
#######################################################
#                                                     #
#                        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  131 (  131),  selected  131 , name T0379TS677_2-D1
# Molecule2: number of CA atoms  140 ( 1126),  selected  140 , name T0379_D1.pdb
# PARAMETERS: T0379TS677_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          2.702
LGA    I       2      I       2          1.681
LGA    R       3      R       3          1.485
LGA    N       4      N       4          1.238
LGA    I       5      I       5          1.215
LGA    V       6      V       6          1.167
LGA    F       7      F       7          0.846
LGA    D       8      D       8          0.679
LGA    L       9      L       9          1.151
LGA    G      10      G      10          0.932
LGA    G      11      G      11          0.954
LGA    V      12      V      12          0.318
LGA    L      13      L      13          0.275
LGA    I      14      I      14          0.341
LGA    H      15      H      15          1.501
LGA    L      16      L      16          1.872
LGA    L      84      L      84          6.159
LGA    E      85      E      85          5.614
LGA    E      86      E      86          3.252
LGA    I      87      I      87          1.936
LGA    S      88      S      88          2.711
LGA    A      89      A      89          5.111
LGA    E      90      E      90          3.279
LGA    K      91      K      91          0.742
LGA    F      92      F      92          2.462
LGA    D      93      D      93          2.570
LGA    Y      94      Y      94          1.420
LGA    I      95      I      95          0.956
LGA    D      96      D      96          1.953
LGA    S      97      S      97          1.994
LGA    L      98      L      98          1.450
LGA    R      99      R      99          1.669
LGA    P     100      P     100          4.021
LGA    D     101      D     101          1.802
LGA    Y     102      Y     102          0.930
LGA    R     103      R     103          1.286
LGA    L     104      L     104          1.150
LGA    F     105      F     105          1.323
LGA    L     106      L     106          1.068
LGA    L     107      L     107          1.288
LGA    S     108      S     108          1.457
LGA    N     109      N     109          2.212
LGA    T     110      T     110          2.655
LGA    -       -      N     111           -
LGA    N     111      P     112          4.130
LGA    P     112      Y     113           -
LGA    -       -      V     114           -
LGA    Y     113      L     115          4.288
LGA    V     114      D     116          3.487
LGA    L     115      -       -           -
LGA    D     116      -       -           -
LGA    L     117      L     117          3.024
LGA    A     118      A     118          2.089
LGA    P     125      M     119           #
LGA    S     126      S     120          4.452
LGA    -       -      P     121           -
LGA    G     127      R     122          3.004
LGA    R     128      F     123          2.963
LGA    T     129      L     124          3.164
LGA    -       -      P     125           -
LGA    -       -      S     126           -
LGA    -       -      G     127           -
LGA    L     130      R     128          4.336
LGA    D     131      T     129          2.641
LGA    -       -      L     130           -
LGA    -       -      D     131           -
LGA    S     132      S     132          2.226
LGA    F     133      F     133          1.495
LGA    F     134      F     134          1.531
LGA    D     135      D     135          1.503
LGA    K     136      K     136          0.879
LGA    V     137      V     137          1.189
LGA    Y     138      Y     138          1.136
LGA    A     139      A     139          1.660
LGA    S     140      S     140          2.343
LGA    C     141      C     141          3.659
LGA    -       -      Q     142           -
LGA    Q     142      M     143          2.353
LGA    M     143      G     144          4.091
LGA    G     144      K     145          3.846
LGA    K     145      -       -           -
LGA    Y     146      Y     146          2.153
LGA    K     147      K     147          1.577
LGA    P     148      P     148          1.330
LGA    N     149      N     149          1.049
LGA    E     150      E     150          0.666
LGA    D     151      D     151          0.534
LGA    I     152      I     152          1.124
LGA    F     153      F     153          0.923
LGA    L     154      L     154          0.811
LGA    E     155      E     155          1.871
LGA    M     156      M     156          2.050
LGA    I     157      I     157          1.291
LGA    A     158      A     158          2.091
LGA    D     159      D     159          2.665
LGA    S     160      S     160          1.891
LGA    G     161      G     161          1.765
LGA    M     162      M     162          1.527
LGA    K     163      K     163          1.545
LGA    P     164      P     164          1.408
LGA    E     165      E     165          1.358
LGA    E     166      E     166          1.619
LGA    T     167      T     167          1.748
LGA    L     168      L     168          1.133
LGA    F     169      F     169          0.729
LGA    I     170      I     170          0.571
LGA    D     171      D     171          0.699
LGA    D     172      D     172          1.326
LGA    G     173      G     173          1.701
LGA    P     174      P     174          1.915
LGA    A     175      A     175          2.196
LGA    N     176      N     176          1.457
LGA    V     177      V     177          0.956
LGA    A     178      A     178          1.210
LGA    T     179      T     179          1.540
LGA    A     180      A     180          1.056
LGA    E     181      E     181          0.794
LGA    R     182      R     182          1.133
LGA    L     183      L     183          1.672
LGA    G     184      G     184          1.392
LGA    F     185      F     185          1.023
LGA    H     186      H     186          0.978
LGA    T     187      T     187          0.656
LGA    Y     188      Y     188          1.182
LGA    C     189      C     189          1.318
LGA    P     190      P     190          1.102
LGA    D     191      D     191          3.039
LGA    -       -      N     192           -
LGA    -       -      G     193           -
LGA    N     192      E     194          2.924
LGA    G     193      N     195           -
LGA    E     194      -       -           -
LGA    N     195      -       -           -
LGA    W     196      -       -           -
LGA    I     197      W     196          3.171
LGA    P     198      I     197          1.216
LGA    A     199      P     198          2.258
LGA    -       -      A     199           -
LGA    I     200      I     200          1.036
LGA    T     201      T     201          2.141
LGA    R     202      R     202          2.866
LGA    L     203      L     203          2.415
LGA    L     204      L     204          2.292
LGA    -       -      R     205           -
LGA    -       -      E     206           -
LGA    -       -      Q     207           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  131  140    5.0    122    2.19    87.70     65.156     5.323

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.246339 * X  +   0.944917 * Y  +  -0.215520 * Z  +  51.710365
  Y_new =  -0.888274 * X  +  -0.309069 * Y  +  -0.339772 * Z  +  37.566586
  Z_new =  -0.387667 * X  +   0.107742 * Y  +   0.915481 * Z  +   3.581999 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.117150   -3.024443  [ DEG:     6.7122   -173.2878 ]
  Theta =   0.398099    2.743494  [ DEG:    22.8094    157.1906 ]
  Phi   =  -1.841321    1.300271  [ DEG:  -105.4999     74.5001 ]
 
# 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: T0379TS677_2-D1                               
REMARK     2: T0379_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS677_2-D1.T0379_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  131  140   5.0  122   2.19   87.70  65.156
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS677_2-D1
PFRMAT TS
TARGET T0379
MODEL  2  REFINED
PARENT 1qh9_A
ATOM      3  CA  MET     1      49.734  19.436 -12.784  1.00 98.00
ATOM      4  CA  ILE     2      51.142  19.380  -9.255  1.00 98.00
ATOM      5  CA  ARG     3      50.378  22.641  -7.447  1.00 98.00
ATOM      6  CA  ASN     4      51.408  21.475  -3.993  1.00 52.00
ATOM      7  CA  ILE     5      53.627  19.039  -2.151  1.00 40.00
ATOM      8  CA  VAL     6      52.963  17.141   1.056  1.00 34.00
ATOM      9  CA  PHE     7      56.165  16.145   2.868  1.00  8.00
ATOM     10  CA  ASP     8      56.973  13.408   5.351  1.00  4.00
ATOM     11  CA  LEU     9      59.290  14.347   8.242  1.00  2.00
ATOM     12  CA  GLY    10      61.761  11.658   9.389  1.00 17.00
ATOM     13  CA  GLY    11      63.868  10.107   6.659  1.00  6.00
ATOM     14  CA  VAL    12      62.476  12.442   4.006  1.00 32.00
ATOM     15  CA  LEU    13      63.643  15.827   5.298  1.00 50.00
ATOM     16  CA  ILE    14      65.360  15.144   8.604  1.00 86.00
ATOM     17  CA  HIS    15      67.997  12.569   9.432  1.00 91.00
ATOM     18  CA  LEU    16      67.140  10.570  12.557  1.00 99.00
ATOM     93  CA  LEU    84      66.810  18.666  17.312  1.00 97.00
ATOM     94  CA  GLU    85      67.306  16.771  14.058  1.00 99.00
ATOM     95  CA  GLU    86      69.485  18.004  11.192  1.00 99.00
ATOM     96  CA  ILE    87      68.085  17.969   7.661  1.00 92.00
ATOM     97  CA  SER    88      69.684  16.079   4.821  1.00 81.00
ATOM     98  CA  ALA    89      72.287  18.226   3.039  1.00 99.00
ATOM     99  CA  GLU    90      70.282  18.709  -0.157  1.00 99.00
ATOM    100  CA  LYS    91      67.099  19.601   1.749  1.00 99.00
ATOM    101  CA  PHE    92      67.535  23.374   2.377  1.00 99.00
ATOM    102  CA  ASP    93      68.460  24.302  -1.201  1.00 99.00
ATOM    103  CA  TYR    94      65.824  21.967  -2.637  1.00 73.00
ATOM    104  CA  ILE    95      63.059  23.493  -0.529  1.00 53.00
ATOM    105  CA  ASP    96      64.137  27.005  -1.473  1.00 36.00
ATOM    106  CA  SER    97      64.160  26.079  -5.138  1.00 42.00
ATOM    107  CA  LEU    98      60.724  24.420  -5.081  1.00 55.00
ATOM    108  CA  ARG    99      59.252  27.454  -3.363  1.00 61.00
ATOM    109  CA  PRO   100      60.892  29.566  -6.073  1.00 42.00
ATOM    111  CA  ASP   101      55.707  28.629  -6.706  1.00 49.00
ATOM    112  CA  TYR   102      54.572  25.301  -5.246  1.00 32.00
ATOM    113  CA  ARG   103      52.617  25.182  -1.988  1.00 16.00
ATOM    114  CA  LEU   104      54.629  23.120   0.501  1.00  0.00
ATOM    115  CA  PHE   105      53.299  21.388   3.612  1.00  7.00
ATOM    116  CA  LEU   106      54.339  18.797   6.206  1.00 10.00
ATOM    117  CA  LEU   107      52.037  16.044   7.464  1.00 36.00
ATOM    118  CA  SER   108      53.430  14.255  10.523  1.00 55.00
ATOM    119  CA  ASN   109      52.334  12.511  13.724  1.00 82.00
ATOM    120  CA  THR   110      53.589  14.897  16.392  1.00 88.00
ATOM    121  CA  ASN   111      51.946  18.051  17.699  1.00 99.00
ATOM    122  CA  PRO   112      52.032  21.167  15.505  1.00 83.00
ATOM    123  CA  TYR   113      54.209  22.792  18.179  1.00 70.00
ATOM    124  CA  VAL   114      56.911  20.114  17.893  1.00 54.00
ATOM    125  CA  LEU   115      56.782  20.002  14.080  1.00 70.00
ATOM    126  CA  ASP   116      57.307  23.779  14.134  1.00 66.00
ATOM    127  CA  LEU   117      60.239  23.325  16.539  1.00 87.00
ATOM    128  CA  ALA   118      62.088  20.862  14.310  1.00 99.00
ATOM    129  CA  PRO   125      61.868  23.110  11.217  1.00 88.00
ATOM    130  CA  SER   126      62.608  26.272  13.209  1.00 99.00
ATOM    131  CA  GLY   127      65.706  24.738  14.824  1.00 99.00
ATOM    132  CA  ARG   128      66.820  23.793  11.312  1.00 99.00
ATOM    133  CA  THR   129      66.036  27.355  10.197  1.00 95.00
ATOM    134  CA  LEU   130      63.681  25.966   7.558  1.00 99.00
ATOM    135  CA  ASP   131      60.416  27.297   9.003  1.00 36.00
ATOM    136  CA  SER   132      59.808  30.040   6.409  1.00  9.00
ATOM    137  CA  PHE   133      59.652  27.498   3.588  1.00 20.00
ATOM    138  CA  PHE   134      56.420  25.785   4.625  1.00 25.00
ATOM    139  CA  ASP   135      52.838  26.943   4.085  1.00 34.00
ATOM    140  CA  LYS   136      51.207  24.327   6.315  1.00 37.00
ATOM    141  CA  VAL   137      52.421  22.274   9.250  1.00 55.00
ATOM    142  CA  TYR   138      49.911  19.485   9.832  1.00 54.00
ATOM    143  CA  ALA   139      49.468  16.881  12.553  1.00 62.00
ATOM    144  CA  SER   140      47.194  13.832  12.555  1.00 61.00
ATOM    145  CA  CYS   141      45.913  14.838  16.015  1.00 81.00
ATOM    146  CA  GLN   142      42.764  16.583  14.742  1.00 69.00
ATOM    147  CA  MET   143      41.456  13.298  13.274  1.00 79.00
ATOM    148  CA  GLY   144      42.455  11.133  16.266  1.00 47.00
ATOM    149  CA  LYS   145      43.872   8.437  13.977  1.00 45.00
ATOM    150  CA  TYR   146      47.178   7.723  12.237  1.00 41.00
ATOM    151  CA  LYS   147      48.301   6.812   8.722  1.00 68.00
ATOM    152  CA  PRO   148      47.560   5.015   6.482  1.00 64.00
ATOM    153  CA  ASN   149      43.957   5.675   7.580  1.00 79.00
ATOM    154  CA  GLU   150      42.513   7.664   4.665  1.00 64.00
ATOM    155  CA  ASP   151      41.109  10.300   7.020  1.00 45.00
ATOM    156  CA  ILE   152      44.649  11.565   7.534  1.00 54.00
ATOM    157  CA  PHE   153      45.160  12.003   3.794  1.00 82.00
ATOM    158  CA  LEU   154      41.927  14.006   3.393  1.00 74.00
ATOM    159  CA  GLU   155      43.227  16.352   6.041  1.00 71.00
ATOM    160  CA  MET   156      46.272  17.077   3.867  1.00 97.00
ATOM    161  CA  ILE   157      43.906  17.582   0.949  1.00 73.00
ATOM    162  CA  ALA   158      41.627  19.962   2.890  1.00 38.00
ATOM    163  CA  ASP   159      44.372  22.070   4.464  1.00 35.00
ATOM    164  CA  SER   160      46.045  22.655   1.079  1.00 49.00
ATOM    165  CA  GLY   161      42.803  23.670  -0.624  1.00 53.00
ATOM    166  CA  MET   162      43.704  21.455  -3.592  1.00 51.00
ATOM    167  CA  LYS   163      42.503  18.150  -5.022  1.00 57.00
ATOM    168  CA  PRO   164      44.717  15.094  -4.344  1.00 91.00
ATOM    169  CA  GLU   165      45.759  14.708  -7.994  1.00 84.00
ATOM    170  CA  GLU   166      47.409  18.135  -7.757  1.00 61.00
ATOM    171  CA  THR   167      49.293  17.368  -4.524  1.00 46.00
ATOM    172  CA  LEU   168      52.524  15.395  -4.766  1.00 33.00
ATOM    173  CA  PHE   169      52.882  13.053  -1.799  1.00 61.00
ATOM    174  CA  ILE   170      56.560  12.712  -0.878  1.00 61.00
ATOM    175  CA  ASP   171      57.683  10.057   1.595  1.00 61.00
ATOM    176  CA  ASP   172      60.605   7.811   2.495  1.00 80.00
ATOM    177  CA  GLY   173      58.250   5.136   3.859  1.00 96.00
ATOM    178  CA  PRO   174      57.019   2.664   1.267  1.00 46.00
ATOM    179  CA  ALA   175      53.981   1.675   3.366  1.00 43.00
ATOM    180  CA  ASN   176      52.945   5.344   3.510  1.00 62.00
ATOM    181  CA  VAL   177      53.541   5.826  -0.228  1.00 60.00
ATOM    182  CA  ALA   178      51.263   2.827  -0.747  1.00 53.00
ATOM    183  CA  THR   179      48.547   4.402   1.388  1.00 58.00
ATOM    184  CA  ALA   180      48.843   7.731  -0.415  1.00 79.00
ATOM    185  CA  GLU   181      48.890   5.980  -3.781  1.00 66.00
ATOM    186  CA  ARG   182      45.631   4.139  -2.985  1.00 55.00
ATOM    187  CA  LEU   183      44.036   7.391  -1.774  1.00 37.00
ATOM    188  CA  GLY   184      44.734   9.214  -5.043  1.00 39.00
ATOM    189  CA  PHE   185      47.876  11.302  -4.507  1.00 20.00
ATOM    190  CA  HIS   186      50.587  11.165  -7.190  1.00 25.00
ATOM    191  CA  THR   187      53.380   9.511  -5.185  1.00 54.00
ATOM    192  CA  TYR   188      57.124  10.107  -4.947  1.00 70.00
ATOM    193  CA  CYS   189      59.122   7.535  -2.948  1.00 64.00
ATOM    194  CA  PRO   190      62.383   8.787  -1.482  1.00 66.00
ATOM    195  CA  ASP   191      64.727   5.788  -1.443  1.00 55.00
ATOM    196  CA  ASN   192      68.255   6.763  -0.456  1.00 47.00
ATOM    197  CA  GLY   193      69.713   3.496   0.895  1.00 51.00
ATOM    198  CA  GLU   194      68.557   1.052  -1.802  1.00 99.00
ATOM    199  CA  ASN   195      65.575  -0.559  -0.083  1.00 99.00
ATOM    200  CA  TRP   196      62.741  -2.291  -1.967  1.00 99.00
ATOM    215  CA  ILE   197      65.133  15.856  -2.979  1.00 99.00
ATOM    216  CA  PRO   198      67.547  17.014  -5.699  1.00 99.00
ATOM    217  CA  ALA   199      65.708  14.728  -8.132  1.00 53.00
ATOM    218  CA  ILE   200      62.336  16.066  -6.950  1.00 43.00
ATOM    219  CA  THR   201      63.225  19.544  -8.303  1.00 69.00
ATOM    220  CA  ARG   202      64.052  18.112 -11.744  1.00 64.00
ATOM    221  CA  LEU   203      60.451  16.875 -12.082  1.00 64.00
ATOM    222  CA  LEU   204      59.227  20.482 -12.211  1.00 64.00
TER
END
