
#######################################################
#                                                     #
#                        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  153 (  153),  selected  153 , name T0330TS168_1-D1
# Molecule2: number of CA atoms  153 ( 1188),  selected  153 , name T0330_D1.pdb
# PARAMETERS: T0330TS168_1-D1.T0330_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       2      S       2           -
LGA    R       3      R       3           -
LGA    T       4      T       4          4.769
LGA    L       5      L       5          3.739
LGA    V       6      V       6          3.033
LGA    L       7      L       7          3.234
LGA    F       8      F       8          2.814
LGA    D       9      D       9           #
LGA    I      10      -       -           -
LGA    D      11      -       -           -
LGA    G      12      I      10          3.578
LGA    -       -      D      11           -
LGA    -       -      G      12           -
LGA    T      13      T      13           #
LGA    L      14      L      14          5.491
LGA    L      15      L      15           #
LGA    K      16      K      16           #
LGA    T      92      T      92          4.404
LGA    L      93      L      93          1.221
LGA    L      94      L      94          2.316
LGA    E      95      E      95          2.573
LGA    G      96      G      96          2.579
LGA    V      97      V      97          2.696
LGA    R      98      R      98          3.309
LGA    E      99      E      99          3.123
LGA    L     100      L     100          2.935
LGA    L     101      L     101          3.569
LGA    D     102      D     102          3.770
LGA    A     103      A     103          3.414
LGA    L     104      L     104          3.965
LGA    S     105      -       -           -
LGA    S     106      S     105           #
LGA    R     107      S     106          1.569
LGA    S     108      R     107          3.563
LGA    D     109      S     108          3.703
LGA    -       -      D     109           -
LGA    V     110      V     110          3.230
LGA    L     111      L     111          2.641
LGA    L     112      L     112          2.905
LGA    G     113      G     113          2.522
LGA    L     114      L     114          2.094
LGA    L     115      L     115          3.855
LGA    T     116      T     116          4.548
LGA    G     117      G     117          2.940
LGA    N     118      N     118          2.037
LGA    F     119      F     119          3.346
LGA    E     120      E     120          1.875
LGA    A     121      A     121          1.603
LGA    S     122      S     122          2.359
LGA    G     123      G     123          2.917
LGA    R     124      R     124          2.890
LGA    H     125      H     125          3.056
LGA    K     126      K     126          4.558
LGA    L     127      L     127          5.114
LGA    K     128      K     128          5.020
LGA    -       -      L     129           -
LGA    L     129      P     130           #
LGA    P     130      G     131          0.980
LGA    G     131      I     132          4.296
LGA    I     132      D     133          4.401
LGA    D     133      H     134          2.280
LGA    H     134      Y     135          3.894
LGA    Y     135      -       -           -
LGA    F     136      F     136          4.140
LGA    P     137      P     137          3.610
LGA    F     138      F     138          3.740
LGA    G     139      G     139          2.660
LGA    A     140      A     140          2.204
LGA    F     141      F     141          4.185
LGA    A     142      -       -           -
LGA    D     143      -       -           -
LGA    D     144      -       -           -
LGA    A     145      -       -           -
LGA    L     146      A     142          4.354
LGA    D     147      D     143           #
LGA    -       -      D     144           -
LGA    R     148      A     145          4.801
LGA    N     149      L     146          4.171
LGA    E     150      D     147          3.293
LGA    L     151      R     148           #
LGA    P     152      N     149          1.066
LGA    H     153      E     150          2.813
LGA    I     154      -       -           -
LGA    A     155      L     151          2.805
LGA    L     156      P     152          1.089
LGA    E     157      H     153          1.927
LGA    R     158      I     154          2.626
LGA    A     159      A     155          1.439
LGA    R     160      L     156          3.352
LGA    R     161      E     157          4.645
LGA    M     162      R     158          4.298
LGA    T     163      A     159          2.997
LGA    -       -      R     160           -
LGA    -       -      R     161           -
LGA    -       -      M     162           -
LGA    G     164      T     163          2.866
LGA    A     165      G     164           -
LGA    -       -      A     165           -
LGA    N     166      N     166          3.598
LGA    Y     167      Y     167          1.914
LGA    S     168      S     168          3.897
LGA    P     169      P     169          3.395
LGA    S     170      S     170          3.048
LGA    Q     171      Q     171          3.554
LGA    -       -      I     172           -
LGA    I     172      V     173          0.786
LGA    V     173      I     174          2.630
LGA    I     174      I     175          3.638
LGA    I     175      G     176          2.034
LGA    G     176      D     177          2.170
LGA    D     177      -       -           -
LGA    T     178      T     178          2.298
LGA    E     179      E     179          1.582
LGA    H     180      H     180          1.097
LGA    D     181      D     181          0.944
LGA    I     182      I     182          1.389
LGA    R     183      R     183          1.939
LGA    C     184      C     184          1.723
LGA    A     185      A     185          2.235
LGA    R     186      -       -           -
LGA    E     187      R     186          3.563
LGA    L     188      E     187          0.845
LGA    D     189      L     188          2.020
LGA    A     190      D     189           #
LGA    R     191      A     190          1.498
LGA    S     192      R     191          2.381
LGA    I     193      S     192          2.311
LGA    A     194      I     193          3.395
LGA    V     195      A     194          1.504
LGA    A     196      V     195          3.362
LGA    T     197      A     196          3.270
LGA    G     198      T     197          3.360
LGA    -       -      G     198           -
LGA    -       -      N     199           -
LGA    -       -      F     200           -
LGA    N     199      T     201          6.032
LGA    F     200      -       -           -
LGA    T     201      M     202          2.353
LGA    M     202      E     203          4.473
LGA    E     203      E     204          3.573
LGA    E     204      L     205          3.405
LGA    L     205      A     206          4.702
LGA    A     206      R     207           #
LGA    R     207      H     208          4.002
LGA    H     208      K     209          3.060
LGA    K     209      P     210          3.418
LGA    P     210      G     211          2.198
LGA    G     211      T     212          2.531
LGA    T     212      L     213           -
LGA    L     213      -       -           -
LGA    F     214      F     214           #
LGA    K     215      K     215           #
LGA    -       -      N     216           -
LGA    N     216      F     217          3.046
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    F     217      T     220          4.362
LGA    A     218      D     221          2.724
LGA    E     219      E     222          2.636
LGA    T     220      V     223          3.933
LGA    D     221      L     224          3.516
LGA    E     222      A     225          2.596
LGA    V     223      S     226          3.446
LGA    -       -      I     227           -
LGA    L     224      L     228          3.427
LGA    A     225      T     229          2.593
LGA    S     226      -       -           -
LGA    I     227      -       -           -
LGA    L     228      -       -           -
LGA    T     229      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    120    3.21    52.50     40.572     3.627

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.570930 * X  +   0.680467 * Y  +  -0.459351 * Z  +  20.210655
  Y_new =  -0.764324 * X  +  -0.236262 * Y  +   0.599991 * Z  +  41.097523
  Z_new =   0.299747 * X  +   0.693646 * Y  +   0.654986 * Z  +  17.972258 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.814056   -2.327536  [ DEG:    46.6420   -133.3580 ]
  Theta =  -0.304428   -2.837165  [ DEG:   -17.4424   -162.5576 ]
  Phi   =  -2.212358    0.929235  [ DEG:  -126.7588     53.2412 ]
 
# 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: T0330TS168_1-D1                               
REMARK     2: T0330_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS168_1-D1.T0330_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  153  153   5.0  120   3.21   52.50  40.572
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS168_1-D1
PFRMAT TS
TARGET T0330
MODEL 1
PARENT N/A
ATOM      2  CA  SER     2      18.855  44.816  37.227  1.00 25.00           C
ATOM      3  CA  ARG     3      21.142  47.773  36.403  1.00 25.00           C
ATOM      4  CA  THR     4      21.872  50.147  33.488  1.00 25.00           C
ATOM      5  CA  LEU     5      21.205  51.265  29.927  1.00 25.00           C
ATOM      6  CA  VAL     6      20.925  47.992  28.029  1.00 25.00           C
ATOM      7  CA  LEU     7      21.315  46.889  24.447  1.00 25.00           C
ATOM      8  CA  PHE     8      20.855  43.632  22.557  1.00 25.00           C
ATOM      9  CA  ASP     9      22.677  40.524  23.934  1.00 25.00           C
ATOM     10  CA  ILE    10      19.607  38.311  23.328  1.00 25.00           C
ATOM     11  CA  ASP    11      19.938  36.097  20.296  1.00 25.00           C
ATOM     12  CA  GLY    12      18.973  39.373  18.598  1.00 25.00           C
ATOM     13  CA  THR    13      18.077  43.047  18.259  1.00 25.00           C
ATOM     14  CA  LEU    14      15.501  45.043  20.266  1.00 25.00           C
ATOM     15  CA  LEU    15      12.199  43.318  19.926  1.00 25.00           C
ATOM     16  CA  LYS    16      13.282  40.650  17.518  1.00 25.00           C
ATOM     92  CA  THR    92       9.513  37.338  16.918  1.00 25.00           C
ATOM     93  CA  LEU    93      11.293  35.600  19.757  1.00 25.00           C
ATOM     94  CA  LEU    94      13.977  33.223  21.188  1.00 25.00           C
ATOM     95  CA  GLU    95      12.787  32.909  24.821  1.00 25.00           C
ATOM     96  CA  GLY    96      15.233  35.280  26.383  1.00 25.00           C
ATOM     97  CA  VAL    97      13.939  37.721  23.706  1.00 25.00           C
ATOM     98  CA  ARG    98      10.197  38.452  24.069  1.00 25.00           C
ATOM     99  CA  GLU    99      10.537  38.425  27.884  1.00 25.00           C
ATOM    100  CA  LEU   100      13.502  40.837  27.661  1.00 25.00           C
ATOM    101  CA  LEU   101      11.474  43.160  25.389  1.00 25.00           C
ATOM    102  CA  ASP   102       8.554  43.074  27.866  1.00 25.00           C
ATOM    103  CA  ALA   103      10.939  43.915  30.743  1.00 25.00           C
ATOM    104  CA  LEU   104      12.372  46.841  28.731  1.00 25.00           C
ATOM    105  CA  SER   105       8.832  48.118  28.018  1.00 25.00           C
ATOM    106  CA  SER   106       7.969  47.881  31.742  1.00 25.00           C
ATOM    107  CA  ARG   107      11.151  49.821  32.627  1.00 25.00           C
ATOM    108  CA  SER   108      10.228  53.495  32.956  1.00 25.00           C
ATOM    109  CA  ASP   109      12.994  55.048  30.856  1.00 25.00           C
ATOM    110  CA  VAL   110      15.971  53.828  28.938  1.00 25.00           C
ATOM    111  CA  LEU   111      16.817  55.230  25.525  1.00 25.00           C
ATOM    112  CA  LEU   112      19.901  53.264  24.385  1.00 25.00           C
ATOM    113  CA  GLY   113      21.085  51.230  21.374  1.00 25.00           C
ATOM    114  CA  LEU   114      20.798  48.104  19.127  1.00 25.00           C
ATOM    115  CA  LEU   115      21.927  46.427  15.895  1.00 25.00           C
ATOM    116  CA  THR   116      22.517  42.667  15.973  1.00 25.00           C
ATOM    117  CA  GLY   117      24.859  43.311  13.073  1.00 25.00           C
ATOM    118  CA  ASN   118      21.892  44.478  10.971  1.00 25.00           C
ATOM    119  CA  PHE   119      22.056  48.185  10.201  1.00 25.00           C
ATOM    120  CA  GLU   120      18.757  49.983  10.897  1.00 25.00           C
ATOM    121  CA  ALA   121      15.382  49.909   9.087  1.00 25.00           C
ATOM    122  CA  SER   122      14.743  46.359  10.371  1.00 25.00           C
ATOM    123  CA  GLY   123      15.598  47.469  13.937  1.00 25.00           C
ATOM    124  CA  ARG   124      13.199  50.436  13.614  1.00 25.00           C
ATOM    125  CA  HIS   125      10.435  48.099  12.363  1.00 25.00           C
ATOM    126  CA  LYS   126      11.053  45.746  15.321  1.00 25.00           C
ATOM    127  CA  LEU   127      10.860  48.703  17.745  1.00 25.00           C
ATOM    128  CA  LYS   128       7.569  49.833  16.146  1.00 25.00           C
ATOM    129  CA  LEU   129       6.163  46.285  16.477  1.00 25.00           C
ATOM    130  CA  PRO   130       6.796  44.145  19.616  1.00 25.00           C
ATOM    131  CA  GLY   131       5.970  46.535  22.505  1.00 25.00           C
ATOM    132  CA  ILE   132       9.597  47.686  22.744  1.00 25.00           C
ATOM    133  CA  ASP   133       8.512  51.370  22.637  1.00 25.00           C
ATOM    134  CA  HIS   134      11.317  53.704  23.800  1.00 25.00           C
ATOM    135  CA  TYR   135      13.301  50.704  25.115  1.00 25.00           C
ATOM    136  CA  PHE   136      16.537  49.491  23.526  1.00 25.00           C
ATOM    137  CA  PRO   137      15.338  52.312  21.261  1.00 25.00           C
ATOM    138  CA  PHE   138      14.556  52.794  17.599  1.00 25.00           C
ATOM    139  CA  GLY   139      18.137  51.870  16.905  1.00 25.00           C
ATOM    140  CA  ALA   140      21.781  51.770  15.866  1.00 25.00           C
ATOM    141  CA  PHE   141      25.434  51.714  14.933  1.00 25.00           C
ATOM    142  CA  ALA   142      25.700  49.628  18.151  1.00 25.00           C
ATOM    143  CA  ASP   143      27.412  46.838  16.146  1.00 25.00           C
ATOM    144  CA  ASP   144      27.995  47.682  12.482  1.00 25.00           C
ATOM    145  CA  ALA   145      29.939  50.983  12.443  1.00 25.00           C
ATOM    146  CA  LEU   146      27.607  52.275   9.720  1.00 25.00           C
ATOM    147  CA  ASP   147      27.775  51.843   5.973  1.00 25.00           C
ATOM    148  CA  ARG   148      31.119  49.952   6.275  1.00 25.00           C
ATOM    149  CA  ASN   149      31.909  47.153   8.715  1.00 25.00           C
ATOM    150  CA  GLU   150      34.874  48.080  10.918  1.00 25.00           C
ATOM    151  CA  LEU   151      34.904  51.896  11.474  1.00 25.00           C
ATOM    152  CA  PRO   152      34.267  51.141  15.154  1.00 25.00           C
ATOM    153  CA  HIS   153      33.374  54.685  16.142  1.00 25.00           C
ATOM    154  CA  ILE   154      31.446  57.970  15.731  1.00 25.00           C
ATOM    155  CA  ALA   155      28.234  56.021  14.987  1.00 25.00           C
ATOM    156  CA  LEU   156      28.789  53.869  18.106  1.00 25.00           C
ATOM    157  CA  GLU   157      29.320  57.020  20.217  1.00 25.00           C
ATOM    158  CA  ARG   158      26.094  58.533  18.814  1.00 25.00           C
ATOM    159  CA  ALA   159      24.194  55.311  19.641  1.00 25.00           C
ATOM    160  CA  ARG   160      25.593  55.372  23.205  1.00 25.00           C
ATOM    161  CA  ARG   161      24.518  59.028  23.590  1.00 25.00           C
ATOM    162  CA  MET   162      21.006  58.152  22.341  1.00 25.00           C
ATOM    163  CA  THR   163      19.203  61.096  23.907  1.00 25.00           C
ATOM    164  CA  GLY   164      20.461  61.342  27.475  1.00 25.00           C
ATOM    165  CA  ALA   165      22.286  58.140  28.321  1.00 25.00           C
ATOM    166  CA  ASN   166      24.904  60.418  29.902  1.00 25.00           C
ATOM    167  CA  TYR   167      27.476  57.682  30.305  1.00 25.00           C
ATOM    168  CA  SER   168      29.345  59.637  27.562  1.00 25.00           C
ATOM    169  CA  PRO   169      31.301  56.455  26.914  1.00 25.00           C
ATOM    170  CA  SER   170      31.395  54.803  30.382  1.00 25.00           C
ATOM    171  CA  GLN   171      28.504  52.447  29.445  1.00 25.00           C
ATOM    172  CA  ILE   172      26.142  49.594  28.739  1.00 25.00           C
ATOM    173  CA  VAL   173      25.339  49.826  25.000  1.00 25.00           C
ATOM    174  CA  ILE   174      25.883  47.226  22.323  1.00 25.00           C
ATOM    175  CA  ILE   175      25.952  43.591  21.262  1.00 25.00           C
ATOM    176  CA  GLY   176      26.007  40.042  19.851  1.00 25.00           C
ATOM    177  CA  ASP   177      25.619  38.595  16.321  1.00 25.00           C
ATOM    178  CA  THR   178      29.125  37.116  16.759  1.00 25.00           C
ATOM    179  CA  GLU   179      32.446  38.592  17.895  1.00 25.00           C
ATOM    180  CA  HIS   180      32.369  41.852  15.886  1.00 25.00           C
ATOM    181  CA  ASP   181      30.498  43.595  18.737  1.00 25.00           C
ATOM    182  CA  ILE   182      33.089  42.315  21.252  1.00 25.00           C
ATOM    183  CA  ARG   183      35.925  43.602  19.023  1.00 25.00           C
ATOM    184  CA  CYS   184      34.214  47.020  18.779  1.00 25.00           C
ATOM    185  CA  ALA   185      33.837  47.131  22.588  1.00 25.00           C
ATOM    186  CA  ARG   186      37.543  46.261  23.005  1.00 25.00           C
ATOM    187  CA  GLU   187      38.497  49.037  20.547  1.00 25.00           C
ATOM    188  CA  LEU   188      35.949  51.853  20.962  1.00 25.00           C
ATOM    189  CA  ASP   189      33.791  54.858  22.069  1.00 25.00           C
ATOM    190  CA  ALA   190      31.434  52.299  23.645  1.00 25.00           C
ATOM    191  CA  ARG   191      33.462  51.098  26.654  1.00 25.00           C
ATOM    192  CA  SER   192      30.929  48.280  26.979  1.00 25.00           C
ATOM    193  CA  ILE   193      28.238  45.645  26.445  1.00 25.00           C
ATOM    194  CA  ALA   194      29.541  42.493  24.828  1.00 25.00           C
ATOM    195  CA  VAL   195      27.042  39.689  24.650  1.00 25.00           C
ATOM    196  CA  ALA   196      28.119  36.312  23.143  1.00 25.00           C
ATOM    197  CA  THR   197      24.784  35.414  21.653  1.00 25.00           C
ATOM    198  CA  GLY   198      23.050  34.668  24.950  1.00 25.00           C
ATOM    199  CA  ASN   199      25.686  32.025  25.755  1.00 25.00           C
ATOM    200  CA  PHE   200      27.200  34.691  27.890  1.00 25.00           C
ATOM    201  CA  THR   201      30.524  33.466  26.574  1.00 25.00           C
ATOM    202  CA  MET   202      32.403  33.245  23.299  1.00 25.00           C
ATOM    203  CA  GLU   203      36.039  33.832  24.348  1.00 25.00           C
ATOM    204  CA  GLU   204      35.983  37.286  22.696  1.00 25.00           C
ATOM    205  CA  LEU   205      32.729  38.136  24.526  1.00 25.00           C
ATOM    206  CA  ALA   206      34.276  37.023  27.848  1.00 25.00           C
ATOM    207  CA  ARG   207      37.356  39.197  27.170  1.00 25.00           C
ATOM    208  CA  HIS   208      38.979  42.582  26.385  1.00 25.00           C
ATOM    209  CA  LYS   209      35.574  44.063  27.156  1.00 25.00           C
ATOM    210  CA  PRO   210      32.143  43.413  28.664  1.00 25.00           C
ATOM    211  CA  GLY   211      30.206  42.762  31.807  1.00 25.00           C
ATOM    212  CA  THR   212      27.389  45.214  31.408  1.00 25.00           C
ATOM    213  CA  LEU   213      25.362  42.572  29.574  1.00 25.00           C
ATOM    214  CA  PHE   214      22.082  41.606  27.912  1.00 25.00           C
ATOM    215  CA  LYS   215      23.010  38.124  29.162  1.00 25.00           C
ATOM    216  CA  ASN   216      19.915  38.488  31.241  1.00 25.00           C
ATOM    217  CA  PHE   217      19.008  41.758  32.938  1.00 25.00           C
ATOM    218  CA  ALA   218      19.139  41.598  36.762  1.00 25.00           C
ATOM    219  CA  GLU   219      22.813  40.528  36.616  1.00 25.00           C
ATOM    220  CA  THR   220      23.592  43.436  34.248  1.00 25.00           C
ATOM    221  CA  ASP   221      21.833  45.872  36.622  1.00 25.00           C
ATOM    222  CA  GLU   222      23.851  44.494  39.570  1.00 25.00           C
ATOM    223  CA  VAL   223      27.094  44.912  37.578  1.00 25.00           C
ATOM    224  CA  LEU   224      26.135  48.521  36.728  1.00 25.00           C
ATOM    225  CA  ALA   225      25.411  49.225  40.422  1.00 25.00           C
ATOM    226  CA  SER   226      28.807  47.748  41.395  1.00 25.00           C
ATOM    227  CA  ILE   227      30.538  49.932  38.768  1.00 25.00           C
ATOM    228  CA  LEU   228      28.725  53.027  40.113  1.00 25.00           C
ATOM    229  CA  THR   229      28.891  53.610  43.906  1.00 25.00           C
TER
END
