
#######################################################
#                                                     #
#                        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  147 (  147),  selected  147 , name T0303TS393_4-D1
# Molecule2: number of CA atoms  147 ( 1151),  selected  147 , name T0303_D1.pdb
# PARAMETERS: T0303TS393_4-D1.T0303_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      T       2           #
LGA    Q       3      Q       3          1.940
LGA    F       4      F       4          1.855
LGA    K       5      K       5          2.400
LGA    L       6      L       6          2.197
LGA    I       7      I       7          3.352
LGA    G       8      G       8          3.544
LGA    F       9      F       9          2.200
LGA    D      10      D      10          0.740
LGA    L      11      L      11          1.704
LGA    D      12      D      12          2.011
LGA    G      13      -       -           -
LGA    T      14      G      13          0.602
LGA    L      15      T      14          2.736
LGA    V      16      L      15          2.796
LGA    N      17      V      16          1.837
LGA    R      95      N      17           -
LGA    -       -      R      95           -
LGA    L      96      L      96          3.274
LGA    Y      97      Y      97          1.467
LGA    P      98      P      98          0.741
LGA    N      99      N      99          2.482
LGA    V     100      V     100          1.503
LGA    K     101      K     101          1.234
LGA    E     102      E     102          1.648
LGA    T     103      T     103          1.797
LGA    L     104      L     104          0.922
LGA    E     105      E     105          0.809
LGA    A     106      A     106          1.490
LGA    L     107      L     107          1.143
LGA    K     108      K     108          0.294
LGA    A     109      A     109          1.230
LGA    Q     110      Q     110          0.801
LGA    G     111      G     111          4.182
LGA    Y     112      Y     112          1.449
LGA    I     113      I     113           #
LGA    L     114      L     114           #
LGA    A     115      A     115          4.546
LGA    V     116      V     116          1.386
LGA    V     117      V     117          1.061
LGA    T     118      T     118          2.221
LGA    N     119      N     119          2.326
LGA    K     120      K     120          1.805
LGA    P     121      P     121          1.837
LGA    T     122      T     122          2.812
LGA    K     123      K     123          1.318
LGA    H     124      H     124          0.928
LGA    V     125      V     125          2.387
LGA    Q     126      Q     126          4.323
LGA    P     127      P     127          2.815
LGA    I     128      I     128          3.818
LGA    L     129      L     129           #
LGA    T     130      -       -           -
LGA    A     131      T     130          2.472
LGA    F     132      A     131          5.345
LGA    -       -      F     132           -
LGA    G     133      G     133          4.020
LGA    I     134      I     134          2.302
LGA    -       -      D     135           -
LGA    D     135      H     136          3.173
LGA    H     136      L     137          3.501
LGA    L     137      F     138          2.982
LGA    F     138      -       -           -
LGA    S     139      S     139          2.535
LGA    E     140      E     140          2.045
LGA    M     141      M     141          3.923
LGA    L     142      L     142          3.068
LGA    G     143      G     143          2.960
LGA    G     144      G     144          2.724
LGA    Q     145      Q     145          1.246
LGA    S     146      S     146          2.691
LGA    L     147      L     147          2.620
LGA    P     148      P     148          2.011
LGA    E     149      E     149          2.849
LGA    I     150      I     150          2.786
LGA    K     151      K     151          3.151
LGA    P     152      P     152          2.035
LGA    H     153      H     153          1.294
LGA    P     154      P     154          0.343
LGA    A     155      A     155          0.567
LGA    P     156      P     156          1.052
LGA    F     157      F     157          1.364
LGA    Y     158      Y     158          1.496
LGA    Y     159      Y     159          1.817
LGA    L     160      L     160          2.793
LGA    C     161      C     161          3.128
LGA    G     162      G     162          3.323
LGA    K     163      K     163          3.921
LGA    F     164      F     164          3.899
LGA    G     165      G     165          4.079
LGA    L     166      L     166          2.042
LGA    Y     167      Y     167          2.458
LGA    P     168      P     168          1.334
LGA    K     169      K     169          1.691
LGA    Q     170      Q     170          3.453
LGA    I     171      I     171          4.764
LGA    L     172      L     172          2.712
LGA    F     173      F     173          3.165
LGA    V     174      V     174          2.573
LGA    G     175      G     175           #
LGA    D     176      D     176          3.670
LGA    S     177      S     177          3.623
LGA    Q     178      Q     178          3.216
LGA    N     179      N     179          1.075
LGA    D     180      D     180          2.232
LGA    I     181      I     181          3.155
LGA    F     182      F     182          2.374
LGA    A     183      A     183          1.310
LGA    A     184      A     184          2.533
LGA    H     185      H     185          2.864
LGA    S     186      S     186          1.889
LGA    A     187      A     187          1.210
LGA    G     188      G     188          0.371
LGA    C     189      C     189          0.966
LGA    A     190      A     190          2.311
LGA    V     191      V     191          1.762
LGA    V     192      V     192          2.747
LGA    G     193      G     193          2.436
LGA    L     194      L     194          1.568
LGA    -       -      T     195           -
LGA    -       -      Y     196           -
LGA    T     195      G     197          3.112
LGA    Y     196      Y     198           -
LGA    G     197      -       -           -
LGA    Y     198      -       -           -
LGA    N     199      -       -           -
LGA    Y     200      -       -           -
LGA    N     201      N     199           #
LGA    -       -      Y     200           -
LGA    -       -      N     201           -
LGA    I     202      I     202           #
LGA    P     203      P     203          4.656
LGA    I     204      I     204          2.185
LGA    A     205      A     205          1.680
LGA    Q     206      Q     206          3.284
LGA    S     207      S     207          4.115
LGA    K     208      K     208          3.754
LGA    P     209      P     209          1.978
LGA    D     210      D     210          0.833
LGA    W     211      W     211          3.342
LGA    I     212      I     212          4.175
LGA    F     213      F     213          3.806
LGA    D     214      -       -           -
LGA    D     215      D     214          4.645
LGA    F     216      -       -           -
LGA    A     217      -       -           -
LGA    D     218      -       -           -
LGA    I     219      D     215           #
LGA    L     220      F     216           -
LGA    K     221      A     217           -
LGA    I     222      D     218           -
LGA    T     223      I     219           -
LGA    Q     224      L     220           -
LGA    -       -      K     221           -
LGA    -       -      I     222           -
LGA    -       -      T     223           -
LGA    -       -      Q     224           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  147  147    5.0    120    2.63    91.67     48.697     4.393

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.907796 * X  +   0.401412 * Y  +   0.121552 * Z  + -11.608697
  Y_new =  -0.087620 * X  +   0.101911 * Y  +  -0.990927 * Z  +  79.776825
  Z_new =  -0.410158 * X  +  -0.910210 * Y  +  -0.057343 * Z  +  17.938311 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.633712    1.507880  [ DEG:   -93.6048     86.3952 ]
  Theta =   0.422627    2.718965  [ DEG:    24.2148    155.7852 ]
  Phi   =  -3.045371    0.096222  [ DEG:  -174.4869      5.5131 ]
 
# 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: T0303TS393_4-D1                               
REMARK     2: T0303_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS393_4-D1.T0303_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  147  147   5.0  120   2.63   91.67  48.697
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS393_4-D1
PFRMAT TS
TARGET T0303
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1     -16.218  49.671   9.790  1.00 25.00           C
ATOM      2  CA  THR     2     -18.181  52.624   8.615  1.00 25.00           C
ATOM      3  CA  GLN     3     -17.365  56.211   7.866  1.00 25.00           C
ATOM      4  CA  PHE     4     -14.980  57.552  10.485  1.00 25.00           C
ATOM      5  CA  LYS     5     -13.341  59.276  13.451  1.00 25.00           C
ATOM      6  CA  LEU     6     -12.414  62.388  15.453  1.00 25.00           C
ATOM      7  CA  ILE     7     -11.120  65.349  13.479  1.00 25.00           C
ATOM      8  CA  GLY     8      -8.908  68.443  13.450  1.00 25.00           C
ATOM      9  CA  PHE     9     -10.798  71.642  14.075  1.00 25.00           C
ATOM     10  CA  ASP    10      -9.670  74.363  16.455  1.00 25.00           C
ATOM     11  CA  LEU    11     -10.227  74.896  20.150  1.00 25.00           C
ATOM     12  CA  ASP    12      -9.607  78.681  19.967  1.00 25.00           C
ATOM     13  CA  GLY    13      -8.483  79.794  16.448  1.00 25.00           C
ATOM     14  CA  THR    14     -12.178  80.272  15.506  1.00 25.00           C
ATOM     15  CA  LEU    15     -14.021  77.757  17.736  1.00 25.00           C
ATOM     16  CA  VAL    16     -15.259  76.345  21.020  1.00 25.00           C
ATOM     17  CA  ASN    17     -16.363  79.911  21.785  1.00 25.00           C
ATOM     95  CA  ARG    95     -24.319  80.717  24.250  1.00 25.00           C
ATOM     96  CA  LEU    96     -22.491  78.626  21.648  1.00 25.00           C
ATOM     97  CA  TYR    97     -20.412  79.983  18.793  1.00 25.00           C
ATOM     98  CA  PRO    98     -23.746  79.506  16.995  1.00 25.00           C
ATOM     99  CA  ASN    99     -23.177  76.042  15.567  1.00 25.00           C
ATOM    100  CA  VAL   100     -20.422  75.093  18.039  1.00 25.00           C
ATOM    101  CA  LYS   101     -22.025  73.386  21.070  1.00 25.00           C
ATOM    102  CA  GLU   102     -24.974  72.256  18.904  1.00 25.00           C
ATOM    103  CA  THR   103     -22.550  70.856  16.291  1.00 25.00           C
ATOM    104  CA  LEU   104     -20.646  68.974  19.029  1.00 25.00           C
ATOM    105  CA  GLU   105     -23.934  67.528  20.357  1.00 25.00           C
ATOM    106  CA  ALA   106     -24.899  66.413  16.822  1.00 25.00           C
ATOM    107  CA  LEU   107     -21.479  64.747  16.387  1.00 25.00           C
ATOM    108  CA  LYS   108     -21.904  62.942  19.738  1.00 25.00           C
ATOM    109  CA  ALA   109     -25.379  61.736  18.674  1.00 25.00           C
ATOM    110  CA  GLN   110     -24.269  59.755  15.564  1.00 25.00           C
ATOM    111  CA  GLY   111     -21.337  58.245  13.597  1.00 25.00           C
ATOM    112  CA  TYR   112     -18.724  60.552  15.145  1.00 25.00           C
ATOM    113  CA  ILE   113     -17.327  63.495  13.106  1.00 25.00           C
ATOM    114  CA  LEU   114     -15.943  66.895  14.101  1.00 25.00           C
ATOM    115  CA  ALA   115     -13.803  68.646  16.724  1.00 25.00           C
ATOM    116  CA  VAL   116     -10.902  69.894  18.793  1.00 25.00           C
ATOM    117  CA  VAL   117      -7.221  70.672  18.773  1.00 25.00           C
ATOM    118  CA  THR   118      -4.663  72.658  16.805  1.00 25.00           C
ATOM    119  CA  ASN   119      -3.729  76.311  16.819  1.00 25.00           C
ATOM    120  CA  LYS   120      -4.648  76.347  20.551  1.00 25.00           C
ATOM    121  CA  PRO   121      -1.886  77.326  23.031  1.00 25.00           C
ATOM    122  CA  THR   122      -0.993  75.674  26.338  1.00 25.00           C
ATOM    123  CA  LYS   123      -2.663  76.092  29.758  1.00 25.00           C
ATOM    124  CA  HIS   124      -5.735  77.660  28.093  1.00 25.00           C
ATOM    125  CA  VAL   125      -5.907  74.749  25.612  1.00 25.00           C
ATOM    126  CA  GLN   126      -5.685  72.243  28.500  1.00 25.00           C
ATOM    127  CA  PRO   127      -8.501  74.076  30.338  1.00 25.00           C
ATOM    128  CA  ILE   128     -10.654  73.996  27.173  1.00 25.00           C
ATOM    129  CA  LEU   129     -10.001  70.242  26.793  1.00 25.00           C
ATOM    130  CA  THR   130     -10.984  69.676  30.451  1.00 25.00           C
ATOM    131  CA  ALA   131     -14.205  71.678  29.921  1.00 25.00           C
ATOM    132  CA  PHE   132     -17.640  72.632  28.516  1.00 25.00           C
ATOM    133  CA  GLY   133     -19.915  69.597  28.142  1.00 25.00           C
ATOM    134  CA  ILE   134     -18.460  69.519  24.658  1.00 25.00           C
ATOM    135  CA  ASP   135     -18.183  65.728  25.296  1.00 25.00           C
ATOM    136  CA  HIS   136     -16.443  63.387  22.816  1.00 25.00           C
ATOM    137  CA  LEU   137     -15.020  66.400  20.930  1.00 25.00           C
ATOM    138  CA  PHE   138     -13.742  67.887  24.220  1.00 25.00           C
ATOM    139  CA  SER   139     -12.096  64.548  25.118  1.00 25.00           C
ATOM    140  CA  GLU   140     -10.433  64.412  21.671  1.00 25.00           C
ATOM    141  CA  MET   141      -6.760  64.258  22.623  1.00 25.00           C
ATOM    142  CA  LEU   142      -5.513  67.257  24.609  1.00 25.00           C
ATOM    143  CA  GLY   143      -3.782  69.431  21.938  1.00 25.00           C
ATOM    144  CA  GLY   144      -0.805  71.535  20.825  1.00 25.00           C
ATOM    145  CA  GLN   145       1.533  71.345  23.797  1.00 25.00           C
ATOM    146  CA  SER   146       2.960  68.062  22.554  1.00 25.00           C
ATOM    147  CA  LEU   147       3.241  69.014  18.894  1.00 25.00           C
ATOM    148  CA  PRO   148       6.801  69.152  17.628  1.00 25.00           C
ATOM    149  CA  GLU   149       6.318  71.835  14.962  1.00 25.00           C
ATOM    150  CA  ILE   150       3.382  73.521  16.634  1.00 25.00           C
ATOM    151  CA  LYS   151       1.062  75.033  13.955  1.00 25.00           C
ATOM    152  CA  PRO   152       1.178  72.216  11.423  1.00 25.00           C
ATOM    153  CA  HIS   153       3.195  69.049  10.609  1.00 25.00           C
ATOM    154  CA  PRO   154       0.051  66.839  10.516  1.00 25.00           C
ATOM    155  CA  ALA   155       1.463  65.496  13.813  1.00 25.00           C
ATOM    156  CA  PRO   156      -1.456  67.066  15.731  1.00 25.00           C
ATOM    157  CA  PHE   157      -3.945  65.476  13.293  1.00 25.00           C
ATOM    158  CA  TYR   158      -2.251  62.071  13.747  1.00 25.00           C
ATOM    159  CA  TYR   159      -2.441  62.456  17.552  1.00 25.00           C
ATOM    160  CA  LEU   160      -6.159  63.340  17.303  1.00 25.00           C
ATOM    161  CA  CYS   161      -6.769  60.260  15.109  1.00 25.00           C
ATOM    162  CA  GLY   162      -4.930  58.058  17.646  1.00 25.00           C
ATOM    163  CA  LYS   163      -7.049  59.515  20.483  1.00 25.00           C
ATOM    164  CA  PHE   164     -10.243  58.823  18.486  1.00 25.00           C
ATOM    165  CA  GLY   165      -9.569  55.913  16.184  1.00 25.00           C
ATOM    166  CA  LEU   166      -9.064  56.387  12.416  1.00 25.00           C
ATOM    167  CA  TYR   167      -5.631  57.000  10.981  1.00 25.00           C
ATOM    168  CA  PRO   168      -6.154  60.364   9.324  1.00 25.00           C
ATOM    169  CA  LYS   169      -9.257  58.992   7.547  1.00 25.00           C
ATOM    170  CA  GLN   170     -11.453  61.564   9.344  1.00 25.00           C
ATOM    171  CA  ILE   171     -14.967  62.062   7.932  1.00 25.00           C
ATOM    172  CA  LEU   172     -15.433  65.737   8.927  1.00 25.00           C
ATOM    173  CA  PHE   173     -14.205  69.289   9.665  1.00 25.00           C
ATOM    174  CA  VAL   174     -15.490  72.454  11.347  1.00 25.00           C
ATOM    175  CA  GLY   175     -16.762  75.638  13.030  1.00 25.00           C
ATOM    176  CA  ASP   176     -12.942  76.072  12.676  1.00 25.00           C
ATOM    177  CA  SER   177      -9.548  77.621  11.854  1.00 25.00           C
ATOM    178  CA  GLN   178      -7.436  78.084   8.702  1.00 25.00           C
ATOM    179  CA  ASN   179      -3.965  76.781   9.661  1.00 25.00           C
ATOM    180  CA  ASP   180      -5.560  74.051  11.823  1.00 25.00           C
ATOM    181  CA  ILE   181      -7.845  73.052   8.917  1.00 25.00           C
ATOM    182  CA  PHE   182      -4.825  72.878   6.568  1.00 25.00           C
ATOM    183  CA  ALA   183      -2.957  70.687   9.094  1.00 25.00           C
ATOM    184  CA  ALA   184      -5.994  68.371   9.369  1.00 25.00           C
ATOM    185  CA  HIS   185      -6.176  68.115   5.553  1.00 25.00           C
ATOM    186  CA  SER   186      -2.444  67.269   5.407  1.00 25.00           C
ATOM    187  CA  ALA   187      -3.388  63.980   7.067  1.00 25.00           C
ATOM    188  CA  GLY   188      -5.342  62.868   3.999  1.00 25.00           C
ATOM    189  CA  CYS   189      -8.693  63.770   5.483  1.00 25.00           C
ATOM    190  CA  ALA   190     -10.868  66.596   6.675  1.00 25.00           C
ATOM    191  CA  VAL   191     -10.392  70.175   5.333  1.00 25.00           C
ATOM    192  CA  VAL   192     -12.209  73.329   6.285  1.00 25.00           C
ATOM    193  CA  GLY   193     -12.230  76.899   7.584  1.00 25.00           C
ATOM    194  CA  LEU   194     -15.143  78.856   9.088  1.00 25.00           C
ATOM    195  CA  THR   195     -15.809  81.263  11.868  1.00 25.00           C
ATOM    196  CA  TYR   196     -19.163  80.236  13.275  1.00 25.00           C
ATOM    197  CA  GLY   197     -20.572  80.067   9.770  1.00 25.00           C
ATOM    198  CA  TYR   198     -19.190  78.830   6.414  1.00 25.00           C
ATOM    199  CA  ASN   199     -17.181  78.494   3.215  1.00 25.00           C
ATOM    200  CA  TYR   200     -14.285  80.825   4.018  1.00 25.00           C
ATOM    201  CA  ASN   201     -11.897  83.034   2.153  1.00 25.00           C
ATOM    202  CA  ILE   202     -10.163  82.434  -1.208  1.00 25.00           C
ATOM    203  CA  PRO   203      -7.075  81.071   0.601  1.00 25.00           C
ATOM    204  CA  ILE   204      -9.291  78.737   2.678  1.00 25.00           C
ATOM    205  CA  ALA   205     -11.018  77.502  -0.510  1.00 25.00           C
ATOM    206  CA  GLN   206      -7.612  76.857  -2.136  1.00 25.00           C
ATOM    207  CA  SER   207      -5.323  73.893  -1.844  1.00 25.00           C
ATOM    208  CA  LYS   208      -6.909  73.060   1.509  1.00 25.00           C
ATOM    209  CA  PRO   209     -10.249  71.541   0.517  1.00 25.00           C
ATOM    210  CA  ASP   210     -13.169  69.146   1.057  1.00 25.00           C
ATOM    211  CA  TRP   211     -16.510  68.687   2.689  1.00 25.00           C
ATOM    212  CA  ILE   212     -18.434  71.878   3.409  1.00 25.00           C
ATOM    213  CA  PHE   213     -21.277  73.116   5.676  1.00 25.00           C
ATOM    214  CA  ASP   214     -23.539  75.435   3.598  1.00 25.00           C
ATOM    215  CA  ASP   215     -22.695  78.997   2.572  1.00 25.00           C
ATOM    216  CA  PHE   216     -21.373  82.537   2.982  1.00 25.00           C
ATOM    217  CA  ALA   217     -20.936  86.317   2.549  1.00 25.00           C
ATOM    218  CA  ASP   218     -21.051  86.789   6.347  1.00 25.00           C
ATOM    219  CA  ILE   219     -18.417  84.045   6.794  1.00 25.00           C
ATOM    220  CA  LEU   220     -16.187  85.724   4.173  1.00 25.00           C
ATOM    221  CA  LYS   221     -16.564  89.085   5.969  1.00 25.00           C
ATOM    222  CA  ILE   222     -15.633  87.438   9.299  1.00 25.00           C
ATOM    223  CA  THR   223     -12.549  85.847   7.678  1.00 25.00           C
ATOM    224  CA  GLN   224     -10.944  88.709   5.691  1.00 25.00           C
TER
END
