
#######################################################
#                                                     #
#                        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  142 (  142),  selected  142 , name T0378TS393_3-D2
# Molecule2: number of CA atoms  142 ( 1079),  selected  142 , name T0378_D2.pdb
# PARAMETERS: T0378TS393_3-D2.T0378_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     100      G     100          1.317
LGA    L     101      L     101          0.755
LGA    T     102      T     102          1.314
LGA    L     103      L     103          2.736
LGA    L     104      L     104          3.962
LGA    L     105      L     105          1.089
LGA    D     106      D     106          1.229
LGA    G     107      G     107          1.038
LGA    V     108      V     108          1.223
LGA    Q     109      Q     109          1.944
LGA    D     110      D     110          1.162
LGA    P     111      P     111          0.964
LGA    G     112      G     112          1.076
LGA    N     113      N     113          0.862
LGA    V     114      V     114          0.914
LGA    G     115      G     115          1.034
LGA    T     116      T     116          1.088
LGA    I     117      I     117          1.030
LGA    L     118      L     118          1.053
LGA    R     119      R     119          0.982
LGA    T     120      T     120          1.073
LGA    A     121      A     121          1.076
LGA    D     122      D     122          0.917
LGA    W     123      W     123          1.146
LGA    F     124      F     124          1.154
LGA    G     125      G     125          1.518
LGA    I     126      I     126          1.467
LGA    R     127      R     127          1.517
LGA    H     128      H     128          1.063
LGA    V     129      V     129          0.879
LGA    W     130      W     130          1.083
LGA    L     131      L     131          0.831
LGA    G     132      G     132          0.508
LGA    T     133      T     133          2.779
LGA    G     134      G     134          2.630
LGA    S     135      S     135          3.850
LGA    A     136      A     136          3.088
LGA    D     137      D     137          2.994
LGA    V     138      V     138          2.738
LGA    F     139      F     139          3.861
LGA    S     140      S     140          2.242
LGA    P     141      P     141          1.292
LGA    K     142      K     142          1.166
LGA    V     143      V     143          1.015
LGA    V     144      V     144          0.794
LGA    Q     145      Q     145          1.131
LGA    A     146      A     146          1.592
LGA    S     147      S     147          1.296
LGA    M     148      M     148          0.496
LGA    G     149      G     149          0.773
LGA    A     150      A     150          2.581
LGA    L     151      L     151          1.128
LGA    A     152      A     152          3.718
LGA    R     153      R     153          1.644
LGA    V     154      V     154          1.614
LGA    Q     155      Q     155          3.466
LGA    P     156      P     156          2.105
LGA    T     157      T     157          1.120
LGA    P     158      P     158          1.265
LGA    L     159      L     159          1.189
LGA    K     160      K     160          1.130
LGA    N     161      N     161          1.048
LGA    T     162      T     162          1.059
LGA    V     163      V     163          2.064
LGA    D     164      D     164          2.352
LGA    T     165      T     165          1.586
LGA    L     166      L     166          1.300
LGA    A     167      A     167          3.805
LGA    Y     168      Y     168          4.210
LGA    F     169      F     169          2.355
LGA    R     170      R     170          3.672
LGA    R     171      R     171           #
LGA    Q     172      Q     172          3.321
LGA    G     173      G     173          4.299
LGA    I     174      I     174          1.183
LGA    P     175      P     175          0.948
LGA    V     176      V     176          1.091
LGA    Y     177      Y     177          1.135
LGA    G     178      G     178          0.962
LGA    A     179      A     179          1.381
LGA    F     180      F     180          4.018
LGA    L     181      L     181          5.469
LGA    D     182      -       -           -
LGA    G     183      -       -           -
LGA    Q     184      D     182          4.573
LGA    S     185      G     183          1.818
LGA    L     186      Q     184          1.356
LGA    Y     187      S     185          4.154
LGA    E     188      L     186          0.711
LGA    A     189      Y     187          1.104
LGA    P     190      E     188          2.145
LGA    L     191      A     189          1.800
LGA    P     192      P     190          2.178
LGA    N     193      L     191          2.947
LGA    F     194      P     192          3.628
LGA    T     195      N     193          3.478
LGA    -       -      F     194           -
LGA    -       -      T     195           -
LGA    E     196      E     196          4.532
LGA    P     197      P     197          2.868
LGA    A     198      A     198          1.350
LGA    I     199      I     199          1.961
LGA    L     200      L     200          2.002
LGA    V     201      V     201          2.061
LGA    L     202      L     202          1.569
LGA    G     203      G     203          3.120
LGA    S     204      S     204          0.819
LGA    E     205      E     205          2.983
LGA    G     206      G     206          0.936
LGA    R     207      R     207          1.337
LGA    G     208      G     208          0.821
LGA    I     209      I     209          0.624
LGA    S     210      S     210          1.319
LGA    P     211      P     211          2.068
LGA    E     212      E     212          3.013
LGA    V     213      V     213          2.831
LGA    A     214      A     214          1.572
LGA    A     215      A     215          1.363
LGA    E     216      E     216          1.896
LGA    I     217      I     217          1.288
LGA    T     218      T     218          2.803
LGA    D     219      D     219          4.368
LGA    R     220      R     220          4.196
LGA    L     221      L     221          3.833
LGA    T     222      T     222          4.420
LGA    I     223      I     223           #
LGA    L     237      L     237          2.253
LGA    N     238      N     238          2.482
LGA    V     239      V     239          2.318
LGA    A     240      A     240          2.017
LGA    I     241      I     241          0.908
LGA    A     242      A     242          1.213
LGA    T     243      T     243          1.512
LGA    A     244      A     244          0.649
LGA    I     245      I     245          1.019
LGA    L     246      L     246          1.817
LGA    C     247      C     247          1.078
LGA    S     248      S     248          1.234
LGA    E     249      E     249          2.622
LGA    W     250      W     250          2.079
LGA    R     251      R     251          1.092
LGA    R     252      R     252          3.271
LGA    R     253      R     253          2.653
LGA    S     254      S     254          2.578

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  142  142    5.0    138    2.24    92.03     68.513     5.907

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.959958 * X  +  -0.278242 * Y  +  -0.032600 * Z  +  20.339151
  Y_new =   0.079748 * X  +  -0.159861 * Y  +  -0.983913 * Z  +   9.149332
  Z_new =   0.268555 * X  +  -0.947115 * Y  +   0.175649 * Z  +  45.290237 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.387423    1.754170  [ DEG:   -79.4935    100.5065 ]
  Theta =  -0.271892   -2.869701  [ DEG:   -15.5783   -164.4217 ]
  Phi   =   3.058708   -0.082885  [ DEG:   175.2511     -4.7489 ]
 
# 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: T0378TS393_3-D2                               
REMARK     2: T0378_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS393_3-D2.T0378_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  142  142   5.0  138   2.24   92.03  68.513
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS393_3-D2
PFRMAT TS
TARGET T0378
MODEL 3
PARENT N/A
ATOM    100  CA  GLY   100      19.062  -6.707  47.298  1.00 25.00           C
ATOM    101  CA  LEU   101      21.045  -4.348  45.142  1.00 25.00           C
ATOM    102  CA  THR   102      21.567  -0.706  46.093  1.00 25.00           C
ATOM    103  CA  LEU   103      21.914   1.299  42.862  1.00 25.00           C
ATOM    104  CA  LEU   104      23.961   4.415  43.108  1.00 25.00           C
ATOM    105  CA  LEU   105      26.600   7.120  43.093  1.00 25.00           C
ATOM    106  CA  ASP   106      30.250   8.069  43.361  1.00 25.00           C
ATOM    107  CA  GLY   107      30.930  11.674  42.244  1.00 25.00           C
ATOM    108  CA  VAL   108      27.553  12.057  40.562  1.00 25.00           C
ATOM    109  CA  GLN   109      28.406  15.206  38.606  1.00 25.00           C
ATOM    110  CA  ASP   110      25.185  15.468  36.705  1.00 25.00           C
ATOM    111  CA  PRO   111      22.224  15.266  39.006  1.00 25.00           C
ATOM    112  CA  GLY   112      20.346  13.941  35.942  1.00 25.00           C
ATOM    113  CA  ASN   113      22.463  10.750  35.995  1.00 25.00           C
ATOM    114  CA  VAL   114      21.721  10.290  39.724  1.00 25.00           C
ATOM    115  CA  GLY   115      17.977  10.747  39.060  1.00 25.00           C
ATOM    116  CA  THR   116      18.134   8.153  36.246  1.00 25.00           C
ATOM    117  CA  ILE   117      19.939   5.704  38.571  1.00 25.00           C
ATOM    118  CA  LEU   118      17.269   6.252  41.261  1.00 25.00           C
ATOM    119  CA  ARG   119      14.507   5.617  38.685  1.00 25.00           C
ATOM    120  CA  THR   120      16.251   2.394  37.573  1.00 25.00           C
ATOM    121  CA  ALA   121      16.523   1.255  41.220  1.00 25.00           C
ATOM    122  CA  ASP   122      12.799   1.980  41.749  1.00 25.00           C
ATOM    123  CA  TRP   123      11.936  -0.027  38.604  1.00 25.00           C
ATOM    124  CA  PHE   124      13.764  -3.330  39.055  1.00 25.00           C
ATOM    125  CA  GLY   125      14.340  -2.970  42.795  1.00 25.00           C
ATOM    126  CA  ILE   126      16.266  -1.341  45.657  1.00 25.00           C
ATOM    127  CA  ARG   127      15.557  -0.533  49.247  1.00 25.00           C
ATOM    128  CA  HIS   128      17.985   2.368  49.547  1.00 25.00           C
ATOM    129  CA  VAL   129      21.002   3.696  47.575  1.00 25.00           C
ATOM    130  CA  TRP   130      24.495   4.896  48.657  1.00 25.00           C
ATOM    131  CA  LEU   131      25.814   8.257  47.466  1.00 25.00           C
ATOM    132  CA  GLY   132      29.486   8.851  48.250  1.00 25.00           C
ATOM    133  CA  THR   133      30.333  11.599  50.695  1.00 25.00           C
ATOM    134  CA  GLY   134      31.994  13.339  47.759  1.00 25.00           C
ATOM    135  CA  SER   135      30.573  15.794  45.226  1.00 25.00           C
ATOM    136  CA  ALA   136      27.116  14.242  45.142  1.00 25.00           C
ATOM    137  CA  ASP   137      24.545  16.967  44.539  1.00 25.00           C
ATOM    138  CA  VAL   138      21.787  14.972  46.336  1.00 25.00           C
ATOM    139  CA  PHE   139      20.510  18.237  47.809  1.00 25.00           C
ATOM    140  CA  SER   140      19.653  18.964  44.164  1.00 25.00           C
ATOM    141  CA  PRO   141      16.121  20.093  43.407  1.00 25.00           C
ATOM    142  CA  LYS   142      16.861  18.700  39.917  1.00 25.00           C
ATOM    143  CA  VAL   143      17.391  15.207  41.397  1.00 25.00           C
ATOM    144  CA  VAL   144      14.069  15.476  43.285  1.00 25.00           C
ATOM    145  CA  GLN   145      12.294  16.537  40.062  1.00 25.00           C
ATOM    146  CA  ALA   146      13.834  13.562  38.206  1.00 25.00           C
ATOM    147  CA  SER   147      12.677  11.197  40.986  1.00 25.00           C
ATOM    148  CA  MET   148       9.673  10.313  38.779  1.00 25.00           C
ATOM    149  CA  GLY   149       7.759   9.527  41.971  1.00 25.00           C
ATOM    150  CA  ALA   150       9.364   6.810  44.076  1.00 25.00           C
ATOM    151  CA  LEU   151      12.390   8.770  45.370  1.00 25.00           C
ATOM    152  CA  ALA   152      12.028   7.111  48.802  1.00 25.00           C
ATOM    153  CA  ARG   153      11.790   3.605  47.520  1.00 25.00           C
ATOM    154  CA  VAL   154      14.985   4.433  45.658  1.00 25.00           C
ATOM    155  CA  GLN   155      17.151   6.993  47.374  1.00 25.00           C
ATOM    156  CA  PRO   156      20.401   8.687  48.604  1.00 25.00           C
ATOM    157  CA  THR   157      22.473   8.649  51.756  1.00 25.00           C
ATOM    158  CA  PRO   158      24.597  11.556  52.801  1.00 25.00           C
ATOM    159  CA  LEU   159      27.438   9.551  54.450  1.00 25.00           C
ATOM    160  CA  LYS   160      30.774  10.648  55.951  1.00 25.00           C
ATOM    161  CA  ASN   161      33.477   8.295  54.559  1.00 25.00           C
ATOM    162  CA  THR   162      33.081   5.454  52.127  1.00 25.00           C
ATOM    163  CA  VAL   163      35.162   3.231  54.448  1.00 25.00           C
ATOM    164  CA  ASP   164      32.509   3.566  57.189  1.00 25.00           C
ATOM    165  CA  THR   165      29.768   2.623  54.686  1.00 25.00           C
ATOM    166  CA  LEU   166      31.792  -0.435  53.584  1.00 25.00           C
ATOM    167  CA  ALA   167      32.248  -1.481  57.240  1.00 25.00           C
ATOM    168  CA  TYR   168      28.485  -1.109  57.842  1.00 25.00           C
ATOM    169  CA  PHE   169      27.755  -3.243  54.747  1.00 25.00           C
ATOM    170  CA  ARG   170      30.191  -5.924  55.990  1.00 25.00           C
ATOM    171  CA  ARG   171      28.494  -5.909  59.424  1.00 25.00           C
ATOM    172  CA  GLN   172      27.699  -9.486  58.592  1.00 25.00           C
ATOM    173  CA  GLY   173      26.566  -9.829  54.935  1.00 25.00           C
ATOM    174  CA  ILE   174      27.583  -7.610  52.006  1.00 25.00           C
ATOM    175  CA  PRO   175      29.802  -7.546  48.916  1.00 25.00           C
ATOM    176  CA  VAL   176      30.550  -4.998  46.215  1.00 25.00           C
ATOM    177  CA  TYR   177      30.477  -4.264  42.478  1.00 25.00           C
ATOM    178  CA  GLY   178      32.654  -1.252  41.897  1.00 25.00           C
ATOM    179  CA  ALA   179      31.073  -0.266  38.646  1.00 25.00           C
ATOM    180  CA  PHE   180      31.951   1.732  35.539  1.00 25.00           C
ATOM    181  CA  LEU   181      31.575  -1.673  33.788  1.00 25.00           C
ATOM    182  CA  ASP   182      32.837  -4.816  32.092  1.00 25.00           C
ATOM    183  CA  GLY   183      33.895  -6.639  28.914  1.00 25.00           C
ATOM    184  CA  GLN   184      37.348  -6.522  30.501  1.00 25.00           C
ATOM    185  CA  SER   185      36.531  -7.342  34.126  1.00 25.00           C
ATOM    186  CA  LEU   186      34.789 -10.584  34.840  1.00 25.00           C
ATOM    187  CA  TYR   187      31.941  -8.493  36.262  1.00 25.00           C
ATOM    188  CA  GLU   188      29.137  -9.273  33.743  1.00 25.00           C
ATOM    189  CA  ALA   189      26.881 -11.984  32.249  1.00 25.00           C
ATOM    190  CA  PRO   190      28.629 -14.646  34.377  1.00 25.00           C
ATOM    191  CA  LEU   191      28.654 -13.029  37.772  1.00 25.00           C
ATOM    192  CA  PRO   192      25.781 -15.192  38.950  1.00 25.00           C
ATOM    193  CA  ASN   193      27.186 -14.479  42.409  1.00 25.00           C
ATOM    194  CA  PHE   194      25.858 -11.006  41.728  1.00 25.00           C
ATOM    195  CA  THR   195      23.157 -11.992  44.111  1.00 25.00           C
ATOM    196  CA  GLU   196      24.264 -12.717  47.645  1.00 25.00           C
ATOM    197  CA  PRO   197      24.286  -8.927  47.975  1.00 25.00           C
ATOM    198  CA  ALA   198      25.252  -5.227  47.842  1.00 25.00           C
ATOM    199  CA  ILE   199      26.187  -2.338  45.483  1.00 25.00           C
ATOM    200  CA  LEU   200      27.700  -0.096  42.810  1.00 25.00           C
ATOM    201  CA  VAL   201      29.850   3.042  42.696  1.00 25.00           C
ATOM    202  CA  LEU   202      28.320   3.950  39.340  1.00 25.00           C
ATOM    203  CA  GLY   203      29.308   7.450  38.153  1.00 25.00           C
ATOM    204  CA  SER   204      32.142   9.887  37.630  1.00 25.00           C
ATOM    205  CA  GLU   205      31.550  11.377  34.193  1.00 25.00           C
ATOM    206  CA  GLY   206      35.196  12.473  34.075  1.00 25.00           C
ATOM    207  CA  ARG   207      36.760   9.401  35.769  1.00 25.00           C
ATOM    208  CA  GLY   208      35.544   6.094  37.099  1.00 25.00           C
ATOM    209  CA  ILE   209      35.431   4.821  40.677  1.00 25.00           C
ATOM    210  CA  SER   210      38.619   5.703  42.630  1.00 25.00           C
ATOM    211  CA  PRO   211      40.234   4.056  45.654  1.00 25.00           C
ATOM    212  CA  GLU   212      38.675   2.572  48.823  1.00 25.00           C
ATOM    213  CA  VAL   213      35.946   0.896  46.724  1.00 25.00           C
ATOM    214  CA  ALA   214      38.604  -0.555  44.380  1.00 25.00           C
ATOM    215  CA  ALA   215      40.562  -1.891  47.389  1.00 25.00           C
ATOM    216  CA  GLU   216      37.375  -3.493  48.784  1.00 25.00           C
ATOM    217  CA  ILE   217      35.628  -4.477  45.523  1.00 25.00           C
ATOM    218  CA  THR   218      37.310  -7.517  43.972  1.00 25.00           C
ATOM    219  CA  ASP   219      37.808  -5.924  40.539  1.00 25.00           C
ATOM    220  CA  ARG   220      37.840  -2.310  39.499  1.00 25.00           C
ATOM    221  CA  LEU   221      35.439  -3.030  36.667  1.00 25.00           C
ATOM    222  CA  THR   222      35.694  -0.935  33.467  1.00 25.00           C
ATOM    223  CA  ILE   223      35.718  -1.144  29.734  1.00 25.00           C
ATOM    237  CA  LEU   237      29.704   6.875  28.872  1.00 25.00           C
ATOM    238  CA  ASN   238      27.449   9.727  30.112  1.00 25.00           C
ATOM    239  CA  VAL   239      26.172   7.954  33.232  1.00 25.00           C
ATOM    240  CA  ALA   240      22.445   7.154  32.852  1.00 25.00           C
ATOM    241  CA  ILE   241      23.277   4.317  30.418  1.00 25.00           C
ATOM    242  CA  ALA   242      25.853   2.922  32.884  1.00 25.00           C
ATOM    243  CA  THR   243      23.265   3.063  35.704  1.00 25.00           C
ATOM    244  CA  ALA   244      20.726   1.229  33.499  1.00 25.00           C
ATOM    245  CA  ILE   245      23.334  -1.455  32.687  1.00 25.00           C
ATOM    246  CA  LEU   246      24.106  -1.870  36.415  1.00 25.00           C
ATOM    247  CA  CYS   247      20.368  -2.221  37.175  1.00 25.00           C
ATOM    248  CA  SER   248      20.033  -4.865  34.424  1.00 25.00           C
ATOM    249  CA  GLU   249      23.025  -6.775  35.861  1.00 25.00           C
ATOM    250  CA  TRP   250      21.459  -6.648  39.354  1.00 25.00           C
ATOM    251  CA  ARG   251      18.149  -7.962  37.945  1.00 25.00           C
ATOM    252  CA  ARG   252      20.003 -10.812  36.183  1.00 25.00           C
ATOM    253  CA  ARG   253      21.005 -13.869  38.201  1.00 25.00           C
ATOM    254  CA  SER   254      18.789 -12.261  40.843  1.00 25.00           C
TER
END
