
#######################################################
#                                                     #
#                        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  155 (  155),  selected  155 , name T0321TS599_1-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS599_1-D2.T0321_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      97      -       -           -
LGA    I      98      -       -           -
LGA    F      99      -       -           -
LGA    S     100      -       -           -
LGA    D     101      -       -           -
LGA    A     102      -       -           -
LGA    K     103      -       -           -
LGA    R     104      -       -           -
LGA    V     105      -       -           -
LGA    E     106      -       -           -
LGA    D     107      -       -           -
LGA    R     108      -       -           -
LGA    M     109      -       -           -
LGA    N     110      -       -           -
LGA    D     111      -       -           -
LGA    P     112      -       -           -
LGA    F     113      -       -           -
LGA    I     114      -       -           -
LGA    M     115      -       -           -
LGA    S     116      -       -           -
LGA    Q     117      -       -           -
LGA    N     118      -       -           -
LGA    E     119      -       -           -
LGA    V     120      -       -           -
LGA    K     121      -       -           -
LGA    G     122      -       -           -
LGA    K     123      -       -           -
LGA    K     124      -       -           -
LGA    V     125      -       -           -
LGA    G     126      V      97           #
LGA    V     127      I      98           -
LGA    V     128      F      99           -
LGA    -       -      S     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      N     110           -
LGA    -       -      D     111           -
LGA    G     129      P     112           #
LGA    H     130      F     113           -
LGA    F     131      I     114           -
LGA    P     132      M     115           #
LGA    H     133      -       -           -
LGA    L     134      -       -           -
LGA    E     135      S     116          5.090
LGA    S     136      Q     117           #
LGA    L     137      N     118           #
LGA    L     138      E     119          3.779
LGA    E     139      V     120          2.089
LGA    P     140      K     121          2.554
LGA    I     141      G     122          2.503
LGA    C     142      K     123          4.076
LGA    D     143      K     124          3.112
LGA    L     144      V     125          2.295
LGA    S     145      G     126          1.628
LGA    I     146      V     127          0.870
LGA    L     147      V     128          0.554
LGA    E     148      G     129          1.551
LGA    W     149      H     130           -
LGA    -       -      F     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      E     135           -
LGA    -       -      S     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    -       -      E     139           -
LGA    -       -      P     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    -       -      L     144           -
LGA    -       -      S     145           -
LGA    -       -      I     146           -
LGA    -       -      L     147           -
LGA    S     150      E     148           #
LGA    P     151      W     149          2.954
LGA    E     152      S     150          4.375
LGA    E     153      -       -           -
LGA    G     154      -       -           -
LGA    D     155      P     151          1.830
LGA    Y     156      E     152          5.041
LGA    -       -      E     153           -
LGA    -       -      G     154           -
LGA    -       -      D     155           -
LGA    P     157      Y     156          3.414
LGA    L     158      P     157          2.341
LGA    P     159      L     158           -
LGA    A     160      P     159           -
LGA    S     161      A     160          4.220
LGA    -       -      S     161           -
LGA    E     162      E     162           #
LGA    F     163      F     163          4.796
LGA    I     164      I     164          4.098
LGA    L     165      L     165          2.623
LGA    P     166      P     166          4.187
LGA    E     167      E     167          3.348
LGA    C     168      C     168          2.262
LGA    D     169      D     169          1.207
LGA    Y     170      Y     170          0.796
LGA    V     171      V     171          0.932
LGA    Y     172      Y     172          0.830
LGA    I     173      I     173          0.258
LGA    T     174      T     174          0.414
LGA    C     175      C     175          1.100
LGA    A     176      A     176          1.458
LGA    S     177      S     177          2.033
LGA    V     178      V     178          4.147
LGA    V     179      V     179          4.291
LGA    -       -      D     180           -
LGA    D     180      K     181          1.390
LGA    K     181      T     182          1.762
LGA    T     182      L     183          3.230
LGA    L     183      P     184          2.839
LGA    P     184      R     185          1.656
LGA    R     185      L     186          2.195
LGA    L     186      L     187          2.718
LGA    L     187      E     188          2.677
LGA    E     188      L     189          2.744
LGA    L     189      S     190          2.904
LGA    S     190      R     191          2.964
LGA    R     191      -       -           -
LGA    N     192      N     192          3.776
LGA    A     193      A     193          4.489
LGA    R     194      R     194           #
LGA    R     195      R     195          3.410
LGA    I     196      I     196          1.792
LGA    T     197      T     197          1.642
LGA    L     198      L     198          1.518
LGA    V     199      V     199          2.390
LGA    G     200      G     200          4.730
LGA    -       -      P     201           -
LGA    P     201      G     202          2.339
LGA    G     202      T     203          4.446
LGA    T     203      P     204          3.793
LGA    P     204      L     205           #
LGA    L     205      A     206          3.391
LGA    A     206      -       -           -
LGA    P     207      P     207          3.938
LGA    V     208      V     208          2.630
LGA    L     209      L     209          3.483
LGA    F     210      F     210           #
LGA    E     211      -       -           -
LGA    H     212      E     211          4.504
LGA    G     213      H     212           -
LGA    -       -      G     213           -
LGA    L     214      L     214           #
LGA    Q     215      Q     215           #
LGA    E     216      E     216          5.001
LGA    L     217      L     217          4.753
LGA    S     218      S     218          2.875
LGA    G     219      G     219          3.436
LGA    F     220      F     220          2.697
LGA    M     221      M     221          4.782
LGA    V     222      V     222           #
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    K     223      A     228          5.249
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    D     224      I     231          4.086
LGA    N     225      V     232           #
LGA    A     226      A     233           -
LGA    R     227      G     234           #
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    A     228      K     239          4.423
LGA    F     229      I     240           -
LGA    R     230      -       -           -
LGA    I     231      -       -           -
LGA    V     232      -       -           -
LGA    A     233      -       -           -
LGA    G     234      -       -           -
LGA    A     235      -       -           -
LGA    E     236      -       -           -
LGA    K     237      -       -           -
LGA    V     238      -       -           -
LGA    K     239      Y     241           #
LGA    I     240      S     242           -
LGA    Y     241      A     243           -
LGA    S     242      G     244           -
LGA    -       -      Q     245           -
LGA    A     243      K     246           #
LGA    G     244      V     247           -
LGA    Q     245      T     248           -
LGA    K     246      I     249           -
LGA    V     247      K     250           -
LGA    T     248      K     251           -
LGA    I     249      -       -           -
LGA    K     250      -       -           -
LGA    K     251      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  155  148    5.0     72    3.19    48.61     29.844     2.186

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.774869 * X  +  -0.552362 * Y  +   0.307367 * Z  +   8.638841
  Y_new =  -0.102037 * X  +  -0.370573 * Y  +  -0.923182 * Z  +  33.378513
  Z_new =   0.623832 * X  +  -0.746707 * Y  +   0.230784 * Z  +  68.943420 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.271040    1.870553  [ DEG:   -72.8252    107.1748 ]
  Theta =  -0.673637   -2.467956  [ DEG:   -38.5965   -141.4035 ]
  Phi   =  -3.010664    0.130929  [ DEG:  -172.4983      7.5017 ]
 
# 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: T0321TS599_1-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS599_1-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  155  148   5.0   72   3.19   48.61  29.844
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS599_1-D2
PFRMAT TS                                                                       
TARGET T0321                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     97  CA  VAL    97      -8.261  25.949  60.137  1.00  0.00              
ATOM     98  CA  ILE    98      -5.569  25.024  57.987  1.00  0.00              
ATOM     99  CA  PHE    99      -4.685  27.291  54.727  1.00  0.00              
ATOM    100  CA  SER   100      -3.018  25.572  52.612  1.00  0.00              
ATOM    101  CA  ASP   101      -0.320  27.868  51.302  1.00  0.00              
ATOM    102  CA  ALA   102      -1.646  31.006  52.898  1.00  0.00              
ATOM    103  CA  LYS   103      -1.065  33.875  50.555  1.00  0.00              
ATOM    104  CA  ARG   104      -4.566  35.294  49.988  1.00  0.00              
ATOM    105  CA  VAL   105      -4.657  38.815  51.454  1.00  0.00              
ATOM    106  CA  GLU   106      -7.763  39.040  53.569  1.00  0.00              
ATOM    107  CA  ASP   107      -9.339  42.475  52.930  1.00  0.00              
ATOM    108  CA  ARG   108     -10.651  43.104  56.474  1.00  0.00              
ATOM    109  CA  MET   109      -7.340  43.094  58.278  1.00  0.00              
ATOM    110  CA  ASN   110      -5.127  45.465  56.312  1.00  0.00              
ATOM    111  CA  ASP   111      -7.494  48.478  56.304  1.00  0.00              
ATOM    112  CA  PRO   112      -8.108  48.219  60.084  1.00  0.00              
ATOM    113  CA  PHE   113      -4.428  48.046  61.052  1.00  0.00              
ATOM    114  CA  ILE   114      -3.550  51.010  58.870  1.00  0.00              
ATOM    115  CA  MET   115      -6.461  53.089  60.322  1.00  0.00              
ATOM    116  CA  SER   116      -5.414  52.248  63.870  1.00  0.00              
ATOM    117  CA  GLN   117      -1.803  53.282  63.219  1.00  0.00              
ATOM    118  CA  ASN   118      -2.796  56.624  61.626  1.00  0.00              
ATOM    119  CA  GLU   119      -5.167  57.711  64.407  1.00  0.00              
ATOM    120  CA  VAL   120      -2.660  57.041  67.080  1.00  0.00              
ATOM    121  CA  LYS   121      -2.235  59.547  69.850  1.00  0.00              
ATOM    122  CA  GLY   122      -3.429  57.821  73.081  1.00  0.00              
ATOM    123  CA  LYS   123      -3.531  54.398  71.658  1.00  0.00              
ATOM    124  CA  LYS   124      -2.436  51.468  73.623  1.00  0.00              
ATOM    125  CA  VAL   125      -0.382  48.934  71.743  1.00  0.00              
ATOM    126  CA  GLY   126       0.089  45.352  73.185  1.00  0.00              
ATOM    127  CA  VAL   127       3.239  43.543  72.300  1.00  0.00              
ATOM    128  CA  VAL   128       3.252  39.784  72.528  1.00  0.00              
ATOM    129  CA  GLY   129       6.524  38.287  73.332  1.00  0.00              
ATOM    130  CA  HIS   130       6.766  34.646  74.107  1.00  0.00              
ATOM    131  CA  PHE   131       7.253  32.932  77.317  1.00  0.00              
ATOM    132  CA  PRO   132       9.359  34.375  79.984  1.00  0.00              
ATOM    133  CA  HIS   133      12.173  31.785  80.128  1.00  0.00              
ATOM    134  CA  LEU   134      12.618  31.922  76.315  1.00  0.00              
ATOM    135  CA  GLU   135      12.794  35.736  76.166  1.00  0.00              
ATOM    136  CA  SER   136      15.304  35.689  78.915  1.00  0.00              
ATOM    137  CA  LEU   137      17.503  33.072  77.105  1.00  0.00              
ATOM    138  CA  LEU   138      17.518  35.034  73.871  1.00  0.00              
ATOM    139  CA  GLU   139      18.566  38.206  75.646  1.00  0.00              
ATOM    140  CA  PRO   140      21.286  36.438  77.665  1.00  0.00              
ATOM    141  CA  ILE   141      22.914  34.777  74.700  1.00  0.00              
ATOM    142  CA  CYS   142      22.504  37.741  72.331  1.00  0.00              
ATOM    143  CA  ASP   143      21.198  37.464  69.145  1.00  0.00              
ATOM    144  CA  LEU   144      18.023  39.975  68.300  1.00  0.00              
ATOM    145  CA  SER   145      17.048  40.848  65.074  1.00  0.00              
ATOM    146  CA  ILE   146      15.130  43.708  64.730  1.00  0.00              
ATOM    147  CA  LEU   147      12.413  44.306  61.298  1.00  0.00              
ATOM    148  CA  GLU   148      11.235  47.415  60.938  1.00  0.00              
ATOM    149  CA  TRP   149       8.890  48.325  57.820  1.00  0.00              
ATOM    150  CA  SER   150       9.961  51.861  57.266  1.00  0.00              
ATOM    151  CA  PRO   151      13.297  52.119  55.391  1.00  0.00              
ATOM    152  CA  GLU   152      14.184  55.565  56.682  1.00  0.00              
ATOM    153  CA  GLU   153      14.048  54.897  60.424  1.00  0.00              
ATOM    154  CA  GLY   154      16.290  51.784  60.571  1.00  0.00              
ATOM    155  CA  ASP   155      18.700  51.796  57.630  1.00  0.00              
ATOM    156  CA  TYR   156      19.176  48.220  56.925  1.00  0.00              
ATOM    157  CA  PRO   157      20.246  47.146  53.450  1.00  0.00              
ATOM    158  CA  LEU   158      18.033  44.296  52.249  1.00  0.00              
ATOM    159  CA  PRO   159      20.820  41.711  52.002  1.00  0.00              
ATOM    160  CA  ALA   160      22.048  42.419  55.562  1.00  0.00              
ATOM    161  CA  SER   161      18.684  42.191  57.007  1.00  0.00              
ATOM    162  CA  GLU   162      17.917  39.016  55.449  1.00  0.00              
ATOM    163  CA  PHE   163      21.177  37.477  56.569  1.00  0.00              
ATOM    164  CA  ILE   164      20.467  38.628  60.116  1.00  0.00              
ATOM    165  CA  LEU   165      16.952  37.118  60.014  1.00  0.00              
ATOM    166  CA  PRO   166      18.346  33.727  59.023  1.00  0.00              
ATOM    167  CA  GLU   167      20.664  33.670  61.944  1.00  0.00              
ATOM    168  CA  CYS   168      18.853  34.861  64.265  1.00  0.00              
ATOM    169  CA  ASP   169      17.063  33.138  67.387  1.00  0.00              
ATOM    170  CA  TYR   170      14.522  35.783  68.078  1.00  0.00              
ATOM    171  CA  VAL   171      13.185  37.924  65.836  1.00  0.00              
ATOM    172  CA  TYR   172      10.833  41.467  66.372  1.00  0.00              
ATOM    173  CA  ILE   173       8.798  42.868  64.380  1.00  0.00              
ATOM    174  CA  THR   174       7.404  46.251  64.524  1.00  0.00              
ATOM    175  CA  CYS   175       4.194  47.514  63.587  1.00  0.00              
ATOM    176  CA  ALA   176       4.205  48.425  59.845  1.00  0.00              
ATOM    177  CA  SER   177       6.202  45.378  58.814  1.00  0.00              
ATOM    178  CA  VAL   178       3.954  42.920  60.681  1.00  0.00              
ATOM    179  CA  VAL   179       0.656  44.319  59.337  1.00  0.00              
ATOM    180  CA  ASP   180       1.617  44.964  55.700  1.00  0.00              
ATOM    181  CA  LYS   181       3.206  41.667  54.845  1.00  0.00              
ATOM    182  CA  THR   182       1.034  39.810  57.218  1.00  0.00              
ATOM    183  CA  LEU   183       0.710  36.479  55.479  1.00  0.00              
ATOM    184  CA  PRO   184       4.248  36.081  54.511  1.00  0.00              
ATOM    185  CA  ARG   185       5.665  36.853  57.898  1.00  0.00              
ATOM    186  CA  LEU   186       3.299  34.682  59.859  1.00  0.00              
ATOM    187  CA  LEU   187       3.744  31.780  57.689  1.00  0.00              
ATOM    188  CA  GLU   188       7.498  31.889  57.788  1.00  0.00              
ATOM    189  CA  LEU   189       7.658  32.278  61.510  1.00  0.00              
ATOM    190  CA  SER   190       5.359  29.397  62.309  1.00  0.00              
ATOM    191  CA  ARG   191       7.201  26.994  60.069  1.00  0.00              
ATOM    192  CA  ASN   192      10.794  27.677  60.807  1.00  0.00              
ATOM    193  CA  ALA   193      10.705  27.659  64.555  1.00  0.00              
ATOM    194  CA  ARG   194      12.370  31.066  65.387  1.00  0.00              
ATOM    195  CA  ARG   195      10.781  32.666  67.502  1.00  0.00              
ATOM    196  CA  ILE   196       8.549  36.117  66.456  1.00  0.00              
ATOM    197  CA  THR   197       7.654  38.547  68.649  1.00  0.00              
ATOM    198  CA  LEU   198       4.870  41.319  67.266  1.00  0.00              
ATOM    199  CA  VAL   199       4.712  44.640  68.295  1.00  0.00              
ATOM    200  CA  GLY   200       2.218  46.930  67.008  1.00  0.00              
ATOM    201  CA  PRO   201       0.374  49.815  69.413  1.00  0.00              
ATOM    202  CA  GLY   202      -3.401  48.984  68.470  1.00  0.00              
ATOM    203  CA  THR   203      -5.384  47.757  71.258  1.00  0.00              
ATOM    204  CA  PRO   204      -7.392  45.043  69.592  1.00  0.00              
ATOM    205  CA  LEU   205      -4.503  42.864  68.421  1.00  0.00              
ATOM    206  CA  ALA   206      -3.057  42.719  71.899  1.00  0.00              
ATOM    207  CA  PRO   207      -6.048  41.288  73.587  1.00  0.00              
ATOM    208  CA  VAL   208      -6.189  38.609  70.884  1.00  0.00              
ATOM    209  CA  LEU   209      -2.466  37.694  71.472  1.00  0.00              
ATOM    210  CA  PHE   210      -2.997  37.417  75.269  1.00  0.00              
ATOM    211  CA  GLU   211      -6.117  35.195  74.613  1.00  0.00              
ATOM    212  CA  HIS   212      -3.869  32.916  72.473  1.00  0.00              
ATOM    213  CA  GLY   213      -1.486  32.163  75.238  1.00  0.00              
ATOM    214  CA  LEU   214       1.354  34.440  74.309  1.00  0.00              
ATOM    215  CA  GLN   215       3.652  35.049  77.172  1.00  0.00              
ATOM    216  CA  GLU   216       5.006  38.356  77.801  1.00  0.00              
ATOM    217  CA  LEU   217       3.285  41.438  76.981  1.00  0.00              
ATOM    218  CA  SER   218       4.999  44.497  76.266  1.00  0.00              
ATOM    219  CA  GLY   219       2.974  47.547  76.415  1.00  0.00              
ATOM    220  CA  PHE   220       3.627  50.085  74.113  1.00  0.00              
ATOM    221  CA  MET   221       1.942  54.024  74.459  1.00  0.00              
ATOM    222  CA  VAL   222       1.613  55.631  71.747  1.00  0.00              
ATOM    223  CA  LYS   223       2.117  59.694  71.831  1.00  0.00              
ATOM    224  CA  ASP   224       1.732  61.433  69.054  1.00  0.00              
ATOM    225  CA  ASN   225       2.888  59.396  66.072  1.00  0.00              
ATOM    226  CA  ALA   226       4.685  62.077  64.220  1.00  0.00              
ATOM    227  CA  ARG   227       6.759  63.094  67.174  1.00  0.00              
ATOM    228  CA  ALA   228       7.757  59.527  67.994  1.00  0.00              
ATOM    229  CA  PHE   229       8.648  58.710  64.521  1.00  0.00              
ATOM    230  CA  ARG   230      10.873  61.773  64.145  1.00  0.00              
ATOM    231  CA  ILE   231      12.581  60.984  67.426  1.00  0.00              
ATOM    232  CA  VAL   232      13.162  57.342  66.490  1.00  0.00              
ATOM    233  CA  ALA   233      14.593  58.091  63.024  1.00  0.00              
ATOM    234  CA  GLY   234      16.898  60.665  64.561  1.00  0.00              
ATOM    235  CA  ALA   235      18.219  58.619  67.489  1.00  0.00              
ATOM    236  CA  GLU   236      16.714  60.580  70.288  1.00  0.00              
ATOM    237  CA  LYS   237      13.317  60.256  72.019  1.00  0.00              
ATOM    238  CA  VAL   238      13.881  58.522  75.244  1.00  0.00              
ATOM    239  CA  LYS   239      10.783  56.393  75.466  1.00  0.00              
ATOM    240  CA  ILE   240      10.767  55.320  71.822  1.00  0.00              
ATOM    241  CA  TYR   241      14.454  54.262  71.655  1.00  0.00              
ATOM    242  CA  SER   242      14.496  52.063  74.748  1.00  0.00              
ATOM    243  CA  ALA   243      11.400  50.070  73.747  1.00  0.00              
ATOM    244  CA  GLY   244      12.351  49.523  70.128  1.00  0.00              
ATOM    245  CA  GLN   245      16.162  48.651  70.335  1.00  0.00              
ATOM    246  CA  LYS   246      17.132  46.741  67.989  1.00  0.00              
ATOM    247  CA  VAL   247      20.261  44.048  68.139  1.00  0.00              
ATOM    248  CA  THR   248      21.597  42.687  65.042  1.00  0.00              
ATOM    249  CA  ILE   249      23.671  39.650  65.253  1.00  0.00              
ATOM    250  CA  LYS   250      26.524  39.025  62.655  1.00  0.00              
ATOM    251  CA  LYS   251      25.063  42.217  63.471  1.00  0.00              
TER                                                                             
END
