
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  153 ( 1188),  selected  153 , name T0330_D1.pdb
# PARAMETERS: T0330TS393_3-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      L       5          4.286
LGA    V       6      V       6          3.872
LGA    L       7      L       7           #
LGA    F       8      F       8          3.800
LGA    D       9      D       9          2.749
LGA    -       -      I      10           -
LGA    I      10      D      11           #
LGA    D      11      G      12          3.833
LGA    G      12      T      13           #
LGA    T      13      L      14           #
LGA    L      14      L      15           #
LGA    L      15      K      16          3.331
LGA    K      16      -       -           -
LGA    T      92      -       -           -
LGA    L      93      T      92           #
LGA    L      94      L      93          2.578
LGA    E      95      L      94          4.797
LGA    G      96      E      95          4.215
LGA    -       -      G      96           -
LGA    V      97      V      97          2.458
LGA    R      98      R      98          3.074
LGA    E      99      E      99          2.935
LGA    L     100      L     100          1.900
LGA    L     101      L     101          1.869
LGA    D     102      D     102          2.147
LGA    A     103      A     103          2.205
LGA    L     104      L     104          1.869
LGA    S     105      S     105          2.220
LGA    S     106      S     106          2.109
LGA    R     107      R     107          2.657
LGA    S     108      S     108          2.915
LGA    D     109      D     109           #
LGA    V     110      V     110          2.867
LGA    L     111      L     111          3.457
LGA    L     112      L     112          3.964
LGA    G     113      G     113          4.142
LGA    L     114      L     114          3.184
LGA    L     115      L     115          3.750
LGA    T     116      T     116          3.414
LGA    G     117      G     117          3.219
LGA    N     118      N     118          2.589
LGA    F     119      F     119          3.197
LGA    E     120      E     120          2.965
LGA    A     121      A     121          2.470
LGA    S     122      S     122          2.035
LGA    G     123      G     123          1.087
LGA    R     124      R     124          1.873
LGA    H     125      H     125          1.057
LGA    K     126      K     126          3.327
LGA    L     127      L     127          4.196
LGA    K     128      K     128          3.378
LGA    -       -      L     129           -
LGA    L     129      P     130          4.703
LGA    P     130      G     131          3.228
LGA    G     131      I     132          3.096
LGA    I     132      D     133          2.924
LGA    D     133      H     134          0.965
LGA    H     134      Y     135          2.128
LGA    Y     135      F     136          2.427
LGA    F     136      -       -           -
LGA    P     137      P     137          5.274
LGA    F     138      F     138          4.084
LGA    G     139      G     139          2.682
LGA    A     140      A     140          2.617
LGA    F     141      F     141          4.970
LGA    A     142      A     142          5.165
LGA    D     143      D     143           -
LGA    D     144      D     144           -
LGA    A     145      -       -           -
LGA    L     146      A     145           #
LGA    D     147      L     146          1.111
LGA    R     148      -       -           -
LGA    N     149      -       -           -
LGA    E     150      -       -           -
LGA    L     151      D     147          1.712
LGA    P     152      R     148          2.728
LGA    H     153      N     149          2.964
LGA    I     154      E     150          4.060
LGA    A     155      L     151          4.367
LGA    L     156      P     152          3.379
LGA    E     157      H     153          2.219
LGA    R     158      I     154          2.156
LGA    A     159      A     155          1.633
LGA    R     160      L     156          4.698
LGA    R     161      E     157          5.266
LGA    M     162      R     158          2.937
LGA    T     163      A     159          2.949
LGA    -       -      R     160           -
LGA    -       -      R     161           -
LGA    G     164      M     162          2.037
LGA    -       -      T     163           -
LGA    -       -      G     164           -
LGA    A     165      A     165          5.004
LGA    N     166      -       -           -
LGA    Y     167      -       -           -
LGA    S     168      N     166           #
LGA    P     169      Y     167           #
LGA    S     170      S     168          4.558
LGA    Q     171      P     169           #
LGA    -       -      S     170           -
LGA    -       -      Q     171           -
LGA    I     172      I     172           #
LGA    V     173      V     173          3.209
LGA    I     174      I     174          2.084
LGA    I     175      I     175          1.703
LGA    G     176      G     176          2.734
LGA    D     177      D     177          3.931
LGA    T     178      T     178          3.080
LGA    E     179      E     179          2.488
LGA    H     180      H     180          1.164
LGA    D     181      D     181          1.462
LGA    I     182      I     182          2.799
LGA    R     183      R     183          2.424
LGA    C     184      C     184          0.996
LGA    A     185      A     185          1.625
LGA    R     186      R     186          1.753
LGA    E     187      E     187          0.819
LGA    L     188      L     188          0.668
LGA    D     189      D     189          1.690
LGA    A     190      A     190          2.228
LGA    R     191      R     191          3.253
LGA    S     192      S     192           #
LGA    I     193      -       -           -
LGA    A     194      -       -           -
LGA    V     195      I     193           #
LGA    A     196      -       -           -
LGA    T     197      A     194           #
LGA    G     198      V     195          3.771
LGA    N     199      A     196          0.928
LGA    -       -      T     197           -
LGA    -       -      G     198           -
LGA    -       -      N     199           -
LGA    -       -      F     200           -
LGA    F     200      T     201           #
LGA    T     201      M     202          2.656
LGA    M     202      E     203          3.631
LGA    E     203      E     204          4.121
LGA    -       -      L     205           -
LGA    E     204      A     206          3.232
LGA    L     205      R     207           #
LGA    A     206      -       -           -
LGA    R     207      H     208          4.039
LGA    H     208      K     209          2.859
LGA    K     209      P     210          3.042
LGA    P     210      G     211          4.933
LGA    G     211      T     212          3.089
LGA    T     212      -       -           -
LGA    L     213      -       -           -
LGA    F     214      -       -           -
LGA    K     215      L     213           #
LGA    N     216      F     214           #
LGA    -       -      K     215           -
LGA    -       -      N     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      T     220           -
LGA    -       -      D     221           -
LGA    -       -      E     222           -
LGA    F     217      V     223          3.423
LGA    A     218      L     224          3.419
LGA    -       -      A     225           -
LGA    E     219      S     226          2.178
LGA    T     220      I     227          3.846
LGA    D     221      L     228          2.521
LGA    E     222      T     229          1.377
LGA    V     223      -       -           -
LGA    L     224      -       -           -
LGA    A     225      -       -           -
LGA    S     226      -       -           -
LGA    I     227      -       -           -
LGA    L     228      -       -           -
LGA    T     229      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    106    3.12    61.32     37.332     3.297

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.886159 * X  +  -0.216675 * Y  +   0.409602 * Z  +  18.877291
  Y_new =  -0.304862 * X  +   0.393083 * Y  +   0.867494 * Z  +  39.752087
  Z_new =  -0.348972 * X  +  -0.893609 * Y  +   0.282278 * Z  +  21.726242 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.264830    1.876762  [ DEG:   -72.4694    107.5306 ]
  Theta =   0.356474    2.785119  [ DEG:    20.4245    159.5755 ]
  Phi   =  -0.331343    2.810250  [ DEG:   -18.9846    161.0154 ]
 
# 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_3-D1                               
REMARK     2: T0330_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS393_3-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  106   3.12   61.32  37.332
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS393_3-D1
PFRMAT TS
TARGET T0330
MODEL 3
PARENT N/A
ATOM      2  CA  SER     2      19.382  42.725  36.899  1.00 25.00           C
ATOM      3  CA  ARG     3      20.700  46.053  35.455  1.00 25.00           C
ATOM      4  CA  THR     4      22.095  49.230  33.821  1.00 25.00           C
ATOM      5  CA  LEU     5      22.945  50.499  30.399  1.00 25.00           C
ATOM      6  CA  VAL     6      21.481  47.270  28.905  1.00 25.00           C
ATOM      7  CA  LEU     7      22.118  44.782  26.101  1.00 25.00           C
ATOM      8  CA  PHE     8      19.727  43.289  23.547  1.00 25.00           C
ATOM      9  CA  ASP     9      21.854  42.283  20.633  1.00 25.00           C
ATOM     10  CA  ILE    10      20.787  38.651  20.586  1.00 25.00           C
ATOM     11  CA  ASP    11      19.280  39.653  17.210  1.00 25.00           C
ATOM     12  CA  GLY    12      16.592  41.557  19.148  1.00 25.00           C
ATOM     13  CA  THR    13      16.926  44.075  16.239  1.00 25.00           C
ATOM     14  CA  LEU    14      16.485  41.867  13.163  1.00 25.00           C
ATOM     15  CA  LEU    15      16.312  38.068  13.318  1.00 25.00           C
ATOM     16  CA  LYS    16      19.621  36.283  12.907  1.00 25.00           C
ATOM     92  CA  THR    92       6.669  38.628  19.652  1.00 25.00           C
ATOM     93  CA  LEU    93       9.781  40.776  19.568  1.00 25.00           C
ATOM     94  CA  LEU    94      12.485  38.434  20.889  1.00 25.00           C
ATOM     95  CA  GLU    95      11.693  37.109  24.336  1.00 25.00           C
ATOM     96  CA  GLY    96      15.043  37.796  26.112  1.00 25.00           C
ATOM     97  CA  VAL    97      14.549  41.239  24.604  1.00 25.00           C
ATOM     98  CA  ARG    98      11.076  42.798  24.183  1.00 25.00           C
ATOM     99  CA  GLU    99      10.182  41.834  27.780  1.00 25.00           C
ATOM    100  CA  LEU   100      13.443  43.397  29.037  1.00 25.00           C
ATOM    101  CA  LEU   101      12.685  46.607  27.090  1.00 25.00           C
ATOM    102  CA  ASP   102       9.165  46.716  28.595  1.00 25.00           C
ATOM    103  CA  ALA   103      10.625  46.256  32.106  1.00 25.00           C
ATOM    104  CA  LEU   104      13.116  49.095  31.468  1.00 25.00           C
ATOM    105  CA  SER   105      10.270  51.357  30.265  1.00 25.00           C
ATOM    106  CA  SER   106       8.246  50.521  33.408  1.00 25.00           C
ATOM    107  CA  ARG   107      11.274  51.337  35.605  1.00 25.00           C
ATOM    108  CA  SER   108      11.305  54.762  33.865  1.00 25.00           C
ATOM    109  CA  ASP   109      13.022  55.595  30.528  1.00 25.00           C
ATOM    110  CA  VAL   110      16.280  54.268  29.167  1.00 25.00           C
ATOM    111  CA  LEU   111      17.912  51.922  26.615  1.00 25.00           C
ATOM    112  CA  LEU   112      17.535  48.236  25.913  1.00 25.00           C
ATOM    113  CA  GLY   113      20.025  48.421  23.066  1.00 25.00           C
ATOM    114  CA  LEU   114      19.847  46.807  19.608  1.00 25.00           C
ATOM    115  CA  LEU   115      20.991  47.181  15.965  1.00 25.00           C
ATOM    116  CA  THR   116      22.443  43.710  15.247  1.00 25.00           C
ATOM    117  CA  GLY   117      23.769  42.618  11.850  1.00 25.00           C
ATOM    118  CA  ASN   118      20.440  43.422  10.158  1.00 25.00           C
ATOM    119  CA  PHE   119      20.690  47.256  10.542  1.00 25.00           C
ATOM    120  CA  GLU   120      18.098  48.780   8.189  1.00 25.00           C
ATOM    121  CA  ALA   121      14.554  47.759   7.156  1.00 25.00           C
ATOM    122  CA  SER   122      14.817  44.591   9.292  1.00 25.00           C
ATOM    123  CA  GLY   123      16.004  46.675  12.279  1.00 25.00           C
ATOM    124  CA  ARG   124      13.063  49.081  11.800  1.00 25.00           C
ATOM    125  CA  HIS   125      10.633  46.123  11.676  1.00 25.00           C
ATOM    126  CA  LYS   126      12.153  44.707  14.893  1.00 25.00           C
ATOM    127  CA  LEU   127      11.790  48.118  16.595  1.00 25.00           C
ATOM    128  CA  LYS   128       8.131  48.313  15.482  1.00 25.00           C
ATOM    129  CA  LEU   129       7.499  44.796  16.862  1.00 25.00           C
ATOM    130  CA  PRO   130       5.088  46.587  19.226  1.00 25.00           C
ATOM    131  CA  GLY   131       7.217  46.148  22.347  1.00 25.00           C
ATOM    132  CA  ILE   132      10.736  47.018  21.195  1.00 25.00           C
ATOM    133  CA  ASP   133       9.252  50.350  20.226  1.00 25.00           C
ATOM    134  CA  HIS   134       9.810  51.396  23.868  1.00 25.00           C
ATOM    135  CA  TYR   135      13.577  50.815  23.483  1.00 25.00           C
ATOM    136  CA  PHE   136      15.203  48.127  21.418  1.00 25.00           C
ATOM    137  CA  PRO   137      16.068  51.021  19.026  1.00 25.00           C
ATOM    138  CA  PHE   138      17.597  53.191  21.692  1.00 25.00           C
ATOM    139  CA  GLY   139      20.468  52.118  19.447  1.00 25.00           C
ATOM    140  CA  ALA   140      23.060  51.472  16.718  1.00 25.00           C
ATOM    141  CA  PHE   141      26.234  50.409  15.060  1.00 25.00           C
ATOM    142  CA  ALA   142      25.305  47.443  12.911  1.00 25.00           C
ATOM    143  CA  ASP   143      28.430  46.588  14.862  1.00 25.00           C
ATOM    144  CA  ASP   144      28.773  43.763  12.290  1.00 25.00           C
ATOM    145  CA  ALA   145      31.437  45.687  10.397  1.00 25.00           C
ATOM    146  CA  LEU   146      28.870  46.315   7.660  1.00 25.00           C
ATOM    147  CA  ASP   147      29.034  49.879   6.507  1.00 25.00           C
ATOM    148  CA  ARG   148      26.257  52.408   6.481  1.00 25.00           C
ATOM    149  CA  ASN   149      28.164  53.950   9.386  1.00 25.00           C
ATOM    150  CA  GLU   150      31.936  53.493   9.476  1.00 25.00           C
ATOM    151  CA  LEU   151      33.457  50.317  10.942  1.00 25.00           C
ATOM    152  CA  PRO   152      32.524  50.050  14.561  1.00 25.00           C
ATOM    153  CA  HIS   153      33.769  53.618  14.894  1.00 25.00           C
ATOM    154  CA  ILE   154      33.110  57.197  16.089  1.00 25.00           C
ATOM    155  CA  ALA   155      29.787  57.247  14.185  1.00 25.00           C
ATOM    156  CA  LEU   156      28.800  53.905  15.771  1.00 25.00           C
ATOM    157  CA  GLU   157      29.665  55.269  19.243  1.00 25.00           C
ATOM    158  CA  ARG   158      27.552  58.391  18.571  1.00 25.00           C
ATOM    159  CA  ALA   159      24.620  56.196  17.451  1.00 25.00           C
ATOM    160  CA  ARG   160      24.952  54.089  20.632  1.00 25.00           C
ATOM    161  CA  ARG   161      24.968  57.269  22.766  1.00 25.00           C
ATOM    162  CA  MET   162      21.831  58.525  20.963  1.00 25.00           C
ATOM    163  CA  THR   163      18.902  59.313  23.321  1.00 25.00           C
ATOM    164  CA  GLY   164      19.696  62.881  24.519  1.00 25.00           C
ATOM    165  CA  ALA   165      23.191  61.440  24.922  1.00 25.00           C
ATOM    166  CA  ASN   166      24.267  63.237  21.751  1.00 25.00           C
ATOM    167  CA  TYR   167      27.668  61.884  22.669  1.00 25.00           C
ATOM    168  CA  SER   168      30.367  60.482  24.939  1.00 25.00           C
ATOM    169  CA  PRO   169      29.845  56.761  24.348  1.00 25.00           C
ATOM    170  CA  SER   170      28.029  56.877  27.673  1.00 25.00           C
ATOM    171  CA  GLN   171      26.247  53.674  26.698  1.00 25.00           C
ATOM    172  CA  ILE   172      23.340  51.749  25.070  1.00 25.00           C
ATOM    173  CA  VAL   173      25.398  48.553  25.209  1.00 25.00           C
ATOM    174  CA  ILE   174      28.332  46.479  23.928  1.00 25.00           C
ATOM    175  CA  ILE   175      26.250  43.365  23.389  1.00 25.00           C
ATOM    176  CA  GLY   176      27.871  40.125  22.142  1.00 25.00           C
ATOM    177  CA  ASP   177      30.358  38.592  19.706  1.00 25.00           C
ATOM    178  CA  THR   178      31.765  38.636  16.183  1.00 25.00           C
ATOM    179  CA  GLU   179      34.674  40.848  16.984  1.00 25.00           C
ATOM    180  CA  HIS   180      32.188  43.644  16.167  1.00 25.00           C
ATOM    181  CA  ASP   181      31.255  43.931  19.869  1.00 25.00           C
ATOM    182  CA  ILE   182      34.962  44.133  20.812  1.00 25.00           C
ATOM    183  CA  ARG   183      35.504  46.875  18.194  1.00 25.00           C
ATOM    184  CA  CYS   184      32.506  48.818  19.572  1.00 25.00           C
ATOM    185  CA  ALA   185      33.902  48.501  23.124  1.00 25.00           C
ATOM    186  CA  ARG   186      37.312  49.765  21.924  1.00 25.00           C
ATOM    187  CA  GLU   187      35.628  52.742  20.201  1.00 25.00           C
ATOM    188  CA  LEU   188      34.381  54.089  23.516  1.00 25.00           C
ATOM    189  CA  ASP   189      34.334  53.137  27.161  1.00 25.00           C
ATOM    190  CA  ALA   190      30.788  52.448  28.537  1.00 25.00           C
ATOM    191  CA  ARG   191      31.108  49.385  26.359  1.00 25.00           C
ATOM    192  CA  SER   192      29.918  51.671  23.636  1.00 25.00           C
ATOM    193  CA  ILE   193      27.735  50.072  20.901  1.00 25.00           C
ATOM    194  CA  ALA   194      26.617  46.671  19.570  1.00 25.00           C
ATOM    195  CA  VAL   195      26.520  43.127  18.081  1.00 25.00           C
ATOM    196  CA  ALA   196      26.495  40.160  15.769  1.00 25.00           C
ATOM    197  CA  THR   197      25.568  37.637  18.394  1.00 25.00           C
ATOM    198  CA  GLY   198      25.605  35.653  21.687  1.00 25.00           C
ATOM    199  CA  ASN   199      26.172  33.287  24.623  1.00 25.00           C
ATOM    200  CA  PHE   200      27.794  35.930  26.825  1.00 25.00           C
ATOM    201  CA  THR   201      30.364  33.217  27.445  1.00 25.00           C
ATOM    202  CA  MET   202      32.109  32.281  24.191  1.00 25.00           C
ATOM    203  CA  GLU   203      35.578  33.063  25.612  1.00 25.00           C
ATOM    204  CA  GLU   204      35.966  35.959  23.135  1.00 25.00           C
ATOM    205  CA  LEU   205      32.531  37.316  24.147  1.00 25.00           C
ATOM    206  CA  ALA   206      33.504  37.095  27.844  1.00 25.00           C
ATOM    207  CA  ARG   207      36.770  38.960  27.122  1.00 25.00           C
ATOM    208  CA  HIS   208      37.363  41.706  24.621  1.00 25.00           C
ATOM    209  CA  LYS   209      34.598  43.792  26.055  1.00 25.00           C
ATOM    210  CA  PRO   210      31.072  42.385  26.077  1.00 25.00           C
ATOM    211  CA  GLY   211      30.269  43.020  29.785  1.00 25.00           C
ATOM    212  CA  THR   212      28.195  45.861  28.382  1.00 25.00           C
ATOM    213  CA  LEU   213      25.230  43.465  28.341  1.00 25.00           C
ATOM    214  CA  PHE   214      21.880  41.669  28.285  1.00 25.00           C
ATOM    215  CA  LYS   215      23.377  38.798  30.283  1.00 25.00           C
ATOM    216  CA  ASN   216      22.977  39.852  33.859  1.00 25.00           C
ATOM    217  CA  PHE   217      22.500  43.565  33.155  1.00 25.00           C
ATOM    218  CA  ALA   218      22.225  44.745  36.789  1.00 25.00           C
ATOM    219  CA  GLU   219      25.767  43.471  37.496  1.00 25.00           C
ATOM    220  CA  THR   220      27.074  45.316  34.405  1.00 25.00           C
ATOM    221  CA  ASP   221      25.339  48.530  35.559  1.00 25.00           C
ATOM    222  CA  GLU   222      26.896  48.150  39.037  1.00 25.00           C
ATOM    223  CA  VAL   223      30.352  47.649  37.463  1.00 25.00           C
ATOM    224  CA  LEU   224      29.856  50.784  35.319  1.00 25.00           C
ATOM    225  CA  ALA   225      28.834  52.776  38.426  1.00 25.00           C
ATOM    226  CA  SER   226      31.946  51.531  40.278  1.00 25.00           C
ATOM    227  CA  ILE   227      34.148  52.551  37.316  1.00 25.00           C
ATOM    228  CA  LEU   228      32.534  56.024  37.280  1.00 25.00           C
ATOM    229  CA  THR   229      31.171  56.508  40.848  1.00 25.00           C
TER
END
