
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  153 ( 1188),  selected  153 , name T0330_D1.pdb
# PARAMETERS: T0330TS168_4-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           #
LGA    L       5      L       5           #
LGA    V       6      V       6          5.082
LGA    L       7      L       7           #
LGA    F       8      F       8          4.364
LGA    D       9      D       9          3.968
LGA    I      10      I      10          1.595
LGA    D      11      D      11          3.248
LGA    G      12      -       -           -
LGA    T      13      G      12          1.704
LGA    L      14      T      13           #
LGA    L      15      L      14           -
LGA    K      16      L      15          3.236
LGA    T      92      K      16           #
LGA    L      93      T      92          3.432
LGA    L      94      L      93          1.171
LGA    E      95      L      94          1.971
LGA    G      96      E      95          3.753
LGA    V      97      -       -           -
LGA    R      98      -       -           -
LGA    E      99      G      96          2.024
LGA    L     100      V      97          2.456
LGA    L     101      R      98          2.883
LGA    D     102      E      99          1.742
LGA    A     103      L     100          1.170
LGA    L     104      L     101          1.939
LGA    S     105      D     102          0.642
LGA    S     106      A     103          2.517
LGA    R     107      L     104          3.490
LGA    -       -      S     105           -
LGA    S     108      S     106          0.910
LGA    D     109      R     107          1.917
LGA    -       -      S     108           -
LGA    -       -      D     109           -
LGA    V     110      V     110          3.528
LGA    L     111      L     111          5.077
LGA    L     112      L     112           #
LGA    G     113      G     113           #
LGA    L     114      L     114          3.445
LGA    L     115      L     115          3.620
LGA    T     116      T     116          1.857
LGA    G     117      G     117          2.017
LGA    N     118      N     118          2.977
LGA    F     119      F     119          2.742
LGA    E     120      E     120          2.972
LGA    A     121      A     121          2.879
LGA    S     122      S     122          3.747
LGA    G     123      G     123          3.947
LGA    R     124      R     124          3.797
LGA    H     125      H     125          3.388
LGA    -       -      K     126           -
LGA    K     126      L     127          3.989
LGA    L     127      K     128           -
LGA    K     128      L     129           -
LGA    -       -      P     130           -
LGA    L     129      G     131           #
LGA    P     130      I     132          1.404
LGA    G     131      D     133           #
LGA    I     132      H     134           #
LGA    D     133      Y     135          1.710
LGA    H     134      F     136          1.324
LGA    Y     135      P     137           #
LGA    F     136      F     138          5.088
LGA    P     137      G     139          2.840
LGA    F     138      -       -           -
LGA    G     139      A     140           #
LGA    A     140      -       -           -
LGA    F     141      -       -           -
LGA    A     142      -       -           -
LGA    D     143      -       -           -
LGA    D     144      F     141          2.010
LGA    A     145      A     142          2.852
LGA    L     146      D     143           #
LGA    D     147      D     144           -
LGA    R     148      A     145          5.743
LGA    N     149      L     146          5.311
LGA    E     150      D     147          4.610
LGA    L     151      -       -           -
LGA    P     152      R     148          3.148
LGA    H     153      N     149          3.935
LGA    I     154      E     150          1.684
LGA    A     155      L     151          3.167
LGA    L     156      -       -           -
LGA    E     157      P     152          2.057
LGA    R     158      H     153          2.319
LGA    A     159      I     154          3.810
LGA    R     160      A     155          4.203
LGA    R     161      L     156          2.442
LGA    M     162      E     157          3.425
LGA    -       -      R     158           -
LGA    T     163      A     159          0.842
LGA    G     164      R     160          2.987
LGA    -       -      R     161           -
LGA    -       -      M     162           -
LGA    -       -      T     163           -
LGA    -       -      G     164           -
LGA    A     165      A     165          5.577
LGA    N     166      N     166          5.038
LGA    Y     167      Y     167          3.612
LGA    S     168      S     168          2.878
LGA    P     169      P     169          0.768
LGA    S     170      S     170          2.480
LGA    Q     171      Q     171           #
LGA    -       -      I     172           -
LGA    I     172      V     173          1.026
LGA    V     173      I     174          3.747
LGA    I     174      I     175          0.998
LGA    I     175      G     176          2.857
LGA    G     176      D     177          3.106
LGA    D     177      -       -           -
LGA    T     178      T     178          3.201
LGA    E     179      E     179          1.633
LGA    H     180      -       -           -
LGA    D     181      H     180          1.854
LGA    I     182      D     181          1.643
LGA    R     183      I     182          3.038
LGA    C     184      R     183          2.364
LGA    A     185      C     184          1.154
LGA    R     186      A     185          2.205
LGA    E     187      R     186          1.586
LGA    L     188      E     187          2.895
LGA    D     189      L     188          2.624
LGA    A     190      D     189          5.039
LGA    R     191      A     190          4.342
LGA    -       -      R     191           -
LGA    S     192      S     192          2.244
LGA    I     193      I     193          3.455
LGA    A     194      A     194          2.248
LGA    V     195      V     195          2.219
LGA    A     196      A     196          3.338
LGA    T     197      T     197          2.634
LGA    -       -      G     198           -
LGA    G     198      N     199          2.659
LGA    N     199      F     200          3.578
LGA    F     200      T     201          4.170
LGA    T     201      M     202          1.559
LGA    M     202      E     203          4.322
LGA    E     203      E     204          2.699
LGA    E     204      L     205          3.504
LGA    L     205      -       -           -
LGA    A     206      A     206          2.103
LGA    R     207      R     207          3.785
LGA    H     208      H     208          3.124
LGA    K     209      K     209          4.543
LGA    P     210      P     210          4.697
LGA    G     211      G     211          1.292
LGA    T     212      T     212          3.139
LGA    L     213      L     213          3.847
LGA    F     214      F     214          4.340
LGA    K     215      K     215          3.433
LGA    N     216      N     216          1.814
LGA    F     217      F     217          1.978
LGA    -       -      A     218           -
LGA    A     218      E     219          2.635
LGA    E     219      T     220           -
LGA    -       -      D     221           -
LGA    T     220      E     222          5.071
LGA    D     221      V     223          2.856
LGA    E     222      -       -           -
LGA    V     223      -       -           -
LGA    L     224      L     224           #
LGA    A     225      A     225          4.166
LGA    S     226      S     226           #
LGA    -       -      I     227           -
LGA    -       -      L     228           -
LGA    I     227      T     229          4.599
LGA    L     228      -       -           -
LGA    T     229      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    113    3.18    46.90     38.202     3.442

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.016057 * X  +   0.376393 * Y  +   0.926321 * Z  +  15.054917
  Y_new =  -0.356375 * X  +  -0.863443 * Y  +   0.357021 * Z  +  44.919846
  Z_new =   0.934205 * X  +  -0.335850 * Y  +   0.120273 * Z  +  20.072311 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.226911    1.914681  [ DEG:   -70.2968    109.7032 ]
  Theta =  -1.206024   -1.935568  [ DEG:   -69.1001   -110.8999 ]
  Phi   =  -1.525770    1.615822  [ DEG:   -87.4202     92.5798 ]
 
# 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_4-D1                               
REMARK     2: T0330_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS168_4-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  113   3.18   46.90  38.202
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS168_4-D1
PFRMAT TS
TARGET T0330
MODEL 4
PARENT N/A
ATOM      2  CA  SER     2       7.676  57.176  28.983  1.00 25.00           C
ATOM      3  CA  ARG     3      11.291  56.276  28.516  1.00 25.00           C
ATOM      4  CA  THR     4      15.043  56.319  29.030  1.00 25.00           C
ATOM      5  CA  LEU     5      17.432  54.168  27.002  1.00 25.00           C
ATOM      6  CA  VAL     6      17.204  50.626  25.605  1.00 25.00           C
ATOM      7  CA  LEU     7      16.739  46.909  25.045  1.00 25.00           C
ATOM      8  CA  PHE     8      18.894  43.815  24.551  1.00 25.00           C
ATOM      9  CA  ASP     9      19.236  42.874  20.917  1.00 25.00           C
ATOM     10  CA  ILE    10      17.795  42.923  17.416  1.00 25.00           C
ATOM     11  CA  ASP    11      18.919  41.876  13.967  1.00 25.00           C
ATOM     12  CA  GLY    12      22.000  40.668  15.911  1.00 25.00           C
ATOM     13  CA  THR    13      20.237  37.417  17.016  1.00 25.00           C
ATOM     14  CA  LEU    14      20.524  37.035  13.203  1.00 25.00           C
ATOM     15  CA  LEU    15      17.066  36.975  11.550  1.00 25.00           C
ATOM     16  CA  LYS    16      15.430  36.994  14.961  1.00 25.00           C
ATOM     92  CA  THR    92      11.337  31.164  17.454  1.00 25.00           C
ATOM     93  CA  LEU    93       9.654  33.976  19.389  1.00 25.00           C
ATOM     94  CA  LEU    94      13.136  35.455  19.397  1.00 25.00           C
ATOM     95  CA  GLU    95      13.874  33.441  22.556  1.00 25.00           C
ATOM     96  CA  GLY    96      16.876  35.609  23.362  1.00 25.00           C
ATOM     97  CA  VAL    97      15.660  38.954  21.974  1.00 25.00           C
ATOM     98  CA  ARG    98      12.209  38.274  23.489  1.00 25.00           C
ATOM     99  CA  GLU    99      13.807  37.672  26.918  1.00 25.00           C
ATOM    100  CA  LEU   100      15.755  40.956  26.614  1.00 25.00           C
ATOM    101  CA  LEU   101      12.533  42.811  25.693  1.00 25.00           C
ATOM    102  CA  ASP   102      10.756  41.276  28.719  1.00 25.00           C
ATOM    103  CA  ALA   103      13.647  42.348  30.991  1.00 25.00           C
ATOM    104  CA  LEU   104      13.473  45.903  29.578  1.00 25.00           C
ATOM    105  CA  SER   105       9.695  45.991  30.198  1.00 25.00           C
ATOM    106  CA  SER   106      10.234  44.799  33.798  1.00 25.00           C
ATOM    107  CA  ARG   107      12.877  47.519  34.329  1.00 25.00           C
ATOM    108  CA  SER   108      10.722  50.638  33.647  1.00 25.00           C
ATOM    109  CA  ASP   109      13.980  52.494  32.825  1.00 25.00           C
ATOM    110  CA  VAL   110      16.755  50.784  30.844  1.00 25.00           C
ATOM    111  CA  LEU   111      20.391  51.044  29.629  1.00 25.00           C
ATOM    112  CA  LEU   112      20.519  47.445  28.405  1.00 25.00           C
ATOM    113  CA  GLY   113      21.644  48.415  24.896  1.00 25.00           C
ATOM    114  CA  LEU   114      20.393  47.481  21.459  1.00 25.00           C
ATOM    115  CA  LEU   115      21.745  46.232  18.178  1.00 25.00           C
ATOM    116  CA  THR   116      21.203  46.863  14.480  1.00 25.00           C
ATOM    117  CA  GLY   117      22.907  44.458  12.128  1.00 25.00           C
ATOM    118  CA  ASN   118      20.550  43.118   9.403  1.00 25.00           C
ATOM    119  CA  PHE   119      21.249  46.675   8.144  1.00 25.00           C
ATOM    120  CA  GLU   120      19.931  49.947   9.567  1.00 25.00           C
ATOM    121  CA  ALA   121      16.572  48.563   8.353  1.00 25.00           C
ATOM    122  CA  SER   122      16.481  46.127  11.307  1.00 25.00           C
ATOM    123  CA  GLY   123      17.227  48.998  13.730  1.00 25.00           C
ATOM    124  CA  ARG   124      14.416  51.078  12.169  1.00 25.00           C
ATOM    125  CA  HIS   125      12.001  48.127  12.523  1.00 25.00           C
ATOM    126  CA  LYS   126      13.007  47.713  16.195  1.00 25.00           C
ATOM    127  CA  LEU   127      12.428  51.449  16.801  1.00 25.00           C
ATOM    128  CA  LYS   128       8.979  51.207  15.153  1.00 25.00           C
ATOM    129  CA  LEU   129       8.112  48.196  17.354  1.00 25.00           C
ATOM    130  CA  PRO   130       9.830  45.626  19.619  1.00 25.00           C
ATOM    131  CA  GLY   131       8.413  47.796  22.412  1.00 25.00           C
ATOM    132  CA  ILE   132      11.889  47.384  23.827  1.00 25.00           C
ATOM    133  CA  ASP   133      11.760  51.221  24.161  1.00 25.00           C
ATOM    134  CA  HIS   134      14.087  52.793  21.557  1.00 25.00           C
ATOM    135  CA  TYR   135      15.762  49.399  20.970  1.00 25.00           C
ATOM    136  CA  PHE   136      18.080  50.796  18.307  1.00 25.00           C
ATOM    137  CA  PRO   137      18.873  54.031  20.152  1.00 25.00           C
ATOM    138  CA  PHE   138      21.064  53.553  23.287  1.00 25.00           C
ATOM    139  CA  GLY   139      23.066  51.401  20.861  1.00 25.00           C
ATOM    140  CA  ALA   140      25.366  48.397  21.015  1.00 25.00           C
ATOM    141  CA  PHE   141      27.065  45.205  19.883  1.00 25.00           C
ATOM    142  CA  ALA   142      27.971  47.315  16.866  1.00 25.00           C
ATOM    143  CA  ASP   143      25.995  48.098  13.738  1.00 25.00           C
ATOM    144  CA  ASP   144      24.315  50.976  11.884  1.00 25.00           C
ATOM    145  CA  ALA   145      26.673  50.790   8.939  1.00 25.00           C
ATOM    146  CA  LEU   146      27.156  46.969   8.954  1.00 25.00           C
ATOM    147  CA  ASP   147      29.903  45.380   6.881  1.00 25.00           C
ATOM    148  CA  ARG   148      31.301  48.880   6.138  1.00 25.00           C
ATOM    149  CA  ASN   149      34.621  47.833   7.769  1.00 25.00           C
ATOM    150  CA  GLU   150      33.845  45.548  10.668  1.00 25.00           C
ATOM    151  CA  LEU   151      36.567  47.470  12.560  1.00 25.00           C
ATOM    152  CA  PRO   152      33.600  49.297  14.000  1.00 25.00           C
ATOM    153  CA  HIS   153      30.569  50.631  12.163  1.00 25.00           C
ATOM    154  CA  ILE   154      31.044  54.422  12.431  1.00 25.00           C
ATOM    155  CA  ALA   155      27.273  54.884  12.917  1.00 25.00           C
ATOM    156  CA  LEU   156      27.272  52.205  15.654  1.00 25.00           C
ATOM    157  CA  GLU   157      30.207  53.946  17.392  1.00 25.00           C
ATOM    158  CA  ARG   158      28.354  57.293  17.226  1.00 25.00           C
ATOM    159  CA  ALA   159      25.227  55.662  18.720  1.00 25.00           C
ATOM    160  CA  ARG   160      27.331  54.155  21.542  1.00 25.00           C
ATOM    161  CA  ARG   161      28.891  57.581  22.243  1.00 25.00           C
ATOM    162  CA  MET   162      25.409  59.173  22.352  1.00 25.00           C
ATOM    163  CA  THR   163      21.884  59.549  23.775  1.00 25.00           C
ATOM    164  CA  GLY   164      23.538  61.237  26.796  1.00 25.00           C
ATOM    165  CA  ALA   165      22.629  57.925  28.491  1.00 25.00           C
ATOM    166  CA  ASN   166      25.948  58.447  30.281  1.00 25.00           C
ATOM    167  CA  TYR   167      27.643  56.694  27.340  1.00 25.00           C
ATOM    168  CA  SER   168      31.051  58.318  28.146  1.00 25.00           C
ATOM    169  CA  PRO   169      31.856  54.781  29.345  1.00 25.00           C
ATOM    170  CA  SER   170      29.225  52.803  31.288  1.00 25.00           C
ATOM    171  CA  GLN   171      29.692  49.571  29.339  1.00 25.00           C
ATOM    172  CA  ILE   172      26.255  50.343  27.907  1.00 25.00           C
ATOM    173  CA  VAL   173      25.533  46.644  28.098  1.00 25.00           C
ATOM    174  CA  ILE   174      24.976  44.185  25.310  1.00 25.00           C
ATOM    175  CA  ILE   175      23.476  41.164  23.449  1.00 25.00           C
ATOM    176  CA  GLY   176      23.914  39.613  20.050  1.00 25.00           C
ATOM    177  CA  ASP   177      27.282  38.339  18.837  1.00 25.00           C
ATOM    178  CA  THR   178      29.099  39.365  15.638  1.00 25.00           C
ATOM    179  CA  GLU   179      32.212  39.089  17.686  1.00 25.00           C
ATOM    180  CA  HIS   180      35.026  41.191  16.160  1.00 25.00           C
ATOM    181  CA  ASP   181      32.626  44.143  15.737  1.00 25.00           C
ATOM    182  CA  ILE   182      31.517  43.796  19.386  1.00 25.00           C
ATOM    183  CA  ARG   183      35.175  43.743  20.518  1.00 25.00           C
ATOM    184  CA  CYS   184      35.885  46.889  18.453  1.00 25.00           C
ATOM    185  CA  ALA   185      32.853  48.630  20.015  1.00 25.00           C
ATOM    186  CA  ARG   186      34.067  47.660  23.515  1.00 25.00           C
ATOM    187  CA  GLU   187      37.550  49.036  22.714  1.00 25.00           C
ATOM    188  CA  LEU   188      36.289  52.426  23.809  1.00 25.00           C
ATOM    189  CA  ASP   189      33.553  53.667  21.512  1.00 25.00           C
ATOM    190  CA  ALA   190      31.271  53.278  24.570  1.00 25.00           C
ATOM    191  CA  ARG   191      29.510  49.955  24.087  1.00 25.00           C
ATOM    192  CA  SER   192      29.546  46.335  25.257  1.00 25.00           C
ATOM    193  CA  ILE   193      30.387  42.684  25.359  1.00 25.00           C
ATOM    194  CA  ALA   194      28.485  40.145  23.347  1.00 25.00           C
ATOM    195  CA  VAL   195      27.442  36.570  24.112  1.00 25.00           C
ATOM    196  CA  ALA   196      23.916  35.613  23.065  1.00 25.00           C
ATOM    197  CA  THR   197      23.224  34.134  19.619  1.00 25.00           C
ATOM    198  CA  GLY   198      26.639  33.308  18.314  1.00 25.00           C
ATOM    199  CA  ASN   199      26.860  30.474  20.828  1.00 25.00           C
ATOM    200  CA  PHE   200      27.033  31.564  24.507  1.00 25.00           C
ATOM    201  CA  THR   201      30.461  32.762  25.779  1.00 25.00           C
ATOM    202  CA  MET   202      32.557  32.640  22.608  1.00 25.00           C
ATOM    203  CA  GLU   203      36.204  32.963  23.730  1.00 25.00           C
ATOM    204  CA  GLU   204      36.530  36.256  21.802  1.00 25.00           C
ATOM    205  CA  LEU   205      33.327  37.563  23.444  1.00 25.00           C
ATOM    206  CA  ALA   206      34.670  36.591  26.896  1.00 25.00           C
ATOM    207  CA  ARG   207      37.965  38.396  26.149  1.00 25.00           C
ATOM    208  CA  HIS   208      37.746  41.753  24.382  1.00 25.00           C
ATOM    209  CA  LYS   209      37.098  44.443  26.950  1.00 25.00           C
ATOM    210  CA  PRO   210      33.699  45.655  28.124  1.00 25.00           C
ATOM    211  CA  GLY   211      33.383  42.099  29.436  1.00 25.00           C
ATOM    212  CA  THR   212      29.982  43.327  30.575  1.00 25.00           C
ATOM    213  CA  LEU   213      27.767  40.526  29.294  1.00 25.00           C
ATOM    214  CA  PHE   214      24.360  39.128  28.179  1.00 25.00           C
ATOM    215  CA  LYS   215      25.304  35.510  28.878  1.00 25.00           C
ATOM    216  CA  ASN   216      21.982  33.752  29.526  1.00 25.00           C
ATOM    217  CA  PHE   217      19.286  35.720  31.308  1.00 25.00           C
ATOM    218  CA  ALA   218      19.974  34.355  34.819  1.00 25.00           C
ATOM    219  CA  GLU   219      23.745  34.647  34.222  1.00 25.00           C
ATOM    220  CA  THR   220      23.300  38.261  33.031  1.00 25.00           C
ATOM    221  CA  ASP   221      21.237  39.062  36.157  1.00 25.00           C
ATOM    222  CA  GLU   222      23.951  37.519  38.374  1.00 25.00           C
ATOM    223  CA  VAL   223      26.626  39.603  36.593  1.00 25.00           C
ATOM    224  CA  LEU   224      24.536  42.771  37.107  1.00 25.00           C
ATOM    225  CA  ALA   225      24.141  41.936  40.824  1.00 25.00           C
ATOM    226  CA  SER   226      27.921  41.407  41.132  1.00 25.00           C
ATOM    227  CA  ILE   227      28.556  44.774  39.422  1.00 25.00           C
ATOM    228  CA  LEU   228      26.109  46.483  41.821  1.00 25.00           C
ATOM    229  CA  THR   229      28.532  45.459  44.607  1.00 25.00           C
TER
END
