
#######################################################
#                                                     #
#                        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 T0324TS393_5-D1
# Molecule2: number of CA atoms  142 ( 1080),  selected  142 , name T0324_D1.pdb
# PARAMETERS: T0324TS393_5-D1.T0324_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    Y       3      M       1           #
LGA    -       -      T       2           -
LGA    Q       4      Y       3          2.973
LGA    A       5      Q       4          3.754
LGA    L       6      A       5          2.931
LGA    -       -      L       6           -
LGA    M       7      M       7          1.430
LGA    F       8      F       8          1.647
LGA    D       9      D       9          2.185
LGA    I      10      I      10          2.227
LGA    D      11      D      11          2.815
LGA    -       -      G      12           -
LGA    G      12      T      13          0.807
LGA    T      13      L      14          2.773
LGA    L      14      -       -           -
LGA    T      15      -       -           -
LGA    N      16      T      15          4.966
LGA    E      82      N      16           -
LGA    -       -      E      82           -
LGA    L      83      L      83          3.683
LGA    -       -      Y      84           -
LGA    Y      84      P      85          3.910
LGA    P      85      G      86          3.017
LGA    -       -      I      87           -
LGA    -       -      T      88           -
LGA    G      86      S      89          2.249
LGA    I      87      L      90          4.423
LGA    T      88      F      91          2.802
LGA    S      89      E      92          1.036
LGA    L      90      Q      93          4.092
LGA    F      91      -       -           -
LGA    E      92      -       -           -
LGA    Q      93      L      94          1.965
LGA    L      94      P      95          3.008
LGA    P      95      S      96          2.186
LGA    S      96      E      97          2.990
LGA    E      97      L      98          3.548
LGA    L      98      -       -           -
LGA    R      99      R      99          2.208
LGA    L     100      L     100          2.569
LGA    G     101      G     101          2.269
LGA    I     102      I     102          0.559
LGA    V     103      V     103          0.728
LGA    T     104      T     104          0.756
LGA    S     105      S     105          3.495
LGA    Q     106      Q     106          2.958
LGA    R     107      R     107          3.727
LGA    R     108      R     108          2.155
LGA    N     109      N     109          2.173
LGA    E     110      E     110          2.737
LGA    L     111      L     111          2.563
LGA    E     112      E     112          2.665
LGA    S     113      S     113          3.425
LGA    G     114      G     114          4.978
LGA    M     115      M     115          5.040
LGA    R     116      R     116          2.255
LGA    S     117      S     117          1.031
LGA    Y     118      Y     118          2.188
LGA    P     119      P     119          2.789
LGA    F     120      F     120          2.198
LGA    M     121      M     121          3.133
LGA    M     122      M     122          2.542
LGA    R     123      R     123          3.446
LGA    M     124      M     124          0.642
LGA    A     125      A     125          0.620
LGA    V     126      V     126          2.349
LGA    T     127      T     127          1.274
LGA    I     128      I     128          1.275
LGA    S     129      S     129          1.864
LGA    A     130      A     130          2.537
LGA    D     131      D     131          3.586
LGA    D     132      D     132          3.500
LGA    T     133      T     133          2.892
LGA    P     134      P     134          3.613
LGA    K     135      K     135          1.298
LGA    R     136      R     136          2.865
LGA    K     137      K     137          2.029
LGA    P     138      P     138          5.271
LGA    D     139      D     139           #
LGA    P     140      P     140          3.250
LGA    L     141      L     141          1.915
LGA    P     142      P     142          2.122
LGA    L     143      L     143          2.344
LGA    L     144      L     144          1.880
LGA    T     145      T     145          1.420
LGA    A     146      A     146          1.704
LGA    L     147      L     147          1.620
LGA    E     148      E     148          1.188
LGA    K     149      K     149          1.076
LGA    V     150      V     150          1.617
LGA    N     151      N     151          2.560
LGA    V     152      V     152          2.737
LGA    A     153      A     153          3.632
LGA    P     154      P     154          3.170
LGA    Q     155      Q     155          3.567
LGA    N     156      N     156          1.931
LGA    A     157      A     157          2.584
LGA    L     158      L     158          1.976
LGA    F     159      F     159          5.076
LGA    I     160      I     160           #
LGA    G     161      G     161          3.140
LGA    D     162      D     162          2.047
LGA    S     163      S     163          1.230
LGA    V     164      V     164          0.743
LGA    S     165      S     165          0.821
LGA    D     166      D     166          0.590
LGA    E     167      E     167          0.707
LGA    Q     168      Q     168          0.809
LGA    T     169      T     169          0.783
LGA    A     170      A     170          0.528
LGA    Q     171      Q     171          0.758
LGA    A     172      A     172          1.219
LGA    A     173      A     173          1.149
LGA    N     174      N     174          2.034
LGA    V     175      V     175          1.381
LGA    D     176      D     176           #
LGA    F     177      -       -           -
LGA    G     178      F     177          5.080
LGA    L     179      G     178          3.567
LGA    A     180      L     179          4.047
LGA    V     181      A     180          2.246
LGA    W     182      V     181          1.777
LGA    G     183      W     182           #
LGA    M     184      G     183           -
LGA    D     185      M     184           -
LGA    P     186      -       -           -
LGA    N     187      -       -           -
LGA    A     188      -       -           -
LGA    D     189      -       -           -
LGA    H     190      -       -           -
LGA    Q     191      -       -           -
LGA    K     192      -       -           -
LGA    V     193      -       -           -
LGA    A     194      -       -           -
LGA    H     195      -       -           -
LGA    R     196      -       -           -
LGA    F     197      -       -           -
LGA    Q     198      -       -           -
LGA    K     199      D     185          4.173
LGA    P     200      P     186          3.822
LGA    L     201      N     187           #
LGA    -       -      A     188           -
LGA    -       -      D     189           -
LGA    -       -      H     190           -
LGA    -       -      Q     191           -
LGA    -       -      K     192           -
LGA    -       -      V     193           -
LGA    -       -      A     194           -
LGA    -       -      H     195           -
LGA    -       -      R     196           -
LGA    D     202      F     197           #
LGA    I     203      -       -           -
LGA    L     204      -       -           -
LGA    E     205      Q     198           #
LGA    L     206      K     199           #
LGA    F     207      P     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      I     203           -
LGA    -       -      L     204           -
LGA    -       -      E     205           -
LGA    -       -      L     206           -
LGA    -       -      F     207           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  142  142    5.0    106    2.70    77.36     44.599     3.784

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.627900 * X  +  -0.770155 * Y  +  -0.112265 * Z  +  25.874210
  Y_new =   0.664905 * X  +  -0.605785 * Y  +   0.436951 * Z  +  21.342585
  Z_new =  -0.404528 * X  +   0.199715 * Y  +   0.892452 * Z  +  21.210316 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.220155   -2.921437  [ DEG:    12.6140   -167.3860 ]
  Theta =   0.416463    2.725130  [ DEG:    23.8616    156.1384 ]
  Phi   =   2.327578   -0.814014  [ DEG:   133.3604    -46.6396 ]
 
# 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: T0324TS393_5-D1                               
REMARK     2: T0324_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS393_5-D1.T0324_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  142  142   5.0  106   2.70   77.36  44.599
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS393_5-D1
PFRMAT TS
TARGET T0324
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      34.675  33.200  47.575  1.00 25.00           C
ATOM      2  CA  THR     2      32.386  32.269  44.695  1.00 25.00           C
ATOM      3  CA  TYR     3      32.892  30.403  41.475  1.00 25.00           C
ATOM      4  CA  GLN     4      30.589  31.762  38.711  1.00 25.00           C
ATOM      5  CA  ALA     5      29.093  28.588  37.176  1.00 25.00           C
ATOM      6  CA  LEU     6      29.083  27.253  33.568  1.00 25.00           C
ATOM      7  CA  MET     7      27.703  26.681  30.100  1.00 25.00           C
ATOM      8  CA  PHE     8      27.961  26.235  26.275  1.00 25.00           C
ATOM      9  CA  ASP     9      24.815  24.043  26.144  1.00 25.00           C
ATOM     10  CA  ILE    10      26.552  22.211  23.375  1.00 25.00           C
ATOM     11  CA  ASP    11      24.893  23.371  20.104  1.00 25.00           C
ATOM     12  CA  GLY    12      28.048  25.294  19.203  1.00 25.00           C
ATOM     13  CA  THR    13      30.605  25.525  22.011  1.00 25.00           C
ATOM     14  CA  LEU    14      32.062  23.634  24.898  1.00 25.00           C
ATOM     15  CA  THR    15      33.601  20.255  24.160  1.00 25.00           C
ATOM     16  CA  ASN    16      33.708  19.803  20.358  1.00 25.00           C
ATOM     82  CA  GLU    82      40.668  22.835  13.800  1.00 25.00           C
ATOM     83  CA  LEU    83      38.524  21.988  16.826  1.00 25.00           C
ATOM     84  CA  TYR    84      37.386  25.429  18.071  1.00 25.00           C
ATOM     85  CA  PRO    85      40.886  26.912  18.341  1.00 25.00           C
ATOM     86  CA  GLY    86      40.011  27.636  21.941  1.00 25.00           C
ATOM     87  CA  ILE    87      38.033  24.777  23.603  1.00 25.00           C
ATOM     88  CA  THR    88      40.499  23.254  26.107  1.00 25.00           C
ATOM     89  CA  SER    89      42.463  26.539  26.209  1.00 25.00           C
ATOM     90  CA  LEU    90      39.223  28.487  26.823  1.00 25.00           C
ATOM     91  CA  PHE    91      38.291  26.089  29.660  1.00 25.00           C
ATOM     92  CA  GLU    92      41.763  26.539  31.214  1.00 25.00           C
ATOM     93  CA  GLN    93      41.398  30.345  30.989  1.00 25.00           C
ATOM     94  CA  LEU    94      37.961  30.139  32.667  1.00 25.00           C
ATOM     95  CA  PRO    95      39.428  27.969  35.461  1.00 25.00           C
ATOM     96  CA  SER    96      39.930  31.005  37.687  1.00 25.00           C
ATOM     97  CA  GLU    97      36.124  31.080  37.696  1.00 25.00           C
ATOM     98  CA  LEU    98      34.148  28.539  35.574  1.00 25.00           C
ATOM     99  CA  ARG    99      34.204  24.942  34.315  1.00 25.00           C
ATOM    100  CA  LEU   100      33.718  24.866  30.560  1.00 25.00           C
ATOM    101  CA  GLY   101      30.727  22.715  29.672  1.00 25.00           C
ATOM    102  CA  ILE   102      27.971  20.445  28.393  1.00 25.00           C
ATOM    103  CA  VAL   103      24.374  20.262  29.543  1.00 25.00           C
ATOM    104  CA  THR   104      23.647  18.444  26.270  1.00 25.00           C
ATOM    105  CA  SER   105      21.401  20.094  23.722  1.00 25.00           C
ATOM    106  CA  GLN   106      20.849  16.623  22.145  1.00 25.00           C
ATOM    107  CA  ARG   107      23.395  14.184  23.535  1.00 25.00           C
ATOM    108  CA  ARG   108      24.405  11.591  26.185  1.00 25.00           C
ATOM    109  CA  ASN   109      26.449   9.078  24.143  1.00 25.00           C
ATOM    110  CA  GLU   110      27.670  11.894  21.853  1.00 25.00           C
ATOM    111  CA  LEU   111      28.674  13.975  24.906  1.00 25.00           C
ATOM    112  CA  GLU   112      30.576  10.981  26.353  1.00 25.00           C
ATOM    113  CA  SER   113      32.382  10.485  23.013  1.00 25.00           C
ATOM    114  CA  GLY   114      33.325  14.196  22.943  1.00 25.00           C
ATOM    115  CA  MET   115      34.663  13.948  26.523  1.00 25.00           C
ATOM    116  CA  ARG   116      36.728  10.869  25.566  1.00 25.00           C
ATOM    117  CA  SER   117      38.145  12.731  22.534  1.00 25.00           C
ATOM    118  CA  TYR   118      38.443  15.498  19.882  1.00 25.00           C
ATOM    119  CA  PRO   119      41.449  16.653  21.846  1.00 25.00           C
ATOM    120  CA  PHE   120      38.911  18.325  24.180  1.00 25.00           C
ATOM    121  CA  MET   121      39.622  16.021  27.079  1.00 25.00           C
ATOM    122  CA  MET   122      39.825  18.799  29.644  1.00 25.00           C
ATOM    123  CA  ARG   123      36.743  20.749  28.504  1.00 25.00           C
ATOM    124  CA  MET   124      34.420  19.415  31.251  1.00 25.00           C
ATOM    125  CA  ALA   125      33.390  18.655  34.860  1.00 25.00           C
ATOM    126  CA  VAL   126      29.918  19.936  33.965  1.00 25.00           C
ATOM    127  CA  THR   127      29.482  16.893  31.699  1.00 25.00           C
ATOM    128  CA  ILE   128      25.819  15.705  31.425  1.00 25.00           C
ATOM    129  CA  SER   129      22.542  14.348  30.005  1.00 25.00           C
ATOM    130  CA  ALA   130      20.043  15.744  27.471  1.00 25.00           C
ATOM    131  CA  ASP   131      17.927  12.775  28.557  1.00 25.00           C
ATOM    132  CA  ASP   132      17.531  12.463  32.327  1.00 25.00           C
ATOM    133  CA  THR   133      14.955  13.837  34.718  1.00 25.00           C
ATOM    134  CA  PRO   134      11.823  15.422  33.367  1.00 25.00           C
ATOM    135  CA  LYS   135      13.622  16.218  30.055  1.00 25.00           C
ATOM    136  CA  ARG   136      12.064  18.341  27.370  1.00 25.00           C
ATOM    137  CA  LYS   137      13.763  21.587  26.363  1.00 25.00           C
ATOM    138  CA  PRO   138      16.962  19.508  26.208  1.00 25.00           C
ATOM    139  CA  ASP   139      18.745  22.199  28.090  1.00 25.00           C
ATOM    140  CA  PRO   140      16.274  21.580  30.883  1.00 25.00           C
ATOM    141  CA  LEU   141      16.032  19.001  33.703  1.00 25.00           C
ATOM    142  CA  PRO   142      19.205  17.275  32.431  1.00 25.00           C
ATOM    143  CA  LEU   143      21.026  20.642  32.329  1.00 25.00           C
ATOM    144  CA  LEU   144      19.900  21.388  35.913  1.00 25.00           C
ATOM    145  CA  THR   145      21.149  17.950  37.046  1.00 25.00           C
ATOM    146  CA  ALA   146      24.521  18.588  35.345  1.00 25.00           C
ATOM    147  CA  LEU   147      24.780  21.993  37.079  1.00 25.00           C
ATOM    148  CA  GLU   148      23.998  20.361  40.454  1.00 25.00           C
ATOM    149  CA  LYS   149      26.690  17.711  39.825  1.00 25.00           C
ATOM    150  CA  VAL   150      29.217  20.452  38.944  1.00 25.00           C
ATOM    151  CA  ASN   151      30.125  21.845  42.341  1.00 25.00           C
ATOM    152  CA  VAL   152      30.130  25.580  41.474  1.00 25.00           C
ATOM    153  CA  ALA   153      26.425  25.520  42.281  1.00 25.00           C
ATOM    154  CA  PRO   154      24.602  27.490  39.586  1.00 25.00           C
ATOM    155  CA  GLN   155      25.400  30.928  41.073  1.00 25.00           C
ATOM    156  CA  ASN   156      25.732  32.401  37.553  1.00 25.00           C
ATOM    157  CA  ALA   157      27.207  32.234  34.110  1.00 25.00           C
ATOM    158  CA  LEU   158      25.540  32.270  30.744  1.00 25.00           C
ATOM    159  CA  PHE   159      22.950  33.282  28.151  1.00 25.00           C
ATOM    160  CA  ILE   160      22.260  32.518  24.493  1.00 25.00           C
ATOM    161  CA  GLY   161      22.800  30.117  21.578  1.00 25.00           C
ATOM    162  CA  ASP   162      21.851  27.352  19.235  1.00 25.00           C
ATOM    163  CA  SER   163      18.276  27.167  20.492  1.00 25.00           C
ATOM    164  CA  VAL   164      15.332  29.192  21.900  1.00 25.00           C
ATOM    165  CA  SER   165      15.146  26.023  24.041  1.00 25.00           C
ATOM    166  CA  ASP   166      18.556  26.835  25.583  1.00 25.00           C
ATOM    167  CA  GLU   167      17.385  30.398  26.358  1.00 25.00           C
ATOM    168  CA  GLN   168      14.209  29.024  27.998  1.00 25.00           C
ATOM    169  CA  THR   169      16.311  26.613  30.105  1.00 25.00           C
ATOM    170  CA  ALA   170      18.584  29.500  31.184  1.00 25.00           C
ATOM    171  CA  GLN   171      15.520  31.583  32.154  1.00 25.00           C
ATOM    172  CA  ALA   172      14.139  28.647  34.190  1.00 25.00           C
ATOM    173  CA  ALA   173      17.517  28.184  35.972  1.00 25.00           C
ATOM    174  CA  ASN   174      19.105  31.437  37.137  1.00 25.00           C
ATOM    175  CA  VAL   175      21.729  32.313  34.531  1.00 25.00           C
ATOM    176  CA  ASP   176      22.018  28.595  33.954  1.00 25.00           C
ATOM    177  CA  PHE   177      22.785  27.811  30.321  1.00 25.00           C
ATOM    178  CA  GLY   178      23.097  28.448  26.586  1.00 25.00           C
ATOM    179  CA  LEU   179      26.418  30.224  26.158  1.00 25.00           C
ATOM    180  CA  ALA   180      27.657  30.768  22.613  1.00 25.00           C
ATOM    181  CA  VAL   181      28.888  31.147  18.988  1.00 25.00           C
ATOM    182  CA  TRP   182      26.861  34.361  19.132  1.00 25.00           C
ATOM    183  CA  GLY   183      28.665  36.003  22.065  1.00 25.00           C
ATOM    184  CA  MET   184      31.969  34.793  20.668  1.00 25.00           C
ATOM    185  CA  ASP   185      32.637  38.487  19.903  1.00 25.00           C
ATOM    186  CA  PRO   186      30.683  41.354  21.461  1.00 25.00           C
ATOM    187  CA  ASN   187      27.929  43.299  19.719  1.00 25.00           C
ATOM    188  CA  ALA   188      26.031  45.312  22.367  1.00 25.00           C
ATOM    189  CA  ASP   189      23.062  42.906  22.103  1.00 25.00           C
ATOM    190  CA  HIS   190      25.418  39.914  22.510  1.00 25.00           C
ATOM    191  CA  GLN   191      26.995  41.545  25.595  1.00 25.00           C
ATOM    192  CA  LYS   192      23.518  42.156  27.080  1.00 25.00           C
ATOM    193  CA  VAL   193      22.298  38.711  27.877  1.00 25.00           C
ATOM    194  CA  ALA   194      18.814  40.073  27.267  1.00 25.00           C
ATOM    195  CA  HIS   195      19.339  39.056  23.678  1.00 25.00           C
ATOM    196  CA  ARG   196      20.149  38.294  19.975  1.00 25.00           C
ATOM    197  CA  PHE   197      19.417  34.601  20.219  1.00 25.00           C
ATOM    198  CA  GLN   198      17.342  34.066  17.144  1.00 25.00           C
ATOM    199  CA  LYS   199      16.844  31.775  14.091  1.00 25.00           C
ATOM    200  CA  PRO   200      20.016  29.704  13.624  1.00 25.00           C
ATOM    201  CA  LEU   201      21.401  31.929  16.417  1.00 25.00           C
ATOM    202  CA  ASP   202      24.971  31.297  15.184  1.00 25.00           C
ATOM    203  CA  ILE   203      23.925  32.199  11.613  1.00 25.00           C
ATOM    204  CA  LEU   204      22.295  35.425  12.879  1.00 25.00           C
ATOM    205  CA  GLU   205      25.485  36.310  14.804  1.00 25.00           C
ATOM    206  CA  LEU   206      27.583  35.684  11.662  1.00 25.00           C
ATOM    207  CA  PHE   207      25.242  37.924   9.622  1.00 25.00           C
TER
END
