for the ??-helix, Protein Engineering, Design and Selection, vol.15, issue.5, pp.353-361, 2002.
DOI : 10.1093/protein/15.5.353

G. Pollastri, D. Przybylski, B. Rost, and P. Baldi, Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles, Proteins: Structure, Function, and Genetics, vol.47, issue.2, pp.228-263, 2002.
DOI : 10.1002/prot.10069

S. Wang, W. Li, S. Liu, and J. Xu, RaptorX-Property: a web server for protein structure property prediction, Nucleic Acids Research, vol.44, issue.W1, pp.430-435, 2016.
DOI : 10.1093/nar/gkw306

URL : http://doi.org/10.1093/nar/gkw306

R. Pancsa, D. Raimondi, E. Cilia, and W. Vranken, Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity, Biophysical Journal, vol.110, issue.3, pp.572-83, 2016.
DOI : 10.1016/j.bpj.2015.12.028

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744172

G. Millhauser, Views of Helical Peptides: A Proposal for the Position of 310-Helix along the Thermodynamic Folding Pathway, Biochemistry, vol.34, issue.12, pp.3873-3880, 1995.
DOI : 10.1021/bi00012a001

G. Millhauser, C. Stenland, K. Bolin, and F. Van-de-ven, Local helix content in an alanine-rich peptide as determined by the complete set of 3JHN?? coupling constants, Journal of Biomolecular NMR, vol.7, issue.4, pp.331-335, 1996.
DOI : 10.1007/BF00200434

R. Armen, D. Alonso, and V. Daggett, -, and ??-helix in helix???coil transitions, Protein Science, vol.31, issue.102, pp.1145-57, 2003.
DOI : 10.1110/ps.9.1.201

B. Goyal, A. Kumar, K. Srivastava, and S. Durani, Scrutiny of chain-length and N-terminal effects in ??-helix folding: a molecular dynamics study on polyalanine peptides, Journal of Biomolecular Structure and Dynamics, vol.35, issue.9, pp.1923-1958, 2016.
DOI : 10.1063/1.1730390

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat et al., The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-277, 2000.
DOI : 10.1093/nar/28.1.235

N. Fox, S. Brenner, and J. Chandonia, SCOPe: Structural Classification of Proteins???extended, integrating SCOP and ASTRAL data and classification of new structures, Nucleic Acids Research, vol.42, issue.D1, pp.304-309, 2014.
DOI : 10.1093/nar/gkt1240

J. Chandonia, G. Hon, N. Walker, L. Conte, L. Koehl et al., The ASTRAL Compendium in 2004, Nucleic Acids Research, vol.32, issue.90001, pp.189-192, 2004.
DOI : 10.1093/nar/gkh034

P. Craveur, J. Rebehmed, and A. De-brevern, PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins, Database, vol.2014, issue.0, p.41, 2014.
DOI : 10.1093/database/bau041

S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar et al., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics, vol.29, issue.7, pp.845-54, 2013.
DOI : 10.1093/bioinformatics/btt055

W. Van-gunsteren, S. Billeter, A. Eising, P. Hünenberger, P. Krüger et al., Biomolecular Simulation: The GROMOS96 Manual and User Guide. Zürich, Switzerland: Vdf Hochschulverlag AG an der ETH Zürich, p.1042, 1996.

W. Jorgensen and J. Madura, Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water, Journal of the American Chemical Society, vol.105, issue.6, pp.1407-1420, 1983.
DOI : 10.1021/ja00344a001

H. Berendsen, J. Postma, W. Van-gunsteren, A. Dinola, and J. Haak, Molecular dynamics with coupling to an external bath, The Journal of Chemical Physics, vol.15, issue.8, pp.3684-90, 1984.
DOI : 10.1039/fs9821700055

M. Parrinello and A. Rahman, Polymorphic transitions in single crystals: A new molecular dynamics method, Journal of Applied Physics, vol.52, issue.12, pp.7182-90, 1981.
DOI : 10.1103/PhysRevA.22.1690

B. Hess, H. Bekker, H. Berendsen, and J. Fraaije, LINCS: A linear constraint solver for molecular simulations, Journal of Computational Chemistry, vol.19, issue.12, pp.1463-72, 1997.
DOI : 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.475.1767

T. Darden, L. Perera, L. Li, and L. Pedersen, New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations, Structure, vol.7, issue.3, pp.55-60, 1999.
DOI : 10.1016/S0969-2126(99)80033-1

A. Bornot, C. Etchebest, and A. De-brevern, Predicting protein flexibility through the prediction of local structures, Proteins: Structure, Function, and Bioinformatics, vol.48, issue.Suppl 7, pp.839-52, 2011.
DOI : 10.1002/anie.200900476

URL : https://hal.archives-ouvertes.fr/inserm-00568171

W. Kabsch and C. Sander, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-637, 1983.
DOI : 10.1016/0005-2795(73)90350-4

A. De-brevern, C. Etchebest, and S. Hazout, Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks, Proteins: Structure, Function, and Genetics, vol.7, issue.3, pp.271-87, 2000.
DOI : 10.1007/BF02337561

URL : https://hal.archives-ouvertes.fr/inserm-00132821

A. Joseph, G. Agarwal, S. Mahajan, J. Gelly, L. Swapna et al., A short survey on protein blocks, Biophysical Reviews, vol.30, issue.3, pp.137-184, 2010.
DOI : 10.1021/jp012090f

URL : https://hal.archives-ouvertes.fr/inserm-00512823

S. Leonard, A. Joseph, N. Srinivasan, J. Gelly, and A. De-brevern, mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet, Journal of Biomolecular Structure and Dynamics, vol.48, issue.4, pp.661-669, 2014.
DOI : 10.1021/ci800178a

URL : https://hal.archives-ouvertes.fr/inserm-00926338

V. Jallu, P. Poulain, P. Fuchs, C. Kaplan, and A. De-brevern, Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit ??3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants, Biochimie, vol.105, pp.84-90, 2014.
DOI : 10.1016/j.biochi.2014.06.017

J. Barnoud, H. Santuz, P. Craveur, A. Joseph, V. Jallu et al., PBxplore: A Tool To Analyze Local Protein Structure And Deformability With Protein Blocks, 2017.
DOI : 10.1101/136408

J. Hartigan and M. Wong, A K-Means Clustering Algorithm, Journal of the Royal Statistical Society Series C (Applied Statistics), vol.28, issue.1, pp.100-108, 1979.

M. Tyagi, A. Bornot, B. Offmann, and A. De-brevern, Analysis of loop boundaries using different local structure assignment methods, Protein Science, vol.34, issue.9, pp.1869-81, 2009.
DOI : 10.1016/j.bbagen.2005.05.016

URL : https://hal.archives-ouvertes.fr/inserm-00392504

P. Craveur, A. Joseph, J. Esque, T. Narwani, F. Noel et al., Protein flexibility in the light of structural alphabets, Frontiers in Molecular Biosciences, vol.48, issue.10, p.20, 2015.
DOI : 10.1021/ci800178a

A. Schlessinger and B. Rost, Protein flexibility and rigidity predicted from sequence, Proteins: Structure, Function, and Bioinformatics, vol.6, issue.Suppl 6, pp.115-141, 2005.
DOI : 10.1007/978-1-4757-3092-0

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.567.9405

A. Schlessinger, G. Yachdav, and B. Rost, PROFbval: predict flexible and rigid residues in proteins, Bioinformatics, vol.22, issue.7, pp.891-894, 2006.
DOI : 10.1093/bioinformatics/btl032

URL : https://academic.oup.com/bioinformatics/article-pdf/22/7/891/523458/btl032.pdf

O. Carugo and P. Argos, Correlation between side chain mobility and conformation in protein structures, Protein Engineering Design and Selection, vol.10, issue.7, pp.777-87, 1997.
DOI : 10.1093/protein/10.7.777

URL : https://academic.oup.com/peds/article-pdf/10/7/777/18542004/100777.pdf

A. De-brevern, A. Bornot, P. Craveur, C. Etchebest, and J. Gelly, PredyFlexy: flexibility and local structure prediction from sequence, Nucleic Acids Research, vol.40, issue.W1, pp.317-322, 2012.
DOI : 10.1093/nar/gks482

URL : https://hal.archives-ouvertes.fr/inserm-00750270

K. Patapati and N. Glykos, Three Force Fields' Views of the 310 Helix, Biophysical Journal, vol.101, issue.7, pp.1766-71, 2011.
DOI : 10.1016/j.bpj.2011.08.044

A. De-brevern, Extension of the classical classification of beta-turns. Sci Rep, p.33191, 2016.

J. Richardson, The Anatomy and Taxonomy of Protein Structure, Adv Protein Chem, vol.34, pp.167-339, 1981.
DOI : 10.1016/S0065-3233(08)60520-3

W. Touw, C. Baakman, J. Black, T. Beek, E. Krieger et al., A series of PDB-related databanks for everyday needs, Nucleic Acids Research, vol.43, issue.D1, pp.364-368, 2015.
DOI : 10.1093/nar/gku1028

P. Craveur, A. Joseph, J. Rebehmed, and A. De-brevern, beta-Bulges: extensive structural analyses of beta-sheets irregularities, Protein Sci, vol.22, issue.10, pp.1366-78, 2013.

Y. Mansiaux, A. Joseph, J. Gelly, and A. De-brevern, Assignment of PolyProline II Conformation and Analysis of Sequence ??? Structure Relationship, PLoS ONE, vol.59, issue.3, p.18401, 2011.
DOI : 10.1371/journal.pone.0018401.s008

URL : https://hal.archives-ouvertes.fr/inserm-00586725

R. Chebrek, S. Leonard, A. De-brevern, and J. Gelly, PolyprOnline: polyproline helix II and secondary structure assignment database, Database, vol.2014, issue.0, p.102, 2014.
DOI : 10.1093/database/bau102

URL : https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau102/8248386/bau102.pdf

T. Narwani, H. Santuz, N. Shinada, A. Vattekatte, Y. Ghouzam et al., Recent advances on polyproline II, Amino Acids, vol.55, issue.Pt 2, pp.705-718, 2017.
DOI : 10.1016/j.jmgm.2014.10.005

URL : https://hal.archives-ouvertes.fr/inserm-01573940

P. Kumar and M. Bansal, Structural and functional analyses of PolyProline-II helices in globular proteins, Journal of Structural Biology, vol.196, issue.3, pp.414-439, 2016.
DOI : 10.1016/j.jsb.2016.09.006

A. Bornot and A. De-brevern, Protein beta-turn assignments, Bioinformation, vol.1, issue.5, pp.153-158, 2006.
DOI : 10.6026/97320630001153

URL : https://hal.archives-ouvertes.fr/inserm-00133658

J. Luo, Z. Liu, Y. Guo, and M. Li, A structural dissection of large protein-protein crystal packing contacts, Scientific Reports, vol.13, issue.1, p.14214, 2015.
DOI : 10.1093/protein/13.3.149

O. Carugo and P. Argos, Protein-protein crystal-packing contacts, Protein Science, vol.29, issue.10, pp.2261-2264, 1997.
DOI : 10.1107/S0108768194011249

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143556

V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg et al., Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins: Structure, Function, and Bioinformatics, vol.43, issue.3, pp.712-737, 2006.
DOI : 10.1002/prot.21123

G. Pavlovic-lazetic, N. Mitic, J. Kovacevic, Z. Obradovic, S. Malkov et al., Bioinformatics analysis of disordered proteins in prokaryotes, BMC Bioinformatics, vol.12, issue.1, p.66, 2011.
DOI : 10.1093/protein/1.6.477