How To Identify Cis And Trans Conformation Of Proline?

Question

[aleeha]

How can I find a proline is in cis and trans conformations? Is it possible to find from pdb files? or any tools available to find it?

Answer 1

[wdiwdi]

If you do not have a turnkey application for this problem, it is a typical application for a Cheminformatics Scripting Toolkit, such as our Cactvs software (see www.xemistry.com/academic for free academic packages)..

The approach is simple: Read the file, match a proline substructure, and compute the torsion angle of the relevant matched atoms: Here is a sample solution with the default Tcl interface language of the toolkit:

(The test PDB file with cis and trans proline fragments is from here)

set st [molfile read PRO-CONF.PDB]
# create proline substructure with C(=O)C stub.
# substructure atoms 1,2,4 and 5 are the atoms defining the torsion (atom 3 is the amide O)
set ss [ens create CC(=O)N1C(C=O)CCC1 smarts]  
# match the substructure and capture the atom mappings
match ss -mode all $ss $st amap          
# loop over all matches and compute the torsion angles
foreach match $amap {
    lassign [unzip $match 1] a1 a2 a3 a4 a5
    set torsion [atom torsion $st $a1 $a2 $a4 $a5]
    if {range($torsion,-10,10)} {
        puts "link $a1 $a2 $a4 $a5 is cis"
    } else {
        puts "link $a1 $a2 $a4 $a5 is trans"
    }
}

And in the current releases of the toolkit you can now also use Python as an alternative interface language, thanks to sponsorship by Vertex Inc:

st=Molfile.Read('PRO-CONF.PDB') 
ss=Ens('CC(=O)N1C(C=O)CCC1','smarts')
match('ss',ss,st,mode='all',atommapvariable='amap')
for match in amap:
    statoms=unzip(match,1)
    torsion=statoms[0].torsion(statoms[1],statoms[3],statoms[4])
    if torsion>=-10 and torsion<=10:
        print("link",statoms[0],statoms[1],statoms[3],statoms[4],"is cis")
    else:
        print("link",statoms[0],statoms[1],statoms[3],statoms[4],"is trans")

[anna.chailyan]

Hey guys,

I just installed and started to play around with cactvs toolkit. Thanks a lot for the idea! I used the above script to get the cis/trans state for proline. I would like to know if it is possible to run it for each chain in the pdb and also to write the residue number rather than the atom number.

Thanks!

[Hassan Rasouli]

Thank you for your mentions.

I installed Cactvs software. really it is a good software for finding any cis or trans conformation.

Thanks!