
#######################################################
#                                                     #
#                        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  153 (  153),  selected  153 , name T0330TS393_2-D1
# Molecule2: number of CA atoms  153 ( 1188),  selected  153 , name T0330_D1.pdb
# PARAMETERS: T0330TS393_2-D1.T0330_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       2      S       2           -
LGA    R       3      R       3           -
LGA    T       4      T       4           -
LGA    -       -      L       5           -
LGA    L       5      V       6           #
LGA    V       6      L       7           -
LGA    L       7      -       -           -
LGA    F       8      F       8           #
LGA    D       9      D       9          3.305
LGA    I      10      I      10          2.123
LGA    D      11      D      11          2.581
LGA    G      12      G      12          1.423
LGA    T      13      T      13          3.809
LGA    L      14      L      14          2.748
LGA    L      15      L      15          4.927
LGA    K      16      K      16          4.302
LGA    T      92      -       -           -
LGA    L      93      T      92           #
LGA    L      94      L      93          1.812
LGA    E      95      L      94          3.772
LGA    G      96      E      95           #
LGA    -       -      G      96           -
LGA    V      97      V      97          2.413
LGA    R      98      R      98          1.312
LGA    E      99      E      99          1.770
LGA    L     100      L     100          2.840
LGA    L     101      L     101          2.549
LGA    D     102      D     102          1.887
LGA    A     103      A     103          2.785
LGA    L     104      L     104          4.249
LGA    S     105      S     105          4.279
LGA    S     106      S     106          2.926
LGA    R     107      R     107          3.673
LGA    S     108      S     108          1.110
LGA    D     109      D     109           #
LGA    V     110      V     110          1.953
LGA    L     111      L     111          4.437
LGA    L     112      L     112          3.318
LGA    G     113      G     113           #
LGA    L     114      L     114          3.206
LGA    L     115      L     115          3.938
LGA    T     116      T     116          2.565
LGA    G     117      G     117          1.887
LGA    N     118      N     118          2.461
LGA    F     119      F     119          2.329
LGA    E     120      E     120          2.662
LGA    A     121      A     121          2.219
LGA    S     122      S     122          4.639
LGA    G     123      G     123          4.417
LGA    R     124      R     124          3.585
LGA    H     125      H     125          5.035
LGA    -       -      K     126           -
LGA    -       -      L     127           -
LGA    K     126      K     128          4.223
LGA    L     127      L     129           -
LGA    K     128      P     130           -
LGA    L     129      -       -           -
LGA    P     130      G     131          4.125
LGA    G     131      I     132          4.019
LGA    I     132      D     133          4.317
LGA    D     133      H     134          2.937
LGA    H     134      Y     135          2.785
LGA    Y     135      F     136          1.708
LGA    -       -      P     137           -
LGA    F     136      F     138          4.278
LGA    P     137      G     139           #
LGA    F     138      -       -           -
LGA    G     139      -       -           -
LGA    A     140      -       -           -
LGA    F     141      -       -           -
LGA    A     142      -       -           -
LGA    D     143      A     140          1.164
LGA    D     144      F     141          3.617
LGA    A     145      A     142          2.512
LGA    L     146      D     143           -
LGA    -       -      D     144           -
LGA    D     147      A     145          3.438
LGA    R     148      L     146          3.434
LGA    N     149      D     147           #
LGA    E     150      -       -           -
LGA    L     151      -       -           -
LGA    P     152      R     148          2.815
LGA    H     153      N     149          2.305
LGA    I     154      E     150          1.328
LGA    A     155      L     151          1.355
LGA    L     156      P     152          2.626
LGA    E     157      H     153          1.521
LGA    R     158      I     154          2.080
LGA    A     159      A     155          3.449
LGA    R     160      L     156          3.509
LGA    R     161      E     157          3.527
LGA    M     162      R     158          5.090
LGA    T     163      A     159          1.749
LGA    G     164      R     160          1.751
LGA    -       -      R     161           -
LGA    -       -      M     162           -
LGA    -       -      T     163           -
LGA    -       -      G     164           -
LGA    A     165      A     165          4.283
LGA    N     166      N     166          3.145
LGA    Y     167      Y     167          2.831
LGA    S     168      S     168          3.410
LGA    P     169      P     169          1.907
LGA    S     170      S     170          3.100
LGA    Q     171      Q     171          3.284
LGA    I     172      I     172          3.074
LGA    V     173      V     173          3.608
LGA    I     174      I     174          2.045
LGA    I     175      I     175          2.461
LGA    G     176      G     176          3.322
LGA    D     177      D     177          1.522
LGA    T     178      T     178          1.090
LGA    E     179      E     179          1.150
LGA    H     180      H     180          0.878
LGA    D     181      D     181          1.374
LGA    I     182      I     182          1.815
LGA    R     183      R     183          1.349
LGA    C     184      C     184          1.096
LGA    A     185      A     185          1.773
LGA    R     186      R     186          1.680
LGA    E     187      E     187          1.724
LGA    L     188      L     188          2.234
LGA    D     189      D     189          3.111
LGA    A     190      A     190          3.099
LGA    R     191      -       -           -
LGA    S     192      R     191          1.910
LGA    I     193      S     192          1.358
LGA    A     194      I     193          3.937
LGA    V     195      A     194          1.478
LGA    A     196      V     195          1.115
LGA    T     197      A     196          5.155
LGA    G     198      T     197          0.331
LGA    N     199      G     198          4.080
LGA    -       -      N     199           -
LGA    F     200      F     200          2.149
LGA    T     201      T     201          1.830
LGA    M     202      M     202          2.500
LGA    E     203      E     203          4.034
LGA    -       -      E     204           -
LGA    -       -      L     205           -
LGA    E     204      A     206          1.435
LGA    L     205      R     207           #
LGA    A     206      -       -           -
LGA    R     207      H     208           #
LGA    H     208      K     209          1.480
LGA    K     209      P     210          4.190
LGA    P     210      G     211          2.189
LGA    G     211      T     212          3.295
LGA    T     212      L     213           #
LGA    L     213      -       -           -
LGA    F     214      F     214           #
LGA    K     215      K     215           #
LGA    -       -      N     216           -
LGA    N     216      F     217          1.197
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    F     217      T     220          2.915
LGA    A     218      D     221          2.035
LGA    E     219      E     222          1.880
LGA    T     220      V     223          2.037
LGA    D     221      L     224          2.334
LGA    E     222      A     225          2.915
LGA    V     223      S     226          2.929
LGA    L     224      I     227          4.436
LGA    A     225      L     228           #
LGA    S     226      -       -           -
LGA    I     227      -       -           -
LGA    L     228      T     229          4.022
LGA    T     229      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    116    2.94    61.21     42.677     3.812

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.526190 * X  +   0.278333 * Y  +   0.803527 * Z  +  16.154911
  Y_new =  -0.794702 * X  +   0.497210 * Y  +   0.348183 * Z  +  41.108170
  Z_new =  -0.302611 * X  +  -0.821774 * Y  +   0.482818 * Z  +  20.032114 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.039595    2.101997  [ DEG:   -59.5644    120.4356 ]
  Theta =   0.307431    2.834162  [ DEG:    17.6145    162.3855 ]
  Phi   =  -0.985947    2.155646  [ DEG:   -56.4906    123.5094 ]
 
# 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: T0330TS393_2-D1                               
REMARK     2: T0330_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS393_2-D1.T0330_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  153  153   5.0  116   2.94   61.21  42.677
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS393_2-D1
PFRMAT TS
TARGET T0330
MODEL 2
PARENT N/A
ATOM      2  CA  SER     2      15.476  39.742  36.272  1.00 25.00           C
ATOM      3  CA  ARG     3      18.010  42.328  35.164  1.00 25.00           C
ATOM      4  CA  THR     4      21.264  44.223  34.881  1.00 25.00           C
ATOM      5  CA  LEU     5      21.778  47.420  32.820  1.00 25.00           C
ATOM      6  CA  VAL     6      20.058  45.370  30.039  1.00 25.00           C
ATOM      7  CA  LEU     7      20.809  43.744  26.639  1.00 25.00           C
ATOM      8  CA  PHE     8      21.881  41.065  24.116  1.00 25.00           C
ATOM      9  CA  ASP     9      20.427  43.234  21.380  1.00 25.00           C
ATOM     10  CA  ILE    10      21.313  42.158  17.834  1.00 25.00           C
ATOM     11  CA  ASP    11      22.868  39.632  15.413  1.00 25.00           C
ATOM     12  CA  GLY    12      22.426  36.130  16.818  1.00 25.00           C
ATOM     13  CA  THR    13      18.987  37.504  17.836  1.00 25.00           C
ATOM     14  CA  LEU    14      16.229  40.108  18.271  1.00 25.00           C
ATOM     15  CA  LEU    15      15.841  41.044  14.608  1.00 25.00           C
ATOM     16  CA  LYS    16      18.228  38.684  12.922  1.00 25.00           C
ATOM     92  CA  THR    92       9.261  40.516  13.568  1.00 25.00           C
ATOM     93  CA  LEU    93      10.409  40.325  17.201  1.00 25.00           C
ATOM     94  CA  LEU    94      12.040  37.405  19.092  1.00 25.00           C
ATOM     95  CA  GLU    95      12.204  36.778  22.841  1.00 25.00           C
ATOM     96  CA  GLY    96      15.766  38.121  23.030  1.00 25.00           C
ATOM     97  CA  VAL    97      15.175  41.230  25.088  1.00 25.00           C
ATOM     98  CA  ARG    98      11.363  41.294  25.455  1.00 25.00           C
ATOM     99  CA  GLU    99      11.711  41.738  29.243  1.00 25.00           C
ATOM    100  CA  LEU   100      14.178  44.617  28.704  1.00 25.00           C
ATOM    101  CA  LEU   101      11.749  46.270  26.246  1.00 25.00           C
ATOM    102  CA  ASP   102       8.902  45.914  28.782  1.00 25.00           C
ATOM    103  CA  ALA   103      11.095  47.482  31.503  1.00 25.00           C
ATOM    104  CA  LEU   104      11.957  50.390  29.164  1.00 25.00           C
ATOM    105  CA  SER   105       8.240  50.910  28.400  1.00 25.00           C
ATOM    106  CA  SER   106       7.445  50.917  32.146  1.00 25.00           C
ATOM    107  CA  ARG   107      10.214  53.494  32.753  1.00 25.00           C
ATOM    108  CA  SER   108      12.580  56.111  34.061  1.00 25.00           C
ATOM    109  CA  ASP   109      13.586  56.793  30.471  1.00 25.00           C
ATOM    110  CA  VAL   110      16.319  54.202  30.310  1.00 25.00           C
ATOM    111  CA  LEU   111      18.656  51.184  29.853  1.00 25.00           C
ATOM    112  CA  LEU   112      18.098  49.127  26.661  1.00 25.00           C
ATOM    113  CA  GLY   113      17.893  46.983  23.526  1.00 25.00           C
ATOM    114  CA  LEU   114      17.848  47.496  19.728  1.00 25.00           C
ATOM    115  CA  LEU   115      20.271  47.191  16.804  1.00 25.00           C
ATOM    116  CA  THR   116      21.548  45.236  13.836  1.00 25.00           C
ATOM    117  CA  GLY   117      24.274  43.891  11.469  1.00 25.00           C
ATOM    118  CA  ASN   118      22.971  46.708   9.281  1.00 25.00           C
ATOM    119  CA  PHE   119      20.893  49.872   9.694  1.00 25.00           C
ATOM    120  CA  GLU   120      17.784  48.349  11.389  1.00 25.00           C
ATOM    121  CA  ALA   121      14.230  48.658   9.996  1.00 25.00           C
ATOM    122  CA  SER   122      13.039  45.880  12.348  1.00 25.00           C
ATOM    123  CA  GLY   123      14.680  47.657  15.318  1.00 25.00           C
ATOM    124  CA  ARG   124      12.973  50.940  14.327  1.00 25.00           C
ATOM    125  CA  HIS   125       9.599  49.143  14.094  1.00 25.00           C
ATOM    126  CA  LYS   126      10.150  47.606  17.558  1.00 25.00           C
ATOM    127  CA  LEU   127      11.006  51.058  18.980  1.00 25.00           C
ATOM    128  CA  LYS   128       7.830  52.517  17.415  1.00 25.00           C
ATOM    129  CA  LEU   129       5.750  49.680  18.928  1.00 25.00           C
ATOM    130  CA  PRO   130       4.812  46.768  21.200  1.00 25.00           C
ATOM    131  CA  GLY   131       6.643  44.416  23.536  1.00 25.00           C
ATOM    132  CA  ILE   132       9.832  46.084  22.350  1.00 25.00           C
ATOM    133  CA  ASP   133       8.529  49.448  23.521  1.00 25.00           C
ATOM    134  CA  HIS   134      10.731  52.581  23.579  1.00 25.00           C
ATOM    135  CA  TYR   135      13.766  50.497  22.526  1.00 25.00           C
ATOM    136  CA  PHE   136      16.780  52.072  20.870  1.00 25.00           C
ATOM    137  CA  PRO   137      17.583  54.660  23.554  1.00 25.00           C
ATOM    138  CA  PHE   138      20.382  52.731  25.199  1.00 25.00           C
ATOM    139  CA  GLY   139      22.409  50.791  22.559  1.00 25.00           C
ATOM    140  CA  ALA   140      23.550  47.910  20.377  1.00 25.00           C
ATOM    141  CA  PHE   141      26.512  48.171  17.943  1.00 25.00           C
ATOM    142  CA  ALA   142      24.875  49.188  14.617  1.00 25.00           C
ATOM    143  CA  ASP   143      23.307  52.546  15.320  1.00 25.00           C
ATOM    144  CA  ASP   144      24.730  54.144  12.142  1.00 25.00           C
ATOM    145  CA  ALA   145      25.853  51.397   9.815  1.00 25.00           C
ATOM    146  CA  LEU   146      29.039  49.369  10.082  1.00 25.00           C
ATOM    147  CA  ASP   147      30.988  51.260   7.395  1.00 25.00           C
ATOM    148  CA  ARG   148      32.162  47.626   7.045  1.00 25.00           C
ATOM    149  CA  ASN   149      31.296  44.183   8.482  1.00 25.00           C
ATOM    150  CA  GLU   150      33.765  44.891  11.292  1.00 25.00           C
ATOM    151  CA  LEU   151      36.056  47.810  12.203  1.00 25.00           C
ATOM    152  CA  PRO   152      33.112  48.987  14.405  1.00 25.00           C
ATOM    153  CA  HIS   153      34.204  52.637  14.121  1.00 25.00           C
ATOM    154  CA  ILE   154      31.396  55.029  13.094  1.00 25.00           C
ATOM    155  CA  ALA   155      28.774  52.496  14.267  1.00 25.00           C
ATOM    156  CA  LEU   156      30.591  52.131  17.618  1.00 25.00           C
ATOM    157  CA  GLU   157      30.680  55.938  18.014  1.00 25.00           C
ATOM    158  CA  ARG   158      26.929  56.128  17.256  1.00 25.00           C
ATOM    159  CA  ALA   159      26.241  53.402  19.855  1.00 25.00           C
ATOM    160  CA  ARG   160      28.327  55.306  22.441  1.00 25.00           C
ATOM    161  CA  ARG   161      26.389  58.518  21.676  1.00 25.00           C
ATOM    162  CA  MET   162      23.074  56.646  22.088  1.00 25.00           C
ATOM    163  CA  THR   163      21.735  60.132  21.273  1.00 25.00           C
ATOM    164  CA  GLY   164      23.016  61.342  24.644  1.00 25.00           C
ATOM    165  CA  ALA   165      21.696  59.753  27.838  1.00 25.00           C
ATOM    166  CA  ASN   166      25.088  60.747  29.162  1.00 25.00           C
ATOM    167  CA  TYR   167      26.532  57.627  27.641  1.00 25.00           C
ATOM    168  CA  SER   168      29.741  59.726  28.003  1.00 25.00           C
ATOM    169  CA  PRO   169      31.295  56.743  29.689  1.00 25.00           C
ATOM    170  CA  SER   170      28.785  55.141  32.048  1.00 25.00           C
ATOM    171  CA  GLN   171      28.322  51.420  31.322  1.00 25.00           C
ATOM    172  CA  ILE   172      25.409  50.784  29.070  1.00 25.00           C
ATOM    173  CA  VAL   173      23.187  48.289  27.304  1.00 25.00           C
ATOM    174  CA  ILE   174      25.306  46.307  24.879  1.00 25.00           C
ATOM    175  CA  ILE   175      25.991  43.792  22.067  1.00 25.00           C
ATOM    176  CA  GLY   176      26.533  42.470  18.553  1.00 25.00           C
ATOM    177  CA  ASP   177      27.259  38.851  19.469  1.00 25.00           C
ATOM    178  CA  THR   178      30.893  38.637  18.572  1.00 25.00           C
ATOM    179  CA  GLU   179      34.362  40.049  18.284  1.00 25.00           C
ATOM    180  CA  HIS   180      32.859  43.200  16.709  1.00 25.00           C
ATOM    181  CA  ASP   181      31.086  44.030  20.001  1.00 25.00           C
ATOM    182  CA  ILE   182      34.370  43.564  21.916  1.00 25.00           C
ATOM    183  CA  ARG   183      36.168  45.869  19.442  1.00 25.00           C
ATOM    184  CA  CYS   184      33.426  48.507  19.869  1.00 25.00           C
ATOM    185  CA  ALA   185      33.746  48.259  23.678  1.00 25.00           C
ATOM    186  CA  ARG   186      37.543  48.679  23.411  1.00 25.00           C
ATOM    187  CA  GLU   187      37.070  51.755  21.178  1.00 25.00           C
ATOM    188  CA  LEU   188      33.635  52.893  22.345  1.00 25.00           C
ATOM    189  CA  ASP   189      33.586  54.364  25.850  1.00 25.00           C
ATOM    190  CA  ALA   190      30.017  53.293  26.662  1.00 25.00           C
ATOM    191  CA  ARG   191      29.151  50.374  24.480  1.00 25.00           C
ATOM    192  CA  SER   192      30.595  48.715  27.572  1.00 25.00           C
ATOM    193  CA  ILE   193      30.143  45.413  25.665  1.00 25.00           C
ATOM    194  CA  ALA   194      29.747  41.807  24.384  1.00 25.00           C
ATOM    195  CA  VAL   195      27.339  38.867  24.520  1.00 25.00           C
ATOM    196  CA  ALA   196      24.691  36.186  25.017  1.00 25.00           C
ATOM    197  CA  THR   197      22.916  36.714  21.729  1.00 25.00           C
ATOM    198  CA  GLY   198      22.799  32.921  21.745  1.00 25.00           C
ATOM    199  CA  ASN   199      26.162  31.184  21.378  1.00 25.00           C
ATOM    200  CA  PHE   200      29.356  33.113  20.712  1.00 25.00           C
ATOM    201  CA  THR   201      30.754  31.057  23.578  1.00 25.00           C
ATOM    202  CA  MET   202      30.020  33.449  26.502  1.00 25.00           C
ATOM    203  CA  GLU   203      33.613  32.839  27.682  1.00 25.00           C
ATOM    204  CA  GLU   204      34.918  35.317  25.070  1.00 25.00           C
ATOM    205  CA  LEU   205      32.359  37.921  26.226  1.00 25.00           C
ATOM    206  CA  ALA   206      33.429  37.392  29.865  1.00 25.00           C
ATOM    207  CA  ARG   207      37.103  37.825  28.874  1.00 25.00           C
ATOM    208  CA  HIS   208      38.812  40.660  27.001  1.00 25.00           C
ATOM    209  CA  LYS   209      36.899  43.870  26.236  1.00 25.00           C
ATOM    210  CA  PRO   210      33.975  43.791  28.638  1.00 25.00           C
ATOM    211  CA  GLY   211      30.646  43.529  30.515  1.00 25.00           C
ATOM    212  CA  THR   212      27.573  45.582  29.615  1.00 25.00           C
ATOM    213  CA  LEU   213      25.157  42.845  28.581  1.00 25.00           C
ATOM    214  CA  PHE   214      21.856  41.215  27.918  1.00 25.00           C
ATOM    215  CA  LYS   215      22.686  37.981  29.712  1.00 25.00           C
ATOM    216  CA  ASN   216      19.296  36.557  30.527  1.00 25.00           C
ATOM    217  CA  PHE   217      18.283  39.676  32.573  1.00 25.00           C
ATOM    218  CA  ALA   218      18.208  39.210  36.373  1.00 25.00           C
ATOM    219  CA  GLU   219      21.864  38.071  36.331  1.00 25.00           C
ATOM    220  CA  THR   220      22.822  41.138  34.247  1.00 25.00           C
ATOM    221  CA  ASP   221      20.986  43.419  36.716  1.00 25.00           C
ATOM    222  CA  GLU   222      22.818  41.764  39.644  1.00 25.00           C
ATOM    223  CA  VAL   223      26.170  42.264  37.861  1.00 25.00           C
ATOM    224  CA  LEU   224      25.326  45.950  37.255  1.00 25.00           C
ATOM    225  CA  ALA   225      24.419  46.376  40.951  1.00 25.00           C
ATOM    226  CA  SER   226      27.732  44.747  41.976  1.00 25.00           C
ATOM    227  CA  ILE   227      29.640  47.094  39.626  1.00 25.00           C
ATOM    228  CA  LEU   228      27.819  50.113  41.119  1.00 25.00           C
ATOM    229  CA  THR   229      30.536  49.955  43.731  1.00 25.00           C
TER
END
