
#######################################################
#                                                     #
#                        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 T0330TS393_5-D1
# Molecule2: number of CA atoms  153 ( 1188),  selected  153 , name T0330_D1.pdb
# PARAMETERS: T0330TS393_5-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          4.773
LGA    V       6      V       6          3.069
LGA    L       7      L       7          3.611
LGA    F       8      F       8          4.101
LGA    D       9      D       9          1.527
LGA    I      10      I      10          3.797
LGA    -       -      D      11           -
LGA    D      11      G      12          4.379
LGA    G      12      T      13          4.545
LGA    T      13      -       -           -
LGA    L      14      L      14          3.449
LGA    L      15      L      15          3.497
LGA    K      16      K      16           #
LGA    T      92      T      92           #
LGA    L      93      L      93          2.947
LGA    L      94      L      94          2.263
LGA    E      95      E      95          1.797
LGA    G      96      G      96          2.583
LGA    V      97      V      97          2.884
LGA    R      98      R      98          2.920
LGA    E      99      E      99          2.933
LGA    L     100      L     100          3.317
LGA    L     101      L     101          3.625
LGA    D     102      D     102          3.228
LGA    A     103      A     103          3.372
LGA    L     104      L     104          4.128
LGA    S     105      S     105          3.982
LGA    S     106      S     106          2.639
LGA    R     107      R     107          2.970
LGA    S     108      S     108          4.060
LGA    D     109      D     109           #
LGA    V     110      V     110          4.896
LGA    L     111      L     111          2.037
LGA    L     112      L     112          2.129
LGA    G     113      G     113          3.861
LGA    L     114      L     114          1.177
LGA    L     115      L     115          3.639
LGA    T     116      T     116          3.142
LGA    G     117      G     117          0.893
LGA    N     118      N     118          1.744
LGA    F     119      F     119          1.381
LGA    E     120      E     120          1.344
LGA    A     121      A     121          0.846
LGA    S     122      S     122          1.715
LGA    G     123      G     123          2.576
LGA    R     124      R     124          2.876
LGA    H     125      H     125          2.681
LGA    K     126      K     126          3.955
LGA    L     127      L     127          4.606
LGA    K     128      K     128          4.165
LGA    L     129      L     129          4.699
LGA    -       -      P     130           -
LGA    -       -      G     131           -
LGA    P     130      I     132          0.441
LGA    G     131      D     133          4.662
LGA    I     132      H     134          2.439
LGA    D     133      Y     135          4.882
LGA    H     134      F     136          4.396
LGA    Y     135      P     137          3.018
LGA    F     136      F     138          3.789
LGA    P     137      -       -           -
LGA    F     138      -       -           -
LGA    G     139      G     139           #
LGA    A     140      A     140          3.844
LGA    F     141      F     141          4.891
LGA    A     142      A     142          4.007
LGA    D     143      D     143           #
LGA    D     144      D     144          1.654
LGA    A     145      A     145          1.766
LGA    L     146      L     146          4.599
LGA    D     147      -       -           -
LGA    R     148      -       -           -
LGA    N     149      -       -           -
LGA    E     150      -       -           -
LGA    L     151      D     147          1.802
LGA    P     152      R     148          2.545
LGA    H     153      N     149          3.667
LGA    I     154      E     150          2.812
LGA    A     155      L     151          0.986
LGA    L     156      P     152          2.346
LGA    E     157      H     153          2.104
LGA    R     158      I     154          1.264
LGA    A     159      A     155          2.008
LGA    R     160      L     156          1.934
LGA    R     161      E     157          0.918
LGA    M     162      R     158          3.067
LGA    T     163      A     159          2.502
LGA    G     164      R     160          0.700
LGA    -       -      R     161           -
LGA    -       -      M     162           -
LGA    -       -      T     163           -
LGA    A     165      G     164          3.843
LGA    N     166      A     165          2.423
LGA    Y     167      N     166           #
LGA    S     168      Y     167          2.633
LGA    P     169      S     168          1.768
LGA    S     170      P     169          1.610
LGA    -       -      S     170           -
LGA    -       -      Q     171           -
LGA    Q     171      I     172          2.317
LGA    I     172      V     173          3.308
LGA    V     173      -       -           -
LGA    I     174      I     174          5.050
LGA    I     175      I     175          4.559
LGA    G     176      G     176          2.793
LGA    D     177      D     177          1.872
LGA    T     178      T     178          2.804
LGA    E     179      E     179          2.033
LGA    H     180      H     180          1.896
LGA    D     181      D     181          1.785
LGA    I     182      I     182          1.837
LGA    R     183      R     183          2.211
LGA    C     184      C     184          1.751
LGA    A     185      A     185          1.720
LGA    R     186      R     186          2.321
LGA    E     187      E     187          3.420
LGA    L     188      L     188          3.769
LGA    D     189      D     189           #
LGA    A     190      A     190          3.660
LGA    R     191      -       -           -
LGA    S     192      -       -           -
LGA    I     193      -       -           -
LGA    A     194      R     191           #
LGA    V     195      S     192          3.854
LGA    -       -      I     193           -
LGA    A     196      A     194          4.496
LGA    T     197      V     195           #
LGA    G     198      A     196          1.675
LGA    -       -      T     197           -
LGA    -       -      G     198           -
LGA    -       -      N     199           -
LGA    -       -      F     200           -
LGA    -       -      T     201           -
LGA    N     199      M     202          4.063
LGA    F     200      E     203           -
LGA    T     201      E     204           #
LGA    M     202      L     205          4.079
LGA    E     203      A     206          4.726
LGA    E     204      R     207          4.920
LGA    L     205      H     208          2.936
LGA    A     206      K     209          3.099
LGA    R     207      P     210           #
LGA    H     208      -       -           -
LGA    K     209      -       -           -
LGA    P     210      G     211           #
LGA    G     211      T     212           -
LGA    T     212      L     213           -
LGA    L     213      -       -           -
LGA    F     214      -       -           -
LGA    K     215      -       -           -
LGA    N     216      F     214          4.012
LGA    -       -      K     215           -
LGA    -       -      N     216           -
LGA    F     217      F     217          2.146
LGA    -       -      A     218           -
LGA    A     218      E     219          3.249
LGA    -       -      T     220           -
LGA    -       -      D     221           -
LGA    E     219      E     222          4.996
LGA    T     220      V     223          2.905
LGA    D     221      L     224          2.930
LGA    E     222      A     225          3.719
LGA    V     223      S     226          1.710
LGA    L     224      I     227          3.214
LGA    A     225      L     228           #
LGA    S     226      -       -           -
LGA    I     227      T     229          1.187
LGA    L     228      -       -           -
LGA    T     229      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    115    3.16    61.74     40.005     3.523

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.513254 * X  +   0.685786 * Y  +   0.516012 * Z  +  17.739172
  Y_new =  -0.347902 * X  +  -0.715882 * Y  +   0.605373 * Z  +  42.299374
  Z_new =   0.784560 * X  +   0.131189 * Y  +   0.606016 * Z  +  18.249744 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.213188   -2.928405  [ DEG:    12.2148   -167.7852 ]
  Theta =  -0.901987   -2.239606  [ DEG:   -51.6800   -128.3200 ]
  Phi   =  -2.545897    0.595695  [ DEG:  -145.8692     34.1308 ]
 
# 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: T0330TS393_5-D1                               
REMARK     2: T0330_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS393_5-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  115   3.16   61.74  40.005
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS393_5-D1
PFRMAT TS
TARGET T0330
MODEL 5
PARENT N/A
ATOM      2  CA  SER     2      16.555  44.268  36.404  1.00 25.00           C
ATOM      3  CA  ARG     3      17.315  47.862  35.316  1.00 25.00           C
ATOM      4  CA  THR     4      19.664  50.565  34.071  1.00 25.00           C
ATOM      5  CA  LEU     5      22.049  50.473  31.121  1.00 25.00           C
ATOM      6  CA  VAL     6      21.162  48.017  28.402  1.00 25.00           C
ATOM      7  CA  LEU     7      21.930  46.496  25.014  1.00 25.00           C
ATOM      8  CA  PHE     8      23.968  43.548  23.591  1.00 25.00           C
ATOM      9  CA  ASP     9      23.326  44.760  20.012  1.00 25.00           C
ATOM     10  CA  ILE    10      22.152  41.243  19.336  1.00 25.00           C
ATOM     11  CA  ASP    11      21.691  38.366  21.796  1.00 25.00           C
ATOM     12  CA  GLY    12      21.169  39.859  25.249  1.00 25.00           C
ATOM     13  CA  THR    13      18.361  42.138  26.497  1.00 25.00           C
ATOM     14  CA  LEU    14      17.669  42.609  22.851  1.00 25.00           C
ATOM     15  CA  LEU    15      17.174  40.264  19.964  1.00 25.00           C
ATOM     16  CA  LYS    16      16.348  41.121  16.369  1.00 25.00           C
ATOM     92  CA  THR    92      18.427  32.997  20.627  1.00 25.00           C
ATOM     93  CA  LEU    93      14.815  34.355  20.603  1.00 25.00           C
ATOM     94  CA  LEU    94      16.705  36.140  23.424  1.00 25.00           C
ATOM     95  CA  GLU    95      13.783  34.747  25.312  1.00 25.00           C
ATOM     96  CA  GLY    96      13.675  38.298  26.786  1.00 25.00           C
ATOM     97  CA  VAL    97      12.845  40.047  23.513  1.00 25.00           C
ATOM     98  CA  ARG    98       9.202  41.148  23.937  1.00 25.00           C
ATOM     99  CA  GLU    99       9.618  41.144  27.744  1.00 25.00           C
ATOM    100  CA  LEU   100      12.802  43.248  27.423  1.00 25.00           C
ATOM    101  CA  LEU   101      10.965  45.726  25.153  1.00 25.00           C
ATOM    102  CA  ASP   102       8.104  45.966  27.687  1.00 25.00           C
ATOM    103  CA  ALA   103      10.619  46.608  30.503  1.00 25.00           C
ATOM    104  CA  LEU   104      12.292  49.350  28.416  1.00 25.00           C
ATOM    105  CA  SER   105       8.881  50.959  27.751  1.00 25.00           C
ATOM    106  CA  SER   106       8.078  50.863  31.494  1.00 25.00           C
ATOM    107  CA  ARG   107      11.453  52.491  32.284  1.00 25.00           C
ATOM    108  CA  SER   108      10.016  56.013  32.359  1.00 25.00           C
ATOM    109  CA  ASP   109      12.575  57.061  29.831  1.00 25.00           C
ATOM    110  CA  VAL   110      14.678  54.613  27.852  1.00 25.00           C
ATOM    111  CA  LEU   111      18.203  53.138  27.575  1.00 25.00           C
ATOM    112  CA  LEU   112      16.953  50.115  25.600  1.00 25.00           C
ATOM    113  CA  GLY   113      17.988  48.500  22.249  1.00 25.00           C
ATOM    114  CA  LEU   114      19.432  48.912  18.744  1.00 25.00           C
ATOM    115  CA  LEU   115      21.271  47.114  15.940  1.00 25.00           C
ATOM    116  CA  THR   116      23.022  43.919  14.919  1.00 25.00           C
ATOM    117  CA  GLY   117      23.811  45.072  11.364  1.00 25.00           C
ATOM    118  CA  ASN   118      20.135  44.455  10.681  1.00 25.00           C
ATOM    119  CA  PHE   119      19.783  47.696   8.688  1.00 25.00           C
ATOM    120  CA  GLU   120      18.256  51.097   9.657  1.00 25.00           C
ATOM    121  CA  ALA   121      14.698  50.446   8.398  1.00 25.00           C
ATOM    122  CA  SER   122      14.911  46.815   9.595  1.00 25.00           C
ATOM    123  CA  GLY   123      16.127  47.993  13.029  1.00 25.00           C
ATOM    124  CA  ARG   124      13.224  50.481  13.232  1.00 25.00           C
ATOM    125  CA  HIS   125      10.748  47.706  12.318  1.00 25.00           C
ATOM    126  CA  LYS   126      12.244  45.447  15.025  1.00 25.00           C
ATOM    127  CA  LEU   127      11.932  48.274  17.589  1.00 25.00           C
ATOM    128  CA  LYS   128       8.278  48.817  16.583  1.00 25.00           C
ATOM    129  CA  LEU   129       7.591  45.068  16.959  1.00 25.00           C
ATOM    130  CA  PRO   130       9.423  44.580  20.298  1.00 25.00           C
ATOM    131  CA  GLY   131       7.187  47.261  21.831  1.00 25.00           C
ATOM    132  CA  ILE   132       9.788  49.957  22.687  1.00 25.00           C
ATOM    133  CA  ASP   133       8.694  52.519  20.098  1.00 25.00           C
ATOM    134  CA  HIS   134      11.294  55.153  21.079  1.00 25.00           C
ATOM    135  CA  TYR   135      13.989  52.440  21.311  1.00 25.00           C
ATOM    136  CA  PHE   136      17.595  53.629  21.640  1.00 25.00           C
ATOM    137  CA  PRO   137      20.732  54.598  23.505  1.00 25.00           C
ATOM    138  CA  PHE   138      22.379  51.580  25.032  1.00 25.00           C
ATOM    139  CA  GLY   139      23.228  50.756  21.432  1.00 25.00           C
ATOM    140  CA  ALA   140      24.039  50.986  17.756  1.00 25.00           C
ATOM    141  CA  PHE   141      25.756  49.177  14.832  1.00 25.00           C
ATOM    142  CA  ALA   142      22.902  50.551  12.665  1.00 25.00           C
ATOM    143  CA  ASP   143      23.449  54.296  13.049  1.00 25.00           C
ATOM    144  CA  ASP   144      25.739  53.838  10.011  1.00 25.00           C
ATOM    145  CA  ALA   145      28.466  51.552   8.649  1.00 25.00           C
ATOM    146  CA  LEU   146      28.125  48.190  10.335  1.00 25.00           C
ATOM    147  CA  ASP   147      28.146  46.498   6.873  1.00 25.00           C
ATOM    148  CA  ARG   148      30.903  43.902   7.151  1.00 25.00           C
ATOM    149  CA  ASN   149      33.493  43.182   9.848  1.00 25.00           C
ATOM    150  CA  GLU   150      35.426  46.174  11.323  1.00 25.00           C
ATOM    151  CA  LEU   151      33.492  48.615   9.127  1.00 25.00           C
ATOM    152  CA  PRO   152      32.226  50.507  12.152  1.00 25.00           C
ATOM    153  CA  HIS   153      33.530  53.901  13.223  1.00 25.00           C
ATOM    154  CA  ILE   154      30.219  55.435  12.059  1.00 25.00           C
ATOM    155  CA  ALA   155      28.286  53.096  14.395  1.00 25.00           C
ATOM    156  CA  LEU   156      30.564  54.084  17.311  1.00 25.00           C
ATOM    157  CA  GLU   157      30.003  57.791  16.525  1.00 25.00           C
ATOM    158  CA  ARG   158      26.216  57.226  16.446  1.00 25.00           C
ATOM    159  CA  ALA   159      26.389  55.426  19.822  1.00 25.00           C
ATOM    160  CA  ARG   160      28.412  58.326  21.292  1.00 25.00           C
ATOM    161  CA  ARG   161      25.833  60.829  19.968  1.00 25.00           C
ATOM    162  CA  MET   162      23.002  58.770  21.521  1.00 25.00           C
ATOM    163  CA  THR   163      21.203  62.076  21.980  1.00 25.00           C
ATOM    164  CA  GLY   164      24.056  63.266  24.157  1.00 25.00           C
ATOM    165  CA  ALA   165      21.649  62.364  26.974  1.00 25.00           C
ATOM    166  CA  ASN   166      23.804  61.027  29.773  1.00 25.00           C
ATOM    167  CA  TYR   167      25.382  58.644  27.191  1.00 25.00           C
ATOM    168  CA  SER   168      28.190  61.125  27.768  1.00 25.00           C
ATOM    169  CA  PRO   169      30.045  58.177  29.390  1.00 25.00           C
ATOM    170  CA  SER   170      31.497  55.161  31.281  1.00 25.00           C
ATOM    171  CA  GLN   171      28.800  52.641  30.507  1.00 25.00           C
ATOM    172  CA  ILE   172      26.963  49.392  31.375  1.00 25.00           C
ATOM    173  CA  VAL   173      25.757  45.877  30.731  1.00 25.00           C
ATOM    174  CA  ILE   174      28.061  44.230  28.216  1.00 25.00           C
ATOM    175  CA  ILE   175      26.771  40.878  26.914  1.00 25.00           C
ATOM    176  CA  GLY   176      26.351  39.529  23.347  1.00 25.00           C
ATOM    177  CA  ASP   177      27.465  39.447  19.685  1.00 25.00           C
ATOM    178  CA  THR   178      28.442  38.425  16.149  1.00 25.00           C
ATOM    179  CA  GLU   179      31.911  39.518  17.316  1.00 25.00           C
ATOM    180  CA  HIS   180      31.311  42.522  15.015  1.00 25.00           C
ATOM    181  CA  ASP   181      29.462  44.341  17.833  1.00 25.00           C
ATOM    182  CA  ILE   182      32.359  43.622  20.232  1.00 25.00           C
ATOM    183  CA  ARG   183      34.856  44.967  17.660  1.00 25.00           C
ATOM    184  CA  CYS   184      32.746  48.134  17.232  1.00 25.00           C
ATOM    185  CA  ALA   185      32.636  48.604  21.031  1.00 25.00           C
ATOM    186  CA  ARG   186      36.439  48.189  21.218  1.00 25.00           C
ATOM    187  CA  GLU   187      36.882  50.778  18.431  1.00 25.00           C
ATOM    188  CA  LEU   188      34.813  53.320  20.471  1.00 25.00           C
ATOM    189  CA  ASP   189      32.640  55.502  22.731  1.00 25.00           C
ATOM    190  CA  ALA   190      30.838  54.213  25.847  1.00 25.00           C
ATOM    191  CA  ARG   191      27.058  53.903  25.546  1.00 25.00           C
ATOM    192  CA  SER   192      28.148  51.519  22.791  1.00 25.00           C
ATOM    193  CA  ILE   193      27.762  48.388  20.719  1.00 25.00           C
ATOM    194  CA  ALA   194      28.607  45.410  22.853  1.00 25.00           C
ATOM    195  CA  VAL   195      30.445  42.375  24.352  1.00 25.00           C
ATOM    196  CA  ALA   196      31.832  39.271  22.741  1.00 25.00           C
ATOM    197  CA  THR   197      29.820  36.095  22.188  1.00 25.00           C
ATOM    198  CA  GLY   198      26.463  34.278  22.289  1.00 25.00           C
ATOM    199  CA  ASN   199      27.465  33.042  25.670  1.00 25.00           C
ATOM    200  CA  PHE   200      29.064  35.915  27.532  1.00 25.00           C
ATOM    201  CA  THR   201      32.715  35.021  27.125  1.00 25.00           C
ATOM    202  CA  MET   202      35.921  36.724  25.889  1.00 25.00           C
ATOM    203  CA  GLU   203      38.594  38.016  28.308  1.00 25.00           C
ATOM    204  CA  GLU   204      40.326  39.873  25.442  1.00 25.00           C
ATOM    205  CA  LEU   205      36.987  41.435  24.404  1.00 25.00           C
ATOM    206  CA  ALA   206      36.350  42.535  28.017  1.00 25.00           C
ATOM    207  CA  ARG   207      39.846  44.090  28.187  1.00 25.00           C
ATOM    208  CA  HIS   208      38.422  46.659  25.788  1.00 25.00           C
ATOM    209  CA  LYS   209      35.931  48.373  28.096  1.00 25.00           C
ATOM    210  CA  PRO   210      33.126  47.169  25.918  1.00 25.00           C
ATOM    211  CA  GLY   211      29.937  48.892  26.904  1.00 25.00           C
ATOM    212  CA  THR   212      26.197  48.553  26.311  1.00 25.00           C
ATOM    213  CA  LEU   213      23.707  45.681  26.300  1.00 25.00           C
ATOM    214  CA  PHE   214      21.013  43.905  28.333  1.00 25.00           C
ATOM    215  CA  LYS   215      21.361  40.646  26.517  1.00 25.00           C
ATOM    216  CA  ASN   216      23.263  37.674  27.911  1.00 25.00           C
ATOM    217  CA  PHE   217      20.553  37.199  30.591  1.00 25.00           C
ATOM    218  CA  ALA   218      20.602  36.328  34.320  1.00 25.00           C
ATOM    219  CA  GLU   219      24.326  37.205  34.501  1.00 25.00           C
ATOM    220  CA  THR   220      23.648  40.550  32.765  1.00 25.00           C
ATOM    221  CA  ASP   221      20.824  41.292  35.244  1.00 25.00           C
ATOM    222  CA  GLU   222      23.147  40.468  38.175  1.00 25.00           C
ATOM    223  CA  VAL   223      25.829  42.792  36.735  1.00 25.00           C
ATOM    224  CA  LEU   224      23.240  45.589  36.360  1.00 25.00           C
ATOM    225  CA  ALA   225      22.122  45.072  39.987  1.00 25.00           C
ATOM    226  CA  SER   226      25.764  45.235  41.158  1.00 25.00           C
ATOM    227  CA  ILE   227      26.282  48.474  39.181  1.00 25.00           C
ATOM    228  CA  LEU   228      23.124  49.967  40.752  1.00 25.00           C
ATOM    229  CA  THR   229      23.331  48.398  44.260  1.00 25.00           C
TER
END
