
#######################################################
#                                                     #
#                        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  140 (  140),  selected  140 , name T0379TS393_2-D1
# Molecule2: number of CA atoms  140 ( 1126),  selected  140 , name T0379_D1.pdb
# PARAMETERS: T0379TS393_2-D1.T0379_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    I       2      I       2          5.184
LGA    R       3      R       3          0.855
LGA    N       4      N       4          0.772
LGA    I       5      I       5          1.142
LGA    V       6      V       6          1.806
LGA    F       7      F       7          2.499
LGA    D       8      D       8          2.725
LGA    L       9      L       9          1.566
LGA    G      10      G      10          1.476
LGA    G      11      G      11          2.799
LGA    V      12      V      12          2.517
LGA    L      13      L      13          5.541
LGA    I      14      -       -           -
LGA    H      15      I      14           #
LGA    L      16      H      15          2.711
LGA    L      84      L      16           -
LGA    E      85      L      84           -
LGA    E      86      E      85           -
LGA    -       -      E      86           -
LGA    I      87      I      87          4.143
LGA    S      88      S      88          3.746
LGA    A      89      A      89          1.639
LGA    E      90      E      90          2.450
LGA    K      91      K      91          3.599
LGA    F      92      F      92          2.371
LGA    D      93      D      93          1.748
LGA    Y      94      Y      94          3.434
LGA    I      95      I      95          3.196
LGA    D      96      D      96          1.654
LGA    S      97      S      97          3.137
LGA    L      98      L      98          3.845
LGA    R      99      R      99          2.970
LGA    P     100      P     100          3.024
LGA    D     101      D     101          1.446
LGA    Y     102      Y     102          2.088
LGA    R     103      R     103          1.390
LGA    L     104      L     104          1.468
LGA    F     105      F     105          2.764
LGA    L     106      L     106          3.100
LGA    L     107      L     107          2.043
LGA    S     108      S     108          3.671
LGA    N     109      -       -           -
LGA    T     110      -       -           -
LGA    N     111      N     109          3.126
LGA    P     112      T     110          2.026
LGA    Y     113      N     111          1.707
LGA    V     114      P     112           #
LGA    L     115      Y     113           -
LGA    D     116      V     114           #
LGA    L     117      L     115          1.695
LGA    A     118      D     116           #
LGA    M     119      L     117           -
LGA    S     120      A     118           -
LGA    P     121      M     119          3.473
LGA    R     122      S     120          3.369
LGA    F     123      -       -           -
LGA    L     124      -       -           -
LGA    P     125      -       -           -
LGA    S     126      P     121          4.823
LGA    -       -      R     122           -
LGA    -       -      F     123           -
LGA    -       -      L     124           -
LGA    -       -      P     125           -
LGA    -       -      S     126           -
LGA    -       -      G     127           -
LGA    G     127      R     128          4.165
LGA    R     128      T     129          5.017
LGA    T     129      L     130           #
LGA    L     130      D     131          4.867
LGA    D     131      S     132          2.481
LGA    S     132      F     133          5.002
LGA    F     133      F     134          1.089
LGA    F     134      D     135           #
LGA    D     135      K     136          2.523
LGA    K     136      V     137          4.218
LGA    V     137      Y     138          3.585
LGA    Y     138      A     139          3.331
LGA    A     139      S     140          3.527
LGA    S     140      C     141           #
LGA    -       -      Q     142           -
LGA    C     141      M     143          4.413
LGA    Q     142      G     144          4.577
LGA    M     143      K     145          4.192
LGA    G     144      Y     146          4.728
LGA    K     145      -       -           -
LGA    Y     146      -       -           -
LGA    K     147      K     147          5.037
LGA    P     148      P     148          0.883
LGA    N     149      N     149          1.353
LGA    E     150      E     150          2.438
LGA    D     151      D     151          1.992
LGA    I     152      I     152          1.861
LGA    F     153      F     153          2.000
LGA    L     154      L     154          1.955
LGA    E     155      E     155          2.122
LGA    M     156      M     156          2.285
LGA    I     157      I     157          2.487
LGA    A     158      A     158          2.831
LGA    D     159      D     159          3.002
LGA    S     160      S     160          2.057
LGA    G     161      G     161          2.763
LGA    M     162      M     162          1.893
LGA    K     163      -       -           -
LGA    P     164      -       -           -
LGA    E     165      K     163          1.211
LGA    E     166      P     164          1.576
LGA    T     167      E     165           -
LGA    -       -      E     166           -
LGA    -       -      T     167           -
LGA    L     168      L     168          4.685
LGA    F     169      F     169          3.075
LGA    I     170      I     170          1.999
LGA    D     171      D     171          1.386
LGA    D     172      D     172          1.932
LGA    G     173      G     173          1.902
LGA    P     174      P     174          1.493
LGA    A     175      A     175          1.096
LGA    N     176      N     176          1.547
LGA    V     177      V     177          1.374
LGA    A     178      A     178          1.162
LGA    T     179      T     179          1.248
LGA    A     180      A     180          1.008
LGA    E     181      E     181          1.305
LGA    R     182      R     182          1.826
LGA    L     183      L     183          2.373
LGA    G     184      G     184          2.702
LGA    F     185      F     185          1.131
LGA    H     186      H     186          1.620
LGA    T     187      T     187          0.955
LGA    Y     188      Y     188          1.710
LGA    C     189      C     189          1.686
LGA    P     190      P     190          2.016
LGA    D     191      D     191          1.656
LGA    N     192      N     192           #
LGA    G     193      G     193           -
LGA    E     194      E     194           #
LGA    N     195      N     195           -
LGA    W     196      -       -           -
LGA    I     197      W     196           #
LGA    P     198      I     197           -
LGA    A     199      P     198           -
LGA    I     200      A     199           #
LGA    -       -      I     200           -
LGA    T     201      T     201           #
LGA    R     202      R     202           #
LGA    L     203      L     203          4.189
LGA    L     204      L     204          2.976
LGA    R     205      R     205          2.954
LGA    E     206      E     206          1.293
LGA    Q     207      Q     207          1.006

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  140  140    5.0    104    2.80    78.85     46.519     3.588

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.237373 * X  +   0.397004 * Y  +  -0.886590 * Z  +  58.704712
  Y_new =   0.658884 * X  +  -0.736445 * Y  +  -0.153363 * Z  +  13.793081
  Z_new =  -0.713811 * X  +  -0.547756 * Y  +  -0.436391 * Z  +   9.973497 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.243515    0.898077  [ DEG:  -128.5440     51.4560 ]
  Theta =   0.794925    2.346668  [ DEG:    45.5458    134.4542 ]
  Phi   =   1.225006   -1.916586  [ DEG:    70.1877   -109.8123 ]
 
# 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: T0379TS393_2-D1                               
REMARK     2: T0379_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS393_2-D1.T0379_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  140  140   5.0  104   2.80   78.85  46.519
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS393_2-D1
PFRMAT TS
TARGET T0379
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      47.285  21.442 -12.923  1.00 25.00           C
ATOM      2  CA  ILE     2      47.609  20.923  -9.152  1.00 25.00           C
ATOM      3  CA  ARG     3      51.322  21.379  -8.521  1.00 25.00           C
ATOM      4  CA  ASN     4      50.943  20.253  -4.943  1.00 25.00           C
ATOM      5  CA  ILE     5      54.517  19.143  -4.324  1.00 25.00           C
ATOM      6  CA  VAL     6      54.856  17.011  -1.129  1.00 25.00           C
ATOM      7  CA  PHE     7      57.651  18.303   1.155  1.00 25.00           C
ATOM      8  CA  ASP     8      58.366  15.159   3.105  1.00 25.00           C
ATOM      9  CA  LEU     9      58.260  15.754   6.871  1.00 25.00           C
ATOM     10  CA  GLY    10      60.651  13.680   8.969  1.00 25.00           C
ATOM     11  CA  GLY    11      62.465  12.823   5.711  1.00 25.00           C
ATOM     12  CA  VAL    12      63.383  14.675   2.593  1.00 25.00           C
ATOM     13  CA  LEU    13      66.048  15.994   0.303  1.00 25.00           C
ATOM     14  CA  ILE    14      68.418  15.275   3.168  1.00 25.00           C
ATOM     15  CA  HIS    15      70.918  15.790   5.986  1.00 25.00           C
ATOM     16  CA  LEU    16      68.107  14.246   8.053  1.00 25.00           C
ATOM     84  CA  LEU    84      63.999  18.747  18.780  1.00 25.00           C
ATOM     85  CA  GLU    85      64.682  22.411  17.901  1.00 25.00           C
ATOM     86  CA  GLU    86      67.120  22.800  15.070  1.00 25.00           C
ATOM     87  CA  ILE    87      66.366  20.972  11.772  1.00 25.00           C
ATOM     88  CA  SER    88      69.098  19.984   9.276  1.00 25.00           C
ATOM     89  CA  ALA    89      70.697  22.355   6.703  1.00 25.00           C
ATOM     90  CA  GLU    90      70.168  20.216   3.570  1.00 25.00           C
ATOM     91  CA  LYS    91      66.628  19.336   4.740  1.00 25.00           C
ATOM     92  CA  PHE    92      65.879  23.043   5.342  1.00 25.00           C
ATOM     93  CA  ASP    93      67.170  23.899   1.839  1.00 25.00           C
ATOM     94  CA  TYR    94      64.963  21.157   0.330  1.00 25.00           C
ATOM     95  CA  ILE    95      61.929  22.516   2.233  1.00 25.00           C
ATOM     96  CA  ASP    96      62.682  26.048   0.958  1.00 25.00           C
ATOM     97  CA  SER    97      62.944  24.725  -2.626  1.00 25.00           C
ATOM     98  CA  LEU    98      59.593  22.914  -2.230  1.00 25.00           C
ATOM     99  CA  ARG    99      57.986  26.129  -0.908  1.00 25.00           C
ATOM    100  CA  PRO   100      57.984  28.554  -3.802  1.00 25.00           C
ATOM    101  CA  ASP   101      56.054  27.397  -6.939  1.00 25.00           C
ATOM    102  CA  TYR   102      55.501  24.123  -5.017  1.00 25.00           C
ATOM    103  CA  ARG   103      52.945  24.476  -2.298  1.00 25.00           C
ATOM    104  CA  LEU   104      54.454  22.114   0.337  1.00 25.00           C
ATOM    105  CA  PHE   105      51.128  20.271   0.402  1.00 25.00           C
ATOM    106  CA  LEU   106      52.126  17.827   3.142  1.00 25.00           C
ATOM    107  CA  LEU   107      53.625  14.971   5.047  1.00 25.00           C
ATOM    108  CA  SER   108      51.256  12.861   7.113  1.00 25.00           C
ATOM    109  CA  ASN   109      52.693   9.356   6.549  1.00 25.00           C
ATOM    110  CA  THR   110      55.514   8.670   9.032  1.00 25.00           C
ATOM    111  CA  ASN   111      55.695  12.433   9.879  1.00 25.00           C
ATOM    112  CA  PRO   112      54.072  12.657  13.321  1.00 25.00           C
ATOM    113  CA  TYR   113      55.126  13.960  16.764  1.00 25.00           C
ATOM    114  CA  VAL   114      57.865  16.092  15.146  1.00 25.00           C
ATOM    115  CA  LEU   115      55.324  17.506  12.654  1.00 25.00           C
ATOM    116  CA  ASP   116      52.933  18.340  15.527  1.00 25.00           C
ATOM    117  CA  LEU   117      55.769  20.094  17.411  1.00 25.00           C
ATOM    118  CA  ALA   118      56.640  22.110  14.272  1.00 25.00           C
ATOM    119  CA  MET   119      52.967  23.114  13.869  1.00 25.00           C
ATOM    120  CA  SER   120      52.837  24.208  17.536  1.00 25.00           C
ATOM    121  CA  PRO   121      56.020  26.282  17.056  1.00 25.00           C
ATOM    122  CA  ARG   122      59.638  25.112  17.234  1.00 25.00           C
ATOM    123  CA  PHE   123      60.424  25.525  13.557  1.00 25.00           C
ATOM    124  CA  LEU   124      59.968  29.281  14.072  1.00 25.00           C
ATOM    125  CA  PRO   125      63.742  29.333  14.404  1.00 25.00           C
ATOM    126  CA  SER   126      65.217  32.082  12.198  1.00 25.00           C
ATOM    127  CA  GLY   127      61.780  32.964  10.701  1.00 25.00           C
ATOM    128  CA  ARG   128      63.025  30.603   7.941  1.00 25.00           C
ATOM    129  CA  THR   129      61.955  30.086   4.316  1.00 25.00           C
ATOM    130  CA  LEU   130      59.075  28.017   5.794  1.00 25.00           C
ATOM    131  CA  ASP   131      55.919  30.083   6.461  1.00 25.00           C
ATOM    132  CA  SER   132      54.175  28.425   3.481  1.00 25.00           C
ATOM    133  CA  PHE   133      55.173  24.966   4.789  1.00 25.00           C
ATOM    134  CA  PHE   134      53.806  25.857   8.254  1.00 25.00           C
ATOM    135  CA  ASP   135      50.520  27.038   6.683  1.00 25.00           C
ATOM    136  CA  LYS   136      50.264  23.769   4.703  1.00 25.00           C
ATOM    137  CA  VAL   137      51.926  21.208   6.971  1.00 25.00           C
ATOM    138  CA  TYR   138      51.994  17.911   8.881  1.00 25.00           C
ATOM    139  CA  ALA   139      49.224  17.037  11.293  1.00 25.00           C
ATOM    140  CA  SER   140      49.683  13.309  11.507  1.00 25.00           C
ATOM    141  CA  CYS   141      47.089  13.036  14.256  1.00 25.00           C
ATOM    142  CA  GLN   142      44.219  11.182  12.661  1.00 25.00           C
ATOM    143  CA  MET   143      46.653   8.699  11.024  1.00 25.00           C
ATOM    144  CA  GLY   144      45.341   5.996  13.412  1.00 25.00           C
ATOM    145  CA  LYS   145      47.724   3.748  11.479  1.00 25.00           C
ATOM    146  CA  TYR   146      50.868   5.939  11.448  1.00 25.00           C
ATOM    147  CA  LYS   147      52.507   4.611   8.275  1.00 25.00           C
ATOM    148  CA  PRO   148      49.210   5.746   6.828  1.00 25.00           C
ATOM    149  CA  ASN   149      45.358   5.868   6.769  1.00 25.00           C
ATOM    150  CA  GLU   150      45.039   8.881   4.480  1.00 25.00           C
ATOM    151  CA  ASP   151      43.123  10.799   7.186  1.00 25.00           C
ATOM    152  CA  ILE   152      46.224  12.928   7.906  1.00 25.00           C
ATOM    153  CA  PHE   153      46.611  13.674   4.171  1.00 25.00           C
ATOM    154  CA  LEU   154      42.924  14.690   3.966  1.00 25.00           C
ATOM    155  CA  GLU   155      43.367  16.995   6.993  1.00 25.00           C
ATOM    156  CA  MET   156      46.448  18.582   5.366  1.00 25.00           C
ATOM    157  CA  ILE   157      44.484  19.130   2.124  1.00 25.00           C
ATOM    158  CA  ALA   158      41.633  20.756   4.097  1.00 25.00           C
ATOM    159  CA  ASP   159      44.135  23.046   5.874  1.00 25.00           C
ATOM    160  CA  SER   160      45.667  24.029   2.503  1.00 25.00           C
ATOM    161  CA  GLY   161      44.640  23.029  -1.025  1.00 25.00           C
ATOM    162  CA  MET   162      45.501  21.557  -4.483  1.00 25.00           C
ATOM    163  CA  LYS   163      41.842  21.977  -5.464  1.00 25.00           C
ATOM    164  CA  PRO   164      41.174  18.579  -3.932  1.00 25.00           C
ATOM    165  CA  GLU   165      43.166  17.250  -6.923  1.00 25.00           C
ATOM    166  CA  GLU   166      45.817  15.824  -4.555  1.00 25.00           C
ATOM    167  CA  THR   167      47.688  17.214  -1.566  1.00 25.00           C
ATOM    168  CA  LEU   168      50.421  14.598  -1.821  1.00 25.00           C
ATOM    169  CA  PHE   169      52.062  11.908   0.270  1.00 25.00           C
ATOM    170  CA  ILE   170      55.823  11.277   0.228  1.00 25.00           C
ATOM    171  CA  ASP   171      57.707  10.106   3.283  1.00 25.00           C
ATOM    172  CA  ASP   172      59.114   6.887   4.866  1.00 25.00           C
ATOM    173  CA  GLY   173      57.411   3.723   3.662  1.00 25.00           C
ATOM    174  CA  PRO   174      55.003   2.372   0.990  1.00 25.00           C
ATOM    175  CA  ALA   175      51.998   3.064   3.263  1.00 25.00           C
ATOM    176  CA  ASN   176      52.244   6.807   2.489  1.00 25.00           C
ATOM    177  CA  VAL   177      52.366   6.047  -1.264  1.00 25.00           C
ATOM    178  CA  ALA   178      49.281   3.801  -0.934  1.00 25.00           C
ATOM    179  CA  THR   179      47.433   6.573   0.955  1.00 25.00           C
ATOM    180  CA  ALA   180      48.363   9.089  -1.778  1.00 25.00           C
ATOM    181  CA  GLU   181      47.090   6.676  -4.466  1.00 25.00           C
ATOM    182  CA  ARG   182      43.807   6.231  -2.547  1.00 25.00           C
ATOM    183  CA  LEU   183      42.709   9.609  -1.077  1.00 25.00           C
ATOM    184  CA  GLY   184      44.261  10.944  -4.244  1.00 25.00           C
ATOM    185  CA  PHE   185      47.507  11.409  -6.225  1.00 25.00           C
ATOM    186  CA  HIS   186      51.046  12.550  -6.856  1.00 25.00           C
ATOM    187  CA  THR   187      53.332  10.213  -4.945  1.00 25.00           C
ATOM    188  CA  TYR   188      56.436   8.238  -3.917  1.00 25.00           C
ATOM    189  CA  CYS   189      57.933   6.129  -1.084  1.00 25.00           C
ATOM    190  CA  PRO   190      61.228   7.441   0.361  1.00 25.00           C
ATOM    191  CA  ASP   191      64.633   5.779  -0.019  1.00 25.00           C
ATOM    192  CA  ASN   192      64.951   2.030  -0.678  1.00 25.00           C
ATOM    193  CA  GLY   193      61.822   1.767  -2.924  1.00 25.00           C
ATOM    194  CA  GLU   194      64.343   2.830  -5.605  1.00 25.00           C
ATOM    195  CA  ASN   195      61.776   2.087  -8.348  1.00 25.00           C
ATOM    196  CA  TRP   196      59.148   4.157  -6.484  1.00 25.00           C
ATOM    197  CA  ILE   197      61.628   7.057  -6.157  1.00 25.00           C
ATOM    198  CA  PRO   198      62.395   6.855  -9.905  1.00 25.00           C
ATOM    199  CA  ALA   199      58.649   6.901 -10.699  1.00 25.00           C
ATOM    200  CA  ILE   200      58.183   9.962  -8.446  1.00 25.00           C
ATOM    201  CA  THR   201      61.092  11.729 -10.203  1.00 25.00           C
ATOM    202  CA  ARG   202      59.549  10.929 -13.615  1.00 25.00           C
ATOM    203  CA  LEU   203      56.177  12.315 -12.442  1.00 25.00           C
ATOM    204  CA  LEU   204      57.893  15.509 -11.207  1.00 25.00           C
ATOM    205  CA  ARG   205      59.669  15.889 -14.578  1.00 25.00           C
ATOM    206  CA  GLU   206      56.337  15.439 -16.412  1.00 25.00           C
ATOM    207  CA  GLN   207      54.573  18.314 -18.205  1.00 25.00           C
TER
END
