
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms  140 ( 1126),  selected  140 , name T0379_D1.pdb
# PARAMETERS: T0379TS393_1-D1.T0379_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    M       1      I       2          4.338
LGA    I       2      R       3          1.163
LGA    R       3      N       4          2.130
LGA    N       4      I       5          1.299
LGA    I       5      V       6          4.555
LGA    V       6      F       7          0.977
LGA    F       7      -       -           -
LGA    D       8      D       8          1.681
LGA    L       9      L       9          2.471
LGA    G      10      G      10          2.290
LGA    G      11      G      11          0.817
LGA    V      12      V      12          0.635
LGA    L      13      L      13          2.238
LGA    I      14      I      14          2.697
LGA    H      15      H      15           #
LGA    L      16      L      16          4.313
LGA    L      84      L      84          4.937
LGA    E      85      -       -           -
LGA    E      86      E      85           #
LGA    I      87      E      86          1.036
LGA    S      88      -       -           -
LGA    A      89      -       -           -
LGA    E      90      -       -           -
LGA    K      91      I      87           #
LGA    F      92      S      88          1.756
LGA    -       -      A      89           -
LGA    D      93      E      90          1.168
LGA    Y      94      K      91          1.994
LGA    I      95      F      92          3.222
LGA    D      96      D      93          2.497
LGA    S      97      Y      94          0.981
LGA    L      98      I      95          2.599
LGA    R      99      D      96          3.283
LGA    P     100      S      97          1.825
LGA    D     101      L      98          3.632
LGA    Y     102      R      99          2.795
LGA    -       -      P     100           -
LGA    -       -      D     101           -
LGA    -       -      Y     102           -
LGA    R     103      R     103          4.377
LGA    L     104      L     104          2.554
LGA    F     105      F     105          2.004
LGA    -       -      L     106           -
LGA    L     106      L     107          0.976
LGA    L     107      S     108          2.115
LGA    S     108      -       -           -
LGA    N     109      -       -           -
LGA    T     110      -       -           -
LGA    N     111      N     109          2.152
LGA    P     112      T     110          2.194
LGA    Y     113      N     111          2.099
LGA    -       -      P     112           -
LGA    V     114      Y     113           #
LGA    L     115      -       -           -
LGA    D     116      V     114          5.217
LGA    L     117      L     115          1.839
LGA    A     118      -       -           -
LGA    M     119      D     116           #
LGA    S     120      L     117          4.852
LGA    P     121      A     118          2.924
LGA    R     122      M     119           #
LGA    -       -      S     120           -
LGA    -       -      P     121           -
LGA    -       -      R     122           -
LGA    F     123      F     123          2.027
LGA    L     124      L     124          2.973
LGA    P     125      P     125           -
LGA    S     126      -       -           -
LGA    G     127      S     126          4.613
LGA    R     128      G     127          2.996
LGA    T     129      R     128          4.444
LGA    L     130      T     129           #
LGA    D     131      L     130          4.707
LGA    -       -      D     131           -
LGA    S     132      S     132          2.238
LGA    F     133      F     133          2.461
LGA    F     134      F     134           #
LGA    D     135      D     135           #
LGA    K     136      K     136          3.285
LGA    V     137      V     137          3.475
LGA    Y     138      Y     138          2.312
LGA    A     139      A     139          0.647
LGA    S     140      S     140          2.890
LGA    C     141      C     141          3.739
LGA    Q     142      Q     142          3.873
LGA    M     143      M     143          4.251
LGA    G     144      G     144          5.252
LGA    K     145      K     145          3.420
LGA    Y     146      Y     146          3.632
LGA    K     147      K     147          3.563
LGA    P     148      P     148          1.037
LGA    N     149      N     149          1.729
LGA    E     150      E     150          2.306
LGA    D     151      D     151          2.038
LGA    I     152      I     152          1.855
LGA    F     153      F     153          1.952
LGA    L     154      L     154          2.030
LGA    E     155      E     155          2.075
LGA    M     156      M     156          2.086
LGA    I     157      I     157          2.177
LGA    A     158      A     158          2.370
LGA    D     159      D     159          2.726
LGA    S     160      S     160          2.137
LGA    G     161      G     161          3.370
LGA    M     162      M     162          3.503
LGA    K     163      K     163          3.743
LGA    P     164      P     164          3.378
LGA    E     165      E     165          3.946
LGA    -       -      E     166           -
LGA    E     166      T     167          2.798
LGA    T     167      L     168           #
LGA    L     168      F     169          1.689
LGA    F     169      I     170          3.588
LGA    I     170      D     171          1.681
LGA    D     171      D     172          2.851
LGA    D     172      G     173          3.735
LGA    G     173      -       -           -
LGA    P     174      P     174          1.943
LGA    A     175      A     175          1.401
LGA    N     176      N     176          1.034
LGA    V     177      V     177          1.379
LGA    A     178      A     178          0.978
LGA    T     179      T     179          0.758
LGA    A     180      A     180          1.100
LGA    E     181      E     181          1.126
LGA    R     182      R     182          0.801
LGA    L     183      L     183          1.670
LGA    G     184      G     184          2.551
LGA    F     185      F     185          3.203
LGA    H     186      H     186          3.042
LGA    T     187      T     187          1.929
LGA    Y     188      Y     188          2.264
LGA    C     189      C     189          0.993
LGA    P     190      -       -           -
LGA    D     191      -       -           -
LGA    N     192      -       -           -
LGA    G     193      -       -           -
LGA    E     194      P     190          4.966
LGA    N     195      D     191           -
LGA    W     196      N     192           -
LGA    -       -      G     193           -
LGA    -       -      E     194           -
LGA    -       -      N     195           -
LGA    I     197      W     196           #
LGA    P     198      I     197           -
LGA    A     199      P     198           -
LGA    -       -      A     199           -
LGA    I     200      I     200           #
LGA    T     201      T     201           #
LGA    R     202      R     202           #
LGA    L     203      L     203          4.907
LGA    L     204      L     204          3.454
LGA    R     205      R     205          3.020
LGA    E     206      E     206          2.734
LGA    Q     207      Q     207          1.101

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  140  140    5.0    105    2.84    68.57     44.358     3.577

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.828040 * X  +  -0.193728 * Y  +  -0.526137 * Z  +  59.456852
  Y_new =  -0.034124 * X  +  -0.954082 * Y  +   0.297596 * Z  +  13.002159
  Z_new =  -0.559630 * X  +  -0.228468 * Y  +  -0.796628 * Z  +  10.790260 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.862296    0.279297  [ DEG:  -163.9975     16.0025 ]
  Theta =   0.593940    2.547653  [ DEG:    34.0302    145.9698 ]
  Phi   =  -0.041187    3.100406  [ DEG:    -2.3598    177.6402 ]
 
# 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_1-D1                               
REMARK     2: T0379_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS393_1-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  105   2.84   68.57  44.358
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS393_1-D1
PFRMAT TS
TARGET T0379
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      51.800  23.075 -11.653  1.00 25.00           C
ATOM      2  CA  ILE     2      51.340  21.048  -8.437  1.00 25.00           C
ATOM      3  CA  ARG     3      52.741  22.478  -5.204  1.00 25.00           C
ATOM      4  CA  ASN     4      54.992  19.719  -3.835  1.00 25.00           C
ATOM      5  CA  ILE     5      57.689  17.969  -1.833  1.00 25.00           C
ATOM      6  CA  VAL     6      57.279  16.874   1.786  1.00 25.00           C
ATOM      7  CA  PHE     7      57.637  17.673   5.452  1.00 25.00           C
ATOM      8  CA  ASP     8      57.536  14.139   6.807  1.00 25.00           C
ATOM      9  CA  LEU     9      59.974  13.849   9.673  1.00 25.00           C
ATOM     10  CA  GLY    10      60.973  10.164  10.065  1.00 25.00           C
ATOM     11  CA  GLY    11      63.355  10.845   7.106  1.00 25.00           C
ATOM     12  CA  VAL    12      63.022  12.578   3.692  1.00 25.00           C
ATOM     13  CA  LEU    13      62.102  16.290   3.950  1.00 25.00           C
ATOM     14  CA  ILE    14      63.626  16.442   7.409  1.00 25.00           C
ATOM     15  CA  HIS    15      65.104  17.281  10.819  1.00 25.00           C
ATOM     16  CA  LEU    16      65.313  13.481  11.228  1.00 25.00           C
ATOM     84  CA  LEU    84      67.714  17.611  16.658  1.00 25.00           C
ATOM     85  CA  GLU    85      70.404  18.285  14.017  1.00 25.00           C
ATOM     86  CA  GLU    86      73.720  17.531  12.354  1.00 25.00           C
ATOM     87  CA  ILE    87      71.558  15.309  10.103  1.00 25.00           C
ATOM     88  CA  SER    88      73.497  14.468   6.919  1.00 25.00           C
ATOM     89  CA  ALA    89      72.816  18.128   5.894  1.00 25.00           C
ATOM     90  CA  GLU    90      71.818  16.444   2.603  1.00 25.00           C
ATOM     91  CA  LYS    91      68.240  15.990   3.891  1.00 25.00           C
ATOM     92  CA  PHE    92      68.110  19.682   4.903  1.00 25.00           C
ATOM     93  CA  ASP    93      69.362  20.702   1.431  1.00 25.00           C
ATOM     94  CA  TYR    94      66.686  18.506  -0.207  1.00 25.00           C
ATOM     95  CA  ILE    95      63.993  20.097   2.002  1.00 25.00           C
ATOM     96  CA  ASP    96      65.233  23.590   1.040  1.00 25.00           C
ATOM     97  CA  SER    97      65.126  22.635  -2.667  1.00 25.00           C
ATOM     98  CA  LEU    98      61.552  21.323  -2.250  1.00 25.00           C
ATOM     99  CA  ARG    99      60.530  24.583  -0.520  1.00 25.00           C
ATOM    100  CA  PRO   100      61.804  27.062  -3.122  1.00 25.00           C
ATOM    101  CA  ASP   101      58.683  28.979  -4.155  1.00 25.00           C
ATOM    102  CA  TYR   102      57.010  25.594  -3.931  1.00 25.00           C
ATOM    103  CA  ARG   103      55.488  25.295  -0.442  1.00 25.00           C
ATOM    104  CA  LEU   104      55.327  21.924   1.280  1.00 25.00           C
ATOM    105  CA  PHE   105      53.141  19.400   3.141  1.00 25.00           C
ATOM    106  CA  LEU   106      52.747  16.528   5.676  1.00 25.00           C
ATOM    107  CA  LEU   107      52.338  13.519   8.024  1.00 25.00           C
ATOM    108  CA  SER   108      50.513  11.370   5.455  1.00 25.00           C
ATOM    109  CA  ASN   109      53.794   9.653   6.482  1.00 25.00           C
ATOM    110  CA  THR   110      55.460   9.805   9.898  1.00 25.00           C
ATOM    111  CA  ASN   111      52.227  10.017  11.904  1.00 25.00           C
ATOM    112  CA  PRO   112      53.610  13.262  13.251  1.00 25.00           C
ATOM    113  CA  TYR   113      55.604  13.744  16.485  1.00 25.00           C
ATOM    114  CA  VAL   114      58.709  14.698  14.458  1.00 25.00           C
ATOM    115  CA  LEU   115      56.648  17.218  12.442  1.00 25.00           C
ATOM    116  CA  ASP   116      55.269  18.721  15.683  1.00 25.00           C
ATOM    117  CA  LEU   117      58.820  19.012  17.087  1.00 25.00           C
ATOM    118  CA  ALA   118      59.977  20.741  13.871  1.00 25.00           C
ATOM    119  CA  MET   119      57.035  23.183  14.097  1.00 25.00           C
ATOM    120  CA  SER   120      57.912  23.939  17.748  1.00 25.00           C
ATOM    121  CA  PRO   121      61.560  24.568  16.767  1.00 25.00           C
ATOM    122  CA  ARG   122      64.267  22.029  16.147  1.00 25.00           C
ATOM    123  CA  PHE   123      64.666  23.424  12.647  1.00 25.00           C
ATOM    124  CA  LEU   124      67.496  25.443  14.107  1.00 25.00           C
ATOM    125  CA  PRO   125      65.741  28.124  16.230  1.00 25.00           C
ATOM    126  CA  SER   126      68.278  30.640  14.827  1.00 25.00           C
ATOM    127  CA  GLY   127      66.289  32.104  11.934  1.00 25.00           C
ATOM    128  CA  ARG   128      65.892  28.957   9.784  1.00 25.00           C
ATOM    129  CA  THR   129      65.751  29.102   5.979  1.00 25.00           C
ATOM    130  CA  LEU   130      63.305  26.248   5.626  1.00 25.00           C
ATOM    131  CA  ASP   131      61.067  28.499   7.770  1.00 25.00           C
ATOM    132  CA  SER   132      58.219  28.120   5.237  1.00 25.00           C
ATOM    133  CA  PHE   133      58.647  24.315   5.288  1.00 25.00           C
ATOM    134  CA  PHE   134      58.548  24.330   9.116  1.00 25.00           C
ATOM    135  CA  ASP   135      55.356  26.443   9.050  1.00 25.00           C
ATOM    136  CA  LYS   136      53.765  24.009   6.558  1.00 25.00           C
ATOM    137  CA  VAL   137      55.200  20.955   8.421  1.00 25.00           C
ATOM    138  CA  TYR   138      51.756  19.857   9.585  1.00 25.00           C
ATOM    139  CA  ALA   139      50.565  16.931  11.710  1.00 25.00           C
ATOM    140  CA  SER   140      48.605  13.812  10.576  1.00 25.00           C
ATOM    141  CA  CYS   141      48.291  12.977  14.282  1.00 25.00           C
ATOM    142  CA  GLN   142      45.790  15.819  14.371  1.00 25.00           C
ATOM    143  CA  MET   143      43.341  13.133  13.296  1.00 25.00           C
ATOM    144  CA  GLY   144      43.323   9.379  13.829  1.00 25.00           C
ATOM    145  CA  LYS   145      46.274   9.207  11.470  1.00 25.00           C
ATOM    146  CA  TYR   146      48.532   6.264  12.351  1.00 25.00           C
ATOM    147  CA  LYS   147      50.578   5.094   9.400  1.00 25.00           C
ATOM    148  CA  PRO   148      47.486   6.266   7.426  1.00 25.00           C
ATOM    149  CA  ASN   149      43.872   6.044   6.300  1.00 25.00           C
ATOM    150  CA  GLU   150      44.520   8.715   3.615  1.00 25.00           C
ATOM    151  CA  ASP   151      42.646  10.960   6.087  1.00 25.00           C
ATOM    152  CA  ILE   152      45.836  12.988   6.702  1.00 25.00           C
ATOM    153  CA  PHE   153      46.346  13.377   2.926  1.00 25.00           C
ATOM    154  CA  LEU   154      42.723  14.552   2.532  1.00 25.00           C
ATOM    155  CA  GLU   155      43.214  17.093   5.356  1.00 25.00           C
ATOM    156  CA  MET   156      46.411  18.374   3.679  1.00 25.00           C
ATOM    157  CA  ILE   157      44.553  18.726   0.349  1.00 25.00           C
ATOM    158  CA  ALA   158      41.745  20.661   2.093  1.00 25.00           C
ATOM    159  CA  ASP   159      44.322  22.975   3.727  1.00 25.00           C
ATOM    160  CA  SER   160      45.978  23.575   0.326  1.00 25.00           C
ATOM    161  CA  GLY   161      43.512  25.436  -1.960  1.00 25.00           C
ATOM    162  CA  MET   162      45.453  23.508  -4.556  1.00 25.00           C
ATOM    163  CA  LYS   163      42.612  20.982  -4.077  1.00 25.00           C
ATOM    164  CA  PRO   164      43.786  17.425  -4.518  1.00 25.00           C
ATOM    165  CA  GLU   165      46.674  17.437  -7.033  1.00 25.00           C
ATOM    166  CA  GLU   166      49.044  18.783  -4.342  1.00 25.00           C
ATOM    167  CA  THR   167      50.307  16.755  -1.404  1.00 25.00           C
ATOM    168  CA  LEU   168      53.248  14.355  -0.969  1.00 25.00           C
ATOM    169  CA  PHE   169      54.471  11.726   1.542  1.00 25.00           C
ATOM    170  CA  ILE   170      58.186  11.217   2.318  1.00 25.00           C
ATOM    171  CA  ASP   171      58.584   8.722   5.167  1.00 25.00           C
ATOM    172  CA  ASP   172      59.683   5.523   6.942  1.00 25.00           C
ATOM    173  CA  GLY   173      56.192   3.881   7.109  1.00 25.00           C
ATOM    174  CA  PRO   174      54.996   1.764   4.163  1.00 25.00           C
ATOM    175  CA  ALA   175      51.364   2.154   5.318  1.00 25.00           C
ATOM    176  CA  ASN   176      51.584   5.944   4.809  1.00 25.00           C
ATOM    177  CA  VAL   177      53.002   5.413   1.291  1.00 25.00           C
ATOM    178  CA  ALA   178      50.155   2.984   0.482  1.00 25.00           C
ATOM    179  CA  THR   179      47.589   5.534   1.741  1.00 25.00           C
ATOM    180  CA  ALA   180      49.191   8.254  -0.428  1.00 25.00           C
ATOM    181  CA  GLU   181      49.064   5.935  -3.474  1.00 25.00           C
ATOM    182  CA  ARG   182      45.370   5.196  -2.787  1.00 25.00           C
ATOM    183  CA  LEU   183      44.156   8.543  -1.396  1.00 25.00           C
ATOM    184  CA  GLY   184      44.564  10.923  -4.334  1.00 25.00           C
ATOM    185  CA  PHE   185      47.506  12.719  -2.728  1.00 25.00           C
ATOM    186  CA  HIS   186      50.391  11.122  -4.564  1.00 25.00           C
ATOM    187  CA  THR   187      53.535   9.664  -3.107  1.00 25.00           C
ATOM    188  CA  TYR   188      57.287  10.365  -2.590  1.00 25.00           C
ATOM    189  CA  CYS   189      58.951   7.411  -0.962  1.00 25.00           C
ATOM    190  CA  PRO   190      59.774   5.029   1.882  1.00 25.00           C
ATOM    191  CA  ASP   191      62.508   2.488   2.689  1.00 25.00           C
ATOM    192  CA  ASN   192      62.740   1.169  -0.798  1.00 25.00           C
ATOM    193  CA  GLY   193      63.200   4.767  -1.860  1.00 25.00           C
ATOM    194  CA  GLU   194      65.414   6.208  -4.634  1.00 25.00           C
ATOM    195  CA  ASN   195      63.204   4.556  -7.290  1.00 25.00           C
ATOM    196  CA  TRP   196      60.077   6.017  -5.632  1.00 25.00           C
ATOM    197  CA  ILE   197      61.691   9.489  -5.589  1.00 25.00           C
ATOM    198  CA  PRO   198      62.577   9.151  -9.299  1.00 25.00           C
ATOM    199  CA  ALA   199      58.973   8.123 -10.091  1.00 25.00           C
ATOM    200  CA  ILE   200      57.659  11.147  -8.143  1.00 25.00           C
ATOM    201  CA  THR   201      60.038  13.452 -10.065  1.00 25.00           C
ATOM    202  CA  ARG   202      58.845  11.956 -13.384  1.00 25.00           C
ATOM    203  CA  LEU   203      55.199  12.499 -12.347  1.00 25.00           C
ATOM    204  CA  LEU   204      55.976  16.134 -11.426  1.00 25.00           C
ATOM    205  CA  ARG   205      57.672  16.657 -14.821  1.00 25.00           C
ATOM    206  CA  GLU   206      54.625  15.168 -16.599  1.00 25.00           C
ATOM    207  CA  GLN   207      54.633  18.460 -18.460  1.00 25.00           C
TER
END
