
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   18 (  144),  selected   18 , name T0301TS193_4_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_4_2-D1.T0301_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      R      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      D      52           -
LGA    -       -      P      53           -
LGA    -       -      Y      54           -
LGA    -       -      A      55           -
LGA    -       -      A      56           -
LGA    -       -      H      57           -
LGA    -       -      I      58           -
LGA    -       -      D      59           -
LGA    -       -      G      60           -
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    -       -      T      68           -
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
LGA    -       -      I      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    -       -      Y      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    -       -      F      97           -
LGA    -       -      V      98           -
LGA    -       -      D      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    R     378      T     109          2.349
LGA    S     379      G     110          3.448
LGA    A     380      A     111          2.938
LGA    -       -      G     112           -
LGA    -       -      A     113           -
LGA    R     381      F     114          1.818
LGA    I     382      A     115          1.044
LGA    L     383      L     116          1.272
LGA    M     384      H     117          5.236
LGA    E     385      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      I     145           -
LGA    -       -      I     146           -
LGA    -       -      A     147           -
LGA    -       -      H     148           -
LGA    -       -      V     149           -
LGA    -       -      P     150           -
LGA    -       -      V     151           -
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    G     386      Q     155          2.490
LGA    W     387      V     156          1.833
LGA    V     388      Q     157          2.960
LGA    R     389      E     158          2.633
LGA    V     390      T     159          1.055
LGA    P     391      G     160          0.878
LGA    G     392      D     161          2.726
LGA    D     393      F     162          3.060
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    A     394      A     172          2.623
LGA    F     395      E     173          2.484
LGA    -       -      I     174           -
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    -       -      R     378           -
LGA    -       -      S     379           -
LGA    -       -      A     380           -
LGA    -       -      R     381           -
LGA    -       -      I     382           -
LGA    -       -      L     383           -
LGA    -       -      M     384           -
LGA    -       -      E     385           -
LGA    -       -      G     386           -
LGA    -       -      W     387           -
LGA    -       -      V     388           -
LGA    -       -      R     389           -
LGA    -       -      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18  200    5.0     17    2.62    17.65      5.682     0.626

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.227730 * X  +   0.724985 * Y  +  -0.650028 * Z  + 104.328857
  Y_new =  -0.875193 * X  +   0.445019 * Y  +   0.189722 * Z  +   6.819586
  Z_new =   0.426820 * X  +   0.525695 * Y  +   0.735846 * Z  +  27.455023 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.620331   -2.521261  [ DEG:    35.5424   -144.4576 ]
  Theta =  -0.440974   -2.700619  [ DEG:   -25.2659   -154.7341 ]
  Phi   =  -1.316236    1.825356  [ DEG:   -75.4148    104.5852 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0301TS193_4_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_4_2-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  200   5.0   17   2.62   17.65   5.682
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      75.986  20.479  16.560  1.00  0.00
ATOM   2790  CA  ARG   378      74.902  20.563  15.589  1.00  0.00
ATOM   2791  C   ARG   378      73.580  20.901  16.266  1.00  0.00
ATOM   2792  O   ARG   378      73.360  20.554  17.427  1.00  0.00
ATOM   2793  CB  ARG   378      74.733  19.229  14.859  1.00  0.00
ATOM   2794  CG  ARG   378      74.193  18.108  15.732  1.00  0.00
ATOM   2795  CD  ARG   378      73.986  16.834  14.928  1.00  0.00
ATOM   2796  NE  ARG   378      73.384  15.772  15.732  1.00  0.00
ATOM   2797  CZ  ARG   378      72.080  15.656  15.961  1.00  0.00
ATOM   2798  NH1 ARG   378      71.624  14.657  16.704  1.00  0.00
ATOM   2799  NH2 ARG   378      71.237  16.540  15.446  1.00  0.00
ATOM   2800  N   SER   379      72.704  21.581  15.535  1.00  0.00
ATOM   2801  CA  SER   379      71.348  21.836  16.006  1.00  0.00
ATOM   2802  C   SER   379      70.490  20.580  15.924  1.00  0.00
ATOM   2803  O   SER   379      70.734  19.704  15.095  1.00  0.00
ATOM   2804  CB  SER   379      70.681  22.921  15.158  1.00  0.00
ATOM   2805  OG  SER   379      71.386  24.147  15.253  1.00  0.00
ATOM   2806  N   ALA   380      70.768  19.448  12.861  1.00  0.00
ATOM   2807  CA  ALA   380      70.327  20.810  12.586  1.00  0.00
ATOM   2808  C   ALA   380      68.921  21.052  13.122  1.00  0.00
ATOM   2809  O   ALA   380      68.571  22.173  13.491  1.00  0.00
ATOM   2810  CB  ALA   380      70.312  21.069  11.087  1.00  0.00
ATOM   2811  N   ARG   381      69.361  22.531  11.415  1.00  0.00
ATOM   2812  CA  ARG   381      68.553  23.723  11.193  1.00  0.00
ATOM   2813  C   ARG   381      67.076  23.371  11.066  1.00  0.00
ATOM   2814  O   ARG   381      66.208  24.122  11.511  1.00  0.00
ATOM   2815  CB  ARG   381      68.983  24.430   9.907  1.00  0.00
ATOM   2816  CG  ARG   381      70.339  25.113   9.997  1.00  0.00
ATOM   2817  CD  ARG   381      70.736  25.731   8.667  1.00  0.00
ATOM   2818  NE  ARG   381      72.049  26.367   8.730  1.00  0.00
ATOM   2819  CZ  ARG   381      72.664  26.917   7.687  1.00  0.00
ATOM   2820  NH1 ARG   381      73.858  27.473   7.839  1.00  0.00
ATOM   2821  NH2 ARG   381      72.082  26.911   6.495  1.00  0.00
ATOM   2822  N   ILE   382      66.796  22.224  10.456  1.00  0.00
ATOM   2823  CA  ILE   382      65.423  21.774  10.261  1.00  0.00
ATOM   2824  C   ILE   382      64.817  21.275  11.567  1.00  0.00
ATOM   2825  O   ILE   382      63.601  21.322  11.756  1.00  0.00
ATOM   2826  CB  ILE   382      65.346  20.621   9.243  1.00  0.00
ATOM   2827  CG1 ILE   382      65.703  21.122   7.842  1.00  0.00
ATOM   2828  CG2 ILE   382      63.940  20.039   9.203  1.00  0.00
ATOM   2829  CD1 ILE   382      65.907  20.014   6.832  1.00  0.00
ATOM   2830  N   LEU   383      65.671  20.798  12.466  1.00  0.00
ATOM   2831  CA  LEU   383      65.220  20.280  13.751  1.00  0.00
ATOM   2832  C   LEU   383      65.208  21.373  14.812  1.00  0.00
ATOM   2833  O   LEU   383      64.855  21.127  15.967  1.00  0.00
ATOM   2834  CB  LEU   383      66.146  19.162  14.234  1.00  0.00
ATOM   2835  CG  LEU   383      66.295  17.957  13.303  1.00  0.00
ATOM   2836  CD1 LEU   383      67.270  16.945  13.885  1.00  0.00
ATOM   2837  CD2 LEU   383      64.957  17.265  13.099  1.00  0.00
ATOM   2838  N   MET   384      67.042  21.637  15.837  1.00  0.00
ATOM   2839  CA  MET   384      67.410  20.850  17.008  1.00  0.00
ATOM   2840  C   MET   384      66.747  21.395  18.267  1.00  0.00
ATOM   2841  O   MET   384      66.227  20.635  19.085  1.00  0.00
ATOM   2842  CB  MET   384      68.925  20.879  17.219  1.00  0.00
ATOM   2843  CG  MET   384      69.401  20.061  18.409  1.00  0.00
ATOM   2844  SD  MET   384      71.189  20.133  18.631  1.00  0.00
ATOM   2845  CE  MET   384      71.386  21.798  19.260  1.00  0.00
ATOM   2846  N   GLU   385      66.767  22.715  18.417  1.00  0.00
ATOM   2847  CA  GLU   385      66.156  23.365  19.570  1.00  0.00
ATOM   2848  C   GLU   385      64.639  23.233  19.536  1.00  0.00
ATOM   2849  O   GLU   385      63.998  23.057  20.572  1.00  0.00
ATOM   2850  CB  GLU   385      66.502  24.855  19.590  1.00  0.00
ATOM   2851  CG  GLU   385      67.988  25.146  19.718  1.00  0.00
ATOM   2852  CD  GLU   385      68.306  26.623  19.597  1.00  0.00
ATOM   2853  OE1 GLU   385      67.365  27.418  19.389  1.00  0.00
ATOM   2854  OE2 GLU   385      69.496  26.986  19.711  1.00  0.00
ATOM   2855  N   GLY   386      62.627  21.313  20.194  1.00  0.00
ATOM   2856  CA  GLY   386      63.671  20.474  19.618  1.00  0.00
ATOM   2857  C   GLY   386      64.347  19.623  20.686  1.00  0.00
ATOM   2858  O   GLY   386      63.981  19.678  21.860  1.00  0.00
ATOM   2859  N   TRP   387      65.335  18.838  20.273  1.00  0.00
ATOM   2860  CA  TRP   387      65.933  17.834  21.145  1.00  0.00
ATOM   2861  C   TRP   387      67.454  17.901  21.100  1.00  0.00
ATOM   2862  O   TRP   387      68.037  18.348  20.112  1.00  0.00
ATOM   2863  CB  TRP   387      65.507  16.429  20.715  1.00  0.00
ATOM   2864  CG  TRP   387      64.025  16.211  20.759  1.00  0.00
ATOM   2865  CD1 TRP   387      63.177  16.134  19.694  1.00  0.00
ATOM   2866  CD2 TRP   387      63.217  16.043  21.931  1.00  0.00
ATOM   2867  NE1 TRP   387      61.889  15.928  20.127  1.00  0.00
ATOM   2868  CE2 TRP   387      61.888  15.868  21.498  1.00  0.00
ATOM   2869  CE3 TRP   387      63.487  16.024  23.302  1.00  0.00
ATOM   2870  CZ2 TRP   387      60.832  15.677  22.388  1.00  0.00
ATOM   2871  CZ3 TRP   387      62.437  15.833  24.180  1.00  0.00
ATOM   2872  CH2 TRP   387      61.126  15.662  23.724  1.00  0.00
ATOM   2873  N   VAL   388      69.652  19.683  20.932  1.00  0.00
ATOM   2874  CA  VAL   388      68.844  20.162  22.049  1.00  0.00
ATOM   2875  C   VAL   388      69.461  21.404  22.681  1.00  0.00
ATOM   2876  O   VAL   388      70.645  21.685  22.494  1.00  0.00
ATOM   2877  CB  VAL   388      68.715  19.095  23.151  1.00  0.00
ATOM   2878  CG1 VAL   388      68.129  19.704  24.416  1.00  0.00
ATOM   2879  CG2 VAL   388      67.805  17.966  22.696  1.00  0.00
ATOM   2880  N   ARG   389      68.651  22.144  23.431  1.00  0.00
ATOM   2881  CA  ARG   389      69.144  23.278  24.202  1.00  0.00
ATOM   2882  C   ARG   389      69.702  22.829  25.547  1.00  0.00
ATOM   2883  O   ARG   389      68.975  22.288  26.381  1.00  0.00
ATOM   2884  CB  ARG   389      68.016  24.277  24.466  1.00  0.00
ATOM   2885  CG  ARG   389      67.502  24.977  23.218  1.00  0.00
ATOM   2886  CD  ARG   389      66.383  25.950  23.552  1.00  0.00
ATOM   2887  NE  ARG   389      65.809  26.556  22.353  1.00  0.00
ATOM   2888  CZ  ARG   389      64.827  27.452  22.366  1.00  0.00
ATOM   2889  NH1 ARG   389      64.368  27.948  21.225  1.00  0.00
ATOM   2890  NH2 ARG   389      64.306  27.848  23.519  1.00  0.00
ATOM   2891  N   VAL   390      71.209  22.248  26.648  1.00  0.00
ATOM   2892  CA  VAL   390      71.375  20.945  26.015  1.00  0.00
ATOM   2893  C   VAL   390      72.301  20.051  26.831  1.00  0.00
ATOM   2894  O   VAL   390      73.441  20.417  27.116  1.00  0.00
ATOM   2895  CB  VAL   390      71.980  21.076  24.605  1.00  0.00
ATOM   2896  CG1 VAL   390      72.235  19.701  24.005  1.00  0.00
ATOM   2897  CG2 VAL   390      71.033  21.832  23.687  1.00  0.00
ATOM   2898  N   PRO   391      71.803  18.877  27.204  1.00  0.00
ATOM   2899  CA  PRO   391      72.592  17.917  27.965  1.00  0.00
ATOM   2900  C   PRO   391      73.891  17.578  27.245  1.00  0.00
ATOM   2901  O   PRO   391      73.896  17.328  26.039  1.00  0.00
ATOM   2902  CB  PRO   391      71.680  16.693  28.077  1.00  0.00
ATOM   2903  CG  PRO   391      70.300  17.244  27.951  1.00  0.00
ATOM   2904  CD  PRO   391      70.386  18.361  26.949  1.00  0.00
ATOM   2905  N   GLY   392      74.991  17.571  27.990  1.00  0.00
ATOM   2906  CA  GLY   392      76.319  17.478  27.396  1.00  0.00
ATOM   2907  C   GLY   392      76.564  16.093  26.809  1.00  0.00
ATOM   2908  O   GLY   392      77.456  15.908  25.982  1.00  0.00
ATOM   2909  N   ASP   393      75.767  15.123  27.242  1.00  0.00
ATOM   2910  CA  ASP   393      75.894  13.754  26.757  1.00  0.00
ATOM   2911  C   ASP   393      74.953  13.494  25.588  1.00  0.00
ATOM   2912  O   ASP   393      74.765  12.351  25.172  1.00  0.00
ATOM   2913  CB  ASP   393      75.555  12.758  27.869  1.00  0.00
ATOM   2914  CG  ASP   393      74.117  12.870  28.333  1.00  0.00
ATOM   2915  OD1 ASP   393      73.387  13.736  27.805  1.00  0.00
ATOM   2916  OD2 ASP   393      73.717  12.092  29.225  1.00  0.00
ATOM   2917  N   ALA   394      74.363  14.562  25.060  1.00  0.00
ATOM   2918  CA  ALA   394      73.459  14.454  23.922  1.00  0.00
ATOM   2919  C   ALA   394      73.937  15.308  22.755  1.00  0.00
ATOM   2920  O   ALA   394      73.333  15.305  21.683  1.00  0.00
ATOM   2921  CB  ALA   394      72.063  14.919  24.309  1.00  0.00
ATOM   2922  N   PHE   395      75.026  16.039  22.970  1.00  0.00
ATOM   2923  CA  PHE   395      75.563  16.932  21.951  1.00  0.00
ATOM   2924  C   PHE   395      76.001  16.156  20.716  1.00  0.00
ATOM   2925  O   PHE   395      75.947  16.669  19.597  1.00  0.00
ATOM   2926  CB  PHE   395      76.777  17.691  22.490  1.00  0.00
ATOM   2927  CG  PHE   395      76.444  18.677  23.573  1.00  0.00
ATOM   2928  CD1 PHE   395      75.138  19.086  23.778  1.00  0.00
ATOM   2929  CD2 PHE   395      77.437  19.195  24.387  1.00  0.00
ATOM   2930  CE1 PHE   395      74.831  19.993  24.774  1.00  0.00
ATOM   2931  CE2 PHE   395      77.130  20.103  25.382  1.00  0.00
ATOM   2932  CZ  PHE   395      75.834  20.502  25.579  1.00  0.00
TER
END
