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Author Topic: Detection of stacking interactions  (Read 2101 times)

Offline miaozhichao

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Detection of stacking interactions
« 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.

Offline xiangjun

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Re: Detection of stacking interactions
« Reply #1 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: Detection of stacking interactions
« Reply #2 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 (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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.