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MatrixPlot 1.2: Column format

Introduction Data format User matrix Mutual Nucl Mutual Prot Dist matrix

The column is a simple format for which each must start with an identifier "R" or "N" for protein or nucleotide sequences respectively. The remaining columns can be interchanged as one wishes. Consult options to pdb2mp. Each column lists a property, here residue, domain assignment (see 3Dee), secondary structure assignment (according to DSSP by Kabsh and Sander. Biopolymers 22 pp 2577-2637, 1983) and the x, y, and z coordinates of the C-alpha atoms. Lines starting with ";" are ignored.


; ENTRY           4mt2 -
; DOMAIN          2  RANGE   1 - 31 , 32 - 61 
; PHYL            EUKARYOTA
; CLASS           Metallothionein
; COMPOUND        Metallothionein Isoform Ii
; AUTHOR          A.H.Robbins,C.D.Stout
; MODEL           type XRAY
; RESOLUTION      2.000000
; ALIGN IDENTITY  100.0% (ATOM vs SEQRES in PDB)
; -----
R   MET   1   .       15.959     19.129     50.206 
R   ASP   1   .       13.885     20.910     47.587 
R   PRO   1   T       10.337     19.460     46.659 
R   ASN   1   T       12.049     17.307     44.026 
R   CYS   1   .       15.082     15.879     45.993 
R   SER   1   .       14.877     15.100     49.767 
R   CYS   1   S       18.635     14.492     50.183 
R   ALA   1   .       21.307     16.274     52.123 
R   THR   1   S       22.711     19.047     49.961 
R   ASP   1   S       26.304     18.918     51.215 
R   GLY   1   S       27.678     16.519     48.573 
R   SER   1   .       27.844     13.528     50.984 
R   CYS   1   .       24.758     11.514     50.000 
R   SER   1   .       25.209      8.017     48.655 
R   CYS   1   .       21.565      7.335     47.731 
R   ALA   1   T       22.738      5.972     44.294 
R   GLY   1   T       19.315      5.425     42.858 
R   SER   1   .       17.563      4.099     45.966 
R   CYS   1   S       15.797      7.389     46.680 
R   LYS   1   .       12.313      8.343     45.853 
R   CYS   1   .       13.352     11.695     44.353 
R   LYS   1   S       11.672     13.074     41.246 
R   GLN   1   S       14.786     15.071     40.286 
R   CYS   1   .       17.596     14.040     42.617 
R   LYS   1   .       20.435     16.445     42.975 
R   CYS   1   .       23.079     13.813     44.196 
R   THR   1   T       26.054     13.067     41.965 
R   SER   1   T       25.822      9.400     43.141 
R   CYS   1   .       22.431      9.000     41.526 
R   LYS   1   .       21.711      7.976     37.987 
R   LYS   1   .       17.946      7.109     37.891 
R   SER   2   .       16.074      7.172     34.577 
R   CYS   2   S       13.929     10.048     33.330 
R   CYS   2   S       10.979      7.586     33.169 
R   SER   2   T        9.629      4.403     34.400 
R   CYS   2   T        9.357      2.837     30.951 
R   CYS   2   S       12.970      3.207     29.896 
R   PRO   2   .       16.409      2.332     31.374 
R   VAL   2   T       18.592      5.304     32.237 
R   GLY   2   T       20.717      4.495     29.101 
R   CYS   2   .       17.812      4.858     26.494 
R   ALA   2   T       19.099      6.505     23.261 
R   LYS   2   T       15.923      8.292     22.202 
R   CYS   2   T       15.544      9.916     25.650 
R   SER   2   T       19.184     11.190     26.073 
R   GLN   2   T       18.576     14.759     24.840 
R   GLY   2   S       15.382     14.935     26.795 
R   CYS   2   .       12.671     12.469     27.879 
R   ILE   2   .       10.161     11.939     25.160 
R   CYS   2   S        7.737      9.559     27.014 
R   LYS   2   .        4.289     10.165     28.455 
R   GLU   2   T        4.521      9.919     32.302 
R   ALA   2   T        1.904      7.145     32.666 
R   SER   2   .        4.610      4.770     34.131 
R   ASP   2   S        4.082      1.124     32.859 
R   LYS   2   .        5.798      0.660     29.459 
R   CYS   2   .        6.157      2.883     26.328 
R   SER   2   S        5.337      2.826     22.671 
R   CYS   2   S        7.882      5.542     21.628 
R   CYS   2   .       11.113      3.719     22.530 
R   ALA   2   .       12.601      0.478     21.366 



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