
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  141 ( 1070),  selected  141 , name T0329_D1.pdb
# PARAMETERS: T0329TS393_3-D1.T0329_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.284
LGA    K       2      K       2          1.189
LGA    Y       3      Y       3          2.585
LGA    K       4      K       4          4.011
LGA    A       5      A       5          1.108
LGA    A       6      A       6          1.795
LGA    I       7      I       7          3.479
LGA    F       8      F       8          3.513
LGA    D       9      D       9          2.859
LGA    M      10      M      10          1.712
LGA    D      11      -       -           -
LGA    G      12      D      11          0.961
LGA    T      13      G      12          2.167
LGA    I      14      T      13          1.687
LGA    L      15      I      14          2.336
LGA    D      16      L      15          2.511
LGA    G     109      D      16           -
LGA    P     110      G     109          1.503
LGA    F     111      P     110          1.959
LGA    -       -      F     111           -
LGA    P     112      P     112          5.432
LGA    G     113      G     113          3.414
LGA    I     114      I     114          2.257
LGA    L     115      L     115          2.544
LGA    D     116      D     116          2.745
LGA    L     117      L     117          2.073
LGA    M     118      M     118          1.888
LGA    K     119      K     119          2.083
LGA    N     120      N     120          2.030
LGA    L     121      L     121          1.848
LGA    R     122      R     122          1.686
LGA    Q     123      Q     123          1.804
LGA    K     124      K     124          2.561
LGA    G     125      G     125          1.130
LGA    V     126      V     126          0.434
LGA    K     127      K     127          2.715
LGA    L     128      L     128          2.439
LGA    A     129      A     129          2.536
LGA    V     130      V     130          2.210
LGA    V     131      V     131          2.441
LGA    S     132      S     132          3.551
LGA    N     133      N     133          2.607
LGA    K     134      K     134          3.731
LGA    P     135      P     135          3.117
LGA    N     136      N     136          2.509
LGA    E     137      E     137          3.656
LGA    A     138      A     138          3.572
LGA    V     139      V     139          1.641
LGA    Q     140      Q     140          1.177
LGA    -       -      V     141           -
LGA    V     141      L     142          3.094
LGA    L     142      V     143          2.523
LGA    V     143      E     144           #
LGA    -       -      E     145           -
LGA    E     144      L     146           #
LGA    E     145      F     147          2.452
LGA    L     146      P     148           #
LGA    F     147      G     149          3.339
LGA    P     148      S     150          3.430
LGA    G     149      -       -           -
LGA    S     150      -       -           -
LGA    F     151      F     151          4.174
LGA    D     152      D     152          1.720
LGA    F     153      F     153          3.338
LGA    A     154      A     154          1.552
LGA    L     155      L     155          2.529
LGA    G     156      G     156          2.058
LGA    R     163      -       -           -
LGA    K     164      R     163          0.162
LGA    P     165      K     164          2.331
LGA    A     166      P     165          2.472
LGA    P     167      A     166          2.540
LGA    D     168      P     167          2.651
LGA    -       -      D     168           -
LGA    M     169      M     169          1.349
LGA    T     170      T     170          1.691
LGA    S     171      S     171          1.687
LGA    E     172      E     172          1.640
LGA    C     173      C     173          1.572
LGA    V     174      V     174          1.533
LGA    K     175      K     175          1.510
LGA    V     176      V     176          1.727
LGA    L     177      L     177          1.468
LGA    G     178      G     178          2.948
LGA    V     179      V     179          2.598
LGA    P     180      P     180          2.934
LGA    R     181      R     181          4.970
LGA    D     182      D     182          4.647
LGA    K     183      K     183          4.405
LGA    C     184      C     184          2.639
LGA    V     185      V     185          2.731
LGA    Y     186      Y     186          2.601
LGA    I     187      I     187          1.451
LGA    G     188      G     188          2.104
LGA    D     189      D     189          5.260
LGA    S     190      S     190          2.884
LGA    E     191      E     191          3.630
LGA    I     192      I     192          2.996
LGA    -       -      D     193           -
LGA    D     193      I     194          2.240
LGA    I     194      Q     195          2.053
LGA    Q     195      T     196          1.913
LGA    T     196      A     197          0.750
LGA    A     197      R     198          3.006
LGA    R     198      N     199          3.918
LGA    N     199      -       -           -
LGA    S     200      S     200          0.948
LGA    E     201      E     201          4.106
LGA    M     202      M     202          1.753
LGA    D     203      D     203          1.171
LGA    E     204      E     204          1.158
LGA    I     205      I     205          2.850
LGA    A     206      -       -           -
LGA    V     207      -       -           -
LGA    N     208      -       -           -
LGA    W     209      -       -           -
LGA    G     210      -       -           -
LGA    F     211      -       -           -
LGA    R     212      -       -           -
LGA    S     213      -       -           -
LGA    V     214      -       -           -
LGA    P     215      -       -           -
LGA    F     216      -       -           -
LGA    L     217      -       -           -
LGA    Q     218      -       -           -
LGA    K     219      -       -           -
LGA    H     220      -       -           -
LGA    G     221      -       -           -
LGA    A     222      -       -           -
LGA    T     223      A     206          3.214
LGA    V     224      V     207          3.439
LGA    I     225      N     208          5.202
LGA    -       -      W     209           -
LGA    -       -      G     210           -
LGA    -       -      F     211           -
LGA    -       -      R     212           -
LGA    -       -      S     213           -
LGA    -       -      V     214           -
LGA    -       -      P     215           -
LGA    -       -      F     216           -
LGA    -       -      L     217           -
LGA    -       -      Q     218           -
LGA    -       -      K     219           -
LGA    -       -      H     220           -
LGA    -       -      G     221           -
LGA    -       -      A     222           -
LGA    -       -      T     223           -
LGA    -       -      V     224           -
LGA    -       -      I     225           -
LGA    -       -      V     226           -
LGA    V     226      D     227          2.948
LGA    D     227      T     228           -
LGA    T     228      A     229           -
LGA    A     229      E     230           -
LGA    -       -      K     231           -
LGA    E     230      L     232          4.014
LGA    K     231      E     233          1.578
LGA    L     232      E     234           #
LGA    E     233      A     235           #
LGA    E     234      I     236           -
LGA    A     235      L     237           -
LGA    I     236      G     238           -
LGA    L     237      E     239           -
LGA    G     238      -       -           -
LGA    E     239      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  141  141    5.0    104    2.72    73.08     44.193     3.683

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.386402 * X  +  -0.208115 * Y  +   0.898544 * Z  +  -2.239356
  Y_new =   0.049353 * X  +  -0.968150 * Y  +  -0.245459 * Z  +  11.325053
  Z_new =   0.921009 * X  +   0.139191 * Y  +  -0.363824 * Z  +  38.809265 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.776194   -0.365399  [ DEG:   159.0642    -20.9358 ]
  Theta =  -1.170664   -1.970929  [ DEG:   -67.0741   -112.9259 ]
  Phi   =   0.127036   -3.014557  [ DEG:     7.2786   -172.7214 ]
 
# 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_3-D1                               
REMARK     2: T0329_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS393_3-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  104   2.72   73.08  44.193
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS393_3-D1
PFRMAT TS
TARGET T0329
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      20.038  -6.616  32.708  1.00 25.00           C
ATOM      2  CA  LYS     2      18.006  -3.530  31.762  1.00 25.00           C
ATOM      3  CA  TYR     3      14.995  -1.738  33.331  1.00 25.00           C
ATOM      4  CA  LYS     4      16.280   1.542  31.859  1.00 25.00           C
ATOM      5  CA  ALA     5      15.914   4.559  34.143  1.00 25.00           C
ATOM      6  CA  ALA     6      12.735   3.185  35.598  1.00 25.00           C
ATOM      7  CA  ILE     7       9.256   4.356  36.445  1.00 25.00           C
ATOM      8  CA  PHE     8       7.420   5.014  39.714  1.00 25.00           C
ATOM      9  CA  ASP     9       4.407   7.132  38.760  1.00 25.00           C
ATOM     10  CA  MET    10       3.702  10.479  40.311  1.00 25.00           C
ATOM     11  CA  ASP    11       1.521  12.972  42.265  1.00 25.00           C
ATOM     12  CA  GLY    12      -1.263  10.745  40.863  1.00 25.00           C
ATOM     13  CA  THR    13      -1.005   6.976  40.133  1.00 25.00           C
ATOM     14  CA  ILE    14       1.603   5.542  42.455  1.00 25.00           C
ATOM     15  CA  LEU    15       2.041   8.524  44.866  1.00 25.00           C
ATOM     16  CA  ASP    16      -1.480   7.559  46.042  1.00 25.00           C
ATOM    109  CA  GLY   109       1.930  11.896  53.653  1.00 25.00           C
ATOM    110  CA  PRO   110       1.123  10.715  50.120  1.00 25.00           C
ATOM    111  CA  PHE   111       0.886   6.973  50.563  1.00 25.00           C
ATOM    112  CA  PRO   112       3.267   6.092  53.461  1.00 25.00           C
ATOM    113  CA  GLY   113       4.177   3.191  51.186  1.00 25.00           C
ATOM    114  CA  ILE   114       4.729   4.865  47.811  1.00 25.00           C
ATOM    115  CA  LEU   115       7.480   7.103  49.256  1.00 25.00           C
ATOM    116  CA  ASP   116       9.194   4.044  50.794  1.00 25.00           C
ATOM    117  CA  LEU   117       9.020   2.223  47.429  1.00 25.00           C
ATOM    118  CA  MET   118      10.537   5.270  45.674  1.00 25.00           C
ATOM    119  CA  LYS   119      13.357   5.387  48.264  1.00 25.00           C
ATOM    120  CA  ASN   120      14.032   1.655  47.734  1.00 25.00           C
ATOM    121  CA  LEU   121      14.150   2.189  43.944  1.00 25.00           C
ATOM    122  CA  ARG   122      16.607   5.090  44.404  1.00 25.00           C
ATOM    123  CA  GLN   123      18.807   2.904  46.650  1.00 25.00           C
ATOM    124  CA  LYS   124      21.536   2.449  43.965  1.00 25.00           C
ATOM    125  CA  GLY   125      22.268   4.048  40.584  1.00 25.00           C
ATOM    126  CA  VAL   126      18.611   3.926  39.611  1.00 25.00           C
ATOM    127  CA  LYS   127      15.451   5.911  38.952  1.00 25.00           C
ATOM    128  CA  LEU   128      12.003   7.199  39.866  1.00 25.00           C
ATOM    129  CA  ALA   129      11.426   8.862  36.520  1.00 25.00           C
ATOM    130  CA  VAL   130       8.067   9.821  38.050  1.00 25.00           C
ATOM    131  CA  VAL   131       5.438  10.936  35.578  1.00 25.00           C
ATOM    132  CA  SER   132       2.407  11.102  33.207  1.00 25.00           C
ATOM    133  CA  ASN   133       1.821  14.847  33.152  1.00 25.00           C
ATOM    134  CA  LYS   134       1.762  14.817  36.993  1.00 25.00           C
ATOM    135  CA  PRO   135       1.240  18.409  38.261  1.00 25.00           C
ATOM    136  CA  ASN   136       1.842  21.615  40.154  1.00 25.00           C
ATOM    137  CA  GLU   137       2.555  21.518  43.915  1.00 25.00           C
ATOM    138  CA  ALA   138       2.183  17.706  43.913  1.00 25.00           C
ATOM    139  CA  VAL   139       4.591  17.449  40.946  1.00 25.00           C
ATOM    140  CA  GLN   140       7.118  19.672  42.773  1.00 25.00           C
ATOM    141  CA  VAL   141       6.824  17.480  45.899  1.00 25.00           C
ATOM    142  CA  LEU   142       7.391  14.341  43.780  1.00 25.00           C
ATOM    143  CA  VAL   143      10.481  15.946  42.184  1.00 25.00           C
ATOM    144  CA  GLU   144      11.833  16.850  45.652  1.00 25.00           C
ATOM    145  CA  GLU   145      11.266  13.253  46.837  1.00 25.00           C
ATOM    146  CA  LEU   146      13.103  11.920  43.752  1.00 25.00           C
ATOM    147  CA  PHE   147      16.024  14.303  44.431  1.00 25.00           C
ATOM    148  CA  PRO   148      16.165  13.130  48.075  1.00 25.00           C
ATOM    149  CA  GLY   149      16.187   9.477  46.924  1.00 25.00           C
ATOM    150  CA  SER   150      19.031  10.240  44.475  1.00 25.00           C
ATOM    151  CA  PHE   151      17.177  10.380  41.123  1.00 25.00           C
ATOM    152  CA  ASP   152      15.332  12.736  38.830  1.00 25.00           C
ATOM    153  CA  PHE   153      11.551  12.799  39.028  1.00 25.00           C
ATOM    154  CA  ALA   154       9.608  15.529  37.192  1.00 25.00           C
ATOM    155  CA  LEU   155       6.375  15.830  35.150  1.00 25.00           C
ATOM    156  CA  GLY   156       5.376  19.506  35.551  1.00 25.00           C
ATOM    163  CA  ARG   163       0.962  16.464  24.420  1.00 25.00           C
ATOM    164  CA  LYS   164       0.350  17.263  28.057  1.00 25.00           C
ATOM    165  CA  PRO   165      -1.400  13.938  28.192  1.00 25.00           C
ATOM    166  CA  ALA   166       2.150  12.603  27.519  1.00 25.00           C
ATOM    167  CA  PRO   167       4.460  12.330  24.563  1.00 25.00           C
ATOM    168  CA  ASP   168       6.322  15.676  24.537  1.00 25.00           C
ATOM    169  CA  MET   169       6.324  15.733  28.366  1.00 25.00           C
ATOM    170  CA  THR   170       7.694  12.157  28.442  1.00 25.00           C
ATOM    171  CA  SER   171      10.448  13.134  25.967  1.00 25.00           C
ATOM    172  CA  GLU   172      11.354  16.161  28.131  1.00 25.00           C
ATOM    173  CA  CYS   173      11.518  13.924  31.235  1.00 25.00           C
ATOM    174  CA  VAL   174      13.787  11.464  29.374  1.00 25.00           C
ATOM    175  CA  LYS   175      16.067  14.346  28.296  1.00 25.00           C
ATOM    176  CA  VAL   176      16.238  15.596  31.912  1.00 25.00           C
ATOM    177  CA  LEU   177      17.131  12.071  33.114  1.00 25.00           C
ATOM    178  CA  GLY   178      20.717  13.277  32.760  1.00 25.00           C
ATOM    179  CA  VAL   179      21.246   9.869  31.117  1.00 25.00           C
ATOM    180  CA  PRO   180      20.696   8.663  27.624  1.00 25.00           C
ATOM    181  CA  ARG   181      17.799  10.121  25.683  1.00 25.00           C
ATOM    182  CA  ASP   182      16.215   6.655  25.302  1.00 25.00           C
ATOM    183  CA  LYS   183      15.987   6.315  29.110  1.00 25.00           C
ATOM    184  CA  CYS   184      12.722   6.147  31.010  1.00 25.00           C
ATOM    185  CA  VAL   185       9.213   4.617  31.246  1.00 25.00           C
ATOM    186  CA  TYR   186       6.652   6.832  32.953  1.00 25.00           C
ATOM    187  CA  ILE   187       4.542   3.980  34.323  1.00 25.00           C
ATOM    188  CA  GLY   188       1.579   6.245  34.715  1.00 25.00           C
ATOM    189  CA  ASP   189      -1.399   8.454  35.314  1.00 25.00           C
ATOM    190  CA  SER   190      -3.626   7.168  32.514  1.00 25.00           C
ATOM    191  CA  GLU   191      -3.181   7.624  28.767  1.00 25.00           C
ATOM    192  CA  ILE   192       0.354   8.105  30.161  1.00 25.00           C
ATOM    193  CA  ASP   193       0.932   4.320  30.065  1.00 25.00           C
ATOM    194  CA  ILE   194      -0.284   4.202  26.435  1.00 25.00           C
ATOM    195  CA  GLN   195       2.079   7.075  25.524  1.00 25.00           C
ATOM    196  CA  THR   196       4.994   5.243  27.202  1.00 25.00           C
ATOM    197  CA  ALA   197       4.137   2.054  25.262  1.00 25.00           C
ATOM    198  CA  ARG   198       4.039   4.041  21.989  1.00 25.00           C
ATOM    199  CA  ASN   199       7.448   5.588  22.798  1.00 25.00           C
ATOM    200  CA  SER   200       8.457   8.646  24.841  1.00 25.00           C
ATOM    201  CA  GLU   201      11.193   6.507  26.248  1.00 25.00           C
ATOM    202  CA  MET   202      11.651   2.849  27.149  1.00 25.00           C
ATOM    203  CA  ASP   203       9.735  -0.473  27.365  1.00 25.00           C
ATOM    204  CA  GLU   204       7.148   0.060  30.162  1.00 25.00           C
ATOM    205  CA  ILE   205       7.614   0.031  33.936  1.00 25.00           C
ATOM    206  CA  ALA   206       5.083  -0.484  36.724  1.00 25.00           C
ATOM    207  CA  VAL   207       3.411   2.152  38.844  1.00 25.00           C
ATOM    208  CA  ASN   208       1.224   0.474  41.452  1.00 25.00           C
ATOM    209  CA  TRP   209      -1.871  -0.493  39.466  1.00 25.00           C
ATOM    210  CA  GLY   210      -1.469   2.730  37.511  1.00 25.00           C
ATOM    211  CA  PHE   211      -4.945   3.848  38.544  1.00 25.00           C
ATOM    212  CA  ARG   212      -6.180   0.509  37.086  1.00 25.00           C
ATOM    213  CA  SER   213      -7.457  -3.021  36.475  1.00 25.00           C
ATOM    214  CA  VAL   214      -8.187  -1.655  32.989  1.00 25.00           C
ATOM    215  CA  PRO   215      -8.544  -4.198  30.148  1.00 25.00           C
ATOM    216  CA  PHE   216      -5.863  -2.354  28.128  1.00 25.00           C
ATOM    217  CA  LEU   217      -3.529  -2.370  31.164  1.00 25.00           C
ATOM    218  CA  GLN   218      -4.112  -6.127  31.624  1.00 25.00           C
ATOM    219  CA  LYS   219      -3.336  -6.726  27.921  1.00 25.00           C
ATOM    220  CA  HIS   220      -0.007  -5.704  26.439  1.00 25.00           C
ATOM    221  CA  GLY   221      -1.054  -2.020  26.503  1.00 25.00           C
ATOM    222  CA  ALA   222       2.166  -1.606  28.486  1.00 25.00           C
ATOM    223  CA  THR   223       2.743  -2.324  32.166  1.00 25.00           C
ATOM    224  CA  VAL   224       0.471  -1.149  34.896  1.00 25.00           C
ATOM    225  CA  ILE   225       1.295  -3.855  37.418  1.00 25.00           C
ATOM    226  CA  VAL   226       1.970  -6.411  40.101  1.00 25.00           C
ATOM    227  CA  ASP   227       4.305  -8.911  38.301  1.00 25.00           C
ATOM    228  CA  THR   228       7.128  -7.689  36.118  1.00 25.00           C
ATOM    229  CA  ALA   229       8.349  -4.598  37.852  1.00 25.00           C
ATOM    230  CA  GLU   230      10.072  -6.025  40.961  1.00 25.00           C
ATOM    231  CA  LYS   231       9.375  -2.778  42.868  1.00 25.00           C
ATOM    232  CA  LEU   232       5.697  -2.919  41.812  1.00 25.00           C
ATOM    233  CA  GLU   233       5.473  -6.557  42.987  1.00 25.00           C
ATOM    234  CA  GLU   234       7.031  -5.593  46.350  1.00 25.00           C
ATOM    235  CA  ALA   235       4.515  -2.730  46.722  1.00 25.00           C
ATOM    236  CA  ILE   236       1.633  -5.129  45.945  1.00 25.00           C
ATOM    237  CA  LEU   237      -1.320  -4.602  48.357  1.00 25.00           C
ATOM    238  CA  GLY   238      -4.694  -2.820  48.503  1.00 25.00           C
ATOM    239  CA  GLU   239      -5.878   0.527  47.013  1.00 25.00           C
TER
END
