
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  147 ( 1151),  selected  147 , name T0303_D1.pdb
# PARAMETERS: T0303TS393_3-D1.T0303_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    Q       3      M       1           #
LGA    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    F       4      F       4          1.759
LGA    K       5      K       5           #
LGA    L       6      L       6          3.556
LGA    I       7      I       7          1.210
LGA    G       8      G       8          4.765
LGA    F       9      F       9          1.703
LGA    D      10      D      10          0.847
LGA    L      11      L      11          1.483
LGA    D      12      D      12          3.195
LGA    G      13      G      13          2.995
LGA    T      14      T      14          2.731
LGA    L      15      L      15          2.062
LGA    V      16      V      16          2.099
LGA    N      17      N      17          3.272
LGA    R      95      R      95          3.945
LGA    L      96      L      96          3.607
LGA    Y      97      Y      97          3.559
LGA    P      98      P      98          4.759
LGA    N      99      N      99          2.394
LGA    V     100      V     100          0.972
LGA    K     101      K     101          0.882
LGA    E     102      E     102          1.428
LGA    T     103      T     103          1.715
LGA    L     104      L     104          1.112
LGA    E     105      E     105          0.808
LGA    A     106      A     106          1.658
LGA    L     107      L     107          1.899
LGA    K     108      K     108          1.020
LGA    A     109      A     109          1.171
LGA    Q     110      Q     110          4.345
LGA    G     111      G     111          1.126
LGA    Y     112      Y     112          0.649
LGA    I     113      I     113          2.192
LGA    L     114      L     114          4.028
LGA    A     115      A     115          3.088
LGA    V     116      V     116          2.791
LGA    V     117      V     117          2.757
LGA    T     118      T     118          1.007
LGA    N     119      N     119          2.210
LGA    K     120      K     120          2.205
LGA    P     121      P     121          2.845
LGA    T     122      T     122          1.661
LGA    K     123      K     123          1.667
LGA    H     124      H     124          2.469
LGA    V     125      V     125          1.804
LGA    Q     126      Q     126          1.868
LGA    P     127      P     127          1.919
LGA    I     128      I     128          2.530
LGA    L     129      L     129          2.938
LGA    T     130      T     130          2.225
LGA    A     131      A     131          1.848
LGA    F     132      F     132          0.463
LGA    G     133      G     133          2.002
LGA    I     134      I     134          1.349
LGA    D     135      D     135          1.928
LGA    H     136      H     136           #
LGA    L     137      L     137           #
LGA    F     138      F     138          2.945
LGA    S     139      S     139          3.959
LGA    E     140      E     140           #
LGA    M     141      M     141           #
LGA    L     142      L     142          4.788
LGA    G     143      G     143          4.423
LGA    G     144      G     144          3.802
LGA    Q     145      Q     145          1.995
LGA    S     146      S     146          3.066
LGA    L     147      L     147          2.816
LGA    P     148      P     148          1.631
LGA    E     149      E     149          3.357
LGA    I     150      I     150          3.082
LGA    K     151      K     151          2.477
LGA    P     152      P     152          2.061
LGA    H     153      H     153          0.825
LGA    P     154      P     154          2.722
LGA    A     155      A     155          2.000
LGA    P     156      P     156          1.988
LGA    F     157      F     157          2.043
LGA    Y     158      Y     158          1.271
LGA    Y     159      Y     159          0.777
LGA    L     160      L     160          1.439
LGA    C     161      C     161          2.276
LGA    G     162      G     162          2.004
LGA    K     163      K     163          2.218
LGA    F     164      F     164          2.729
LGA    G     165      G     165          3.390
LGA    L     166      L     166          3.172
LGA    Y     167      Y     167          1.654
LGA    P     168      P     168          2.097
LGA    K     169      K     169          2.337
LGA    Q     170      Q     170          3.083
LGA    I     171      I     171          1.339
LGA    L     172      L     172          1.194
LGA    F     173      F     173          0.715
LGA    V     174      V     174          2.608
LGA    G     175      G     175          1.805
LGA    D     176      D     176          2.069
LGA    S     177      S     177          3.056
LGA    Q     178      Q     178          1.978
LGA    N     179      N     179          1.607
LGA    D     180      D     180          2.167
LGA    I     181      I     181          2.094
LGA    F     182      F     182          2.395
LGA    A     183      A     183          2.602
LGA    A     184      A     184          2.468
LGA    H     185      H     185          2.543
LGA    S     186      S     186          3.316
LGA    A     187      A     187          2.595
LGA    G     188      G     188          1.944
LGA    C     189      C     189          1.196
LGA    A     190      A     190          1.218
LGA    V     191      V     191          1.592
LGA    V     192      V     192          1.242
LGA    G     193      G     193          1.392
LGA    L     194      L     194          1.379
LGA    T     195      T     195          4.326
LGA    Y     196      -       -           -
LGA    G     197      Y     196          0.827
LGA    Y     198      G     197          3.689
LGA    N     199      Y     198          4.293
LGA    Y     200      N     199          5.562
LGA    -       -      Y     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    N     201      P     203          3.241
LGA    I     202      I     204          5.488
LGA    P     203      A     205          3.310
LGA    I     204      Q     206          4.409
LGA    A     205      -       -           -
LGA    Q     206      -       -           -
LGA    S     207      S     207          2.567
LGA    K     208      K     208          4.154
LGA    P     209      P     209          1.945
LGA    D     210      D     210          2.698
LGA    W     211      -       -           -
LGA    I     212      W     211          0.685
LGA    F     213      I     212          3.064
LGA    D     214      F     213          5.376
LGA    -       -      D     214           -
LGA    D     215      D     215           #
LGA    F     216      F     216          3.871
LGA    A     217      A     217          4.140
LGA    D     218      D     218           #
LGA    I     219      -       -           -
LGA    L     220      I     219           #
LGA    K     221      L     220           -
LGA    I     222      K     221           -
LGA    T     223      I     222           -
LGA    Q     224      T     223           -
LGA    -       -      Q     224           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  147  147    5.0    127    2.67    92.13     53.842     4.586

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.354515 * X  +  -0.912448 * Y  +  -0.204346 * Z  + -10.393612
  Y_new =  -0.262777 * X  +   0.306954 * Y  +  -0.914728 * Z  +  80.222359
  Z_new =   0.897367 * X  +  -0.270588 * Y  +  -0.348590 * Z  +  16.537888 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.481512    0.660081  [ DEG:  -142.1801     37.8199 ]
  Theta =  -1.113766   -2.027827  [ DEG:   -63.8141   -116.1859 ]
  Phi   =  -2.503729    0.637864  [ DEG:  -143.4531     36.5469 ]
 
# 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_3-D1                               
REMARK     2: T0303_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS393_3-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  127   2.67   92.13  53.842
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS393_3-D1
PFRMAT TS
TARGET T0303
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1     -18.561  52.356   4.075  1.00 25.00           C
ATOM      2  CA  THR     2     -15.832  54.938   3.578  1.00 25.00           C
ATOM      3  CA  GLN     3     -17.846  57.138   5.983  1.00 25.00           C
ATOM      4  CA  PHE     4     -17.127  58.172   9.559  1.00 25.00           C
ATOM      5  CA  LYS     5     -18.401  61.746   9.531  1.00 25.00           C
ATOM      6  CA  LEU     6     -15.654  62.305  12.050  1.00 25.00           C
ATOM      7  CA  ILE     7     -14.820  65.569  13.790  1.00 25.00           C
ATOM      8  CA  GLY     8     -15.481  69.334  13.277  1.00 25.00           C
ATOM      9  CA  PHE     9     -13.642  71.136  16.117  1.00 25.00           C
ATOM     10  CA  ASP    10     -10.670  73.443  15.903  1.00 25.00           C
ATOM     11  CA  LEU    11     -10.242  76.647  17.928  1.00 25.00           C
ATOM     12  CA  ASP    12     -10.951  79.316  15.322  1.00 25.00           C
ATOM     13  CA  GLY    13     -14.179  79.665  13.297  1.00 25.00           C
ATOM     14  CA  THR    14     -15.098  76.063  12.885  1.00 25.00           C
ATOM     15  CA  LEU    15     -15.943  75.599  16.513  1.00 25.00           C
ATOM     16  CA  VAL    16     -14.963  78.041  19.237  1.00 25.00           C
ATOM     17  CA  ASN    17     -13.759  81.207  20.964  1.00 25.00           C
ATOM     95  CA  ARG    95     -20.019  83.367  26.779  1.00 25.00           C
ATOM     96  CA  LEU    96     -20.681  80.321  24.502  1.00 25.00           C
ATOM     97  CA  TYR    97     -21.136  81.059  20.765  1.00 25.00           C
ATOM     98  CA  PRO    98     -23.738  78.365  20.866  1.00 25.00           C
ATOM     99  CA  ASN    99     -23.595  77.944  17.045  1.00 25.00           C
ATOM    100  CA  VAL   100     -21.086  75.165  17.713  1.00 25.00           C
ATOM    101  CA  LYS   101     -22.545  73.483  20.828  1.00 25.00           C
ATOM    102  CA  GLU   102     -25.251  71.815  18.693  1.00 25.00           C
ATOM    103  CA  THR   103     -22.584  70.566  16.245  1.00 25.00           C
ATOM    104  CA  LEU   104     -20.535  69.158  19.158  1.00 25.00           C
ATOM    105  CA  GLU   105     -23.645  67.386  20.521  1.00 25.00           C
ATOM    106  CA  ALA   106     -24.344  65.900  17.060  1.00 25.00           C
ATOM    107  CA  LEU   107     -20.722  64.677  16.827  1.00 25.00           C
ATOM    108  CA  LYS   108     -21.012  63.079  20.295  1.00 25.00           C
ATOM    109  CA  ALA   109     -24.264  61.346  19.251  1.00 25.00           C
ATOM    110  CA  GLN   110     -22.854  57.883  19.951  1.00 25.00           C
ATOM    111  CA  GLY   111     -20.671  57.606  16.920  1.00 25.00           C
ATOM    112  CA  TYR   112     -17.988  60.183  16.218  1.00 25.00           C
ATOM    113  CA  ILE   113     -14.653  61.810  17.169  1.00 25.00           C
ATOM    114  CA  LEU   114     -11.126  62.932  18.120  1.00 25.00           C
ATOM    115  CA  ALA   115      -9.056  64.620  20.908  1.00 25.00           C
ATOM    116  CA  VAL   116      -8.871  68.262  22.022  1.00 25.00           C
ATOM    117  CA  VAL   117      -8.352  71.354  19.865  1.00 25.00           C
ATOM    118  CA  THR   118      -6.192  73.594  17.713  1.00 25.00           C
ATOM    119  CA  ASN   119      -2.721  74.835  16.719  1.00 25.00           C
ATOM    120  CA  LYS   120      -3.472  77.250  19.541  1.00 25.00           C
ATOM    121  CA  PRO   121      -2.660  75.204  22.665  1.00 25.00           C
ATOM    122  CA  THR   122      -2.996  72.287  25.157  1.00 25.00           C
ATOM    123  CA  LYS   123      -3.766  74.627  28.090  1.00 25.00           C
ATOM    124  CA  HIS   124      -6.284  76.543  25.932  1.00 25.00           C
ATOM    125  CA  VAL   125      -7.952  73.250  24.911  1.00 25.00           C
ATOM    126  CA  GLN   126      -8.165  72.190  28.585  1.00 25.00           C
ATOM    127  CA  PRO   127      -9.735  75.564  29.493  1.00 25.00           C
ATOM    128  CA  ILE   128     -12.287  75.164  26.665  1.00 25.00           C
ATOM    129  CA  LEU   129     -13.142  71.641  27.902  1.00 25.00           C
ATOM    130  CA  THR   130     -13.604  72.976  31.461  1.00 25.00           C
ATOM    131  CA  ALA   131     -15.900  75.747  30.150  1.00 25.00           C
ATOM    132  CA  PHE   132     -18.659  77.243  27.939  1.00 25.00           C
ATOM    133  CA  GLY   133     -21.560  74.767  27.967  1.00 25.00           C
ATOM    134  CA  ILE   134     -18.853  72.185  27.088  1.00 25.00           C
ATOM    135  CA  ASP   135     -17.215  68.757  26.905  1.00 25.00           C
ATOM    136  CA  HIS   136     -17.821  69.111  23.141  1.00 25.00           C
ATOM    137  CA  LEU   137     -14.329  70.618  22.695  1.00 25.00           C
ATOM    138  CA  PHE   138     -12.799  67.722  24.677  1.00 25.00           C
ATOM    139  CA  SER   139     -14.685  65.200  22.498  1.00 25.00           C
ATOM    140  CA  GLU   140     -13.424  66.953  19.335  1.00 25.00           C
ATOM    141  CA  MET   141     -10.417  67.786  17.145  1.00 25.00           C
ATOM    142  CA  LEU   142      -6.755  67.475  18.010  1.00 25.00           C
ATOM    143  CA  GLY   143      -4.078  68.438  20.473  1.00 25.00           C
ATOM    144  CA  GLY   144      -0.860  70.402  20.860  1.00 25.00           C
ATOM    145  CA  GLN   145       1.645  70.464  23.677  1.00 25.00           C
ATOM    146  CA  SER   146       2.838  66.934  22.739  1.00 25.00           C
ATOM    147  CA  LEU   147       5.325  66.396  19.866  1.00 25.00           C
ATOM    148  CA  PRO   148       7.336  69.559  20.517  1.00 25.00           C
ATOM    149  CA  GLU   149       5.858  72.183  18.147  1.00 25.00           C
ATOM    150  CA  ILE   150       2.783  74.104  16.973  1.00 25.00           C
ATOM    151  CA  LYS   151       1.682  73.415  13.428  1.00 25.00           C
ATOM    152  CA  PRO   152       2.119  73.491   9.600  1.00 25.00           C
ATOM    153  CA  HIS   153       2.379  69.705   9.760  1.00 25.00           C
ATOM    154  CA  PRO   154       0.700  67.909  12.668  1.00 25.00           C
ATOM    155  CA  ALA   155       2.070  65.458  15.273  1.00 25.00           C
ATOM    156  CA  PRO   156      -0.951  66.130  17.529  1.00 25.00           C
ATOM    157  CA  PHE   157      -3.319  65.518  14.581  1.00 25.00           C
ATOM    158  CA  TYR   158      -1.524  62.228  13.790  1.00 25.00           C
ATOM    159  CA  TYR   159      -1.828  61.153  17.453  1.00 25.00           C
ATOM    160  CA  LEU   160      -5.566  61.986  17.413  1.00 25.00           C
ATOM    161  CA  CYS   161      -6.012  59.942  14.205  1.00 25.00           C
ATOM    162  CA  GLY   162      -4.167  56.989  15.799  1.00 25.00           C
ATOM    163  CA  LYS   163      -6.410  57.229  18.895  1.00 25.00           C
ATOM    164  CA  PHE   164      -9.523  57.268  16.667  1.00 25.00           C
ATOM    165  CA  GLY   165      -9.691  54.013  14.609  1.00 25.00           C
ATOM    166  CA  LEU   166     -10.391  55.246  11.071  1.00 25.00           C
ATOM    167  CA  TYR   167      -6.645  55.593  10.642  1.00 25.00           C
ATOM    168  CA  PRO   168      -7.905  58.934   9.370  1.00 25.00           C
ATOM    169  CA  LYS   169     -10.677  57.729   7.019  1.00 25.00           C
ATOM    170  CA  GLN   170     -12.840  60.737   7.988  1.00 25.00           C
ATOM    171  CA  ILE   171     -10.882  62.949  10.365  1.00 25.00           C
ATOM    172  CA  LEU   172     -13.009  65.680   8.841  1.00 25.00           C
ATOM    173  CA  PHE   173     -11.035  68.461  10.548  1.00 25.00           C
ATOM    174  CA  VAL   174     -10.828  72.209  10.961  1.00 25.00           C
ATOM    175  CA  GLY   175     -10.547  75.999  10.328  1.00 25.00           C
ATOM    176  CA  ASP   176     -10.038  79.753  10.449  1.00 25.00           C
ATOM    177  CA  SER   177      -6.328  80.029  11.413  1.00 25.00           C
ATOM    178  CA  GLN   178      -4.965  78.695   8.074  1.00 25.00           C
ATOM    179  CA  ASN   179      -2.847  76.830  10.663  1.00 25.00           C
ATOM    180  CA  ASP   180      -5.858  74.655  11.595  1.00 25.00           C
ATOM    181  CA  ILE   181      -6.473  73.875   7.897  1.00 25.00           C
ATOM    182  CA  PHE   182      -2.789  72.919   7.462  1.00 25.00           C
ATOM    183  CA  ALA   183      -2.997  70.630  10.525  1.00 25.00           C
ATOM    184  CA  ALA   184      -6.149  68.980   9.110  1.00 25.00           C
ATOM    185  CA  HIS   185      -4.388  68.440   5.752  1.00 25.00           C
ATOM    186  CA  SER   186      -1.389  66.877   7.548  1.00 25.00           C
ATOM    187  CA  ALA   187      -2.764  63.744   9.132  1.00 25.00           C
ATOM    188  CA  GLY   188      -4.347  62.379   5.921  1.00 25.00           C
ATOM    189  CA  CYS   189      -7.463  64.046   7.234  1.00 25.00           C
ATOM    190  CA  ALA   190     -10.007  65.423   4.791  1.00 25.00           C
ATOM    191  CA  VAL   191     -10.065  69.153   5.610  1.00 25.00           C
ATOM    192  CA  VAL   192     -13.154  71.294   6.378  1.00 25.00           C
ATOM    193  CA  GLY   193     -14.577  74.838   6.668  1.00 25.00           C
ATOM    194  CA  LEU   194     -14.304  78.310   8.206  1.00 25.00           C
ATOM    195  CA  THR   195     -17.966  78.474   9.283  1.00 25.00           C
ATOM    196  CA  TYR   196     -18.990  80.573  12.357  1.00 25.00           C
ATOM    197  CA  GLY   197     -16.745  83.230  10.779  1.00 25.00           C
ATOM    198  CA  TYR   198     -13.785  83.611   8.391  1.00 25.00           C
ATOM    199  CA  ASN   199     -10.261  84.863   7.695  1.00 25.00           C
ATOM    200  CA  TYR   200     -10.839  83.362   4.250  1.00 25.00           C
ATOM    201  CA  ASN   201     -13.368  82.212   1.696  1.00 25.00           C
ATOM    202  CA  ILE   202     -12.089  81.262  -1.786  1.00 25.00           C
ATOM    203  CA  PRO   203      -8.599  80.605  -0.352  1.00 25.00           C
ATOM    204  CA  ILE   204     -10.115  78.408   2.394  1.00 25.00           C
ATOM    205  CA  ALA   205     -12.102  76.454  -0.231  1.00 25.00           C
ATOM    206  CA  GLN   206      -8.920  75.954  -2.304  1.00 25.00           C
ATOM    207  CA  SER   207      -5.280  76.117  -1.380  1.00 25.00           C
ATOM    208  CA  LYS   208      -5.777  72.767   0.456  1.00 25.00           C
ATOM    209  CA  PRO   209      -9.044  73.109   2.289  1.00 25.00           C
ATOM    210  CA  ASP   210     -10.777  70.727  -0.111  1.00 25.00           C
ATOM    211  CA  TRP   211     -13.998  72.210  -1.528  1.00 25.00           C
ATOM    212  CA  ILE   212     -15.931  72.450   1.661  1.00 25.00           C
ATOM    213  CA  PHE   213     -19.246  73.876   2.781  1.00 25.00           C
ATOM    214  CA  ASP   214     -21.641  71.577   4.591  1.00 25.00           C
ATOM    215  CA  ASP   215     -21.789  72.170   8.377  1.00 25.00           C
ATOM    216  CA  PHE   216     -24.284  72.900  11.138  1.00 25.00           C
ATOM    217  CA  ALA   217     -26.439  74.003   8.170  1.00 25.00           C
ATOM    218  CA  ASP   218     -27.421  77.199  10.038  1.00 25.00           C
ATOM    219  CA  ILE   219     -23.737  77.913  10.802  1.00 25.00           C
ATOM    220  CA  LEU   220     -22.846  77.395   7.113  1.00 25.00           C
ATOM    221  CA  LYS   221     -25.651  79.787   6.075  1.00 25.00           C
ATOM    222  CA  ILE   222     -24.379  82.401   8.569  1.00 25.00           C
ATOM    223  CA  THR   223     -20.827  82.028   7.185  1.00 25.00           C
ATOM    224  CA  GLN   224     -18.914  85.084   6.119  1.00 25.00           C
TER
END
