
#######################################################
#                                                     #
#                        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  121 (  121),  selected  121 , name T0371TS393_1-D2
# Molecule2: number of CA atoms  121 (  915),  selected  121 , name T0371_D2.pdb
# PARAMETERS: T0371TS393_1-D2.T0371_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      82           -
LGA    S      82      G      83          3.520
LGA    G      83      M      84          3.261
LGA    M      84      I      85          0.801
LGA    I      85      T      86          2.157
LGA    T      86      K      87          2.836
LGA    K      87      E      88          1.147
LGA    E      88      Y      89          1.371
LGA    Y      89      I      90          2.413
LGA    I      90      D      91          1.293
LGA    D      91      L      92          1.109
LGA    L      92      K      93          2.229
LGA    K      93      V      94          3.932
LGA    V      94      D      95           #
LGA    D      95      -       -           -
LGA    G      96      -       -           -
LGA    G      97      -       -           -
LGA    I      98      G      96           #
LGA    V      99      G      97           -
LGA    A     100      I      98           -
LGA    Y     101      -       -           -
LGA    L     102      -       -           -
LGA    G     103      -       -           -
LGA    T     104      -       -           -
LGA    A     105      -       -           -
LGA    N     106      V      99           #
LGA    S     107      A     100          0.551
LGA    A     108      Y     101           #
LGA    N     109      L     102           -
LGA    Y     110      G     103           -
LGA    L     111      T     104           -
LGA    V     112      A     105           -
LGA    S     113      N     106           -
LGA    D     114      S     107           -
LGA    -       -      A     108           -
LGA    -       -      N     109           -
LGA    -       -      Y     110           -
LGA    -       -      L     111           -
LGA    -       -      V     112           -
LGA    -       -      S     113           -
LGA    G     115      D     114           #
LGA    I     116      G     115           #
LGA    K     117      I     116          2.425
LGA    M     118      K     117          3.444
LGA    L     119      M     118          3.072
LGA    P     120      L     119          2.702
LGA    V     121      P     120          3.099
LGA    S     122      V     121          5.545
LGA    A     123      S     122          4.341
LGA    I     124      A     123          0.796
LGA    D     125      I     124           #
LGA    D     126      D     125           -
LGA    S     127      D     126           -
LGA    N     128      S     127           -
LGA    I     129      N     128           -
LGA    G     130      I     129           -
LGA    E     131      G     130           -
LGA    V     132      E     131           -
LGA    N     133      V     132           -
LGA    A     134      N     133           -
LGA    -       -      A     134           -
LGA    L     135      L     135           #
LGA    V     136      V     136          4.859
LGA    L     137      L     137          2.941
LGA    L     138      L     138          3.796
LGA    D     139      D     139          1.426
LGA    D     140      D     140          3.574
LGA    E     141      E     141          2.447
LGA    G     142      G     142          4.180
LGA    F     143      F     143          3.172
LGA    N     144      N     144          5.240
LGA    W     145      -       -           -
LGA    F     146      -       -           -
LGA    H     147      -       -           -
LGA    D     148      W     145          2.947
LGA    L     149      F     146           -
LGA    -       -      H     147           -
LGA    -       -      D     148           -
LGA    N     150      L     149          3.228
LGA    K     151      N     150          3.849
LGA    T     152      K     151           #
LGA    V     153      T     152          4.202
LGA    N     154      V     153          1.078
LGA    L     155      N     154          4.408
LGA    L     156      L     155          4.543
LGA    R     157      L     156          1.928
LGA    K     158      R     157          2.477
LGA    R     159      K     158          1.966
LGA    -       -      R     159           -
LGA    T     160      T     160          2.672
LGA    I     161      I     161          3.635
LGA    P     162      P     162          1.093
LGA    A     163      A     163          1.049
LGA    I     164      I     164          2.722
LGA    V     165      V     165          3.403
LGA    A     166      A     166          3.228
LGA    N     167      N     167          5.813
LGA    T     168      T     168          4.476
LGA    D     169      D     169          2.872
LGA    N     170      N     170          3.593
LGA    T     171      T     171          3.873
LGA    Y     172      Y     172          4.731
LGA    P     173      P     173          5.188
LGA    L     174      -       -           -
LGA    T     175      -       -           -
LGA    K     176      -       -           -
LGA    T     177      -       -           -
LGA    D     178      L     174          2.976
LGA    V     179      T     175           -
LGA    A     180      K     176           -
LGA    I     181      T     177           -
LGA    -       -      D     178           -
LGA    -       -      V     179           -
LGA    -       -      A     180           -
LGA    -       -      I     181           -
LGA    A     182      A     182          2.770
LGA    I     183      I     183          2.125
LGA    G     184      G     184          2.228
LGA    G     185      G     185          2.541
LGA    V     186      V     186          2.273
LGA    A     187      A     187          1.657
LGA    T     188      T     188          2.304
LGA    M     189      M     189          2.683
LGA    I     190      I     190          2.262
LGA    E     191      E     191          2.359
LGA    S     192      S     192          2.956
LGA    I     193      I     193          2.069
LGA    L     194      L     194          2.197
LGA    G     195      G     195          3.363
LGA    R     196      -       -           -
LGA    R     197      R     196          2.693
LGA    F     198      R     197          1.758
LGA    I     199      F     198          3.662
LGA    R     200      I     199          1.437
LGA    F     201      R     200          3.765
LGA    G     202      F     201          3.255
LGA    -       -      G     202           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  121  121    5.0     75    3.11    52.00     35.519     2.334

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.452747 * X  +   0.778857 * Y  +   0.434053 * Z  +  35.830509
  Y_new =  -0.758000 * X  +   0.079859 * Y  +   0.647348 * Z  +   4.418457
  Z_new =   0.469528 * X  +  -0.622097 * Y  +   0.626529 * Z  + -55.385052 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.781849    2.359744  [ DEG:   -44.7966    135.2034 ]
  Theta =  -0.488756   -2.652837  [ DEG:   -28.0037   -151.9964 ]
  Phi   =  -1.032370    2.109222  [ DEG:   -59.1505    120.8495 ]
 
# 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: T0371TS393_1-D2                               
REMARK     2: T0371_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0371TS393_1-D2.T0371_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  121  121   5.0   75   3.11   52.00  35.519
REMARK  ---------------------------------------------------------- 
MOLECULE T0371TS393_1-D2
PFRMAT TS
TARGET T0371
MODEL 1
PARENT N/A
ATOM     82  CA  SER    82      37.234   2.612 -56.719  1.00 25.00           C
ATOM     83  CA  GLY    83      36.211   1.586 -60.264  1.00 25.00           C
ATOM     84  CA  MET    84      36.662   5.195 -61.465  1.00 25.00           C
ATOM     85  CA  ILE    85      40.130   5.325 -59.848  1.00 25.00           C
ATOM     86  CA  THR    86      41.077   2.029 -61.554  1.00 25.00           C
ATOM     87  CA  LYS    87      39.882   3.401 -64.923  1.00 25.00           C
ATOM     88  CA  GLU    88      41.953   6.578 -64.392  1.00 25.00           C
ATOM     89  CA  TYR    89      45.032   4.460 -63.552  1.00 25.00           C
ATOM     90  CA  ILE    90      44.493   2.376 -66.720  1.00 25.00           C
ATOM     91  CA  ASP    91      44.204   5.574 -68.804  1.00 25.00           C
ATOM     92  CA  LEU    92      47.445   6.905 -67.257  1.00 25.00           C
ATOM     93  CA  LYS    93      50.680   4.914 -66.867  1.00 25.00           C
ATOM     94  CA  VAL    94      52.601   8.069 -67.710  1.00 25.00           C
ATOM     95  CA  ASP    95      56.229   8.478 -66.582  1.00 25.00           C
ATOM     96  CA  GLY    96      55.238   5.903 -63.895  1.00 25.00           C
ATOM     97  CA  GLY    97      52.314   4.929 -61.606  1.00 25.00           C
ATOM     98  CA  ILE    98      48.872   3.919 -60.311  1.00 25.00           C
ATOM     99  CA  VAL    99      45.584   2.768 -58.689  1.00 25.00           C
ATOM    100  CA  ALA   100      42.747   1.760 -56.365  1.00 25.00           C
ATOM    101  CA  TYR   101      44.738  -0.686 -54.227  1.00 25.00           C
ATOM    102  CA  LEU   102      43.594  -2.725 -51.263  1.00 25.00           C
ATOM    103  CA  GLY   103      43.838  -5.808 -49.119  1.00 25.00           C
ATOM    104  CA  THR   104      47.430  -6.620 -50.020  1.00 25.00           C
ATOM    105  CA  ALA   105      50.887  -6.592 -51.525  1.00 25.00           C
ATOM    106  CA  ASN   106      49.141  -7.734 -54.737  1.00 25.00           C
ATOM    107  CA  SER   107      47.875  -4.170 -55.345  1.00 25.00           C
ATOM    108  CA  ALA   108      51.412  -2.799 -54.823  1.00 25.00           C
ATOM    109  CA  ASN   109      52.802  -5.371 -57.298  1.00 25.00           C
ATOM    110  CA  TYR   110      50.133  -4.382 -59.860  1.00 25.00           C
ATOM    111  CA  LEU   111      51.022  -0.686 -59.398  1.00 25.00           C
ATOM    112  CA  VAL   112      54.734  -1.491 -59.896  1.00 25.00           C
ATOM    113  CA  SER   113      53.907  -3.440 -63.088  1.00 25.00           C
ATOM    114  CA  ASP   114      52.882  -2.276 -66.605  1.00 25.00           C
ATOM    115  CA  GLY   115      49.734  -1.539 -68.671  1.00 25.00           C
ATOM    116  CA  ILE   116      48.227  -0.982 -65.223  1.00 25.00           C
ATOM    117  CA  LYS   117      46.955  -4.183 -63.544  1.00 25.00           C
ATOM    118  CA  MET   118      45.867  -6.345 -60.599  1.00 25.00           C
ATOM    119  CA  LEU   119      44.134  -6.378 -57.245  1.00 25.00           C
ATOM    120  CA  PRO   120      44.868  -9.643 -55.334  1.00 25.00           C
ATOM    121  CA  VAL   121      43.626  -9.835 -51.750  1.00 25.00           C
ATOM    122  CA  SER   122      46.670 -11.930 -50.836  1.00 25.00           C
ATOM    123  CA  ALA   123      49.679 -14.260 -50.218  1.00 25.00           C
ATOM    124  CA  ILE   124      51.498 -11.799 -52.490  1.00 25.00           C
ATOM    125  CA  ASP   125      54.451 -13.988 -53.402  1.00 25.00           C
ATOM    126  CA  ASP   126      53.495 -17.652 -53.547  1.00 25.00           C
ATOM    127  CA  SER   127      50.121 -18.126 -55.211  1.00 25.00           C
ATOM    128  CA  ASN   128      46.696 -16.632 -54.630  1.00 25.00           C
ATOM    129  CA  ILE   129      44.173 -14.493 -56.528  1.00 25.00           C
ATOM    130  CA  GLY   130      47.123 -13.550 -58.688  1.00 25.00           C
ATOM    131  CA  GLU   131      44.842 -11.765 -61.227  1.00 25.00           C
ATOM    132  CA  VAL   132      41.829  -9.696 -60.221  1.00 25.00           C
ATOM    133  CA  ASN   133      41.521  -6.294 -61.980  1.00 25.00           C
ATOM    134  CA  ALA   134      42.398  -2.560 -62.235  1.00 25.00           C
ATOM    135  CA  LEU   135      41.235  -2.439 -58.648  1.00 25.00           C
ATOM    136  CA  VAL   136      40.186  -3.368 -55.083  1.00 25.00           C
ATOM    137  CA  LEU   137      39.202  -0.615 -52.701  1.00 25.00           C
ATOM    138  CA  LEU   138      39.655  -0.305 -48.955  1.00 25.00           C
ATOM    139  CA  ASP   139      38.256  -3.856 -48.768  1.00 25.00           C
ATOM    140  CA  ASP   140      39.443  -6.772 -46.578  1.00 25.00           C
ATOM    141  CA  GLU   141      37.305  -9.950 -46.652  1.00 25.00           C
ATOM    142  CA  GLY   142      37.712 -11.048 -43.029  1.00 25.00           C
ATOM    143  CA  PHE   143      41.329 -10.007 -42.369  1.00 25.00           C
ATOM    144  CA  ASN   144      40.790  -8.012 -39.108  1.00 25.00           C
ATOM    145  CA  TRP   145      39.087  -5.556 -41.486  1.00 25.00           C
ATOM    146  CA  PHE   146      40.585  -2.446 -39.830  1.00 25.00           C
ATOM    147  CA  HIS   147      43.933  -4.257 -39.401  1.00 25.00           C
ATOM    148  CA  ASP   148      43.872  -5.292 -43.088  1.00 25.00           C
ATOM    149  CA  LEU   149      43.147  -1.675 -44.117  1.00 25.00           C
ATOM    150  CA  ASN   150      46.060  -0.449 -41.954  1.00 25.00           C
ATOM    151  CA  LYS   151      48.375  -3.045 -43.557  1.00 25.00           C
ATOM    152  CA  THR   152      47.258  -1.922 -47.045  1.00 25.00           C
ATOM    153  CA  VAL   153      47.933   1.730 -46.111  1.00 25.00           C
ATOM    154  CA  ASN   154      51.416   0.786 -44.829  1.00 25.00           C
ATOM    155  CA  LEU   155      52.134  -1.092 -48.089  1.00 25.00           C
ATOM    156  CA  LEU   156      51.002   1.951 -50.120  1.00 25.00           C
ATOM    157  CA  ARG   157      53.278   4.219 -48.037  1.00 25.00           C
ATOM    158  CA  LYS   158      56.220   1.834 -48.610  1.00 25.00           C
ATOM    159  CA  ARG   159      58.290   3.675 -51.244  1.00 25.00           C
ATOM    160  CA  THR   160      55.827   6.308 -52.457  1.00 25.00           C
ATOM    161  CA  ILE   161      52.069   6.262 -53.039  1.00 25.00           C
ATOM    162  CA  PRO   162      49.256   5.317 -55.371  1.00 25.00           C
ATOM    163  CA  ALA   163      46.226   4.048 -53.541  1.00 25.00           C
ATOM    164  CA  ILE   164      42.903   3.739 -51.618  1.00 25.00           C
ATOM    165  CA  VAL   165      41.040   6.524 -49.909  1.00 25.00           C
ATOM    166  CA  ALA   166      37.777   4.591 -49.674  1.00 25.00           C
ATOM    167  CA  ASN   167      35.196   1.867 -50.382  1.00 25.00           C
ATOM    168  CA  THR   168      33.492   1.244 -47.116  1.00 25.00           C
ATOM    169  CA  ASP   169      33.128   3.976 -44.531  1.00 25.00           C
ATOM    170  CA  ASN   170      32.615   2.746 -40.992  1.00 25.00           C
ATOM    171  CA  THR   171      29.521   1.024 -42.466  1.00 25.00           C
ATOM    172  CA  TYR   172      28.556  -0.607 -45.752  1.00 25.00           C
ATOM    173  CA  PRO   173      25.938  -2.518 -43.761  1.00 25.00           C
ATOM    174  CA  LEU   174      26.835  -5.604 -45.689  1.00 25.00           C
ATOM    175  CA  THR   175      24.256  -8.166 -44.744  1.00 25.00           C
ATOM    176  CA  LYS   176      22.759 -10.141 -41.861  1.00 25.00           C
ATOM    177  CA  THR   177      25.442  -8.522 -39.709  1.00 25.00           C
ATOM    178  CA  ASP   178      27.968  -5.710 -40.211  1.00 25.00           C
ATOM    179  CA  VAL   179      30.780  -4.372 -42.297  1.00 25.00           C
ATOM    180  CA  ALA   180      32.872  -4.414 -45.461  1.00 25.00           C
ATOM    181  CA  ILE   181      35.910  -2.445 -44.177  1.00 25.00           C
ATOM    182  CA  ALA   182      36.704   0.602 -41.965  1.00 25.00           C
ATOM    183  CA  ILE   183      38.309   1.873 -45.170  1.00 25.00           C
ATOM    184  CA  GLY   184      38.208   5.683 -44.793  1.00 25.00           C
ATOM    185  CA  GLY   185      39.550   5.391 -41.218  1.00 25.00           C
ATOM    186  CA  VAL   186      42.377   3.113 -42.441  1.00 25.00           C
ATOM    187  CA  ALA   187      43.245   5.629 -45.194  1.00 25.00           C
ATOM    188  CA  THR   188      43.308   8.463 -42.620  1.00 25.00           C
ATOM    189  CA  MET   189      45.611   6.396 -40.364  1.00 25.00           C
ATOM    190  CA  ILE   190      47.940   5.711 -43.326  1.00 25.00           C
ATOM    191  CA  GLU   191      48.021   9.449 -44.158  1.00 25.00           C
ATOM    192  CA  SER   192      48.856  10.267 -40.511  1.00 25.00           C
ATOM    193  CA  ILE   193      51.677   7.677 -40.549  1.00 25.00           C
ATOM    194  CA  LEU   194      53.055   9.190 -43.787  1.00 25.00           C
ATOM    195  CA  GLY   195      52.115  12.512 -45.377  1.00 25.00           C
ATOM    196  CA  ARG   196      51.254  10.620 -48.527  1.00 25.00           C
ATOM    197  CA  ARG   197      48.132  12.774 -48.623  1.00 25.00           C
ATOM    198  CA  PHE   198      46.448   9.601 -49.871  1.00 25.00           C
ATOM    199  CA  ILE   199      46.781   9.213 -53.627  1.00 25.00           C
ATOM    200  CA  ARG   200      43.215   8.143 -54.358  1.00 25.00           C
ATOM    201  CA  PHE   201      39.957   6.246 -55.128  1.00 25.00           C
ATOM    202  CA  GLY   202      37.731   7.928 -52.545  1.00 25.00           C
TER
END
