
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  140 ( 1126),  selected  140 , name T0379_D1.pdb
# PARAMETERS: T0379TS393_5-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          4.690
LGA    R       3      R       3          2.364
LGA    N       4      N       4          1.564
LGA    I       5      I       5          1.282
LGA    V       6      V       6          2.048
LGA    F       7      F       7          3.478
LGA    D       8      D       8          1.372
LGA    L       9      L       9          1.391
LGA    G      10      G      10          0.923
LGA    G      11      G      11          4.138
LGA    V      12      V      12          4.104
LGA    L      13      -       -           -
LGA    I      14      -       -           -
LGA    H      15      -       -           -
LGA    L      16      L      13          4.604
LGA    -       -      I      14           -
LGA    -       -      H      15           -
LGA    -       -      L      16           -
LGA    L      84      L      84          3.588
LGA    E      85      E      85           -
LGA    E      86      E      86           -
LGA    I      87      I      87          1.780
LGA    S      88      S      88          3.724
LGA    A      89      A      89          1.726
LGA    E      90      E      90          2.781
LGA    K      91      K      91          3.662
LGA    F      92      F      92          2.419
LGA    D      93      D      93          1.932
LGA    Y      94      Y      94          3.368
LGA    I      95      I      95          2.985
LGA    D      96      D      96          1.539
LGA    S      97      S      97          2.917
LGA    L      98      L      98          3.283
LGA    R      99      R      99          2.457
LGA    P     100      P     100          2.880
LGA    D     101      D     101          2.129
LGA    Y     102      Y     102          1.996
LGA    R     103      R     103          1.090
LGA    L     104      L     104          0.989
LGA    F     105      F     105          2.041
LGA    L     106      L     106          4.204
LGA    L     107      L     107          1.795
LGA    S     108      S     108          4.538
LGA    N     109      -       -           -
LGA    T     110      N     109          2.353
LGA    N     111      -       -           -
LGA    P     112      -       -           -
LGA    Y     113      -       -           -
LGA    V     114      T     110          1.910
LGA    L     115      N     111          5.172
LGA    D     116      P     112          3.631
LGA    L     117      Y     113          4.839
LGA    A     118      V     114          4.349
LGA    M     119      L     115          1.919
LGA    S     120      D     116          2.422
LGA    P     121      L     117          2.732
LGA    R     122      A     118          1.467
LGA    F     123      M     119          3.726
LGA    L     124      -       -           -
LGA    P     125      S     120          2.150
LGA    S     126      P     121          1.952
LGA    G     127      R     122           -
LGA    -       -      F     123           -
LGA    -       -      L     124           -
LGA    -       -      P     125           -
LGA    -       -      S     126           -
LGA    -       -      G     127           -
LGA    R     128      R     128          1.096
LGA    T     129      T     129          5.208
LGA    L     130      L     130          2.964
LGA    D     131      D     131          2.117
LGA    S     132      S     132          3.692
LGA    F     133      F     133          3.808
LGA    F     134      F     134           #
LGA    D     135      D     135          4.813
LGA    K     136      K     136          1.736
LGA    V     137      V     137          3.082
LGA    Y     138      Y     138          2.225
LGA    A     139      A     139          2.443
LGA    S     140      S     140          4.414
LGA    -       -      C     141           -
LGA    -       -      Q     142           -
LGA    -       -      M     143           -
LGA    C     141      G     144           #
LGA    Q     142      K     145          3.078
LGA    M     143      Y     146          3.685
LGA    G     144      -       -           -
LGA    K     145      -       -           -
LGA    Y     146      -       -           -
LGA    K     147      K     147          3.748
LGA    P     148      P     148          2.106
LGA    N     149      N     149          3.094
LGA    E     150      E     150          1.060
LGA    D     151      D     151          1.784
LGA    I     152      I     152          1.290
LGA    F     153      F     153          0.768
LGA    L     154      L     154          1.664
LGA    E     155      E     155          1.661
LGA    M     156      M     156          1.366
LGA    I     157      I     157          2.339
LGA    A     158      A     158          2.942
LGA    D     159      D     159          2.939
LGA    S     160      S     160          2.831
LGA    G     161      G     161          4.805
LGA    M     162      M     162          3.813
LGA    K     163      K     163          3.616
LGA    P     164      P     164          3.165
LGA    E     165      E     165          2.397
LGA    E     166      E     166          2.921
LGA    T     167      T     167          3.446
LGA    L     168      L     168          3.084
LGA    F     169      F     169          2.683
LGA    I     170      I     170          2.837
LGA    D     171      D     171          2.755
LGA    D     172      D     172          1.574
LGA    G     173      G     173          2.091
LGA    P     174      P     174          1.416
LGA    A     175      A     175          1.219
LGA    N     176      N     176          1.356
LGA    V     177      V     177          1.650
LGA    A     178      A     178          1.325
LGA    T     179      T     179          1.509
LGA    A     180      A     180          1.801
LGA    E     181      E     181          1.590
LGA    R     182      R     182          1.409
LGA    L     183      L     183          1.781
LGA    G     184      G     184          1.591
LGA    F     185      F     185          0.529
LGA    H     186      H     186          0.583
LGA    T     187      T     187          0.848
LGA    Y     188      Y     188          1.936
LGA    C     189      C     189          1.051
LGA    P     190      P     190          2.711
LGA    D     191      D     191          2.631
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    -       -      I     197           -
LGA    -       -      P     198           -
LGA    P     198      A     199           #
LGA    A     199      -       -           -
LGA    I     200      -       -           -
LGA    T     201      I     200          4.430
LGA    R     202      T     201           -
LGA    -       -      R     202           -
LGA    L     203      L     203          4.669
LGA    L     204      L     204          3.214
LGA    R     205      R     205          3.219
LGA    E     206      E     206          2.596
LGA    Q     207      Q     207          0.945

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  140  140    5.0    113    2.81    85.84     47.786     3.887

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.346372 * X  +   0.561377 * Y  +  -0.751587 * Z  +  60.594692
  Y_new =   0.937175 * X  +   0.242591 * Y  +  -0.250705 * Z  +  12.538970
  Z_new =   0.041588 * X  +  -0.791205 * Y  +  -0.610135 * Z  +   8.010575 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.227694    0.913899  [ DEG:  -127.6375     52.3625 ]
  Theta =  -0.041600   -3.099993  [ DEG:    -2.3835   -177.6165 ]
  Phi   =   1.924817   -1.216776  [ DEG:   110.2839    -69.7161 ]
 
# 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_5-D1                               
REMARK     2: T0379_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS393_5-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  113   2.81   85.84  47.786
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS393_5-D1
PFRMAT TS
TARGET T0379
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      48.330  23.397 -12.077  1.00 25.00           C
ATOM      2  CA  ILE     2      48.495  21.305  -8.877  1.00 25.00           C
ATOM      3  CA  ARG     3      50.933  23.360  -6.754  1.00 25.00           C
ATOM      4  CA  ASN     4      52.806  20.691  -4.819  1.00 25.00           C
ATOM      5  CA  ILE     5      54.889  18.524  -2.503  1.00 25.00           C
ATOM      6  CA  VAL     6      55.464  17.244   0.995  1.00 25.00           C
ATOM      7  CA  PHE     7      55.777  18.725   4.473  1.00 25.00           C
ATOM      8  CA  ASP     8      56.563  15.203   5.833  1.00 25.00           C
ATOM      9  CA  LEU     9      58.709  15.722   8.966  1.00 25.00           C
ATOM     10  CA  GLY    10      60.898  12.686   8.530  1.00 25.00           C
ATOM     11  CA  GLY    11      61.838  13.869   5.029  1.00 25.00           C
ATOM     12  CA  VAL    12      60.130  15.631   2.131  1.00 25.00           C
ATOM     13  CA  LEU    13      60.371  17.569  -1.159  1.00 25.00           C
ATOM     14  CA  ILE    14      63.990  16.645  -0.939  1.00 25.00           C
ATOM     15  CA  HIS    15      67.711  16.181  -0.764  1.00 25.00           C
ATOM     16  CA  LEU    16      67.067  14.436   2.535  1.00 25.00           C
ATOM     84  CA  LEU    84      67.514  16.638  15.452  1.00 25.00           C
ATOM     85  CA  GLU    85      68.292  20.354  14.951  1.00 25.00           C
ATOM     86  CA  GLU    86      69.604  22.335  11.978  1.00 25.00           C
ATOM     87  CA  ILE    87      67.782  19.724   9.894  1.00 25.00           C
ATOM     88  CA  SER    88      71.246  18.758   8.812  1.00 25.00           C
ATOM     89  CA  ALA    89      70.983  21.896   6.605  1.00 25.00           C
ATOM     90  CA  GLU    90      70.130  19.694   3.590  1.00 25.00           C
ATOM     91  CA  LYS    91      66.511  19.390   4.807  1.00 25.00           C
ATOM     92  CA  PHE    92      66.301  23.192   5.212  1.00 25.00           C
ATOM     93  CA  ASP    93      67.673  23.671   1.668  1.00 25.00           C
ATOM     94  CA  TYR    94      65.086  21.196   0.306  1.00 25.00           C
ATOM     95  CA  ILE    95      62.293  23.072   2.137  1.00 25.00           C
ATOM     96  CA  ASP    96      63.530  26.389   0.676  1.00 25.00           C
ATOM     97  CA  SER    97      63.573  24.856  -2.834  1.00 25.00           C
ATOM     98  CA  LEU    98      60.002  23.566  -2.341  1.00 25.00           C
ATOM     99  CA  ARG    99      58.878  27.041  -1.189  1.00 25.00           C
ATOM    100  CA  PRO   100      59.082  29.247  -4.313  1.00 25.00           C
ATOM    101  CA  ASP   101      55.857  28.573  -6.298  1.00 25.00           C
ATOM    102  CA  TYR   102      55.129  25.440  -4.322  1.00 25.00           C
ATOM    103  CA  ARG   103      52.040  24.903  -2.071  1.00 25.00           C
ATOM    104  CA  LEU   104      54.369  23.186   0.446  1.00 25.00           C
ATOM    105  CA  PHE   105      51.534  20.769   0.851  1.00 25.00           C
ATOM    106  CA  LEU   106      50.804  17.659   2.994  1.00 25.00           C
ATOM    107  CA  LEU   107      51.625  14.603   5.101  1.00 25.00           C
ATOM    108  CA  SER   108      53.122  11.212   5.965  1.00 25.00           C
ATOM    109  CA  ASN   109      54.642   8.429   7.959  1.00 25.00           C
ATOM    110  CA  THR   110      54.790  11.595  10.029  1.00 25.00           C
ATOM    111  CA  ASN   111      52.116   9.848  12.144  1.00 25.00           C
ATOM    112  CA  PRO   112      50.924  11.943  15.110  1.00 25.00           C
ATOM    113  CA  TYR   113      54.119  11.406  17.155  1.00 25.00           C
ATOM    114  CA  VAL   114      56.252  12.137  14.058  1.00 25.00           C
ATOM    115  CA  LEU   115      54.256  15.341  13.409  1.00 25.00           C
ATOM    116  CA  ASP   116      54.756  16.419  17.049  1.00 25.00           C
ATOM    117  CA  LEU   117      58.517  15.762  16.754  1.00 25.00           C
ATOM    118  CA  ALA   118      58.650  17.833  13.535  1.00 25.00           C
ATOM    119  CA  MET   119      56.782  20.692  15.267  1.00 25.00           C
ATOM    120  CA  SER   120      59.237  20.549  18.204  1.00 25.00           C
ATOM    121  CA  PRO   121      62.192  20.661  15.770  1.00 25.00           C
ATOM    122  CA  ARG   122      60.639  23.468  13.622  1.00 25.00           C
ATOM    123  CA  PHE   123      57.333  25.094  12.641  1.00 25.00           C
ATOM    124  CA  LEU   124      57.120  27.499  15.583  1.00 25.00           C
ATOM    125  CA  PRO   125      60.844  27.888  16.125  1.00 25.00           C
ATOM    126  CA  SER   126      64.165  28.804  14.479  1.00 25.00           C
ATOM    127  CA  GLY   127      63.115  32.150  13.045  1.00 25.00           C
ATOM    128  CA  ARG   128      63.200  30.195   9.763  1.00 25.00           C
ATOM    129  CA  THR   129      60.487  30.294   7.031  1.00 25.00           C
ATOM    130  CA  LEU   130      59.111  26.868   8.083  1.00 25.00           C
ATOM    131  CA  ASP   131      55.964  28.519   9.511  1.00 25.00           C
ATOM    132  CA  SER   132      54.561  28.963   5.975  1.00 25.00           C
ATOM    133  CA  PHE   133      55.272  25.280   5.203  1.00 25.00           C
ATOM    134  CA  PHE   134      53.505  24.237   8.436  1.00 25.00           C
ATOM    135  CA  ASP   135      50.485  26.404   7.514  1.00 25.00           C
ATOM    136  CA  LYS   136      50.379  24.816   4.030  1.00 25.00           C
ATOM    137  CA  VAL   137      49.804  21.600   5.999  1.00 25.00           C
ATOM    138  CA  TYR   138      51.801  18.968   7.961  1.00 25.00           C
ATOM    139  CA  ALA   139      49.790  16.493  10.035  1.00 25.00           C
ATOM    140  CA  SER   140      49.201  12.837   9.133  1.00 25.00           C
ATOM    141  CA  CYS   141      47.250  11.204  11.922  1.00 25.00           C
ATOM    142  CA  GLN   142      45.462   8.902  14.302  1.00 25.00           C
ATOM    143  CA  MET   143      46.795   6.205  11.996  1.00 25.00           C
ATOM    144  CA  GLY   144      43.212   6.006  10.839  1.00 25.00           C
ATOM    145  CA  LYS   145      44.307   3.419   8.215  1.00 25.00           C
ATOM    146  CA  TYR   146      47.956   2.944   7.125  1.00 25.00           C
ATOM    147  CA  LYS   147      50.882   4.975   8.460  1.00 25.00           C
ATOM    148  CA  PRO   148      48.858   7.890   7.013  1.00 25.00           C
ATOM    149  CA  ASN   149      45.728   7.138   4.975  1.00 25.00           C
ATOM    150  CA  GLU   150      42.568   9.198   4.809  1.00 25.00           C
ATOM    151  CA  ASP   151      40.468  11.950   6.448  1.00 25.00           C
ATOM    152  CA  ILE   152      43.654  13.676   7.689  1.00 25.00           C
ATOM    153  CA  PHE   153      45.153  13.493   4.170  1.00 25.00           C
ATOM    154  CA  LEU   154      41.954  15.000   2.701  1.00 25.00           C
ATOM    155  CA  GLU   155      42.071  17.828   5.281  1.00 25.00           C
ATOM    156  CA  MET   156      45.737  18.507   4.405  1.00 25.00           C
ATOM    157  CA  ILE   157      44.851  18.612   0.679  1.00 25.00           C
ATOM    158  CA  ALA   158      42.000  21.065   1.401  1.00 25.00           C
ATOM    159  CA  ASP   159      44.381  23.277   3.426  1.00 25.00           C
ATOM    160  CA  SER   160      46.912  23.225   0.551  1.00 25.00           C
ATOM    161  CA  GLY   161      44.816  26.222  -0.664  1.00 25.00           C
ATOM    162  CA  MET   162      44.037  24.067  -3.691  1.00 25.00           C
ATOM    163  CA  LYS   163      42.327  20.684  -4.052  1.00 25.00           C
ATOM    164  CA  PRO   164      43.766  17.133  -4.470  1.00 25.00           C
ATOM    165  CA  GLU   165      45.519  14.807  -6.958  1.00 25.00           C
ATOM    166  CA  GLU   166      48.797  16.726  -6.480  1.00 25.00           C
ATOM    167  CA  THR   167      49.090  16.488  -2.688  1.00 25.00           C
ATOM    168  CA  LEU   168      52.090  14.180  -2.787  1.00 25.00           C
ATOM    169  CA  PHE   169      53.015  12.263   0.349  1.00 25.00           C
ATOM    170  CA  ILE   170      56.465  11.881   1.873  1.00 25.00           C
ATOM    171  CA  ASP   171      58.372   9.933   4.495  1.00 25.00           C
ATOM    172  CA  ASP   172      61.078   7.533   3.283  1.00 25.00           C
ATOM    173  CA  GLY   173      58.792   4.787   4.508  1.00 25.00           C
ATOM    174  CA  PRO   174      56.565   1.932   3.196  1.00 25.00           C
ATOM    175  CA  ALA   175      53.072   2.287   4.727  1.00 25.00           C
ATOM    176  CA  ASN   176      53.116   6.050   4.019  1.00 25.00           C
ATOM    177  CA  VAL   177      54.156   5.381   0.393  1.00 25.00           C
ATOM    178  CA  ALA   178      51.313   2.842   0.022  1.00 25.00           C
ATOM    179  CA  THR   179      48.823   5.385   1.436  1.00 25.00           C
ATOM    180  CA  ALA   180      50.094   8.032  -1.022  1.00 25.00           C
ATOM    181  CA  GLU   181      49.706   5.562  -3.922  1.00 25.00           C
ATOM    182  CA  ARG   182      46.133   4.765  -2.796  1.00 25.00           C
ATOM    183  CA  LEU   183      45.028   8.285  -1.932  1.00 25.00           C
ATOM    184  CA  GLY   184      44.328  10.241  -5.164  1.00 25.00           C
ATOM    185  CA  PHE   185      48.105  10.944  -5.016  1.00 25.00           C
ATOM    186  CA  HIS   186      50.990  11.274  -7.422  1.00 25.00           C
ATOM    187  CA  THR   187      53.199   9.669  -4.734  1.00 25.00           C
ATOM    188  CA  TYR   188      56.572   9.809  -3.053  1.00 25.00           C
ATOM    189  CA  CYS   189      59.476   7.923  -1.522  1.00 25.00           C
ATOM    190  CA  PRO   190      62.115  10.616  -0.903  1.00 25.00           C
ATOM    191  CA  ASP   191      64.552   7.686  -0.481  1.00 25.00           C
ATOM    192  CA  ASN   192      66.338   4.299  -0.450  1.00 25.00           C
ATOM    193  CA  GLY   193      63.692   2.941  -2.828  1.00 25.00           C
ATOM    194  CA  GLU   194      65.721   4.099  -5.862  1.00 25.00           C
ATOM    195  CA  ASN   195      62.953   2.878  -8.210  1.00 25.00           C
ATOM    196  CA  TRP   196      60.334   4.755  -6.140  1.00 25.00           C
ATOM    197  CA  ILE   197      62.460   7.937  -6.292  1.00 25.00           C
ATOM    198  CA  PRO   198      62.789   7.566 -10.089  1.00 25.00           C
ATOM    199  CA  ALA   199      58.997   7.124 -10.398  1.00 25.00           C
ATOM    200  CA  ILE   200      58.434  10.261  -8.274  1.00 25.00           C
ATOM    201  CA  THR   201      60.870  12.225 -10.482  1.00 25.00           C
ATOM    202  CA  ARG   202      59.036  11.018 -13.620  1.00 25.00           C
ATOM    203  CA  LEU   203      55.686  12.084 -12.102  1.00 25.00           C
ATOM    204  CA  LEU   204      57.132  15.532 -11.271  1.00 25.00           C
ATOM    205  CA  ARG   205      58.428  15.881 -14.858  1.00 25.00           C
ATOM    206  CA  GLU   206      54.980  14.924 -16.224  1.00 25.00           C
ATOM    207  CA  GLN   207      54.574  18.192 -18.159  1.00 25.00           C
TER
END
