
#######################################################
#                                                     #
#                        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 T0324TS168_1-D1
# Molecule2: number of CA atoms  142 ( 1080),  selected  142 , name T0324_D1.pdb
# PARAMETERS: T0324TS168_1-D1.T0324_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    T       2      -       -           -
LGA    Y       3      T       2           #
LGA    -       -      Y       3           -
LGA    Q       4      Q       4          2.444
LGA    A       5      A       5          1.665
LGA    L       6      L       6          2.567
LGA    M       7      M       7          2.192
LGA    F       8      F       8          1.570
LGA    D       9      D       9          2.447
LGA    I      10      I      10          2.623
LGA    D      11      D      11          2.334
LGA    G      12      G      12          1.788
LGA    T      13      T      13          1.455
LGA    L      14      L      14          1.953
LGA    T      15      -       -           -
LGA    N      16      T      15          3.038
LGA    E      82      N      16           -
LGA    L      83      E      82           #
LGA    Y      84      L      83          2.350
LGA    -       -      Y      84           -
LGA    P      85      P      85          0.793
LGA    G      86      G      86          1.653
LGA    I      87      I      87          1.162
LGA    T      88      T      88          1.827
LGA    S      89      S      89          2.665
LGA    L      90      L      90          2.316
LGA    F      91      F      91          1.202
LGA    E      92      E      92          2.197
LGA    Q      93      Q      93          2.987
LGA    L      94      L      94          2.508
LGA    P      95      P      95          3.984
LGA    S      96      S      96          1.696
LGA    E      97      E      97          1.701
LGA    L      98      L      98          2.167
LGA    R      99      R      99          4.002
LGA    L     100      L     100          3.801
LGA    G     101      G     101          4.715
LGA    I     102      I     102          3.025
LGA    V     103      V     103          2.872
LGA    T     104      T     104          1.663
LGA    S     105      S     105          1.941
LGA    Q     106      Q     106          3.135
LGA    R     107      R     107          1.877
LGA    R     108      R     108          1.952
LGA    N     109      N     109          1.748
LGA    E     110      E     110          2.924
LGA    L     111      L     111          3.255
LGA    E     112      E     112          2.651
LGA    S     113      S     113          3.428
LGA    G     114      G     114          5.496
LGA    M     115      M     115          5.365
LGA    R     116      R     116          1.220
LGA    S     117      S     117          2.768
LGA    Y     118      Y     118          2.958
LGA    P     119      P     119          3.489
LGA    F     120      -       -           -
LGA    M     121      -       -           -
LGA    M     122      F     120          2.874
LGA    R     123      M     121          3.429
LGA    -       -      M     122           -
LGA    M     124      R     123          4.428
LGA    A     125      M     124          3.730
LGA    V     126      A     125          2.965
LGA    T     127      V     126          4.039
LGA    I     128      T     127          1.508
LGA    S     129      I     128          1.512
LGA    A     130      S     129          2.748
LGA    -       -      A     130           -
LGA    D     131      D     131          1.867
LGA    D     132      D     132          2.937
LGA    T     133      T     133          1.187
LGA    P     134      P     134          1.168
LGA    K     135      K     135          1.565
LGA    R     136      R     136          2.322
LGA    K     137      K     137          2.440
LGA    P     138      P     138          1.599
LGA    D     139      D     139          1.951
LGA    P     140      P     140           #
LGA    L     141      L     141          2.337
LGA    P     142      P     142          2.815
LGA    L     143      L     143          3.093
LGA    L     144      L     144          2.133
LGA    T     145      T     145          1.083
LGA    A     146      A     146          1.362
LGA    L     147      L     147          1.751
LGA    E     148      E     148          2.112
LGA    K     149      K     149          1.922
LGA    V     150      V     150          1.789
LGA    N     151      N     151          1.833
LGA    V     152      V     152          1.328
LGA    A     153      A     153          1.238
LGA    P     154      P     154          2.237
LGA    Q     155      Q     155          1.895
LGA    N     156      N     156          1.569
LGA    A     157      A     157          1.673
LGA    L     158      L     158          2.297
LGA    F     159      F     159          2.868
LGA    I     160      I     160          1.958
LGA    G     161      G     161          1.240
LGA    D     162      D     162          1.766
LGA    S     163      S     163          0.429
LGA    V     164      V     164          1.304
LGA    S     165      S     165          1.063
LGA    D     166      D     166          1.794
LGA    E     167      E     167          1.726
LGA    Q     168      Q     168          0.831
LGA    T     169      T     169          0.638
LGA    A     170      A     170          2.005
LGA    Q     171      Q     171          2.165
LGA    A     172      A     172          1.807
LGA    A     173      A     173          1.598
LGA    N     174      N     174          3.423
LGA    V     175      V     175          3.989
LGA    D     176      -       -           -
LGA    F     177      D     176          2.474
LGA    G     178      F     177          1.881
LGA    L     179      G     178          2.066
LGA    A     180      L     179          2.549
LGA    V     181      A     180          2.404
LGA    W     182      V     181          2.860
LGA    -       -      W     182           -
LGA    -       -      G     183           -
LGA    -       -      M     184           -
LGA    -       -      D     185           -
LGA    -       -      P     186           -
LGA    -       -      N     187           -
LGA    G     183      A     188           #
LGA    M     184      D     189          3.062
LGA    D     185      -       -           -
LGA    P     186      -       -           -
LGA    N     187      H     190          0.989
LGA    A     188      Q     191          3.105
LGA    D     189      K     192          3.076
LGA    H     190      V     193          3.218
LGA    Q     191      -       -           -
LGA    K     192      -       -           -
LGA    V     193      -       -           -
LGA    A     194      A     194          2.194
LGA    H     195      H     195          3.189
LGA    R     196      -       -           -
LGA    F     197      R     196          2.616
LGA    Q     198      F     197          5.234
LGA    K     199      Q     198          3.374
LGA    P     200      -       -           -
LGA    L     201      -       -           -
LGA    D     202      K     199          4.562
LGA    I     203      P     200           -
LGA    L     204      L     201           -
LGA    E     205      D     202           -
LGA    L     206      I     203           -
LGA    F     207      L     204           -
LGA    -       -      E     205           -
LGA    -       -      L     206           -
LGA    -       -      F     207           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  142  142    5.0    118    2.57    77.97     52.133     4.422

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.397562 * X  +  -0.818421 * Y  +  -0.414887 * Z  +  25.626759
  Y_new =   0.606428 * X  +  -0.104972 * Y  +   0.788179 * Z  +  22.008593
  Z_new =  -0.688614 * X  +  -0.564949 * Y  +   0.454581 * Z  +  20.739351 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.893232    2.248360  [ DEG:   -51.1785    128.8215 ]
  Theta =   0.759576    2.382017  [ DEG:    43.5205    136.4795 ]
  Phi   =   0.990508   -2.151084  [ DEG:    56.7519   -123.2481 ]
 
# 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: T0324TS168_1-D1                               
REMARK     2: T0324_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_1-D1.T0324_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  142  142   5.0  118   2.57   77.97  52.133
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_1-D1
PFRMAT TS
TARGET T0324
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      38.307  33.249  44.377  1.00 25.00           C
ATOM      2  CA  THR     2      36.144  31.013  42.193  1.00 25.00           C
ATOM      3  CA  TYR     3      34.093  29.358  39.418  1.00 25.00           C
ATOM      4  CA  GLN     4      32.135  29.770  36.151  1.00 25.00           C
ATOM      5  CA  ALA     5      29.852  26.754  35.875  1.00 25.00           C
ATOM      6  CA  LEU     6      28.373  26.363  32.402  1.00 25.00           C
ATOM      7  CA  MET     7      26.075  24.481  30.083  1.00 25.00           C
ATOM      8  CA  PHE     8      26.677  25.362  26.444  1.00 25.00           C
ATOM      9  CA  ASP     9      23.712  22.986  25.784  1.00 25.00           C
ATOM     10  CA  ILE    10      25.378  22.503  22.364  1.00 25.00           C
ATOM     11  CA  ASP    11      23.692  22.333  18.999  1.00 25.00           C
ATOM     12  CA  GLY    12      26.880  24.272  18.212  1.00 25.00           C
ATOM     13  CA  THR    13      29.292  26.095  20.508  1.00 25.00           C
ATOM     14  CA  LEU    14      32.231  23.939  21.671  1.00 25.00           C
ATOM     15  CA  THR    15      32.078  20.280  20.903  1.00 25.00           C
ATOM     16  CA  ASN    16      29.832  19.105  18.134  1.00 25.00           C
ATOM     82  CA  GLU    82      40.178  21.757  14.366  1.00 25.00           C
ATOM     83  CA  LEU    83      37.898  22.276  17.319  1.00 25.00           C
ATOM     84  CA  TYR    84      35.555  23.987  14.855  1.00 25.00           C
ATOM     85  CA  PRO    85      37.721  27.023  14.102  1.00 25.00           C
ATOM     86  CA  GLY    86      38.031  27.694  17.785  1.00 25.00           C
ATOM     87  CA  ILE    87      36.665  26.757  21.256  1.00 25.00           C
ATOM     88  CA  THR    88      40.288  25.944  22.192  1.00 25.00           C
ATOM     89  CA  SER    89      40.834  29.564  23.318  1.00 25.00           C
ATOM     90  CA  LEU    90      37.651  29.409  25.442  1.00 25.00           C
ATOM     91  CA  PHE    91      38.841  26.134  27.031  1.00 25.00           C
ATOM     92  CA  GLU    92      42.241  27.715  27.807  1.00 25.00           C
ATOM     93  CA  GLN    93      40.501  30.732  29.401  1.00 25.00           C
ATOM     94  CA  LEU    94      38.335  28.392  31.523  1.00 25.00           C
ATOM     95  CA  PRO    95      41.458  26.479  32.644  1.00 25.00           C
ATOM     96  CA  SER    96      41.930  25.585  36.338  1.00 25.00           C
ATOM     97  CA  GLU    97      38.537  27.123  37.296  1.00 25.00           C
ATOM     98  CA  LEU    98      35.380  25.883  35.639  1.00 25.00           C
ATOM     99  CA  ARG    99      34.402  23.479  32.780  1.00 25.00           C
ATOM    100  CA  LEU   100      34.263  26.039  29.928  1.00 25.00           C
ATOM    101  CA  GLY   101      31.661  24.248  27.910  1.00 25.00           C
ATOM    102  CA  ILE   102      29.702  21.307  26.390  1.00 25.00           C
ATOM    103  CA  VAL   103      26.514  19.341  27.046  1.00 25.00           C
ATOM    104  CA  THR   104      24.136  17.469  24.741  1.00 25.00           C
ATOM    105  CA  SER   105      20.565  18.567  25.010  1.00 25.00           C
ATOM    106  CA  GLN   106      19.673  15.217  23.489  1.00 25.00           C
ATOM    107  CA  ARG   107      21.477  12.189  24.989  1.00 25.00           C
ATOM    108  CA  ARG   108      23.503   9.893  27.276  1.00 25.00           C
ATOM    109  CA  ASN   109      25.391   8.352  24.324  1.00 25.00           C
ATOM    110  CA  GLU   110      26.016  11.840  22.870  1.00 25.00           C
ATOM    111  CA  LEU   111      27.320  13.047  26.263  1.00 25.00           C
ATOM    112  CA  GLU   112      29.651  10.016  26.473  1.00 25.00           C
ATOM    113  CA  SER   113      30.948  10.738  22.942  1.00 25.00           C
ATOM    114  CA  GLY   114      31.575  14.394  23.892  1.00 25.00           C
ATOM    115  CA  MET   115      33.471  13.279  27.028  1.00 25.00           C
ATOM    116  CA  ARG   116      35.595  10.886  24.923  1.00 25.00           C
ATOM    117  CA  SER   117      36.371  13.709  22.453  1.00 25.00           C
ATOM    118  CA  TYR   118      38.085  15.003  19.244  1.00 25.00           C
ATOM    119  CA  PRO   119      40.963  16.614  21.157  1.00 25.00           C
ATOM    120  CA  PHE   120      38.270  18.327  23.230  1.00 25.00           C
ATOM    121  CA  MET   121      40.038  16.739  26.173  1.00 25.00           C
ATOM    122  CA  MET   122      40.977  19.854  28.172  1.00 25.00           C
ATOM    123  CA  ARG   123      37.290  19.995  29.037  1.00 25.00           C
ATOM    124  CA  MET   124      34.672  17.715  30.632  1.00 25.00           C
ATOM    125  CA  ALA   125      33.673  16.580  34.174  1.00 25.00           C
ATOM    126  CA  VAL   126      30.700  18.940  34.754  1.00 25.00           C
ATOM    127  CA  THR   127      29.699  20.228  31.307  1.00 25.00           C
ATOM    128  CA  ILE   128      27.220  17.299  31.499  1.00 25.00           C
ATOM    129  CA  SER   129      23.782  16.586  30.034  1.00 25.00           C
ATOM    130  CA  ALA   130      20.581  14.876  28.868  1.00 25.00           C
ATOM    131  CA  ASP   131      20.065  11.555  30.587  1.00 25.00           C
ATOM    132  CA  ASP   132      18.455  10.817  33.907  1.00 25.00           C
ATOM    133  CA  THR   133      16.860  14.251  34.074  1.00 25.00           C
ATOM    134  CA  PRO   134      14.049  13.013  31.885  1.00 25.00           C
ATOM    135  CA  LYS   135      14.105  16.356  29.989  1.00 25.00           C
ATOM    136  CA  ARG   136      15.698  16.271  26.499  1.00 25.00           C
ATOM    137  CA  LYS   137      15.585  19.815  25.125  1.00 25.00           C
ATOM    138  CA  PRO   138      13.534  22.040  27.476  1.00 25.00           C
ATOM    139  CA  ASP   139      14.410  21.150  31.076  1.00 25.00           C
ATOM    140  CA  PRO   140      18.045  20.647  30.187  1.00 25.00           C
ATOM    141  CA  LEU   141      17.560  19.114  33.663  1.00 25.00           C
ATOM    142  CA  PRO   142      20.866  17.212  33.313  1.00 25.00           C
ATOM    143  CA  LEU   143      22.642  20.443  32.277  1.00 25.00           C
ATOM    144  CA  LEU   144      21.158  22.258  35.305  1.00 25.00           C
ATOM    145  CA  THR   145      22.336  19.434  37.608  1.00 25.00           C
ATOM    146  CA  ALA   146      25.849  19.635  36.098  1.00 25.00           C
ATOM    147  CA  LEU   147      25.890  23.427  36.639  1.00 25.00           C
ATOM    148  CA  GLU   148      24.801  22.944  40.279  1.00 25.00           C
ATOM    149  CA  LYS   149      27.577  20.357  40.793  1.00 25.00           C
ATOM    150  CA  VAL   150      30.142  22.774  39.293  1.00 25.00           C
ATOM    151  CA  ASN   151      29.787  23.957  42.943  1.00 25.00           C
ATOM    152  CA  VAL   152      28.634  27.204  41.343  1.00 25.00           C
ATOM    153  CA  ALA   153      25.107  27.753  42.666  1.00 25.00           C
ATOM    154  CA  PRO   154      24.202  28.380  38.972  1.00 25.00           C
ATOM    155  CA  GLN   155      24.689  32.092  39.776  1.00 25.00           C
ATOM    156  CA  ASN   156      28.246  31.957  38.361  1.00 25.00           C
ATOM    157  CA  ALA   157      27.810  30.815  34.751  1.00 25.00           C
ATOM    158  CA  LEU   158      27.907  32.986  31.651  1.00 25.00           C
ATOM    159  CA  PHE   159      27.285  30.362  28.988  1.00 25.00           C
ATOM    160  CA  ILE   160      28.181  29.792  25.348  1.00 25.00           C
ATOM    161  CA  GLY   161      25.511  28.841  22.846  1.00 25.00           C
ATOM    162  CA  ASP   162      23.041  27.349  20.351  1.00 25.00           C
ATOM    163  CA  SER   163      19.350  27.798  19.693  1.00 25.00           C
ATOM    164  CA  VAL   164      15.620  28.200  20.574  1.00 25.00           C
ATOM    165  CA  SER   165      14.598  25.429  23.012  1.00 25.00           C
ATOM    166  CA  ASP   166      18.204  25.178  24.278  1.00 25.00           C
ATOM    167  CA  GLU   167      18.319  28.973  24.776  1.00 25.00           C
ATOM    168  CA  GLN   168      15.018  28.844  26.713  1.00 25.00           C
ATOM    169  CA  THR   169      16.394  26.031  28.918  1.00 25.00           C
ATOM    170  CA  ALA   170      19.562  28.075  29.592  1.00 25.00           C
ATOM    171  CA  GLN   171      17.431  31.117  30.529  1.00 25.00           C
ATOM    172  CA  ALA   172      15.348  28.954  32.907  1.00 25.00           C
ATOM    173  CA  ALA   173      16.617  26.484  35.488  1.00 25.00           C
ATOM    174  CA  ASN   174      18.728  28.937  37.559  1.00 25.00           C
ATOM    175  CA  VAL   175      21.604  27.540  35.424  1.00 25.00           C
ATOM    176  CA  ASP   176      22.185  31.081  34.265  1.00 25.00           C
ATOM    177  CA  PHE   177      22.890  32.187  30.664  1.00 25.00           C
ATOM    178  CA  GLY   178      22.210  32.247  26.955  1.00 25.00           C
ATOM    179  CA  LEU   179      24.692  33.649  24.464  1.00 25.00           C
ATOM    180  CA  ALA   180      26.718  34.642  21.381  1.00 25.00           C
ATOM    181  CA  VAL   181      29.605  32.231  20.630  1.00 25.00           C
ATOM    182  CA  TRP   182      27.668  31.470  17.416  1.00 25.00           C
ATOM    183  CA  GLY   183      23.995  32.466  17.553  1.00 25.00           C
ATOM    184  CA  MET   184      21.463  34.418  19.644  1.00 25.00           C
ATOM    185  CA  ASP   185      22.041  37.368  17.221  1.00 25.00           C
ATOM    186  CA  PRO   186      19.037  39.618  16.509  1.00 25.00           C
ATOM    187  CA  ASN   187      17.086  37.460  18.989  1.00 25.00           C
ATOM    188  CA  ALA   188      15.264  39.984  21.218  1.00 25.00           C
ATOM    189  CA  ASP   189      15.195  37.442  24.082  1.00 25.00           C
ATOM    190  CA  HIS   190      18.946  36.807  23.641  1.00 25.00           C
ATOM    191  CA  GLN   191      19.617  40.578  23.716  1.00 25.00           C
ATOM    192  CA  LYS   192      17.538  40.909  26.915  1.00 25.00           C
ATOM    193  CA  VAL   193      18.725  37.794  28.745  1.00 25.00           C
ATOM    194  CA  ALA   194      21.737  39.640  30.154  1.00 25.00           C
ATOM    195  CA  HIS   195      24.101  40.625  27.381  1.00 25.00           C
ATOM    196  CA  ARG   196      24.472  38.672  24.189  1.00 25.00           C
ATOM    197  CA  PHE   197      28.295  38.767  24.637  1.00 25.00           C
ATOM    198  CA  GLN   198      31.027  41.088  23.495  1.00 25.00           C
ATOM    199  CA  LYS   199      31.759  38.783  20.564  1.00 25.00           C
ATOM    200  CA  PRO   200      29.257  40.866  18.571  1.00 25.00           C
ATOM    201  CA  LEU   201      30.673  40.667  15.019  1.00 25.00           C
ATOM    202  CA  ASP   202      30.651  36.841  15.197  1.00 25.00           C
ATOM    203  CA  ILE   203      27.014  36.895  16.394  1.00 25.00           C
ATOM    204  CA  LEU   204      26.072  39.227  13.507  1.00 25.00           C
ATOM    205  CA  GLU   205      27.808  36.889  11.019  1.00 25.00           C
ATOM    206  CA  LEU   206      25.920  33.894  12.478  1.00 25.00           C
ATOM    207  CA  PHE   207      22.610  35.798  12.165  1.00 25.00           C
TER
END
