{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T13:56:50Z","timestamp":1783605410091,"version":"3.55.0"},"reference-count":65,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2017,12,12]],"date-time":"2017-12-12T00:00:00Z","timestamp":1513036800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2017,12,12]],"date-time":"2017-12-12T00:00:00Z","timestamp":1513036800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001412","name":"Council of Scientific and Industrial Research","doi-asserted-by":"publisher","award":["37(1694)\/17\/EMR\u2010II"],"award-info":[{"award-number":["37(1694)\/17\/EMR\u2010II"]}],"id":[{"id":"10.13039\/501100001412","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J of Molecular Recognition"],"published-print":{"date-parts":[[2018,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Protein\u2010DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein\u2010DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein\u2010DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing\/binding residues are identified as key residues. Specifically, stabilizing residues have higher preference to be key residues than binding residues. These key residues include polar, nonpolar, aliphatic, aromatic, and charged amino acids. Moreover, we have analyzed and discussed the key residues in different protein\u2010DNA complexes, which are classified based on protein structural class, function, DNA strand, and their conformations. Especially, Ser, Thr, Tyr, Arg, and Lys residues are commonly found in most of the subclasses of protein\u2010DNA complexes. Further, we analyzed atomic contacts, which show that polar\u2010nonpolar is more enriched than other types of contacts. In addition, the charged contacts are highly preferred in protein\u2010DNA complexes compared with protein\u2010protein and protein\u2010RNA complexes. Finally, we have discussed the sequence and structural features of key residues such as conservation score, surrounding hydrophobicity, solvent accessibility, secondary structure, and long\u2010range order. This study will be helpful to understand the recognition mechanism and structural and functional aspects of protein\u2010DNA complexes.<\/jats:p>","DOI":"10.1002\/jmr.2692","type":"journal-article","created":{"date-parts":[[2017,12,12]],"date-time":"2017-12-12T00:53:18Z","timestamp":1513039998000},"source":"Crossref","is-referenced-by-count":10,"title":["Dissecting and analyzing key residues in protein\u2010DNA complexes"],"prefix":"10.1002","volume":"31","author":[{"given":"A.","family":"Kulandaisamy","sequence":"first","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences Indian Institute of Technology Madras  Chennai 600 036 Tamilnadu India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ambuj","family":"Srivastava","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences Indian Institute of Technology Madras  Chennai 600 036 Tamilnadu India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.","family":"Nagarajan","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences Indian Institute of Technology Madras  Chennai 600 036 Tamilnadu India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1776-4096","authenticated-orcid":false,"given":"M. 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