
#######################################################
#                                                     #
#                        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  142 (  142),  selected  142 , name T0378TS168_4-D2
# Molecule2: number of CA atoms  142 ( 1079),  selected  142 , name T0378_D2.pdb
# PARAMETERS: T0378TS168_4-D2.T0378_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     100      G     100          0.967
LGA    L     101      L     101          0.894
LGA    T     102      T     102          2.847
LGA    L     103      L     103          3.447
LGA    L     104      L     104          2.817
LGA    L     105      L     105          0.599
LGA    D     106      D     106          1.217
LGA    G     107      G     107          0.306
LGA    V     108      V     108          1.269
LGA    Q     109      Q     109          1.415
LGA    D     110      D     110          0.842
LGA    P     111      P     111          1.841
LGA    G     112      G     112          1.987
LGA    N     113      N     113          0.466
LGA    V     114      V     114          1.380
LGA    G     115      G     115          2.178
LGA    T     116      T     116          1.337
LGA    I     117      I     117          0.798
LGA    L     118      L     118          2.213
LGA    R     119      R     119          2.139
LGA    T     120      T     120          0.756
LGA    A     121      A     121          1.493
LGA    D     122      D     122          2.341
LGA    W     123      W     123          1.800
LGA    F     124      F     124          1.693
LGA    G     125      G     125          2.411
LGA    I     126      I     126          1.516
LGA    R     127      R     127          1.629
LGA    H     128      H     128          1.641
LGA    V     129      V     129          1.362
LGA    W     130      W     130          1.627
LGA    L     131      L     131          1.368
LGA    G     132      G     132          1.331
LGA    T     133      T     133          0.693
LGA    G     134      G     134          3.038
LGA    S     135      S     135          4.054
LGA    A     136      A     136          3.249
LGA    D     137      D     137          2.280
LGA    V     138      V     138          3.927
LGA    F     139      F     139          2.862
LGA    S     140      S     140          1.580
LGA    P     141      P     141          2.193
LGA    K     142      K     142          2.572
LGA    V     143      V     143          2.142
LGA    V     144      V     144          2.229
LGA    Q     145      Q     145          3.181
LGA    A     146      A     146          3.137
LGA    S     147      S     147          2.154
LGA    M     148      M     148          3.452
LGA    G     149      G     149          2.702
LGA    A     150      A     150          2.601
LGA    L     151      L     151          1.737
LGA    A     152      A     152          4.185
LGA    R     153      R     153          2.422
LGA    V     154      V     154          2.078
LGA    Q     155      Q     155          2.375
LGA    P     156      P     156          2.510
LGA    T     157      T     157          1.618
LGA    P     158      P     158          0.474
LGA    L     159      L     159          3.604
LGA    K     160      K     160          3.462
LGA    N     161      N     161          1.280
LGA    T     162      T     162          1.093
LGA    V     163      V     163          3.194
LGA    -       -      D     164           -
LGA    D     164      T     165          1.789
LGA    T     165      L     166          3.884
LGA    L     166      A     167          3.744
LGA    A     167      Y     168          1.983
LGA    Y     168      F     169          3.431
LGA    F     169      R     170          4.819
LGA    R     170      R     171          4.199
LGA    R     171      Q     172          3.772
LGA    Q     172      G     173          5.767
LGA    G     173      -       -           -
LGA    I     174      I     174          4.303
LGA    P     175      P     175          4.726
LGA    V     176      V     176          5.678
LGA    Y     177      Y     177          3.733
LGA    G     178      G     178          3.898
LGA    A     179      A     179          2.848
LGA    F     180      F     180           #
LGA    L     181      -       -           -
LGA    D     182      -       -           -
LGA    G     183      L     181          3.947
LGA    Q     184      D     182          2.155
LGA    S     185      G     183          2.146
LGA    L     186      Q     184          1.650
LGA    Y     187      S     185          2.575
LGA    E     188      L     186          2.261
LGA    A     189      Y     187          1.667
LGA    P     190      E     188          1.219
LGA    L     191      A     189          1.343
LGA    P     192      P     190          1.791
LGA    N     193      -       -           -
LGA    F     194      L     191          1.096
LGA    T     195      P     192          0.604
LGA    -       -      N     193           -
LGA    -       -      F     194           -
LGA    -       -      T     195           -
LGA    -       -      E     196           -
LGA    E     196      P     197           #
LGA    P     197      -       -           -
LGA    A     198      A     198           #
LGA    I     199      I     199          3.685
LGA    L     200      L     200          3.095
LGA    V     201      V     201          2.313
LGA    L     202      L     202          2.211
LGA    G     203      G     203          3.196
LGA    S     204      S     204          1.705
LGA    E     205      E     205          3.165
LGA    G     206      G     206          1.406
LGA    R     207      R     207          1.290
LGA    G     208      G     208          2.919
LGA    I     209      I     209          0.649
LGA    S     210      S     210          1.561
LGA    P     211      P     211          2.061
LGA    E     212      E     212          3.275
LGA    V     213      V     213          1.843
LGA    A     214      A     214          1.241
LGA    A     215      A     215          2.707
LGA    E     216      E     216          1.705
LGA    I     217      I     217          1.748
LGA    T     218      T     218          1.904
LGA    D     219      D     219          3.655
LGA    R     220      R     220          2.796
LGA    L     221      L     221          2.708
LGA    T     222      T     222          4.370
LGA    I     223      I     223           #
LGA    L     237      L     237          3.477
LGA    N     238      N     238          2.713
LGA    V     239      V     239          1.725
LGA    A     240      A     240          1.153
LGA    I     241      I     241          1.778
LGA    A     242      A     242          1.589
LGA    T     243      T     243          1.381
LGA    A     244      A     244          1.626
LGA    I     245      I     245          1.270
LGA    L     246      L     246          1.365
LGA    C     247      C     247          1.578
LGA    S     248      S     248          1.184
LGA    E     249      E     249          1.439
LGA    W     250      W     250          2.068
LGA    R     251      R     251          2.097
LGA    R     252      R     252          1.944
LGA    R     253      R     253          1.374
LGA    S     254      S     254          2.336

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  142  142    5.0    133    2.51    85.71     61.992     5.098

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.992733 * X  +  -0.011410 * Y  +  -0.119794 * Z  +  19.326200
  Y_new =   0.119990 * X  +  -0.169277 * Y  +  -0.978237 * Z  +   8.644900
  Z_new =  -0.009116 * X  +  -0.985503 * Y  +   0.169416 * Z  +  45.260555 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.400553    1.741040  [ DEG:   -80.2458     99.7542 ]
  Theta =   0.009116    3.132476  [ DEG:     0.5223    179.4777 ]
  Phi   =   3.021307   -0.120285  [ DEG:   173.1082     -6.8918 ]
 
# 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: T0378TS168_4-D2                               
REMARK     2: T0378_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS168_4-D2.T0378_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  142  142   5.0  133   2.51   85.71  61.992
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS168_4-D2
PFRMAT TS
TARGET T0378
MODEL 4
PARENT N/A
ATOM    100  CA  GLY   100      19.545  -6.928  47.958  1.00 25.00           C
ATOM    101  CA  LEU   101      21.183  -5.172  44.972  1.00 25.00           C
ATOM    102  CA  THR   102      21.819  -1.539  44.190  1.00 25.00           C
ATOM    103  CA  LEU   103      23.161   0.742  41.482  1.00 25.00           C
ATOM    104  CA  LEU   104      25.086   3.297  43.571  1.00 25.00           C
ATOM    105  CA  LEU   105      27.048   6.578  43.253  1.00 25.00           C
ATOM    106  CA  ASP   106      30.658   7.848  43.118  1.00 25.00           C
ATOM    107  CA  GLY   107      31.329  11.593  43.263  1.00 25.00           C
ATOM    108  CA  VAL   108      27.958  12.012  41.516  1.00 25.00           C
ATOM    109  CA  GLN   109      29.587  15.276  40.250  1.00 25.00           C
ATOM    110  CA  ASP   110      26.546  15.800  37.999  1.00 25.00           C
ATOM    111  CA  PRO   111      23.353  15.473  40.075  1.00 25.00           C
ATOM    112  CA  GLY   112      20.561  14.826  37.533  1.00 25.00           C
ATOM    113  CA  ASN   113      22.414  11.731  36.248  1.00 25.00           C
ATOM    114  CA  VAL   114      22.819  10.453  39.835  1.00 25.00           C
ATOM    115  CA  GLY   115      19.082  10.993  40.474  1.00 25.00           C
ATOM    116  CA  THR   116      18.231   9.084  37.266  1.00 25.00           C
ATOM    117  CA  ILE   117      20.519   6.207  38.340  1.00 25.00           C
ATOM    118  CA  LEU   118      18.831   6.116  41.777  1.00 25.00           C
ATOM    119  CA  ARG   119      15.385   6.025  40.108  1.00 25.00           C
ATOM    120  CA  THR   120      16.526   3.150  37.851  1.00 25.00           C
ATOM    121  CA  ALA   121      17.832   1.240  40.904  1.00 25.00           C
ATOM    122  CA  ASP   122      14.493   1.780  42.700  1.00 25.00           C
ATOM    123  CA  TRP   123      12.603   0.502  39.624  1.00 25.00           C
ATOM    124  CA  PHE   124      14.231  -2.802  40.570  1.00 25.00           C
ATOM    125  CA  GLY   125      13.632  -3.927  44.154  1.00 25.00           C
ATOM    126  CA  ILE   126      17.008  -2.328  44.692  1.00 25.00           C
ATOM    127  CA  ARG   127      16.326  -1.380  48.265  1.00 25.00           C
ATOM    128  CA  HIS   128      19.583   0.660  48.533  1.00 25.00           C
ATOM    129  CA  VAL   129      21.831   3.433  47.350  1.00 25.00           C
ATOM    130  CA  TRP   130      24.803   4.533  49.448  1.00 25.00           C
ATOM    131  CA  LEU   131      24.967   7.812  47.498  1.00 25.00           C
ATOM    132  CA  GLY   132      28.266   9.554  47.709  1.00 25.00           C
ATOM    133  CA  THR   133      31.268  11.745  48.394  1.00 25.00           C
ATOM    134  CA  GLY   134      32.871  15.165  48.225  1.00 25.00           C
ATOM    135  CA  SER   135      30.103  16.320  45.835  1.00 25.00           C
ATOM    136  CA  ALA   136      26.649  14.796  46.190  1.00 25.00           C
ATOM    137  CA  ASP   137      23.921  17.166  45.002  1.00 25.00           C
ATOM    138  CA  VAL   138      21.368  16.941  47.738  1.00 25.00           C
ATOM    139  CA  PHE   139      18.516  16.453  45.341  1.00 25.00           C
ATOM    140  CA  SER   140      17.174  19.821  44.196  1.00 25.00           C
ATOM    141  CA  PRO   141      14.545  19.854  41.451  1.00 25.00           C
ATOM    142  CA  LYS   142      16.647  17.402  39.395  1.00 25.00           C
ATOM    143  CA  VAL   143      15.839  14.594  41.871  1.00 25.00           C
ATOM    144  CA  VAL   144      12.108  15.431  41.639  1.00 25.00           C
ATOM    145  CA  GLN   145      12.303  15.357  37.815  1.00 25.00           C
ATOM    146  CA  ALA   146      14.058  11.955  37.946  1.00 25.00           C
ATOM    147  CA  SER   147      11.344  10.619  40.296  1.00 25.00           C
ATOM    148  CA  MET   148       8.498   8.087  40.484  1.00 25.00           C
ATOM    149  CA  GLY   149       8.535   8.198  44.229  1.00 25.00           C
ATOM    150  CA  ALA   150      11.480   5.844  44.657  1.00 25.00           C
ATOM    151  CA  LEU   151      13.466   8.443  46.647  1.00 25.00           C
ATOM    152  CA  ALA   152      11.926   7.160  49.909  1.00 25.00           C
ATOM    153  CA  ARG   153      11.545   3.409  49.169  1.00 25.00           C
ATOM    154  CA  VAL   154      15.289   3.980  48.489  1.00 25.00           C
ATOM    155  CA  GLN   155      17.573   6.872  49.427  1.00 25.00           C
ATOM    156  CA  PRO   156      20.233   9.232  48.088  1.00 25.00           C
ATOM    157  CA  THR   157      21.078   9.540  51.754  1.00 25.00           C
ATOM    158  CA  PRO   158      24.754  10.476  51.853  1.00 25.00           C
ATOM    159  CA  LEU   159      27.990  12.363  52.510  1.00 25.00           C
ATOM    160  CA  LYS   160      31.588  11.898  53.610  1.00 25.00           C
ATOM    161  CA  ASN   161      31.959   8.161  54.141  1.00 25.00           C
ATOM    162  CA  THR   162      32.437   5.042  51.939  1.00 25.00           C
ATOM    163  CA  VAL   163      33.652   3.319  55.137  1.00 25.00           C
ATOM    164  CA  ASP   164      30.058   3.168  56.449  1.00 25.00           C
ATOM    165  CA  THR   165      28.884   1.653  53.133  1.00 25.00           C
ATOM    166  CA  LEU   166      31.679  -0.960  53.309  1.00 25.00           C
ATOM    167  CA  ALA   167      30.674  -1.828  56.902  1.00 25.00           C
ATOM    168  CA  TYR   168      27.021  -2.204  55.815  1.00 25.00           C
ATOM    169  CA  PHE   169      28.087  -4.496  52.938  1.00 25.00           C
ATOM    170  CA  ARG   170      30.163  -6.614  55.361  1.00 25.00           C
ATOM    171  CA  ARG   171      27.168  -6.877  57.734  1.00 25.00           C
ATOM    172  CA  GLN   172      25.353  -9.818  56.147  1.00 25.00           C
ATOM    173  CA  GLY   173      26.082 -11.456  52.780  1.00 25.00           C
ATOM    174  CA  ILE   174      24.269  -8.354  51.594  1.00 25.00           C
ATOM    175  CA  PRO   175      25.465  -7.249  48.126  1.00 25.00           C
ATOM    176  CA  VAL   176      25.622  -3.667  46.858  1.00 25.00           C
ATOM    177  CA  TYR   177      27.214  -4.504  43.517  1.00 25.00           C
ATOM    178  CA  GLY   178      28.584  -2.761  40.504  1.00 25.00           C
ATOM    179  CA  ALA   179      29.138  -1.208  37.092  1.00 25.00           C
ATOM    180  CA  PHE   180      30.071  -1.411  33.448  1.00 25.00           C
ATOM    181  CA  LEU   181      31.397  -3.409  30.416  1.00 25.00           C
ATOM    182  CA  ASP   182      34.936  -3.994  29.248  1.00 25.00           C
ATOM    183  CA  GLY   183      38.331  -3.388  30.713  1.00 25.00           C
ATOM    184  CA  GLN   184      39.997  -5.066  33.750  1.00 25.00           C
ATOM    185  CA  SER   185      37.030  -7.461  33.570  1.00 25.00           C
ATOM    186  CA  LEU   186      34.349 -10.205  33.842  1.00 25.00           C
ATOM    187  CA  TYR   187      31.353  -7.952  34.134  1.00 25.00           C
ATOM    188  CA  GLU   188      28.627  -9.364  31.967  1.00 25.00           C
ATOM    189  CA  ALA   189      27.511 -13.015  32.266  1.00 25.00           C
ATOM    190  CA  PRO   190      30.586 -13.806  34.407  1.00 25.00           C
ATOM    191  CA  LEU   191      30.742 -12.817  38.119  1.00 25.00           C
ATOM    192  CA  PRO   192      29.273 -16.212  39.040  1.00 25.00           C
ATOM    193  CA  ASN   193      25.682 -15.070  38.505  1.00 25.00           C
ATOM    194  CA  PHE   194      24.927 -11.865  40.378  1.00 25.00           C
ATOM    195  CA  THR   195      24.090 -12.536  44.033  1.00 25.00           C
ATOM    196  CA  GLU   196      27.556 -11.370  44.912  1.00 25.00           C
ATOM    197  CA  PRO   197      29.925  -8.803  46.271  1.00 25.00           C
ATOM    198  CA  ALA   198      30.329  -5.257  47.563  1.00 25.00           C
ATOM    199  CA  ILE   199      29.875  -1.454  47.925  1.00 25.00           C
ATOM    200  CA  LEU   200      29.334   0.328  44.627  1.00 25.00           C
ATOM    201  CA  VAL   201      30.096   2.170  41.376  1.00 25.00           C
ATOM    202  CA  LEU   202      29.623   4.791  38.665  1.00 25.00           C
ATOM    203  CA  GLY   203      32.250   6.648  36.633  1.00 25.00           C
ATOM    204  CA  SER   204      29.909   9.497  37.311  1.00 25.00           C
ATOM    205  CA  GLU   205      31.664  11.514  34.599  1.00 25.00           C
ATOM    206  CA  GLY   206      35.423  10.982  35.233  1.00 25.00           C
ATOM    207  CA  ARG   207      38.077   9.497  37.446  1.00 25.00           C
ATOM    208  CA  GLY   208      35.157   8.701  39.720  1.00 25.00           C
ATOM    209  CA  ILE   209      36.263   5.192  40.675  1.00 25.00           C
ATOM    210  CA  SER   210      38.926   5.374  43.352  1.00 25.00           C
ATOM    211  CA  PRO   211      41.870   3.092  43.096  1.00 25.00           C
ATOM    212  CA  GLU   212      42.192   2.113  46.784  1.00 25.00           C
ATOM    213  CA  VAL   213      38.379   2.128  47.147  1.00 25.00           C
ATOM    214  CA  ALA   214      38.050  -0.082  44.035  1.00 25.00           C
ATOM    215  CA  ALA   215      40.646  -2.511  45.458  1.00 25.00           C
ATOM    216  CA  GLU   216      38.742  -2.641  48.778  1.00 25.00           C
ATOM    217  CA  ILE   217      35.381  -3.960  47.679  1.00 25.00           C
ATOM    218  CA  THR   218      37.155  -6.346  45.304  1.00 25.00           C
ATOM    219  CA  ASP   219      36.841  -5.200  41.667  1.00 25.00           C
ATOM    220  CA  ARG   220      35.399  -2.958  38.895  1.00 25.00           C
ATOM    221  CA  LEU   221      33.985  -3.782  35.463  1.00 25.00           C
ATOM    222  CA  THR   222      35.243  -0.689  33.637  1.00 25.00           C
ATOM    223  CA  ILE   223      33.816   1.024  30.563  1.00 25.00           C
ATOM    237  CA  LEU   237      27.612   6.931  27.692  1.00 25.00           C
ATOM    238  CA  ASN   238      25.975   9.321  30.202  1.00 25.00           C
ATOM    239  CA  VAL   239      27.288   7.499  33.193  1.00 25.00           C
ATOM    240  CA  ALA   240      23.876   7.196  34.907  1.00 25.00           C
ATOM    241  CA  ILE   241      22.514   5.245  31.906  1.00 25.00           C
ATOM    242  CA  ALA   242      25.542   2.903  32.024  1.00 25.00           C
ATOM    243  CA  THR   243      24.996   2.345  35.774  1.00 25.00           C
ATOM    244  CA  ALA   244      21.301   1.558  35.143  1.00 25.00           C
ATOM    245  CA  ILE   245      22.274  -0.934  32.403  1.00 25.00           C
ATOM    246  CA  LEU   246      24.775  -2.604  34.776  1.00 25.00           C
ATOM    247  CA  CYS   247      22.077  -2.855  37.482  1.00 25.00           C
ATOM    248  CA  SER   248      19.657  -4.420  34.960  1.00 25.00           C
ATOM    249  CA  GLU   249      22.339  -6.949  33.919  1.00 25.00           C
ATOM    250  CA  TRP   250      22.971  -7.827  37.593  1.00 25.00           C
ATOM    251  CA  ARG   251      19.213  -8.317  38.148  1.00 25.00           C
ATOM    252  CA  ARG   252      19.030 -10.590  35.071  1.00 25.00           C
ATOM    253  CA  ARG   253      20.198 -13.605  37.062  1.00 25.00           C
ATOM    254  CA  SER   254      18.756 -13.134  40.559  1.00 25.00           C
TER
END
