
#######################################################
#                                                     #
#                        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 T0303TS168_5-D1
# Molecule2: number of CA atoms  147 ( 1151),  selected  147 , name T0303_D1.pdb
# PARAMETERS: T0303TS168_5-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           -
LGA    -       -      F       4           -
LGA    Q       3      K       5           #
LGA    F       4      -       -           -
LGA    K       5      -       -           -
LGA    L       6      -       -           -
LGA    I       7      -       -           -
LGA    G       8      -       -           -
LGA    F       9      -       -           -
LGA    D      10      -       -           -
LGA    L      11      -       -           -
LGA    D      12      -       -           -
LGA    G      13      -       -           -
LGA    T      14      -       -           -
LGA    L      15      -       -           -
LGA    V      16      -       -           -
LGA    N      17      -       -           -
LGA    R      95      -       -           -
LGA    L      96      -       -           -
LGA    Y      97      -       -           -
LGA    P      98      -       -           -
LGA    N      99      -       -           -
LGA    V     100      -       -           -
LGA    K     101      -       -           -
LGA    E     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    E     105      -       -           -
LGA    A     106      -       -           -
LGA    L     107      -       -           -
LGA    K     108      -       -           -
LGA    A     109      -       -           -
LGA    Q     110      -       -           -
LGA    G     111      -       -           -
LGA    Y     112      -       -           -
LGA    I     113      L       6          1.898
LGA    L     114      I       7          2.588
LGA    A     115      G       8          1.260
LGA    V     116      F       9          0.322
LGA    V     117      D      10          3.307
LGA    T     118      L      11          2.923
LGA    -       -      D      12           -
LGA    -       -      G      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      V      16           -
LGA    -       -      N      17           -
LGA    -       -      R      95           -
LGA    -       -      L      96           -
LGA    -       -      Y      97           -
LGA    -       -      P      98           -
LGA    -       -      N      99           -
LGA    -       -      V     100           -
LGA    -       -      K     101           -
LGA    -       -      E     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      L     107           -
LGA    -       -      K     108           -
LGA    -       -      A     109           -
LGA    -       -      Q     110           -
LGA    -       -      G     111           -
LGA    -       -      Y     112           -
LGA    -       -      I     113           -
LGA    -       -      L     114           -
LGA    -       -      A     115           -
LGA    -       -      V     116           -
LGA    -       -      V     117           -
LGA    N     119      T     118          2.022
LGA    K     120      N     119          1.948
LGA    P     121      K     120          2.991
LGA    -       -      P     121           -
LGA    T     122      T     122          1.519
LGA    K     123      K     123          1.787
LGA    H     124      H     124          1.694
LGA    V     125      V     125          1.282
LGA    Q     126      Q     126          2.800
LGA    P     127      P     127          1.458
LGA    I     128      I     128          2.610
LGA    L     129      L     129          3.964
LGA    T     130      T     130          3.039
LGA    A     131      A     131          3.182
LGA    F     132      F     132          3.089
LGA    G     133      G     133          2.739
LGA    I     134      I     134          1.273
LGA    D     135      D     135          1.714
LGA    H     136      H     136          4.832
LGA    L     137      L     137          5.225
LGA    F     138      F     138          3.469
LGA    S     139      S     139          2.295
LGA    E     140      E     140          5.362
LGA    M     141      M     141          4.939
LGA    L     142      L     142          4.733
LGA    G     143      G     143           #
LGA    G     144      G     144          3.927
LGA    Q     145      Q     145          2.699
LGA    S     146      S     146          4.156
LGA    L     147      L     147          3.803
LGA    P     148      P     148          3.077
LGA    E     149      E     149          4.928
LGA    I     150      I     150          3.705
LGA    K     151      K     151          3.490
LGA    P     152      P     152          1.534
LGA    H     153      H     153          1.719
LGA    P     154      P     154          1.793
LGA    A     155      A     155          1.988
LGA    P     156      P     156          1.131
LGA    F     157      F     157          0.945
LGA    Y     158      Y     158          1.235
LGA    Y     159      Y     159          1.158
LGA    L     160      L     160          1.132
LGA    C     161      C     161          1.022
LGA    G     162      G     162          1.211
LGA    K     163      K     163          1.965
LGA    F     164      F     164          1.845
LGA    G     165      G     165          0.808
LGA    L     166      L     166          1.001
LGA    Y     167      Y     167          0.567
LGA    P     168      P     168          3.101
LGA    K     169      K     169           #
LGA    Q     170      Q     170          3.366
LGA    I     171      I     171          2.021
LGA    L     172      L     172          1.862
LGA    F     173      F     173          0.763
LGA    V     174      V     174          2.415
LGA    G     175      G     175          2.300
LGA    D     176      D     176          1.771
LGA    S     177      S     177          1.731
LGA    Q     178      Q     178          1.058
LGA    N     179      N     179          0.789
LGA    D     180      D     180          0.621
LGA    I     181      I     181          1.271
LGA    F     182      F     182          1.436
LGA    A     183      A     183          1.544
LGA    A     184      A     184          2.062
LGA    H     185      H     185          2.396
LGA    S     186      S     186          2.838
LGA    A     187      A     187          2.806
LGA    G     188      G     188          3.015
LGA    C     189      C     189          2.022
LGA    A     190      A     190          2.394
LGA    V     191      V     191          2.480
LGA    V     192      -       -           -
LGA    G     193      V     192          1.604
LGA    L     194      G     193          2.358
LGA    T     195      L     194          3.159
LGA    Y     196      T     195           #
LGA    G     197      Y     196          4.264
LGA    Y     198      G     197          3.681
LGA    -       -      Y     198           -
LGA    -       -      N     199           -
LGA    -       -      Y     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    N     199      P     203           #
LGA    Y     200      I     204          2.185
LGA    N     201      -       -           -
LGA    I     202      A     205          1.122
LGA    P     203      Q     206          2.750
LGA    I     204      S     207          3.669
LGA    A     205      K     208          1.502
LGA    Q     206      -       -           -
LGA    S     207      -       -           -
LGA    K     208      -       -           -
LGA    P     209      P     209          3.400
LGA    D     210      D     210          3.168
LGA    W     211      W     211          4.277
LGA    I     212      I     212          3.972
LGA    F     213      F     213           #
LGA    D     214      D     214           #
LGA    -       -      D     215           -
LGA    -       -      F     216           -
LGA    -       -      A     217           -
LGA    -       -      D     218           -
LGA    D     215      I     219          3.101
LGA    F     216      L     220          3.085
LGA    A     217      K     221          4.833
LGA    D     218      -       -           -
LGA    I     219      -       -           -
LGA    L     220      I     222           #
LGA    K     221      T     223           -
LGA    I     222      Q     224           -
LGA    T     223      -       -           -
LGA    Q     224      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  147  147    5.0     94    2.73    76.60     39.864     3.317

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.182423 * X  +   0.982725 * Y  +  -0.031185 * Z  + -12.096717
  Y_new =   0.815842 * X  +   0.133590 * Y  +  -0.562633 * Z  +  79.078262
  Z_new =  -0.548747 * X  +  -0.128080 * Y  +  -0.826119 * Z  +  15.833426 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.987779    0.153813  [ DEG:  -171.1871      8.8128 ]
  Theta =   0.580865    2.560728  [ DEG:    33.2811    146.7189 ]
  Phi   =   1.790779   -1.350814  [ DEG:   102.6041    -77.3959 ]
 
# 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: T0303TS168_5-D1                               
REMARK     2: T0303_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS168_5-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   94   2.73   76.60  39.864
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS168_5-D1
PFRMAT TS
TARGET T0303
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1     -17.451  47.509  17.953  1.00 25.00           C
ATOM      2  CA  THR     2     -14.959  50.222  17.218  1.00 25.00           C
ATOM      3  CA  GLN     3     -13.419  53.677  17.402  1.00 25.00           C
ATOM      4  CA  PHE     4     -12.393  56.237  20.018  1.00 25.00           C
ATOM      5  CA  LYS     5     -10.936  58.925  22.301  1.00 25.00           C
ATOM      6  CA  LEU     6      -8.366  60.982  24.172  1.00 25.00           C
ATOM      7  CA  ILE     7      -7.363  64.641  24.440  1.00 25.00           C
ATOM      8  CA  GLY     8      -7.877  68.117  23.078  1.00 25.00           C
ATOM      9  CA  PHE     9      -7.083  70.078  19.937  1.00 25.00           C
ATOM     10  CA  ASP    10      -6.955  69.679  16.185  1.00 25.00           C
ATOM     11  CA  LEU    11      -6.595  73.395  15.291  1.00 25.00           C
ATOM     12  CA  ASP    12      -6.883  77.217  15.736  1.00 25.00           C
ATOM     13  CA  GLY    13     -10.566  76.567  14.852  1.00 25.00           C
ATOM     14  CA  THR    14     -14.106  75.886  13.549  1.00 25.00           C
ATOM     15  CA  LEU    15     -15.588  74.013  16.482  1.00 25.00           C
ATOM     16  CA  VAL    16     -14.791  76.666  19.098  1.00 25.00           C
ATOM     17  CA  ASN    17     -16.987  79.343  17.467  1.00 25.00           C
ATOM     95  CA  ARG    95     -21.465  81.825  25.512  1.00 25.00           C
ATOM     96  CA  LEU    96     -19.618  80.212  22.631  1.00 25.00           C
ATOM     97  CA  TYR    97     -22.232  77.427  22.622  1.00 25.00           C
ATOM     98  CA  PRO    98     -25.574  77.165  20.854  1.00 25.00           C
ATOM     99  CA  ASN    99     -23.646  76.649  17.596  1.00 25.00           C
ATOM    100  CA  VAL   100     -20.607  74.508  18.604  1.00 25.00           C
ATOM    101  CA  LYS   101     -20.727  72.194  21.654  1.00 25.00           C
ATOM    102  CA  GLU   102     -24.182  70.930  20.589  1.00 25.00           C
ATOM    103  CA  THR   103     -22.876  70.268  17.050  1.00 25.00           C
ATOM    104  CA  LEU   104     -19.888  68.349  18.484  1.00 25.00           C
ATOM    105  CA  GLU   105     -22.245  66.262  20.666  1.00 25.00           C
ATOM    106  CA  ALA   106     -24.428  65.492  17.615  1.00 25.00           C
ATOM    107  CA  LEU   107     -21.327  64.431  15.633  1.00 25.00           C
ATOM    108  CA  LYS   108     -20.235  62.155  18.514  1.00 25.00           C
ATOM    109  CA  ALA   109     -23.729  60.592  18.636  1.00 25.00           C
ATOM    110  CA  GLN   110     -22.788  56.905  19.146  1.00 25.00           C
ATOM    111  CA  GLY   111     -20.620  57.556  16.076  1.00 25.00           C
ATOM    112  CA  TYR   112     -18.208  59.869  14.180  1.00 25.00           C
ATOM    113  CA  ILE   113     -15.038  61.464  15.551  1.00 25.00           C
ATOM    114  CA  LEU   114     -16.145  65.107  15.713  1.00 25.00           C
ATOM    115  CA  ALA   115     -12.945  67.074  15.334  1.00 25.00           C
ATOM    116  CA  VAL   116     -11.764  70.632  15.658  1.00 25.00           C
ATOM    117  CA  VAL   117     -10.936  72.451  18.878  1.00 25.00           C
ATOM    118  CA  THR   118      -8.556  74.961  20.379  1.00 25.00           C
ATOM    119  CA  ASN   119      -4.748  74.934  19.858  1.00 25.00           C
ATOM    120  CA  LYS   120      -1.879  77.459  19.502  1.00 25.00           C
ATOM    121  CA  PRO   121      -1.582  76.924  23.256  1.00 25.00           C
ATOM    122  CA  THR   122      -2.088  74.850  26.439  1.00 25.00           C
ATOM    123  CA  LYS   123      -3.772  76.739  29.314  1.00 25.00           C
ATOM    124  CA  HIS   124      -6.504  77.978  26.932  1.00 25.00           C
ATOM    125  CA  VAL   125      -7.063  74.404  25.676  1.00 25.00           C
ATOM    126  CA  GLN   126      -7.331  73.151  29.285  1.00 25.00           C
ATOM    127  CA  PRO   127      -9.871  75.905  30.078  1.00 25.00           C
ATOM    128  CA  ILE   128     -11.914  74.946  26.985  1.00 25.00           C
ATOM    129  CA  LEU   129     -11.857  71.269  28.056  1.00 25.00           C
ATOM    130  CA  THR   130     -13.026  72.250  31.568  1.00 25.00           C
ATOM    131  CA  ALA   131     -15.870  74.330  30.068  1.00 25.00           C
ATOM    132  CA  PHE   132     -19.634  74.886  29.867  1.00 25.00           C
ATOM    133  CA  GLY   133     -20.223  71.172  30.209  1.00 25.00           C
ATOM    134  CA  ILE   134     -19.791  70.596  26.423  1.00 25.00           C
ATOM    135  CA  ASP   135     -16.477  68.743  26.469  1.00 25.00           C
ATOM    136  CA  HIS   136     -17.598  66.598  23.503  1.00 25.00           C
ATOM    137  CA  LEU   137     -15.452  68.708  21.133  1.00 25.00           C
ATOM    138  CA  PHE   138     -12.439  68.300  23.462  1.00 25.00           C
ATOM    139  CA  SER   139     -12.996  64.513  23.561  1.00 25.00           C
ATOM    140  CA  GLU   140     -13.179  64.415  19.737  1.00 25.00           C
ATOM    141  CA  MET   141      -9.871  66.247  19.283  1.00 25.00           C
ATOM    142  CA  LEU   142      -6.227  65.053  19.676  1.00 25.00           C
ATOM    143  CA  GLY   143      -3.403  67.261  20.965  1.00 25.00           C
ATOM    144  CA  GLY   144      -1.560  70.552  20.626  1.00 25.00           C
ATOM    145  CA  GLN   145       1.417  70.016  22.910  1.00 25.00           C
ATOM    146  CA  SER   146       3.551  67.461  21.094  1.00 25.00           C
ATOM    147  CA  LEU   147       4.011  70.226  18.555  1.00 25.00           C
ATOM    148  CA  PRO   148       7.704  71.148  18.330  1.00 25.00           C
ATOM    149  CA  GLU   149       6.636  74.258  16.473  1.00 25.00           C
ATOM    150  CA  ILE   150       2.844  74.870  16.768  1.00 25.00           C
ATOM    151  CA  LYS   151       2.347  74.494  13.029  1.00 25.00           C
ATOM    152  CA  PRO   152       1.282  72.130  10.194  1.00 25.00           C
ATOM    153  CA  HIS   153       3.941  69.426  10.831  1.00 25.00           C
ATOM    154  CA  PRO   154       0.926  67.352  11.747  1.00 25.00           C
ATOM    155  CA  ALA   155       1.932  65.954  15.168  1.00 25.00           C
ATOM    156  CA  PRO   156      -1.586  66.649  16.513  1.00 25.00           C
ATOM    157  CA  PHE   157      -3.120  64.875  13.486  1.00 25.00           C
ATOM    158  CA  TYR   158      -0.821  61.865  14.053  1.00 25.00           C
ATOM    159  CA  TYR   159      -1.835  61.754  17.744  1.00 25.00           C
ATOM    160  CA  LEU   160      -5.533  61.871  16.756  1.00 25.00           C
ATOM    161  CA  CYS   161      -4.985  59.011  14.268  1.00 25.00           C
ATOM    162  CA  GLY   162      -3.228  56.956  16.981  1.00 25.00           C
ATOM    163  CA  LYS   163      -6.138  57.598  19.387  1.00 25.00           C
ATOM    164  CA  PHE   164      -8.635  56.499  16.698  1.00 25.00           C
ATOM    165  CA  GLY   165      -7.390  52.981  15.829  1.00 25.00           C
ATOM    166  CA  LEU   166      -7.519  54.036  12.210  1.00 25.00           C
ATOM    167  CA  TYR   167      -6.851  55.470   8.769  1.00 25.00           C
ATOM    168  CA  PRO   168      -8.463  58.618  10.215  1.00 25.00           C
ATOM    169  CA  LYS   169     -11.990  57.569  11.279  1.00 25.00           C
ATOM    170  CA  GLN   170     -13.448  60.696   9.620  1.00 25.00           C
ATOM    171  CA  ILE   171     -10.912  63.562   9.872  1.00 25.00           C
ATOM    172  CA  LEU   172     -14.093  65.577  10.571  1.00 25.00           C
ATOM    173  CA  PHE   173     -11.727  68.557  10.710  1.00 25.00           C
ATOM    174  CA  VAL   174     -11.119  72.327  10.638  1.00 25.00           C
ATOM    175  CA  GLY   175     -10.497  75.916   9.358  1.00 25.00           C
ATOM    176  CA  ASP   176     -10.289  79.513  10.629  1.00 25.00           C
ATOM    177  CA  SER   177      -7.619  80.277   8.001  1.00 25.00           C
ATOM    178  CA  GLN   178      -6.170  77.299   6.130  1.00 25.00           C
ATOM    179  CA  ASN   179      -3.542  75.976   8.580  1.00 25.00           C
ATOM    180  CA  ASP   180      -6.196  73.816  10.300  1.00 25.00           C
ATOM    181  CA  ILE   181      -7.308  72.437   6.906  1.00 25.00           C
ATOM    182  CA  PHE   182      -3.673  71.622   6.017  1.00 25.00           C
ATOM    183  CA  ALA   183      -3.229  69.832   9.374  1.00 25.00           C
ATOM    184  CA  ALA   184      -6.424  67.815   8.749  1.00 25.00           C
ATOM    185  CA  HIS   185      -5.164  66.853   5.263  1.00 25.00           C
ATOM    186  CA  SER   186      -1.812  65.751   6.751  1.00 25.00           C
ATOM    187  CA  ALA   187      -1.774  62.695   9.014  1.00 25.00           C
ATOM    188  CA  GLY   188      -4.051  61.153   6.428  1.00 25.00           C
ATOM    189  CA  CYS   189      -7.608  62.065   5.622  1.00 25.00           C
ATOM    190  CA  ALA   190     -11.102  63.125   4.394  1.00 25.00           C
ATOM    191  CA  VAL   191     -10.980  66.685   5.602  1.00 25.00           C
ATOM    192  CA  VAL   192     -13.394  69.452   6.580  1.00 25.00           C
ATOM    193  CA  GLY   193     -14.113  73.200   6.456  1.00 25.00           C
ATOM    194  CA  LEU   194     -15.033  76.808   6.769  1.00 25.00           C
ATOM    195  CA  THR   195     -17.534  75.584   9.325  1.00 25.00           C
ATOM    196  CA  TYR   196     -19.401  77.412  12.059  1.00 25.00           C
ATOM    197  CA  GLY   197     -19.462  80.220   9.448  1.00 25.00           C
ATOM    198  CA  TYR   198     -15.795  80.850  10.177  1.00 25.00           C
ATOM    199  CA  ASN   199     -13.947  81.965   7.044  1.00 25.00           C
ATOM    200  CA  TYR   200     -11.438  82.076   4.261  1.00 25.00           C
ATOM    201  CA  ASN   201     -13.329  79.234   2.696  1.00 25.00           C
ATOM    202  CA  ILE   202     -11.221  80.129  -0.373  1.00 25.00           C
ATOM    203  CA  PRO   203      -8.025  79.191   1.517  1.00 25.00           C
ATOM    204  CA  ILE   204      -9.584  75.845   2.540  1.00 25.00           C
ATOM    205  CA  ALA   205     -10.578  75.169  -1.097  1.00 25.00           C
ATOM    206  CA  GLN   206      -7.015  75.973  -2.247  1.00 25.00           C
ATOM    207  CA  SER   207      -3.883  75.427  -0.159  1.00 25.00           C
ATOM    208  CA  LYS   208      -4.862  71.768  -0.481  1.00 25.00           C
ATOM    209  CA  PRO   209      -8.100  70.998   1.380  1.00 25.00           C
ATOM    210  CA  ASP   210     -10.514  68.274   0.486  1.00 25.00           C
ATOM    211  CA  TRP   211     -12.805  71.158  -0.423  1.00 25.00           C
ATOM    212  CA  ILE   212     -16.117  71.975   1.343  1.00 25.00           C
ATOM    213  CA  PHE   213     -17.763  71.596   4.799  1.00 25.00           C
ATOM    214  CA  ASP   214     -20.954  70.615   2.978  1.00 25.00           C
ATOM    215  CA  ASP   215     -22.355  69.639   6.373  1.00 25.00           C
ATOM    216  CA  PHE   216     -25.328  70.350   8.587  1.00 25.00           C
ATOM    217  CA  ALA   217     -27.795  71.885   6.092  1.00 25.00           C
ATOM    218  CA  ASP   218     -27.894  75.119   8.142  1.00 25.00           C
ATOM    219  CA  ILE   219     -24.066  75.228   8.201  1.00 25.00           C
ATOM    220  CA  LEU   220     -23.969  74.724   4.405  1.00 25.00           C
ATOM    221  CA  LYS   221     -26.503  77.558   3.940  1.00 25.00           C
ATOM    222  CA  ILE   222     -24.392  79.845   6.173  1.00 25.00           C
ATOM    223  CA  THR   223     -21.264  78.985   4.137  1.00 25.00           C
ATOM    224  CA  GLN   224     -19.685  82.448   3.549  1.00 25.00           C
TER
END
