
#######################################################
#                                                     #
#                        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_5_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_5_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    R     378      S      78          2.402
LGA    S     379      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    A     380      V      84          3.169
LGA    R     381      D      85          2.236
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    -       -      T     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      G     112           -
LGA    -       -      A     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -
LGA    -       -      H     117           -
LGA    -       -      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     382      I     136          2.966
LGA    L     383      W     137          1.810
LGA    -       -      Q     138           -
LGA    M     384      A     139          4.072
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    E     385      G     142          2.748
LGA    G     386      K     143          1.397
LGA    W     387      T     144          0.882
LGA    V     388      I     145          1.602
LGA    R     389      I     146          1.809
LGA    V     390      A     147          1.900
LGA    P     391      H     148          2.764
LGA    G     392      V     149          0.621
LGA    D     393      P     150          1.008
LGA    A     394      V     151          2.319
LGA    F     395      S     152          2.882
LGA    -       -      G     153           -
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     17    2.33     5.88      6.842     0.701

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.531364 * X  +   0.594286 * Y  +  -0.603719 * Z  + -14.355137
  Y_new =  -0.691595 * X  +   0.715879 * Y  +   0.095986 * Z  +  15.324767
  Z_new =   0.489233 * X  +   0.366526 * Y  +   0.791397 * Z  +  24.792631 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.433725   -2.707868  [ DEG:    24.8506   -155.1494 ]
  Theta =  -0.511210   -2.630383  [ DEG:   -29.2902   -150.7098 ]
  Phi   =  -0.915675    2.225918  [ DEG:   -52.4643    127.5357 ]
 
# 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_5_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_5_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   2.33    5.88   6.842
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      62.939  19.662  -0.980  1.00  0.00
ATOM   2790  CA  ARG   378      63.712  19.650  -2.216  1.00  0.00
ATOM   2791  C   ARG   378      64.990  20.466  -2.074  1.00  0.00
ATOM   2792  O   ARG   378      66.023  20.125  -2.651  1.00  0.00
ATOM   2793  CB  ARG   378      62.894  20.246  -3.364  1.00  0.00
ATOM   2794  CG  ARG   378      61.744  19.367  -3.829  1.00  0.00
ATOM   2795  CD  ARG   378      60.926  20.054  -4.908  1.00  0.00
ATOM   2796  NE  ARG   378      59.801  19.232  -5.350  1.00  0.00
ATOM   2797  CZ  ARG   378      58.867  19.640  -6.204  1.00  0.00
ATOM   2798  NH1 ARG   378      57.880  18.823  -6.547  1.00  0.00
ATOM   2799  NH2 ARG   378      58.923  20.863  -6.713  1.00  0.00
ATOM   2800  N   SER   379      64.915  21.545  -1.304  1.00  0.00
ATOM   2801  CA  SER   379      66.070  22.403  -1.072  1.00  0.00
ATOM   2802  C   SER   379      67.135  21.684  -0.254  1.00  0.00
ATOM   2803  O   SER   379      68.328  21.793  -0.539  1.00  0.00
ATOM   2804  CB  SER   379      65.658  23.664  -0.309  1.00  0.00
ATOM   2805  OG  SER   379      64.799  24.475  -1.091  1.00  0.00
ATOM   2806  N   ALA   380      66.699  20.951   0.763  1.00  0.00
ATOM   2807  CA  ALA   380      67.612  20.188   1.606  1.00  0.00
ATOM   2808  C   ALA   380      68.280  19.068   0.820  1.00  0.00
ATOM   2809  O   ALA   380      69.485  18.844   0.941  1.00  0.00
ATOM   2810  CB  ALA   380      66.861  19.565   2.773  1.00  0.00
ATOM   2811  N   ARG   381      70.076  19.982   2.790  1.00  0.00
ATOM   2812  CA  ARG   381      71.444  20.218   2.344  1.00  0.00
ATOM   2813  C   ARG   381      72.270  18.940   2.401  1.00  0.00
ATOM   2814  O   ARG   381      72.990  18.611   1.459  1.00  0.00
ATOM   2815  CB  ARG   381      72.124  21.262   3.231  1.00  0.00
ATOM   2816  CG  ARG   381      71.593  22.675   3.047  1.00  0.00
ATOM   2817  CD  ARG   381      72.279  23.650   3.989  1.00  0.00
ATOM   2818  NE  ARG   381      71.745  25.004   3.859  1.00  0.00
ATOM   2819  CZ  ARG   381      72.130  26.033   4.606  1.00  0.00
ATOM   2820  NH1 ARG   381      71.590  27.229   4.416  1.00  0.00
ATOM   2821  NH2 ARG   381      73.057  25.866   5.539  1.00  0.00
ATOM   2822  N   ILE   382      72.162  18.221   3.514  1.00  0.00
ATOM   2823  CA  ILE   382      72.795  16.913   3.646  1.00  0.00
ATOM   2824  C   ILE   382      72.331  15.964   2.548  1.00  0.00
ATOM   2825  O   ILE   382      73.133  15.237   1.965  1.00  0.00
ATOM   2826  CB  ILE   382      72.459  16.257   4.998  1.00  0.00
ATOM   2827  CG1 ILE   382      73.110  17.034   6.144  1.00  0.00
ATOM   2828  CG2 ILE   382      72.968  14.825   5.037  1.00  0.00
ATOM   2829  CD1 ILE   382      72.621  16.624   7.516  1.00  0.00
ATOM   2830  N   LEU   383      71.031  15.977   2.271  1.00  0.00
ATOM   2831  CA  LEU   383      70.461  15.131   1.230  1.00  0.00
ATOM   2832  C   LEU   383      71.030  15.483  -0.139  1.00  0.00
ATOM   2833  O   LEU   383      71.457  14.604  -0.889  1.00  0.00
ATOM   2834  CB  LEU   383      68.942  15.303   1.171  1.00  0.00
ATOM   2835  CG  LEU   383      68.207  14.485   0.108  1.00  0.00
ATOM   2836  CD1 LEU   383      68.398  12.995   0.350  1.00  0.00
ATOM   2837  CD2 LEU   383      66.716  14.783   0.134  1.00  0.00
ATOM   2838  N   MET   384      71.032  16.772  -0.459  1.00  0.00
ATOM   2839  CA  MET   384      71.549  17.242  -1.739  1.00  0.00
ATOM   2840  C   MET   384      73.054  17.026  -1.838  1.00  0.00
ATOM   2841  O   MET   384      73.598  16.879  -2.932  1.00  0.00
ATOM   2842  CB  MET   384      71.272  18.737  -1.912  1.00  0.00
ATOM   2843  CG  MET   384      69.801  19.081  -2.075  1.00  0.00
ATOM   2844  SD  MET   384      69.051  18.273  -3.502  1.00  0.00
ATOM   2845  CE  MET   384      69.893  19.106  -4.844  1.00  0.00
ATOM   2846  N   GLU   385      73.721  17.006  -0.689  1.00  0.00
ATOM   2847  CA  GLU   385      75.172  16.871  -0.647  1.00  0.00
ATOM   2848  C   GLU   385      75.595  15.420  -0.832  1.00  0.00
ATOM   2849  O   GLU   385      76.705  15.138  -1.286  1.00  0.00
ATOM   2850  CB  GLU   385      75.717  17.356   0.697  1.00  0.00
ATOM   2851  CG  GLU   385      75.538  18.846   0.938  1.00  0.00
ATOM   2852  CD  GLU   385      76.069  19.287   2.288  1.00  0.00
ATOM   2853  OE1 GLU   385      76.622  18.435   3.015  1.00  0.00
ATOM   2854  OE2 GLU   385      75.933  20.483   2.618  1.00  0.00
ATOM   2855  N   GLY   386      74.754  14.245  -0.611  1.00  0.00
ATOM   2856  CA  GLY   386      75.358  13.446   0.449  1.00  0.00
ATOM   2857  C   GLY   386      74.359  13.170   1.567  1.00  0.00
ATOM   2858  O   GLY   386      73.252  13.707   1.570  1.00  0.00
ATOM   2859  N   TRP   387      74.758  12.328   2.514  1.00  0.00
ATOM   2860  CA  TRP   387      73.892  11.963   3.629  1.00  0.00
ATOM   2861  C   TRP   387      74.706  11.607   4.866  1.00  0.00
ATOM   2862  O   TRP   387      75.829  11.113   4.761  1.00  0.00
ATOM   2863  CB  TRP   387      73.030  10.753   3.264  1.00  0.00
ATOM   2864  CG  TRP   387      73.827   9.526   2.940  1.00  0.00
ATOM   2865  CD1 TRP   387      74.324   9.169   1.720  1.00  0.00
ATOM   2866  CD2 TRP   387      74.218   8.491   3.852  1.00  0.00
ATOM   2867  NE1 TRP   387      75.001   7.977   1.814  1.00  0.00
ATOM   2868  CE2 TRP   387      74.950   7.540   3.113  1.00  0.00
ATOM   2869  CE3 TRP   387      74.021   8.276   5.219  1.00  0.00
ATOM   2870  CZ2 TRP   387      75.486   6.393   3.696  1.00  0.00
ATOM   2871  CZ3 TRP   387      74.554   7.137   5.792  1.00  0.00
ATOM   2872  CH2 TRP   387      75.277   6.209   5.036  1.00  0.00
ATOM   2873  N   VAL   388      74.134  11.862   6.039  1.00  0.00
ATOM   2874  CA  VAL   388      74.780  11.513   7.298  1.00  0.00
ATOM   2875  C   VAL   388      73.770  11.452   8.436  1.00  0.00
ATOM   2876  O   VAL   388      72.587  11.728   8.244  1.00  0.00
ATOM   2877  CB  VAL   388      75.854  12.547   7.686  1.00  0.00
ATOM   2878  CG1 VAL   388      76.974  12.562   6.657  1.00  0.00
ATOM   2879  CG2 VAL   388      75.250  13.940   7.760  1.00  0.00
ATOM   2880  N   ARG   389      74.246  11.088   9.623  1.00  0.00
ATOM   2881  CA  ARG   389      73.400  11.058  10.810  1.00  0.00
ATOM   2882  C   ARG   389      74.023  11.854  11.950  1.00  0.00
ATOM   2883  O   ARG   389      75.228  11.776  12.188  1.00  0.00
ATOM   2884  CB  ARG   389      73.200   9.619  11.290  1.00  0.00
ATOM   2885  CG  ARG   389      72.398   8.751  10.334  1.00  0.00
ATOM   2886  CD  ARG   389      72.264   7.331  10.857  1.00  0.00
ATOM   2887  NE  ARG   389      71.608   6.451   9.892  1.00  0.00
ATOM   2888  CZ  ARG   389      71.399   5.153  10.087  1.00  0.00
ATOM   2889  NH1 ARG   389      70.795   4.432   9.153  1.00  0.00
ATOM   2890  NH2 ARG   389      71.793   4.580  11.215  1.00  0.00
ATOM   2891  N   VAL   390      73.631  13.330  11.876  1.00  0.00
ATOM   2892  CA  VAL   390      73.908  14.038  13.119  1.00  0.00
ATOM   2893  C   VAL   390      72.999  13.557  14.243  1.00  0.00
ATOM   2894  O   VAL   390      71.777  13.523  14.093  1.00  0.00
ATOM   2895  CB  VAL   390      73.692  15.555  12.966  1.00  0.00
ATOM   2896  CG1 VAL   390      73.852  16.254  14.306  1.00  0.00
ATOM   2897  CG2 VAL   390      74.704  16.142  11.994  1.00  0.00
ATOM   2898  N   PRO   391      73.600  13.185  15.367  1.00  0.00
ATOM   2899  CA  PRO   391      72.843  12.838  16.564  1.00  0.00
ATOM   2900  C   PRO   391      71.923  13.977  16.982  1.00  0.00
ATOM   2901  O   PRO   391      72.349  15.127  17.084  1.00  0.00
ATOM   2902  CB  PRO   391      73.918  12.573  17.619  1.00  0.00
ATOM   2903  CG  PRO   391      75.123  12.177  16.833  1.00  0.00
ATOM   2904  CD  PRO   391      75.104  13.019  15.588  1.00  0.00
ATOM   2905  N   GLY   392      70.657  13.649  17.223  1.00  0.00
ATOM   2906  CA  GLY   392      69.664  14.652  17.591  1.00  0.00
ATOM   2907  C   GLY   392      68.809  14.178  18.759  1.00  0.00
ATOM   2908  O   GLY   392      68.666  12.977  18.989  1.00  0.00
ATOM   2909  N   ASP   393      68.243  15.128  19.495  1.00  0.00
ATOM   2910  CA  ASP   393      67.358  14.808  20.609  1.00  0.00
ATOM   2911  C   ASP   393      66.042  14.220  20.117  1.00  0.00
ATOM   2912  O   ASP   393      65.587  14.528  19.016  1.00  0.00
ATOM   2913  CB  ASP   393      67.040  16.067  21.420  1.00  0.00
ATOM   2914  CG  ASP   393      68.221  16.542  22.244  1.00  0.00
ATOM   2915  OD1 ASP   393      69.213  15.790  22.350  1.00  0.00
ATOM   2916  OD2 ASP   393      68.154  17.666  22.785  1.00  0.00
ATOM   2917  N   ALA   394      65.435  13.371  20.939  1.00  0.00
ATOM   2918  CA  ALA   394      64.083  12.891  20.684  1.00  0.00
ATOM   2919  C   ALA   394      63.090  13.488  21.673  1.00  0.00
ATOM   2920  O   ALA   394      63.216  13.300  22.883  1.00  0.00
ATOM   2921  CB  ALA   394      64.025  11.376  20.811  1.00  0.00
ATOM   2922  N   PHE   395      62.102  14.206  21.152  1.00  0.00
ATOM   2923  CA  PHE   395      61.150  14.922  21.992  1.00  0.00
ATOM   2924  C   PHE   395      59.908  14.080  22.259  1.00  0.00
ATOM   2925  O   PHE   395      59.432  13.363  21.379  1.00  0.00
ATOM   2926  CB  PHE   395      60.706  16.219  21.313  1.00  0.00
ATOM   2927  CG  PHE   395      61.808  17.228  21.154  1.00  0.00
ATOM   2928  CD1 PHE   395      62.444  17.394  19.936  1.00  0.00
ATOM   2929  CD2 PHE   395      62.209  18.011  22.223  1.00  0.00
ATOM   2930  CE1 PHE   395      63.459  18.322  19.791  1.00  0.00
ATOM   2931  CE2 PHE   395      63.222  18.939  22.077  1.00  0.00
ATOM   2932  CZ  PHE   395      63.846  19.096  20.868  1.00  0.00
TER
END
