To add to what Oliver suggested, there is the “PSILO” program that can specifically search the pattern you are interested and even filter some 3D constraints.
Yong Wang From: CCP4 bulletin board <[email protected]> On Behalf Of Oliver Smart Sent: Thursday, September 11, 2025 7:48 AM To: [email protected] Subject: [EXTERNAL] Re: [ccp4bb] Arginine/Carboxyl salt bridges Dear David, It might be worth looking at Janet Thornton's "Atlas of Protein Side-Chain Interactions", although this is probably out-of-date: https: //www. ebi. ac. uk/thornton-srv/databases/sidechains/ It may also be of interest to Dear David, It might be worth looking at Janet Thornton's "Atlas of Protein Side-Chain Interactions", although this is probably out-of-date: https://www.ebi.ac.uk/thornton-srv/databases/sidechains/<https://urldefense.com/v3/__https:/www.ebi.ac.uk/thornton-srv/databases/sidechains/__;!!A_kSX19cfVk!D5RhHDgdFcpLE_sziFUEj2IcZJshEXA16yjSMTJzlWl8XxrKuCtN5DmSqJB6iI9uXG8neEnx25ltgVe-w7xNNIpQndcZR8ExxlS0LA$> It may also be of interest to examine the interactions between these groups in the CSD small molecule database. The CCDC program Isostar allows this: https://www.ccdc.cam.ac.uk/solutions/software/isostar/<https://urldefense.com/v3/__https:/www.ccdc.cam.ac.uk/solutions/software/isostar/__;!!A_kSX19cfVk!D5RhHDgdFcpLE_sziFUEj2IcZJshEXA16yjSMTJzlWl8XxrKuCtN5DmSqJB6iI9uXG8neEnx25ltgVe-w7xNNIpQndcZR8EvP1Pujw$> However, I haven't used it in a few years and am currently at the beach! Hope this is useful Oliver On Wed, 10 Sept 2025 at 17:06, Sanders, David <[email protected]<mailto:[email protected]>> wrote: Hi all, We have recently determined the structure of a protein ligand complex, where there is a Arg/carboxylate salt bridge,, where the plane of the Arg guanidino group is perpendicular to the plane of the carboxyl group. I’m trying to find other examples of the same orientation, but have had little luck (not even fully sure how to do that search !). Does anyone have any examples of such an interaction ? Many thanks for your help, David ------------------------------------------------------------------------------------ Dr. David Sanders Department of Chemistry Professor of Structural Biology web page: https://research-groups.usask.ca/sanders/<https://urldefense.com/v3/__https:/research-groups.usask.ca/sanders/__;!!A_kSX19cfVk!D5RhHDgdFcpLE_sziFUEj2IcZJshEXA16yjSMTJzlWl8XxrKuCtN5DmSqJB6iI9uXG8neEnx25ltgVe-w7xNNIpQndcZR8FNkjdjmg$> Email: [email protected]<mailto:[email protected]> Ph : (306) 966-6788 Mailing Address: Office : Thorv. 153 Department of Chemistry Lab : Thorv. 139 University of Saskatchewan Lab Ph : (306) 966-1936 110 Science Place Fax : (306) 966-4730 Saskatoon, SK, S7N 5C9, CANADA ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!A_kSX19cfVk!D5RhHDgdFcpLE_sziFUEj2IcZJshEXA16yjSMTJzlWl8XxrKuCtN5DmSqJB6iI9uXG8neEnx25ltgVe-w7xNNIpQndcZR8GohnoyqQ$> -- Oliver Smart ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!A_kSX19cfVk!D5RhHDgdFcpLE_sziFUEj2IcZJshEXA16yjSMTJzlWl8XxrKuCtN5DmSqJB6iI9uXG8neEnx25ltgVe-w7xNNIpQndcZR8GohnoyqQ$> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
