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... are the most precisely defined by X-ray crystallography [100]. Table 2 summarizes the different methods analyzed in this study in this research with the number and type of states they focus on. DSSP =-=[101]-=- is the most popular method. Moreover, it is the basis of the secondary structure assignment given by the Protein DataBank [102, 103]. It is based on the hydrogen bonding patterns.Structural alphabet...

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...in this research with the number and type of states they focus on. DSSP [101] is the most popular method. Moreover, it is the basis of the secondary structure assignment given by the Protein DataBank =-=[102, 103]-=-. It is based on the hydrogen bonding patterns.Structural alphabet methods helicoidal state strand state coil states HAL author manuscript inserm-00134564, version 1 DSSP α-helix (‘H’) β-strand (‘b’)...

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...tes and the non-repetitive states. In brackets are given the number of states corresponding to one specific category and in parenthesis is given the one letter code corresponding to the state. STRIDE =-=[104]-=- uses the same criteria with parameters slightly different and the computation of backbone dihedral angles. SECSTR focuses on the correct assignment of 3.10 – and π-helices [24]. Recently, DSSPcont tr...

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...’s, different turns have been excluded, the turns III and III’ which were too close to the 3.10 helix, the turns V, V’ and VII which were too rare and theirStructural alphabet definitions inaccurate =-=[53]-=-. Wilmot and Thornton defined the turn VIII which is associated with HAL author manuscript inserm-00134564, version 1 an important number of observations [54]. It is the first turn not directly associ...

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... be of great interest in proteomics and sequence alignment.Structural alphabet Introduction HAL author manuscript inserm-00134564, version 1 The first protein structure obtained by X-ray diffraction =-=[1]-=- had marked the beginning of the description and analysis of protein structures. Two ways have since been followed with the theoretical methods and the descriptive methods. In the first years, due to ...

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...always agree particularly at the edges. The first software has been developed by Levitt and Greer and used only the Cα positions as these atoms are the most precisely defined by X-ray crystallography =-=[100]-=-. Table 2 summarizes the different methods analyzed in this study in this research with the number and type of states they focus on. DSSP [101] is the most popular method. Moreover, it is the basis of...

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...s used by Thornton’s group [37, 55] are considered as the standard. Nevertheless, some analyses have been done using the excluded turns V, V’ and VII [56, 57]. Shorter turns (e.g. 2 residues δ-turns) =-=[58]-=- and longer ones (e.g. 5 residues α-turns [59, 60] and 6 residues π-turns [61, 62]) have been less studied. The different classes of turns can be overlapping, e.g. two β-turns can have 3 positions in ...

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... identified in the coil state. For instance, the Ω-loops constitute a particular category characterized by a small distance at their extremities and an important number of contacts in their structure =-=[66, 67]-=-. They correspond to compact globular loops mainly located at the surface of the proteins [68]. They may be directly associated with the protein functions [69, 70] and folding [70]. However, even if t...

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...oops in non-complete structures [91 - 95]. Databases of loops useful for molecular modeling have been created [88, 96 - 98]. Even if the repetitive secondary structures have been intensively analyzed =-=[17, 99]-=-, the characterization of the α-helices and the β-strands has led to different assignment methods based upon energetic, geometrical and/or angular criteria, which do not always agree particularly at t...

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...e first years, due to the limited number of available structures, the first kind of approaches was used for proposing potential local structures based on physico-chemical properties (e.g. the γ-helix =-=[2]-=-). Their presence and interest in experimentally determined structures were confirmed or not only in a second step [3]. In this chapter, we focus on the second kind of approaches based on the descript...

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...bed in Table 1. The α-helix (or 3.613 helix) is characterized by intramolecular hydrogen bonds between amino acid residues i and i +4 [5]. Its extremities show specific physicochemical stabilizations =-=[6]-=-. The β-sheet is defined by hydrogen bonds between neighboring parallel (or antiparallel) chains [4]. As for the α-helix, its edges have been widely analyzed [7 - 9]. Many studies have also analyzed t...

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...proach close to Ramachandran method [39], determined small local folds characterized by the reversing of the polypeptide chain maintained by a hydrogen bond between two close residues, i.e. the turns =-=[40]-=-. After this description, a classification was done and has greatly evolved. The tight turns are characterized by precise dihedral angle values and short distance between their ends [41]. The two most...

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...ersion 1 to the ‘L’ structure of orthogonal ββ [79]. Other studies have focused on one precise loop category like α-helix-turn-β-strand [80], or on particular combinations of β-strands like the Ψloop =-=[55, 81]-=-. The second type of classification consists in more systematic analyses of the short and medium loops. Many studies have been carried out for short loops connecting α-helices and β-sheets [82 - 84]. ...

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...tructural alphabet definitions inaccurate [53]. Wilmot and Thornton defined the turn VIII which is associated with HAL author manuscript inserm-00134564, version 1 an important number of observations =-=[54]-=-. It is the first turn not directly associated with a stabilizing bond between its ends. The definitions used by Thornton’s group [37, 55] are considered as the standard. Nevertheless, some analyses h...

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...cation created new categories: the turns III, III’, V and V’, the turn VI characterized by a Proline, the turn VII associated with a kink and the turn IV corresponding to all the non classified turns =-=[48]-=-. The first analyses of turns in protein structures used this classification [49 - 52]. However, at the beginning of the 80’s, different turns have been excluded, the turns III and III’ which were too...

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... identified in the coil state. For instance, the Ω-loops constitute a particular category characterized by a small distance at their extremities and an important number of contacts in their structure =-=[66, 67]-=-. They correspond to compact globular loops mainly located at the surface of the proteins [68]. They may be directly associated with the protein functions [69, 70] and folding [70]. However, even if t...

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.... The average characteristics of these local structures are described in Table 1. The α-helix (or 3.613 helix) is characterized by intramolecular hydrogen bonds between amino acid residues i and i +4 =-=[5]-=-. Its extremities show specific physicochemical stabilizations [6]. The β-sheet is defined by hydrogen bonds between neighboring parallel (or antiparallel) chains [4]. As for the α-helix, its edges ha...

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...umber of contacts in their structure [66, 67]. They correspond to compact globular loops mainly located at the surface of the proteins [68]. They may be directly associated with the protein functions =-=[69, 70]-=- and folding [70]. However, even if the coil state is better characterized, some local folds still remained unassigned. Hence, another approach is developed and consists in classifying the protein fra...

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...tematic analyses of the short and medium loops. Many studies have been carried out for short loops connecting α-helices and β-sheets [82 - 84]. Others have also been done systematically for the short =-=[85, 86]-=- and medium loops [87, 88], whatever the flanking regions. All theses methods can only be used for short length loops [89] or for combination of small loops [90] since longer loops are less frequent a...

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... done systematically for the short [85, 86] and medium loops [87, 88], whatever the flanking regions. All theses methods can only be used for short length loops [89] or for combination of small loops =-=[90]-=- since longer loops are less frequent and considered as too variables. Nevertheless, the different loop classifications have shown their interest in local structure prediction to construct loops in no...

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...ort and medium loops. Many studies have been carried out for short loops connecting α-helices and β-sheets [82 - 84]. Others have also been done systematically for the short [85, 86] and medium loops =-=[87, 88]-=-, whatever the flanking regions. All theses methods can only be used for short length loops [89] or for combination of small loops [90] since longer loops are less frequent and considered as too varia...

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...ngly, the short length hairpins are often characterized by a specific turn [13] and the longer ones by a β-bulge in one of the strands [75]. Sometimes stabilization by disulfide bonds can be observed =-=[76]-=-. The β-hairpins are well studied in molecular dynamics [77, 78]. The same approach was performed for the short loopsStructural alphabet connecting two α-helices and resulted in the characterization ...

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...ered as the standard. Nevertheless, some analyses have been done using the excluded turns V, V’ and VII [56, 57]. Shorter turns (e.g. 2 residues δ-turns) [58] and longer ones (e.g. 5 residues α-turns =-=[59, 60]-=- and 6 residues π-turns [61, 62]) have been less studied. The different classes of turns can be overlapping, e.g. two β-turns can have 3 positions in common. The turns can also be multiple at the same...

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... specific turn [13] and the longer ones by a β-bulge in one of the strands [75]. Sometimes stabilization by disulfide bonds can be observed [76]. The β-hairpins are well studied in molecular dynamics =-=[77, 78]-=-. The same approach was performed for the short loopsStructural alphabet connecting two α-helices and resulted in the characterization of the α-α corners which are similar HAL author manuscript inser...

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...dues). The γ- turns are composed of two categories, classic and inverse [42 - 45]. The β-turns have a more complex history. At the beginning, the four main categories were the types I, I’, II and II’ =-=[46, 47]-=-. The extension of the β-turn classification created new categories: the turns III, III’, V and V’, the turn VI characterized by a Proline, the turn VII associated with a kink and the turn IV correspo...

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...ss, some analyses have been done using the excluded turns V, V’ and VII [56, 57]. Shorter turns (e.g. 2 residues δ-turns) [58] and longer ones (e.g. 5 residues α-turns [59, 60] and 6 residues π-turns =-=[61, 62]-=-) have been less studied. The different classes of turns can be overlapping, e.g. two β-turns can have 3 positions in common. The turns can also be multiple at the same position, e.g. a β-turn can enc...

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...coidalStructural alphabet HAL author manuscript inserm-00134564, version 1 local folds never observed in proteins we can quote the γ-helix (or 5.1117-helix) [2, 3], the 2.27helix and the 4.314-helix =-=[18]-=-. As for the Polyproline I, it is only found in apolar solvents. In the same way, accurate analyses have been carried out for the β-sheet category. An interesting point is that since the description o...

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...cutive strands, have been identified, forming a ‘L’ structure with an angle of 90° [13, 35]. Globally, the irregularities within the β-strands have been classified into 4 distinct classes of β-bulges =-=[36, 37]-=- and can be related to the of proteins’ function and stability [38]. The regions between the repetitive helicoidal and extended structures have been intensively studied too. Thus, Venkatachalam, using...

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...oidal structures [26]. The π-bulges constitute a particular kind of discontinuity in helicoidal structures. Like the π-helices, they are not frequent but seem directly associated to protein functions =-=[23, 27]-=-. The Polyproline II helices correspond to a specific local fold initially found in fibrous proteins [28, 29]. They contribute to the creation of coiled coil supersecondary structures characteristic o...

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...ural alphabet connecting two α-helices and resulted in the characterization of the α-α corners which are similar HAL author manuscript inserm-00134564, version 1 to the ‘L’ structure of orthogonal ββ =-=[79]-=-. Other studies have focused on one precise loop category like α-helix-turn-β-strand [80], or on particular combinations of β-strands like the Ψloop [55, 81]. The second type of classification consist...

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...ort and medium loops. Many studies have been carried out for short loops connecting α-helices and β-sheets [82 - 84]. Others have also been done systematically for the short [85, 86] and medium loops =-=[87, 88]-=-, whatever the flanking regions. All theses methods can only be used for short length loops [89] or for combination of small loops [90] since longer loops are less frequent and considered as too varia...

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... to the state. STRIDE [104] uses the same criteria with parameters slightly different and the computation of backbone dihedral angles. SECSTR focuses on the correct assignment of 3.10 – and π-helices =-=[24]-=-. Recently, DSSPcont tries to optimize the parameters of DSSP by taking into accountStructural alphabet multiple NMR models assignment and tries to compensate at best the fluctuations of the HAL auth...

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...lted in the classification of the β-hairpins [71 - 74]. Interestingly, the short length hairpins are often characterized by a specific turn [13] and the longer ones by a β-bulge in one of the strands =-=[75]-=-. Sometimes stabilization by disulfide bonds can be observed [76]. The β-hairpins are well studied in molecular dynamics [77, 78]. The same approach was performed for the short loopsStructural alphab...

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...sheets [82 - 84]. Others have also been done systematically for the short [85, 86] and medium loops [87, 88], whatever the flanking regions. All theses methods can only be used for short length loops =-=[89]-=- or for combination of small loops [90] since longer loops are less frequent and considered as too variables. Nevertheless, the different loop classifications have shown their interest in local struct...

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...potential local structures based on physico-chemical properties (e.g. the γ-helix [2]). Their presence and interest in experimentally determined structures were confirmed or not only in a second step =-=[3]-=-. In this chapter, we focus on the second kind of approaches based on the description and characterization of particular local fold structures observed in experimentally determined protein structures....

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...urn (‘N’) polyproline II (‘P’) coil SECSTR α-helix β-strand coil 5 310-helix π-helix HELANAL α-helix [5] / / 5 EXTENDED-BETA / β-sheet [5] / 6 β-strand PROMOTIF α-helix β-strand γ-turn [2] 25 β-bulge =-=[10]-=- β-turn [10] β-hairpins SUMMARY α-helix [5] β-sheet [6] γ-turn [2] 310-helix β-strand β-turn [10] π-helix β-bulge [10] β-hairpins polyproline II TOTAL 7 17 14 38 Table 2. Secondary structure assignmen...

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...trand can be found independently of a β-sheet and named the E-strand [34]. Moreover, orthogonal ββ motifs, i.e. consecutive strands, have been identified, forming a ‘L’ structure with an angle of 90° =-=[13, 35]-=-. Globally, the irregularities within the β-strands have been classified into 4 distinct classes of β-bulges [36, 37] and can be related to the of proteins’ function and stability [38]. The regions be...

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...cutive strands, have been identified, forming a ‘L’ structure with an angle of 90° [13, 35]. Globally, the irregularities within the β-strands have been classified into 4 distinct classes of β-bulges =-=[36, 37]-=- and can be related to the of proteins’ function and stability [38]. The regions between the repetitive helicoidal and extended structures have been intensively studied too. Thus, Venkatachalam, using...

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...dues). The γ- turns are composed of two categories, classic and inverse [42 - 45]. The β-turns have a more complex history. At the beginning, the four main categories were the types I, I’, II and II’ =-=[46, 47]-=-. The extension of the β-turn classification created new categories: the turns III, III’, V and V’, the turn VI characterized by a Proline, the turn VII associated with a kink and the turn IV correspo...

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...ered as the standard. Nevertheless, some analyses have been done using the excluded turns V, V’ and VII [56, 57]. Shorter turns (e.g. 2 residues δ-turns) [58] and longer ones (e.g. 5 residues α-turns =-=[59, 60]-=- and 6 residues π-turns [61, 62]) have been less studied. The different classes of turns can be overlapping, e.g. two β-turns can have 3 positions in common. The turns can also be multiple at the same...

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...umber of contacts in their structure [66, 67]. They correspond to compact globular loops mainly located at the surface of the proteins [68]. They may be directly associated with the protein functions =-=[69, 70]-=- and folding [70]. However, even if the coil state is better characterized, some local folds still remained unassigned. Hence, another approach is developed and consists in classifying the protein fra...

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...rners which are similar HAL author manuscript inserm-00134564, version 1 to the ‘L’ structure of orthogonal ββ [79]. Other studies have focused on one precise loop category like α-helix-turn-β-strand =-=[80]-=-, or on particular combinations of β-strands like the Ψloop [55, 81]. The second type of classification consists in more systematic analyses of the short and medium loops. Many studies have been carri...

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...21 - 25]. These two types of helicoidal structures are often encountered at the extremities of longer α-helices and seem to play an important role in the stabilization of longer helicoidal structures =-=[26]-=-. The π-bulges constitute a particular kind of discontinuity in helicoidal structures. Like the π-helices, they are not frequent but seem directly associated to protein functions [23, 27]. The Polypro...

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...oidal structures [26]. The π-bulges constitute a particular kind of discontinuity in helicoidal structures. Like the π-helices, they are not frequent but seem directly associated to protein functions =-=[23, 27]-=-. The Polyproline II helices correspond to a specific local fold initially found in fibrous proteins [28, 29]. They contribute to the creation of coiled coil supersecondary structures characteristic o...

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...for the β-sheet category. An interesting point is that since the description of the β-strands, several analyses have shown that a strand can be found independently of a β-sheet and named the E-strand =-=[34]-=-. Moreover, orthogonal ββ motifs, i.e. consecutive strands, have been identified, forming a ‘L’ structure with an angle of 90° [13, 35]. Globally, the irregularities within the β-strands have been cla...

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...pt inserm-00134564, version 1 an important number of observations [54]. It is the first turn not directly associated with a stabilizing bond between its ends. The definitions used by Thornton’s group =-=[37, 55]-=- are considered as the standard. Nevertheless, some analyses have been done using the excluded turns V, V’ and VII [56, 57]. Shorter turns (e.g. 2 residues δ-turns) [58] and longer ones (e.g. 5 residu...

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...rized by a small distance at their extremities and an important number of contacts in their structure [66, 67]. They correspond to compact globular loops mainly located at the surface of the proteins =-=[68]-=-. They may be directly associated with the protein functions [69, 70] and folding [70]. However, even if the coil state is better characterized, some local folds still remained unassigned. Hence, anot...

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...ike the π-helices, they are not frequent but seem directly associated to protein functions [23, 27]. The Polyproline II helices correspond to a specific local fold initially found in fibrous proteins =-=[28, 29]-=-. They contribute to the creation of coiled coil supersecondary structures characteristic of these proteins. They are also found in globular proteins and are not composed only of Proline [30 - 33]. Am...

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...vents in the protein history is the series of seven consecutive papers of Pauling and Corey in 1951. They described an impressive number of potential local folds including the α-helix and the β-sheet =-=[2, 4]-=-. The average characteristics of these local structures are described in Table 1. The α-helix (or 3.613 helix) is characterized by intramolecular hydrogen bonds between amino acid residues i and i +4 ...

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...oops in non-complete structures [91 - 95]. Databases of loops useful for molecular modeling have been created [88, 96 - 98]. Even if the repetitive secondary structures have been intensively analyzed =-=[17, 99]-=-, the characterization of the α-helices and the β-strands has led to different assignment methods based upon energetic, geometrical and/or angular criteria, which do not always agree particularly at t...

Citation Context

...ike the π-helices, they are not frequent but seem directly associated to protein functions [23, 27]. The Polyproline II helices correspond to a specific local fold initially found in fibrous proteins =-=[28, 29]-=-. They contribute to the creation of coiled coil supersecondary structures characteristic of these proteins. They are also found in globular proteins and are not composed only of Proline [30 - 33]. Am...

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...trand can be found independently of a β-sheet and named the E-strand [34]. Moreover, orthogonal ββ motifs, i.e. consecutive strands, have been identified, forming a ‘L’ structure with an angle of 90° =-=[13, 35]-=-. Globally, the irregularities within the β-strands have been classified into 4 distinct classes of β-bulges [36, 37] and can be related to the of proteins’ function and stability [38]. The regions be...

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...ngle of 90° [13, 35]. Globally, the irregularities within the β-strands have been classified into 4 distinct classes of β-bulges [36, 37] and can be related to the of proteins’ function and stability =-=[38]-=-. The regions between the repetitive helicoidal and extended structures have been intensively studied too. Thus, Venkatachalam, using a theoretical approach close to Ramachandran method [39], determin...

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... stabilizing bond between its ends. The definitions used by Thornton’s group [37, 55] are considered as the standard. Nevertheless, some analyses have been done using the excluded turns V, V’ and VII =-=[56, 57]-=-. Shorter turns (e.g. 2 residues δ-turns) [58] and longer ones (e.g. 5 residues α-turns [59, 60] and 6 residues π-turns [61, 62]) have been less studied. The different classes of turns can be overlapp...

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... stabilizing bond between its ends. The definitions used by Thornton’s group [37, 55] are considered as the standard. Nevertheless, some analyses have been done using the excluded turns V, V’ and VII =-=[56, 57]-=-. Shorter turns (e.g. 2 residues δ-turns) [58] and longer ones (e.g. 5 residues α-turns [59, 60] and 6 residues π-turns [61, 62]) have been less studied. The different classes of turns can be overlapp...

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...ss, some analyses have been done using the excluded turns V, V’ and VII [56, 57]. Shorter turns (e.g. 2 residues δ-turns) [58] and longer ones (e.g. 5 residues α-turns [59, 60] and 6 residues π-turns =-=[61, 62]-=-) have been less studied. The different classes of turns can be overlapping, e.g. two β-turns can have 3 positions in common. The turns can also be multiple at the same position, e.g. a β-turn can enc...

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... specific turn [13] and the longer ones by a β-bulge in one of the strands [75]. Sometimes stabilization by disulfide bonds can be observed [76]. The β-hairpins are well studied in molecular dynamics =-=[77, 78]-=-. The same approach was performed for the short loopsStructural alphabet connecting two α-helices and resulted in the characterization of the α-α corners which are similar HAL author manuscript inser...

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...tematic analyses of the short and medium loops. Many studies have been carried out for short loops connecting α-helices and β-sheets [82 - 84]. Others have also been done systematically for the short =-=[85, 86]-=- and medium loops [87, 88], whatever the flanking regions. All theses methods can only be used for short length loops [89] or for combination of small loops [90] since longer loops are less frequent a...