
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_2_2-D1.T0301_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    R     378      N     106          2.976
LGA    S     379      L     107          1.532
LGA    A     380      S     108          1.850
LGA    R     381      T     109          1.569
LGA    I     382      G     110          1.787
LGA    L     383      A     111          1.377
LGA    M     384      G     112          1.317
LGA    E     385      A     113          2.409
LGA    G     386      F     114          2.142
LGA    W     387      A     115          0.709
LGA    V     388      L     116          2.759
LGA    R     389      H     117           #
LGA    -       -      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    V     390      A     124           #
LGA    -       -      R     125           -
LGA    P     391      I     126          4.702
LGA    G     392      P     127          1.303
LGA    D     393      E     128          2.045
LGA    A     394      D     129          2.770
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    F     395      G     153          2.133
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    -       -      Q     157           -
LGA    -       -      E     158           -
LGA    -       -      T     159           -
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
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     172           -
LGA    -       -      E     173           -
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     16    2.27     0.00      6.473     0.674

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.052520 * X  +   0.995539 * Y  +  -0.078379 * Z  +  80.099937
  Y_new =  -0.598913 * X  +  -0.031404 * Y  +  -0.800198 * Z  +   2.639448
  Z_new =  -0.799090 * X  +   0.088969 * Y  +   0.594592 * Z  +  28.274214 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.148528   -2.993065  [ DEG:     8.5100   -171.4900 ]
  Theta =   0.925780    2.215812  [ DEG:    53.0433    126.9567 ]
  Phi   =  -1.483328    1.658264  [ DEG:   -84.9884     95.0116 ]
 
# 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_2_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_2_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   16   2.27    0.00   6.473
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      82.822  22.724  10.429  1.00  0.00
ATOM   2790  CA  ARG   378      81.372  22.616  10.315  1.00  0.00
ATOM   2791  C   ARG   378      80.680  23.150  11.562  1.00  0.00
ATOM   2792  O   ARG   378      81.305  23.307  12.611  1.00  0.00
ATOM   2793  CB  ARG   378      80.957  21.154  10.132  1.00  0.00
ATOM   2794  CG  ARG   378      81.529  20.499   8.886  1.00  0.00
ATOM   2795  CD  ARG   378      80.899  21.066   7.624  1.00  0.00
ATOM   2796  NE  ARG   378      81.385  20.394   6.421  1.00  0.00
ATOM   2797  CZ  ARG   378      82.460  20.769   5.737  1.00  0.00
ATOM   2798  NH1 ARG   378      82.826  20.098   4.654  1.00  0.00
ATOM   2799  NH2 ARG   378      83.169  21.816   6.139  1.00  0.00
ATOM   2800  N   SER   379      79.386  23.426  11.442  1.00  0.00
ATOM   2801  CA  SER   379      78.595  23.898  12.573  1.00  0.00
ATOM   2802  C   SER   379      77.504  22.899  12.937  1.00  0.00
ATOM   2803  O   SER   379      76.596  22.640  12.145  1.00  0.00
ATOM   2804  CB  SER   379      77.924  25.232  12.238  1.00  0.00
ATOM   2805  OG  SER   379      78.889  26.239  11.988  1.00  0.00
ATOM   2806  N   ALA   380      78.528  21.607  11.631  1.00  0.00
ATOM   2807  CA  ALA   380      77.954  20.838  10.533  1.00  0.00
ATOM   2808  C   ALA   380      76.834  19.931  11.023  1.00  0.00
ATOM   2809  O   ALA   380      75.746  19.907  10.449  1.00  0.00
ATOM   2810  CB  ALA   380      79.019  19.967   9.883  1.00  0.00
ATOM   2811  N   ARG   381      77.106  19.184  12.087  1.00  0.00
ATOM   2812  CA  ARG   381      76.122  18.271  12.656  1.00  0.00
ATOM   2813  C   ARG   381      74.932  19.031  13.228  1.00  0.00
ATOM   2814  O   ARG   381      73.790  18.583  13.125  1.00  0.00
ATOM   2815  CB  ARG   381      76.744  17.445  13.783  1.00  0.00
ATOM   2816  CG  ARG   381      77.744  16.402  13.310  1.00  0.00
ATOM   2817  CD  ARG   381      78.380  15.675  14.483  1.00  0.00
ATOM   2818  NE  ARG   381      79.347  14.671  14.045  1.00  0.00
ATOM   2819  CZ  ARG   381      80.101  13.950  14.870  1.00  0.00
ATOM   2820  NH1 ARG   381      80.953  13.060  14.381  1.00  0.00
ATOM   2821  NH2 ARG   381      79.999  14.122  16.180  1.00  0.00
ATOM   2822  N   ILE   382      75.206  20.184  13.830  1.00  0.00
ATOM   2823  CA  ILE   382      74.171  20.966  14.493  1.00  0.00
ATOM   2824  C   ILE   382      73.176  21.529  13.487  1.00  0.00
ATOM   2825  O   ILE   382      71.977  21.600  13.758  1.00  0.00
ATOM   2826  CB  ILE   382      74.771  22.154  15.267  1.00  0.00
ATOM   2827  CG1 ILE   382      75.600  21.655  16.452  1.00  0.00
ATOM   2828  CG2 ILE   382      73.666  23.057  15.798  1.00  0.00
ATOM   2829  CD1 ILE   382      76.436  22.732  17.109  1.00  0.00
ATOM   2830  N   LEU   383      73.679  21.927  12.324  1.00  0.00
ATOM   2831  CA  LEU   383      72.832  22.466  11.266  1.00  0.00
ATOM   2832  C   LEU   383      71.679  21.523  10.949  1.00  0.00
ATOM   2833  O   LEU   383      70.634  21.947  10.454  1.00  0.00
ATOM   2834  CB  LEU   383      73.641  22.671   9.984  1.00  0.00
ATOM   2835  CG  LEU   383      74.732  23.743  10.036  1.00  0.00
ATOM   2836  CD1 LEU   383      75.540  23.750   8.747  1.00  0.00
ATOM   2837  CD2 LEU   383      74.121  25.124  10.221  1.00  0.00
ATOM   2838  N   MET   384      71.874  20.240  11.238  1.00  0.00
ATOM   2839  CA  MET   384      70.844  19.236  10.998  1.00  0.00
ATOM   2840  C   MET   384      69.535  19.616  11.680  1.00  0.00
ATOM   2841  O   MET   384      68.457  19.214  11.242  1.00  0.00
ATOM   2842  CB  MET   384      71.285  17.876  11.542  1.00  0.00
ATOM   2843  CG  MET   384      70.312  16.745  11.251  1.00  0.00
ATOM   2844  SD  MET   384      70.139  16.413   9.488  1.00  0.00
ATOM   2845  CE  MET   384      71.711  15.630   9.135  1.00  0.00
ATOM   2846  N   GLU   385      69.768  18.953  13.052  1.00  0.00
ATOM   2847  CA  GLU   385      68.671  18.565  13.930  1.00  0.00
ATOM   2848  C   GLU   385      67.610  19.655  13.999  1.00  0.00
ATOM   2849  O   GLU   385      66.413  19.369  14.038  1.00  0.00
ATOM   2850  CB  GLU   385      69.184  18.312  15.349  1.00  0.00
ATOM   2851  CG  GLU   385      68.114  17.841  16.321  1.00  0.00
ATOM   2852  CD  GLU   385      68.670  17.545  17.700  1.00  0.00
ATOM   2853  OE1 GLU   385      69.896  17.691  17.891  1.00  0.00
ATOM   2854  OE2 GLU   385      67.879  17.168  18.590  1.00  0.00
ATOM   2855  N   GLY   386      68.055  20.907  14.015  1.00  0.00
ATOM   2856  CA  GLY   386      67.143  22.044  14.074  1.00  0.00
ATOM   2857  C   GLY   386      66.222  22.074  12.862  1.00  0.00
ATOM   2858  O   GLY   386      65.011  22.259  12.995  1.00  0.00
ATOM   2859  N   TRP   387      66.801  21.893  11.680  1.00  0.00
ATOM   2860  CA  TRP   387      66.033  21.911  10.441  1.00  0.00
ATOM   2861  C   TRP   387      65.142  20.681  10.326  1.00  0.00
ATOM   2862  O   TRP   387      63.977  20.781   9.942  1.00  0.00
ATOM   2863  CB  TRP   387      66.970  21.932   9.230  1.00  0.00
ATOM   2864  CG  TRP   387      67.763  23.196   9.108  1.00  0.00
ATOM   2865  CD1 TRP   387      67.637  24.320   9.873  1.00  0.00
ATOM   2866  CD2 TRP   387      68.807  23.466   8.165  1.00  0.00
ATOM   2867  NE1 TRP   387      68.538  25.274   9.465  1.00  0.00
ATOM   2868  CE2 TRP   387      69.267  24.774   8.416  1.00  0.00
ATOM   2869  CE3 TRP   387      69.397  22.732   7.132  1.00  0.00
ATOM   2870  CZ2 TRP   387      70.291  25.361   7.674  1.00  0.00
ATOM   2871  CZ3 TRP   387      70.410  23.318   6.398  1.00  0.00
ATOM   2872  CH2 TRP   387      70.849  24.618   6.670  1.00  0.00
ATOM   2873  N   VAL   388      64.918  20.056  11.853  1.00  0.00
ATOM   2874  CA  VAL   388      64.485  18.676  11.675  1.00  0.00
ATOM   2875  C   VAL   388      63.489  18.268  12.754  1.00  0.00
ATOM   2876  O   VAL   388      63.641  18.630  13.920  1.00  0.00
ATOM   2877  CB  VAL   388      65.672  17.698  11.745  1.00  0.00
ATOM   2878  CG1 VAL   388      65.179  16.259  11.728  1.00  0.00
ATOM   2879  CG2 VAL   388      66.601  17.901  10.559  1.00  0.00
ATOM   2880  N   ARG   389      62.472  17.510  12.357  1.00  0.00
ATOM   2881  CA  ARG   389      61.458  17.039  13.293  1.00  0.00
ATOM   2882  C   ARG   389      61.668  15.571  13.640  1.00  0.00
ATOM   2883  O   ARG   389      61.639  14.706  12.765  1.00  0.00
ATOM   2884  CB  ARG   389      60.060  17.188  12.688  1.00  0.00
ATOM   2885  CG  ARG   389      58.930  16.849  13.646  1.00  0.00
ATOM   2886  CD  ARG   389      57.573  17.065  12.997  1.00  0.00
ATOM   2887  NE  ARG   389      56.475  16.829  13.933  1.00  0.00
ATOM   2888  CZ  ARG   389      55.199  16.723  13.575  1.00  0.00
ATOM   2889  NH1 ARG   389      54.269  16.509  14.496  1.00  0.00
ATOM   2890  NH2 ARG   389      54.856  16.833  12.299  1.00  0.00
ATOM   2891  N   VAL   390      61.878  15.296  14.923  1.00  0.00
ATOM   2892  CA  VAL   390      62.121  13.934  15.385  1.00  0.00
ATOM   2893  C   VAL   390      60.910  13.380  16.126  1.00  0.00
ATOM   2894  O   VAL   390      60.326  14.057  16.972  1.00  0.00
ATOM   2895  CB  VAL   390      63.323  13.871  16.346  1.00  0.00
ATOM   2896  CG1 VAL   390      63.601  12.433  16.756  1.00  0.00
ATOM   2897  CG2 VAL   390      64.570  14.429  15.677  1.00  0.00
ATOM   2898  N   PRO   391      61.464  15.374  18.397  1.00  0.00
ATOM   2899  CA  PRO   391      61.764  14.295  19.331  1.00  0.00
ATOM   2900  C   PRO   391      60.488  13.696  19.910  1.00  0.00
ATOM   2901  O   PRO   391      60.384  12.482  20.083  1.00  0.00
ATOM   2902  CB  PRO   391      62.607  14.967  20.416  1.00  0.00
ATOM   2903  CG  PRO   391      62.074  16.359  20.495  1.00  0.00
ATOM   2904  CD  PRO   391      61.808  16.783  19.078  1.00  0.00
ATOM   2905  N   GLY   392      59.566  11.364  18.311  1.00  0.00
ATOM   2906  CA  GLY   392      58.870  12.521  17.760  1.00  0.00
ATOM   2907  C   GLY   392      57.871  13.091  18.761  1.00  0.00
ATOM   2908  O   GLY   392      57.778  14.306  18.935  1.00  0.00
ATOM   2909  N   ASP   393      57.127  12.206  19.415  1.00  0.00
ATOM   2910  CA  ASP   393      56.141  12.619  20.408  1.00  0.00
ATOM   2911  C   ASP   393      56.800  13.366  21.560  1.00  0.00
ATOM   2912  O   ASP   393      56.314  14.410  21.995  1.00  0.00
ATOM   2913  CB  ASP   393      55.419  11.399  20.984  1.00  0.00
ATOM   2914  CG  ASP   393      54.449  10.777  19.998  1.00  0.00
ATOM   2915  OD1 ASP   393      54.159  11.418  18.965  1.00  0.00
ATOM   2916  OD2 ASP   393      53.981   9.650  20.257  1.00  0.00
ATOM   2917  N   ALA   394      57.909  12.825  22.052  1.00  0.00
ATOM   2918  CA  ALA   394      58.635  13.438  23.159  1.00  0.00
ATOM   2919  C   ALA   394      59.152  14.820  22.781  1.00  0.00
ATOM   2920  O   ALA   394      59.132  15.744  23.595  1.00  0.00
ATOM   2921  CB  ALA   394      59.828  12.579  23.551  1.00  0.00
ATOM   2922  N   PHE   395      57.644  15.136  25.170  1.00  0.00
ATOM   2923  CA  PHE   395      58.314  15.864  26.242  1.00  0.00
ATOM   2924  C   PHE   395      58.928  14.909  27.256  1.00  0.00
ATOM   2925  O   PHE   395      58.311  13.915  27.640  1.00  0.00
ATOM   2926  CB  PHE   395      57.321  16.764  26.979  1.00  0.00
ATOM   2927  CG  PHE   395      56.771  17.878  26.136  1.00  0.00
ATOM   2928  CD1 PHE   395      55.528  17.763  25.537  1.00  0.00
ATOM   2929  CD2 PHE   395      57.495  19.041  25.941  1.00  0.00
ATOM   2930  CE1 PHE   395      55.021  18.788  24.762  1.00  0.00
ATOM   2931  CE2 PHE   395      56.988  20.066  25.165  1.00  0.00
ATOM   2932  CZ  PHE   395      55.756  19.943  24.576  1.00  0.00
TER
END
