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Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: miaozhichao on August 10, 2015, 03:37:51 am

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Title: Detection of stacking interactions
Post by: miaozhichao on August 10, 2015, 03:37:51 am
Hi Xiangjun,
It was very convenient using SNAP. I am wondering if you have function in detecting aromatic stacking between protein and NA? I need this function for my current job. Can you help me?

Best
Zhichao.
Title: Re: Detection of stacking interactions
Post by: xiangjun on August 10, 2015, 08:12:57 am
Hi Zhichao,

Yes, SNAP has provisions for detecting aromatic stacking interactions. Try the (currently undocumented) option --get-stack to see if it gets what you want.

The output is in format;
Code: [Select]
1 U/G A.U2647 A.G2648 1.0 3.32 6where the last three values are the area of overlap in Å2, vertical distance in Å, and angle between the two planes.

I welcome your suggestions to revise this functionality in order to better fit your needs.

Best regards,

Xiang-Jun
Title: Re: Detection of stacking interactions
Post by: xiangjun on October 23, 2015, 12:01:46 am
Hi Zhichao,

As of SNAP beta-r06-2015oct23, I've added a new section in the main output for aromatic stacking interactions between bases and amino acids. Using PDB entry 3k49 (http://www.rcsb.org/pdb/explore/explore.do?structureId=3k49) (Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site B) as an example, the new part is as below:

Code: [Select]
****************************************************************************
List of 39 base/amino-acid pseudo stacks
      id  nt-aa  nt           aa      vertical-distance   plane-angle
   1 3k49 U-tyr B.U3         A.TYR825        3.16             15
   2 3k49 G-tyr B.G4         A.TYR825        3.43              5
   3 3k49 U-tyr B.U5         A.TYR734        3.13             14
   4 3k49 U-asn B.U5         A.ASN776        3.19              4
   5 3k49 A-arg B.A6         A.ARG698        3.40              6
   6 3k49 A-tyr B.A6         A.TYR734        3.41              2
   7 3k49 A-arg B.A7         A.ARG698        3.43             12
   8 3k49 A-arg B.A8         A.ARG626        3.60             13
   9 3k49 A-his B.A8         A.HIS662        3.28             12
  10 3k49 U-tyr B.U9         A.TYR590        3.05             10
  11 3k49 U-arg B.U9         A.ARG626        3.47             30
  12 3k49 A-arg B.A10        A.ARG554        3.22             26
  13 3k49 A-tyr B.A10        A.TYR590        3.31              2
  14 3k49 U-tyr D.U3         C.TYR825        3.19             16
  15 3k49 G-tyr D.G4         C.TYR825        3.34              5
  16 3k49 U-tyr D.U5         C.TYR734        3.24             14
  17 3k49 U-asn D.U5         C.ASN776        3.14              4
  18 3k49 A-arg D.A6         C.ARG698        3.40              4
  19 3k49 A-tyr D.A6         C.TYR734        3.36              4
  20 3k49 A-arg D.A7         C.ARG698        3.40              9
  21 3k49 A-arg D.A8         C.ARG626        3.57             15
  22 3k49 A-his D.A8         C.HIS662        3.33              8
  23 3k49 U-tyr D.U9         C.TYR590        3.09             13
  24 3k49 U-arg D.U9         C.ARG626        3.46             31
  25 3k49 A-arg D.A10        C.ARG554        3.11             26
  26 3k49 A-tyr D.A10        C.TYR590        3.37              3
  27 3k49 U-tyr F.U3         E.TYR825        3.19             15
  28 3k49 G-tyr F.G4         E.TYR825        3.36              4
  29 3k49 U-tyr F.U5         E.TYR734        3.18             14
  30 3k49 U-asn F.U5         E.ASN776        3.21              1
  31 3k49 A-arg F.A6         E.ARG698        3.37              4
  32 3k49 A-tyr F.A6         E.TYR734        3.43              2
  33 3k49 A-arg F.A7         E.ARG698        3.48             16
  34 3k49 A-arg F.A8         E.ARG626        3.57             12
  35 3k49 A-his F.A8         E.HIS662        3.32              9
  36 3k49 U-tyr F.U9         E.TYR590        3.14             15
  37 3k49 U-arg F.U9         E.ARG626        3.57             28
  38 3k49 A-arg F.A10        E.ARG554        3.41             24
  39 3k49 A-tyr F.A10        E.TYR590        3.27              2

It is tentatively called "pseudo stacks" to match "pseudo pairs".

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.