
#######################################################
#                                                     #
#                        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  141 (  141),  selected  141 , name T0329TS393_2-D1
# Molecule2: number of CA atoms  141 ( 1070),  selected  141 , name T0329_D1.pdb
# PARAMETERS: T0329TS393_2-D1.T0329_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      M       1           #
LGA    Y       3      K       2           -
LGA    -       -      Y       3           -
LGA    K       4      K       4          2.613
LGA    A       5      A       5          3.646
LGA    A       6      A       6           #
LGA    I       7      I       7           #
LGA    F       8      -       -           -
LGA    D       9      -       -           -
LGA    M      10      -       -           -
LGA    D      11      -       -           -
LGA    G      12      -       -           -
LGA    T      13      F       8           #
LGA    -       -      D       9           -
LGA    -       -      M      10           -
LGA    -       -      D      11           -
LGA    -       -      G      12           -
LGA    -       -      T      13           -
LGA    I      14      I      14          1.676
LGA    L      15      L      15          2.247
LGA    D      16      D      16          1.764
LGA    G     109      G     109          3.195
LGA    P     110      P     110          4.589
LGA    F     111      F     111          4.203
LGA    P     112      P     112          4.963
LGA    G     113      G     113          2.676
LGA    I     114      I     114          1.231
LGA    L     115      L     115          0.977
LGA    D     116      D     116          0.738
LGA    L     117      L     117          1.169
LGA    M     118      M     118          1.247
LGA    K     119      K     119          1.362
LGA    N     120      N     120          1.776
LGA    L     121      L     121          2.033
LGA    R     122      R     122          2.001
LGA    Q     123      Q     123          2.493
LGA    K     124      K     124          2.123
LGA    G     125      G     125          1.715
LGA    V     126      V     126          1.914
LGA    K     127      K     127          4.292
LGA    L     128      L     128          3.448
LGA    A     129      A     129          3.785
LGA    V     130      V     130          1.275
LGA    V     131      V     131          4.975
LGA    S     132      S     132          4.576
LGA    N     133      N     133          4.205
LGA    K     134      K     134          2.901
LGA    P     135      P     135          2.673
LGA    N     136      N     136          4.233
LGA    E     137      E     137          3.195
LGA    A     138      A     138          2.535
LGA    V     139      V     139          1.232
LGA    Q     140      Q     140          0.700
LGA    V     141      V     141          2.365
LGA    L     142      L     142          2.795
LGA    V     143      V     143          3.642
LGA    E     144      E     144          4.006
LGA    -       -      E     145           -
LGA    E     145      L     146          4.517
LGA    L     146      F     147          4.773
LGA    F     147      P     148           #
LGA    P     148      G     149          2.826
LGA    G     149      S     150          3.117
LGA    S     150      -       -           -
LGA    F     151      F     151          5.051
LGA    D     152      D     152           -
LGA    F     153      F     153           -
LGA    A     154      -       -           -
LGA    L     155      A     154           #
LGA    -       -      L     155           -
LGA    G     156      G     156           #
LGA    R     163      R     163          2.258
LGA    K     164      K     164          1.333
LGA    P     165      P     165          1.804
LGA    A     166      A     166          2.300
LGA    P     167      P     167          2.270
LGA    D     168      D     168          2.647
LGA    M     169      M     169          2.327
LGA    T     170      T     170          1.922
LGA    S     171      S     171          1.735
LGA    E     172      E     172          1.800
LGA    C     173      C     173          1.194
LGA    V     174      V     174          0.456
LGA    K     175      K     175          0.478
LGA    V     176      V     176          1.637
LGA    L     177      L     177          1.302
LGA    G     178      G     178          2.524
LGA    V     179      V     179          2.470
LGA    P     180      P     180          2.783
LGA    R     181      R     181          4.045
LGA    D     182      D     182          2.958
LGA    K     183      K     183          1.859
LGA    C     184      C     184          3.175
LGA    V     185      V     185          1.877
LGA    Y     186      Y     186          0.934
LGA    I     187      I     187          2.502
LGA    G     188      G     188          2.205
LGA    D     189      D     189          3.218
LGA    S     190      S     190          1.625
LGA    E     191      E     191          1.939
LGA    I     192      I     192          1.517
LGA    D     193      D     193          1.205
LGA    I     194      I     194          1.068
LGA    Q     195      Q     195          0.469
LGA    T     196      T     196          0.729
LGA    A     197      A     197          1.090
LGA    R     198      R     198          1.526
LGA    N     199      N     199          1.734
LGA    S     200      S     200          1.669
LGA    E     201      E     201          2.962
LGA    M     202      M     202          2.564
LGA    D     203      D     203          1.684
LGA    E     204      E     204          2.045
LGA    I     205      I     205          2.210
LGA    A     206      A     206          3.610
LGA    V     207      -       -           -
LGA    N     208      V     207          4.250
LGA    W     209      N     208          3.380
LGA    G     210      W     209          1.827
LGA    F     211      G     210          2.331
LGA    R     212      F     211          3.115
LGA    S     213      R     212          3.634
LGA    -       -      S     213           -
LGA    V     214      V     214          2.177
LGA    P     215      P     215          1.895
LGA    F     216      F     216          1.051
LGA    L     217      L     217          1.937
LGA    Q     218      Q     218          2.698
LGA    K     219      K     219          2.395
LGA    H     220      H     220          1.612
LGA    G     221      G     221          1.650
LGA    A     222      A     222          2.623
LGA    T     223      T     223          2.032
LGA    V     224      V     224          3.280
LGA    I     225      I     225          2.518
LGA    V     226      -       -           -
LGA    D     227      V     226          3.931
LGA    T     228      D     227           #
LGA    A     229      -       -           -
LGA    E     230      -       -           -
LGA    K     231      T     228           #
LGA    -       -      A     229           -
LGA    -       -      E     230           -
LGA    -       -      K     231           -
LGA    L     232      L     232          3.403
LGA    E     233      E     233           -
LGA    E     234      E     234           -
LGA    A     235      A     235           -
LGA    I     236      I     236           -
LGA    L     237      L     237           -
LGA    G     238      G     238           -
LGA    E     239      E     239           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  141  141    5.0    110    2.67    90.00     49.415     3.975

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.912314 * X  +  -0.171329 * Y  +   0.371928 * Z  +  -3.537390
  Y_new =  -0.206891 * X  +  -0.590962 * Y  +  -0.779718 * Z  +  10.646969
  Z_new =   0.353383 * X  +  -0.788296 * Y  +   0.503696 * Z  +  37.203320 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.002215    2.139377  [ DEG:   -57.4227    122.5773 ]
  Theta =  -0.361185   -2.780408  [ DEG:   -20.6944   -159.3056 ]
  Phi   =  -2.918588    0.223005  [ DEG:  -167.2228     12.7772 ]
 
# 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: T0329TS393_2-D1                               
REMARK     2: T0329_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS393_2-D1.T0329_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  141  141   5.0  110   2.67   90.00  49.415
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS393_2-D1
PFRMAT TS
TARGET T0329
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      27.244   1.230  30.367  1.00 25.00           C
ATOM      2  CA  LYS     2      24.167   2.705  32.070  1.00 25.00           C
ATOM      3  CA  TYR     3      21.072   4.631  31.175  1.00 25.00           C
ATOM      4  CA  LYS     4      19.025   5.668  34.188  1.00 25.00           C
ATOM      5  CA  ALA     5      17.298   8.700  35.699  1.00 25.00           C
ATOM      6  CA  ALA     6      15.040  11.127  37.587  1.00 25.00           C
ATOM      7  CA  ILE     7      12.843  13.698  35.883  1.00 25.00           C
ATOM      8  CA  PHE     8       9.342  14.937  35.063  1.00 25.00           C
ATOM      9  CA  ASP     9       5.684  15.351  35.868  1.00 25.00           C
ATOM     10  CA  MET    10       2.432  13.605  35.023  1.00 25.00           C
ATOM     11  CA  ASP    11      -0.478  11.218  34.733  1.00 25.00           C
ATOM     12  CA  GLY    12      -0.653   9.912  38.340  1.00 25.00           C
ATOM     13  CA  THR    13       0.887   6.618  39.629  1.00 25.00           C
ATOM     14  CA  ILE    14       3.535   7.573  42.246  1.00 25.00           C
ATOM     15  CA  LEU    15       0.826   9.981  43.494  1.00 25.00           C
ATOM     16  CA  ASP    16      -1.633   9.084  46.226  1.00 25.00           C
ATOM    109  CA  GLY   109      -1.026  10.842  53.900  1.00 25.00           C
ATOM    110  CA  PRO   110      -1.523   7.631  51.896  1.00 25.00           C
ATOM    111  CA  PHE   111       2.103   7.466  50.806  1.00 25.00           C
ATOM    112  CA  PRO   112       3.600   5.335  53.603  1.00 25.00           C
ATOM    113  CA  GLY   113       4.874   2.498  51.330  1.00 25.00           C
ATOM    114  CA  ILE   114       5.771   4.314  48.069  1.00 25.00           C
ATOM    115  CA  LEU   115       8.957   5.881  49.503  1.00 25.00           C
ATOM    116  CA  ASP   116      10.307   2.404  50.370  1.00 25.00           C
ATOM    117  CA  LEU   117       9.547   1.196  46.817  1.00 25.00           C
ATOM    118  CA  MET   118      11.353   4.244  45.366  1.00 25.00           C
ATOM    119  CA  LYS   119      14.381   3.546  47.606  1.00 25.00           C
ATOM    120  CA  ASN   120      14.416  -0.109  46.462  1.00 25.00           C
ATOM    121  CA  LEU   121      14.270   1.010  42.802  1.00 25.00           C
ATOM    122  CA  ARG   122      17.180   3.428  43.399  1.00 25.00           C
ATOM    123  CA  GLN   123      19.209   0.621  45.034  1.00 25.00           C
ATOM    124  CA  LYS   124      22.141   1.674  42.835  1.00 25.00           C
ATOM    125  CA  GLY   125      21.036   3.420  39.595  1.00 25.00           C
ATOM    126  CA  VAL   126      17.561   2.219  38.620  1.00 25.00           C
ATOM    127  CA  LYS   127      14.529   4.510  38.910  1.00 25.00           C
ATOM    128  CA  LEU   128      12.463   6.879  36.820  1.00 25.00           C
ATOM    129  CA  ALA   129       9.826   9.048  35.238  1.00 25.00           C
ATOM    130  CA  VAL   130       9.062  11.297  38.190  1.00 25.00           C
ATOM    131  CA  VAL   131       5.551  11.511  39.551  1.00 25.00           C
ATOM    132  CA  SER   132       2.428  13.677  40.124  1.00 25.00           C
ATOM    133  CA  ASN   133      -0.642  14.896  38.168  1.00 25.00           C
ATOM    134  CA  LYS   134       1.438  17.850  36.976  1.00 25.00           C
ATOM    135  CA  PRO   135       1.795  21.606  37.645  1.00 25.00           C
ATOM    136  CA  ASN   136       0.572  23.335  40.814  1.00 25.00           C
ATOM    137  CA  GLU   137       2.409  23.706  44.153  1.00 25.00           C
ATOM    138  CA  ALA   138       1.083  20.299  45.290  1.00 25.00           C
ATOM    139  CA  VAL   139       2.250  18.718  42.003  1.00 25.00           C
ATOM    140  CA  GLN   140       5.717  20.284  42.455  1.00 25.00           C
ATOM    141  CA  VAL   141       5.890  18.929  46.032  1.00 25.00           C
ATOM    142  CA  LEU   142       4.908  15.443  44.785  1.00 25.00           C
ATOM    143  CA  VAL   143       7.621  15.617  42.089  1.00 25.00           C
ATOM    144  CA  GLU   144      10.206  16.650  44.719  1.00 25.00           C
ATOM    145  CA  GLU   145       9.140  13.726  46.950  1.00 25.00           C
ATOM    146  CA  LEU   146       9.471  11.316  43.992  1.00 25.00           C
ATOM    147  CA  PHE   147      12.967  12.686  43.236  1.00 25.00           C
ATOM    148  CA  PRO   148      13.967  12.228  46.905  1.00 25.00           C
ATOM    149  CA  GLY   149      12.669   8.626  46.834  1.00 25.00           C
ATOM    150  CA  SER   150      14.665   7.943  43.638  1.00 25.00           C
ATOM    151  CA  PHE   151      11.491   7.998  41.593  1.00 25.00           C
ATOM    152  CA  ASP   152       8.258   6.671  39.969  1.00 25.00           C
ATOM    153  CA  PHE   153       5.708   6.836  37.160  1.00 25.00           C
ATOM    154  CA  ALA   154       4.254   9.423  34.772  1.00 25.00           C
ATOM    155  CA  LEU   155       5.984  11.563  32.074  1.00 25.00           C
ATOM    156  CA  GLY   156       4.330  14.806  30.945  1.00 25.00           C
ATOM    163  CA  ARG   163      -1.902  17.428  27.835  1.00 25.00           C
ATOM    164  CA  LYS   164      -0.318  14.013  28.273  1.00 25.00           C
ATOM    165  CA  PRO   165       0.232  12.594  24.746  1.00 25.00           C
ATOM    166  CA  ALA   166       3.087  12.290  22.190  1.00 25.00           C
ATOM    167  CA  PRO   167       6.260  10.861  23.643  1.00 25.00           C
ATOM    168  CA  ASP   168       7.525  14.475  23.590  1.00 25.00           C
ATOM    169  CA  MET   169       7.046  14.724  27.381  1.00 25.00           C
ATOM    170  CA  THR   170       8.975  11.451  27.864  1.00 25.00           C
ATOM    171  CA  SER   171      11.811  12.767  25.652  1.00 25.00           C
ATOM    172  CA  GLU   172      11.925  16.011  27.684  1.00 25.00           C
ATOM    173  CA  CYS   173      12.077  13.996  30.938  1.00 25.00           C
ATOM    174  CA  VAL   174      14.937  11.880  29.522  1.00 25.00           C
ATOM    175  CA  LYS   175      16.819  15.057  28.507  1.00 25.00           C
ATOM    176  CA  VAL   176      16.331  16.498  32.022  1.00 25.00           C
ATOM    177  CA  LEU   177      17.647  13.248  33.563  1.00 25.00           C
ATOM    178  CA  GLY   178      20.953  13.808  31.712  1.00 25.00           C
ATOM    179  CA  VAL   179      20.206  10.526  30.011  1.00 25.00           C
ATOM    180  CA  PRO   180      18.357   9.117  27.022  1.00 25.00           C
ATOM    181  CA  ARG   181      16.504   7.063  29.657  1.00 25.00           C
ATOM    182  CA  ASP   182      17.246   3.921  27.596  1.00 25.00           C
ATOM    183  CA  LYS   183      15.792   1.724  30.375  1.00 25.00           C
ATOM    184  CA  CYS   184      14.215   3.045  33.614  1.00 25.00           C
ATOM    185  CA  VAL   185      10.445   3.651  33.316  1.00 25.00           C
ATOM    186  CA  TYR   186       7.090   5.221  32.434  1.00 25.00           C
ATOM    187  CA  ILE   187       3.688   3.913  33.578  1.00 25.00           C
ATOM    188  CA  GLY   188       0.591   2.447  35.357  1.00 25.00           C
ATOM    189  CA  ASP   189      -0.628   6.061  35.137  1.00 25.00           C
ATOM    190  CA  SER   190      -3.669   5.942  32.823  1.00 25.00           C
ATOM    191  CA  GLU   191      -4.414   5.995  29.093  1.00 25.00           C
ATOM    192  CA  ILE   192      -2.097   8.981  28.471  1.00 25.00           C
ATOM    193  CA  ASP   193       0.698   7.254  30.438  1.00 25.00           C
ATOM    194  CA  ILE   194       0.200   4.059  28.387  1.00 25.00           C
ATOM    195  CA  GLN   195       0.367   6.086  25.142  1.00 25.00           C
ATOM    196  CA  THR   196       3.596   7.768  26.330  1.00 25.00           C
ATOM    197  CA  ALA   197       5.097   4.347  27.172  1.00 25.00           C
ATOM    198  CA  ARG   198       4.136   3.043  23.702  1.00 25.00           C
ATOM    199  CA  ASN   199       5.759   6.109  22.075  1.00 25.00           C
ATOM    200  CA  SER   200       9.050   6.595  23.917  1.00 25.00           C
ATOM    201  CA  GLU   201      12.426   4.981  24.413  1.00 25.00           C
ATOM    202  CA  MET   202      11.945   3.903  27.982  1.00 25.00           C
ATOM    203  CA  ASP   203      10.543   0.421  27.118  1.00 25.00           C
ATOM    204  CA  GLU   204       8.144   0.666  30.004  1.00 25.00           C
ATOM    205  CA  ILE   205       7.042  -0.193  33.538  1.00 25.00           C
ATOM    206  CA  ALA   206       4.515  -0.328  36.398  1.00 25.00           C
ATOM    207  CA  VAL   207       4.222   2.393  38.942  1.00 25.00           C
ATOM    208  CA  ASN   208       1.562   1.650  41.522  1.00 25.00           C
ATOM    209  CA  TRP   209       0.075  -1.191  39.518  1.00 25.00           C
ATOM    210  CA  GLY   210      -3.236   0.311  40.741  1.00 25.00           C
ATOM    211  CA  PHE   211      -3.667   3.282  38.424  1.00 25.00           C
ATOM    212  CA  ARG   212      -6.996   1.960  37.144  1.00 25.00           C
ATOM    213  CA  SER   213      -9.374  -0.870  37.769  1.00 25.00           C
ATOM    214  CA  VAL   214      -6.786  -3.478  36.994  1.00 25.00           C
ATOM    215  CA  PRO   215      -8.269  -5.288  33.962  1.00 25.00           C
ATOM    216  CA  PHE   216      -8.726  -1.941  32.156  1.00 25.00           C
ATOM    217  CA  LEU   217      -5.093  -1.003  32.926  1.00 25.00           C
ATOM    218  CA  GLN   218      -3.907  -4.384  31.575  1.00 25.00           C
ATOM    219  CA  LYS   219      -5.960  -3.857  28.385  1.00 25.00           C
ATOM    220  CA  HIS   220      -5.790  -1.853  25.158  1.00 25.00           C
ATOM    221  CA  GLY   221      -2.096  -0.957  25.181  1.00 25.00           C
ATOM    222  CA  ALA   222       0.680  -3.056  26.742  1.00 25.00           C
ATOM    223  CA  THR   223       3.068  -5.889  27.298  1.00 25.00           C
ATOM    224  CA  VAL   224       4.364  -3.796  30.184  1.00 25.00           C
ATOM    225  CA  ILE   225       1.994  -4.873  33.009  1.00 25.00           C
ATOM    226  CA  VAL   226      -0.211  -4.999  36.160  1.00 25.00           C
ATOM    227  CA  ASP   227       0.483  -8.604  37.150  1.00 25.00           C
ATOM    228  CA  THR   228       3.907 -10.148  37.730  1.00 25.00           C
ATOM    229  CA  ALA   229       7.131  -8.265  38.285  1.00 25.00           C
ATOM    230  CA  GLU   230       7.080 -10.137  41.625  1.00 25.00           C
ATOM    231  CA  LYS   231       7.465  -6.828  43.514  1.00 25.00           C
ATOM    232  CA  LEU   232       4.581  -5.315  41.500  1.00 25.00           C
ATOM    233  CA  GLU   233       2.397  -8.359  42.291  1.00 25.00           C
ATOM    234  CA  GLU   234       3.238  -8.024  46.014  1.00 25.00           C
ATOM    235  CA  ALA   235       2.329  -4.305  45.910  1.00 25.00           C
ATOM    236  CA  ILE   236      -0.998  -5.141  44.206  1.00 25.00           C
ATOM    237  CA  LEU   237      -2.614  -3.585  47.267  1.00 25.00           C
ATOM    238  CA  GLY   238      -5.981  -1.926  47.870  1.00 25.00           C
ATOM    239  CA  GLU   239      -9.391  -0.609  46.819  1.00 25.00           C
TER
END
