An interaction site with trypsin.Worth and Blundell BMC Evolutionary Biology
An interaction site with trypsin.Worth and Blundell BMC Evolutionary Biology 2010, 10:161 http://www.biomedcentral.com/1471-2148/10/Page 10 ofresidue forms a hydrogen bond to a mainchain atom group.Additional materialAdditional file 1 Table of the 131 non-redundant families which were used in the analysis. Additional file 2 Table of the families and their members that were used in the analysis. Additional file 3 Figures S1 to S6 show the propensity of polar amino acids to form hydrogen bonds to mainchain atoms in the various architectural contexts analysed. Authors’ contributions CLW participated in the design of the study, performed the computational experiments, analysed the data and drafted the manuscript. TLB conceived of the study, participated in its design and refined the manuscript. Both authors read and approved the final manuscript. Acknowledgements This work was supported by a BBSRC studentship to CLW. TLB is supported by the Wellcome Trust. Author Details 1Biocomputing Group, Biochemistry purchase Necrostatin-1 Department, University of Cambridge, Cambridge, CB2 1GA, UK and 2Structural Bioinformatics Group, Institute for PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27663262 Physiology, Charit?Universit smedizin, Arnimallee 22, 14197 Berlin, Germany Received: 2 September 2009 Accepted: 31 May 2010 Published: 31 May?2010 Worth and Blundell; http://www.biomedcentral.com/1471-2148/10/161 This is an Open Access from:licensee BioMed Central Ltd. of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BMC article is available article distributed under the terms Evolutionary Biology 2010, 10:Figure 12 Examples of hydrogen bond interactions from conserved, buried residues to mainchain atoms in coils. Representative structures were chosen for each family based on resolution; residues are coloured by atom type with buried, conserved polar residues shown in magenta. Hydrogen bonds are shown in black. Three examples of polar residues forming hydrogen bonds to coils including, A) a cysteine in the high potential iron-sulphur protein family [PDB: 1isu], two asparates in B) the glycosyl hydrolase family 10 [PDB: 1tax] and C) the serine/threonine protein kinases [PDB: 1hcl].3. -strands – edge strands were distinguished from centre strands by referring to the number of hydrogen bonding partner strands. Strands defined as having >1 hydrogen bonding partner strand were defined as centre and all others as edge. 4. -hairpins 5. Coil regions We also identified polyproline helices using the program SEGNO[34].Calculation of residue propensitiesThe propensity of a particular residue type x to form hydrogen bonds to mainchain atoms in a particular architectural context Parch was calculated using the following equation:Parch( x) =( narch(total)( narch(x)N ( x))N (total))where narch(x) is the number of residues of type x forming hydrogen bonds to mainchain atoms in a particular architectural context, N(x ) is the number of residues of type x in the dataset of 131 families, narch(total) is the total number of residues forming hydrogen bonds to mainchain atoms in a particular architectural context and N(total) is the total number of residues in the dataset of 131 families. Propensities were calculated for: (i) Polar residues which are entirely conserved, buried in each family member and forming a hydrogen bond to a mainchain atom group in each family member. These numbers wer.