
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  140 ( 1126),  selected  140 , name T0379_D1.pdb
# PARAMETERS: T0379TS393_3-D1.T0379_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    I       2      I       2          3.354
LGA    R       3      R       3          0.369
LGA    N       4      N       4          1.018
LGA    I       5      I       5          0.659
LGA    V       6      V       6          2.392
LGA    F       7      F       7          2.342
LGA    D       8      D       8          2.007
LGA    L       9      L       9          1.991
LGA    G      10      G      10          1.676
LGA    G      11      G      11          2.397
LGA    V      12      V      12          1.897
LGA    L      13      -       -           -
LGA    I      14      L      13          1.884
LGA    H      15      -       -           -
LGA    L      16      I      14          3.491
LGA    L      84      H      15           -
LGA    E      85      L      16           -
LGA    E      86      L      84           -
LGA    -       -      E      85           -
LGA    I      87      E      86           #
LGA    S      88      I      87           #
LGA    -       -      S      88           -
LGA    A      89      A      89          2.291
LGA    E      90      E      90          1.064
LGA    K      91      K      91          3.146
LGA    F      92      F      92          2.607
LGA    D      93      D      93          0.547
LGA    Y      94      Y      94          2.028
LGA    I      95      I      95          2.264
LGA    D      96      D      96          0.931
LGA    S      97      S      97          1.753
LGA    L      98      L      98          2.063
LGA    R      99      R      99          0.563
LGA    P     100      P     100          0.657
LGA    D     101      D     101          2.613
LGA    Y     102      Y     102          2.897
LGA    R     103      R     103          3.116
LGA    L     104      L     104          1.300
LGA    F     105      F     105          1.560
LGA    L     106      L     106          4.006
LGA    L     107      L     107          1.517
LGA    S     108      S     108          3.681
LGA    N     109      N     109          4.735
LGA    T     110      -       -           -
LGA    N     111      -       -           -
LGA    P     112      -       -           -
LGA    Y     113      -       -           -
LGA    V     114      -       -           -
LGA    L     115      T     110           #
LGA    -       -      N     111           -
LGA    -       -      P     112           -
LGA    -       -      Y     113           -
LGA    D     116      V     114           #
LGA    L     117      L     115          1.607
LGA    A     118      -       -           -
LGA    M     119      D     116           #
LGA    S     120      L     117           #
LGA    P     121      A     118          1.439
LGA    R     122      M     119          5.401
LGA    -       -      S     120           -
LGA    -       -      P     121           -
LGA    -       -      R     122           -
LGA    -       -      F     123           -
LGA    -       -      L     124           -
LGA    -       -      P     125           -
LGA    -       -      S     126           -
LGA    -       -      G     127           -
LGA    -       -      R     128           -
LGA    F     123      T     129          1.277
LGA    L     124      L     130           #
LGA    P     125      -       -           -
LGA    S     126      -       -           -
LGA    G     127      -       -           -
LGA    R     128      D     131           #
LGA    T     129      S     132           #
LGA    L     130      F     133           #
LGA    D     131      F     134           #
LGA    S     132      D     135          2.793
LGA    F     133      K     136          3.147
LGA    F     134      V     137          3.823
LGA    D     135      -       -           -
LGA    K     136      Y     138          2.444
LGA    V     137      A     139          4.556
LGA    Y     138      -       -           -
LGA    A     139      -       -           -
LGA    S     140      -       -           -
LGA    C     141      S     140          5.165
LGA    -       -      C     141           -
LGA    -       -      Q     142           -
LGA    -       -      M     143           -
LGA    Q     142      G     144           #
LGA    M     143      K     145          1.714
LGA    G     144      Y     146          4.253
LGA    K     145      -       -           -
LGA    Y     146      -       -           -
LGA    K     147      K     147          4.580
LGA    P     148      P     148          1.380
LGA    N     149      N     149          3.072
LGA    E     150      E     150          3.182
LGA    D     151      D     151          2.979
LGA    I     152      I     152          2.616
LGA    F     153      F     153          2.432
LGA    L     154      L     154          2.416
LGA    E     155      E     155          2.479
LGA    M     156      M     156          2.398
LGA    I     157      I     157          2.269
LGA    A     158      A     158          2.412
LGA    D     159      D     159          2.929
LGA    S     160      S     160          2.217
LGA    G     161      G     161          2.273
LGA    M     162      M     162          3.300
LGA    K     163      K     163          3.008
LGA    P     164      P     164          2.730
LGA    E     165      E     165          3.437
LGA    -       -      E     166           -
LGA    E     166      T     167          3.691
LGA    T     167      L     168           #
LGA    L     168      F     169          1.502
LGA    F     169      I     170          2.894
LGA    I     170      D     171          2.774
LGA    D     171      D     172          3.903
LGA    D     172      -       -           -
LGA    G     173      G     173          1.889
LGA    P     174      P     174          1.867
LGA    A     175      A     175          3.205
LGA    N     176      N     176          2.822
LGA    V     177      V     177          1.112
LGA    A     178      A     178          1.653
LGA    T     179      T     179          3.043
LGA    A     180      A     180          2.763
LGA    E     181      E     181          1.015
LGA    R     182      R     182          1.858
LGA    L     183      L     183          2.655
LGA    G     184      G     184          1.913
LGA    F     185      F     185          2.151
LGA    H     186      H     186          0.788
LGA    T     187      T     187          2.121
LGA    Y     188      Y     188          2.202
LGA    C     189      C     189          2.046
LGA    P     190      P     190          4.825
LGA    D     191      D     191          3.402
LGA    N     192      N     192          5.635
LGA    G     193      G     193           -
LGA    E     194      E     194          4.570
LGA    N     195      N     195           -
LGA    W     196      W     196           -
LGA    -       -      I     197           -
LGA    -       -      P     198           -
LGA    I     197      A     199           #
LGA    P     198      -       -           -
LGA    A     199      -       -           -
LGA    I     200      I     200          5.478
LGA    T     201      T     201          5.000
LGA    R     202      R     202          3.218
LGA    L     203      L     203          3.122
LGA    L     204      L     204          3.011
LGA    R     205      R     205          2.298
LGA    E     206      E     206          1.782
LGA    Q     207      Q     207          1.708

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  140  140    5.0     99    2.82    82.83     42.794     3.389

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.941813 * X  +  -0.099062 * Y  +  -0.321208 * Z  +  58.649597
  Y_new =  -0.165518 * X  +  -0.968381 * Y  +  -0.186661 * Z  +  14.445480
  Z_new =  -0.292561 * X  +   0.228965 * Y  +  -0.928430 * Z  +  10.372793 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.899802   -0.241791  [ DEG:   166.1464    -13.8536 ]
  Theta =   0.296904    2.844689  [ DEG:    17.0113    162.9886 ]
  Phi   =  -0.173967    2.967626  [ DEG:    -9.9676    170.0324 ]
 
# 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_3-D1                               
REMARK     2: T0379_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS393_3-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   99   2.82   82.83  42.794
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS393_3-D1
PFRMAT TS
TARGET T0379
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      47.706  23.095 -13.073  1.00 25.00           C
ATOM      2  CA  ILE     2      49.140  20.161 -11.043  1.00 25.00           C
ATOM      3  CA  ARG     3      51.025  22.209  -8.436  1.00 25.00           C
ATOM      4  CA  ASN     4      50.977  21.795  -4.663  1.00 25.00           C
ATOM      5  CA  ILE     5      53.391  19.074  -3.474  1.00 25.00           C
ATOM      6  CA  VAL     6      55.755  17.857  -0.844  1.00 25.00           C
ATOM      7  CA  PHE     7      56.635  18.532   2.742  1.00 25.00           C
ATOM      8  CA  ASP     8      57.333  16.031   5.499  1.00 25.00           C
ATOM      9  CA  LEU     9      59.208  17.239   8.579  1.00 25.00           C
ATOM     10  CA  GLY    10      60.957  13.849   8.654  1.00 25.00           C
ATOM     11  CA  GLY    11      63.316  12.511   6.011  1.00 25.00           C
ATOM     12  CA  VAL    12      63.323  12.824   2.220  1.00 25.00           C
ATOM     13  CA  LEU    13      62.290  16.231   0.984  1.00 25.00           C
ATOM     14  CA  ILE    14      62.717  17.343   4.578  1.00 25.00           C
ATOM     15  CA  HIS    15      63.275  19.852   7.343  1.00 25.00           C
ATOM     16  CA  LEU    16      64.430  17.693  10.300  1.00 25.00           C
ATOM     84  CA  LEU    84      64.102  19.737  17.756  1.00 25.00           C
ATOM     85  CA  GLU    85      66.485  21.909  15.689  1.00 25.00           C
ATOM     86  CA  GLU    86      69.969  22.910  14.434  1.00 25.00           C
ATOM     87  CA  ILE    87      68.456  21.716  11.219  1.00 25.00           C
ATOM     88  CA  SER    88      69.700  21.554   7.582  1.00 25.00           C
ATOM     89  CA  ALA    89      70.662  24.308   5.143  1.00 25.00           C
ATOM     90  CA  GLU    90      69.751  21.732   2.458  1.00 25.00           C
ATOM     91  CA  LYS    91      66.207  21.463   3.885  1.00 25.00           C
ATOM     92  CA  PHE    92      65.874  25.278   3.846  1.00 25.00           C
ATOM     93  CA  ASP    93      67.060  25.369   0.206  1.00 25.00           C
ATOM     94  CA  TYR    94      64.506  22.668  -0.719  1.00 25.00           C
ATOM     95  CA  ILE    95      61.734  24.661   1.014  1.00 25.00           C
ATOM     96  CA  ASP    96      62.776  27.815  -0.891  1.00 25.00           C
ATOM     97  CA  SER    97      62.713  25.873  -4.191  1.00 25.00           C
ATOM     98  CA  LEU    98      59.219  24.539  -3.367  1.00 25.00           C
ATOM     99  CA  ARG    99      58.022  28.091  -2.581  1.00 25.00           C
ATOM    100  CA  PRO   100      56.655  30.370  -5.304  1.00 25.00           C
ATOM    101  CA  ASP   101      54.001  28.191  -6.802  1.00 25.00           C
ATOM    102  CA  TYR   102      53.126  26.333  -3.621  1.00 25.00           C
ATOM    103  CA  ARG   103      52.178  25.374  -0.036  1.00 25.00           C
ATOM    104  CA  LEU   104      54.565  22.417   0.360  1.00 25.00           C
ATOM    105  CA  PHE   105      51.434  20.682   1.812  1.00 25.00           C
ATOM    106  CA  LEU   106      52.110  16.977   2.398  1.00 25.00           C
ATOM    107  CA  LEU   107      51.835  14.660   5.405  1.00 25.00           C
ATOM    108  CA  SER   108      53.299  11.504   6.890  1.00 25.00           C
ATOM    109  CA  ASN   109      50.129  10.526   8.784  1.00 25.00           C
ATOM    110  CA  THR   110      50.220  14.100  10.040  1.00 25.00           C
ATOM    111  CA  ASN   111      47.546  16.570  11.201  1.00 25.00           C
ATOM    112  CA  PRO   112      47.961  16.942  15.012  1.00 25.00           C
ATOM    113  CA  TYR   113      51.064  16.143  17.111  1.00 25.00           C
ATOM    114  CA  VAL   114      53.244  16.227  13.962  1.00 25.00           C
ATOM    115  CA  LEU   115      51.742  19.612  12.983  1.00 25.00           C
ATOM    116  CA  ASP   116      52.442  20.967  16.496  1.00 25.00           C
ATOM    117  CA  LEU   117      56.058  19.726  16.281  1.00 25.00           C
ATOM    118  CA  ALA   118      56.461  21.416  12.868  1.00 25.00           C
ATOM    119  CA  MET   119      55.063  24.684  14.293  1.00 25.00           C
ATOM    120  CA  SER   120      57.504  24.474  17.237  1.00 25.00           C
ATOM    121  CA  PRO   121      60.414  23.893  14.815  1.00 25.00           C
ATOM    122  CA  ARG   122      61.430  24.185  11.124  1.00 25.00           C
ATOM    123  CA  PHE   123      60.244  27.760  10.522  1.00 25.00           C
ATOM    124  CA  LEU   124      59.580  29.801  13.709  1.00 25.00           C
ATOM    125  CA  PRO   125      62.711  30.661  15.691  1.00 25.00           C
ATOM    126  CA  SER   126      63.924  33.190  13.112  1.00 25.00           C
ATOM    127  CA  GLY   127      61.078  34.937  11.351  1.00 25.00           C
ATOM    128  CA  ARG   128      58.691  32.975   9.202  1.00 25.00           C
ATOM    129  CA  THR   129      55.249  32.690   7.641  1.00 25.00           C
ATOM    130  CA  LEU   130      55.146  28.963   8.207  1.00 25.00           C
ATOM    131  CA  ASP   131      51.338  29.355   8.326  1.00 25.00           C
ATOM    132  CA  SER   132      50.958  26.725   5.567  1.00 25.00           C
ATOM    133  CA  PHE   133      53.245  24.335   7.497  1.00 25.00           C
ATOM    134  CA  PHE   134      51.178  24.884  10.675  1.00 25.00           C
ATOM    135  CA  ASP   135      47.956  24.171   8.731  1.00 25.00           C
ATOM    136  CA  LYS   136      49.488  20.959   7.318  1.00 25.00           C
ATOM    137  CA  VAL   137      52.623  18.854   8.031  1.00 25.00           C
ATOM    138  CA  TYR   138      55.012  16.930  10.340  1.00 25.00           C
ATOM    139  CA  ALA   139      55.334  13.145  10.534  1.00 25.00           C
ATOM    140  CA  SER   140      55.260   9.359  11.124  1.00 25.00           C
ATOM    141  CA  CYS   141      53.271  10.843  14.015  1.00 25.00           C
ATOM    142  CA  GLN   142      49.684  10.072  14.906  1.00 25.00           C
ATOM    143  CA  MET   143      46.457  11.412  13.281  1.00 25.00           C
ATOM    144  CA  GLY   144      44.532   8.279  14.229  1.00 25.00           C
ATOM    145  CA  LYS   145      44.960   6.258  11.029  1.00 25.00           C
ATOM    146  CA  TYR   146      48.516   5.093  11.956  1.00 25.00           C
ATOM    147  CA  LYS   147      48.562   3.668   8.421  1.00 25.00           C
ATOM    148  CA  PRO   148      47.629   6.678   6.322  1.00 25.00           C
ATOM    149  CA  ASN   149      44.522   4.849   5.155  1.00 25.00           C
ATOM    150  CA  GLU   150      44.526   7.502   2.446  1.00 25.00           C
ATOM    151  CA  ASP   151      42.631   9.494   5.112  1.00 25.00           C
ATOM    152  CA  ILE   152      45.841  11.375   6.024  1.00 25.00           C
ATOM    153  CA  PHE   153      46.452  12.173   2.329  1.00 25.00           C
ATOM    154  CA  LEU   154      42.861  13.460   1.987  1.00 25.00           C
ATOM    155  CA  GLU   155      43.328  15.658   5.089  1.00 25.00           C
ATOM    156  CA  MET   156      46.588  17.052   3.641  1.00 25.00           C
ATOM    157  CA  ILE   157      44.820  17.813   0.330  1.00 25.00           C
ATOM    158  CA  ALA   158      42.005  19.599   2.214  1.00 25.00           C
ATOM    159  CA  ASP   159      44.581  21.661   4.158  1.00 25.00           C
ATOM    160  CA  SER   160      46.333  22.603   0.885  1.00 25.00           C
ATOM    161  CA  GLY   161      43.963  23.554  -1.904  1.00 25.00           C
ATOM    162  CA  MET   162      41.657  21.390  -4.034  1.00 25.00           C
ATOM    163  CA  LYS   163      41.444  17.619  -4.031  1.00 25.00           C
ATOM    164  CA  PRO   164      42.764  14.124  -4.967  1.00 25.00           C
ATOM    165  CA  GLU   165      44.561  16.580  -7.293  1.00 25.00           C
ATOM    166  CA  GLU   166      46.769  17.749  -4.390  1.00 25.00           C
ATOM    167  CA  THR   167      49.321  16.417  -1.924  1.00 25.00           C
ATOM    168  CA  LEU   168      52.300  13.992  -1.875  1.00 25.00           C
ATOM    169  CA  PHE   169      54.723  12.747   0.837  1.00 25.00           C
ATOM    170  CA  ILE   170      58.332  12.433   1.888  1.00 25.00           C
ATOM    171  CA  ASP   171      58.391  10.260   5.044  1.00 25.00           C
ATOM    172  CA  ASP   172      60.363   7.830   7.146  1.00 25.00           C
ATOM    173  CA  GLY   173      57.896   5.134   6.153  1.00 25.00           C
ATOM    174  CA  PRO   174      55.285   3.413   3.959  1.00 25.00           C
ATOM    175  CA  ALA   175      52.209   5.414   5.053  1.00 25.00           C
ATOM    176  CA  ASN   176      53.283   8.333   2.820  1.00 25.00           C
ATOM    177  CA  VAL   177      53.737   5.940  -0.135  1.00 25.00           C
ATOM    178  CA  ALA   178      50.254   4.472   0.488  1.00 25.00           C
ATOM    179  CA  THR   179      48.760   7.997   0.591  1.00 25.00           C
ATOM    180  CA  ALA   180      50.511   8.862  -2.704  1.00 25.00           C
ATOM    181  CA  GLU   181      49.147   5.658  -4.299  1.00 25.00           C
ATOM    182  CA  ARG   182      45.620   6.526  -3.086  1.00 25.00           C
ATOM    183  CA  LEU   183      45.465  10.346  -2.761  1.00 25.00           C
ATOM    184  CA  GLY   184      46.751  10.224  -6.366  1.00 25.00           C
ATOM    185  CA  PHE   185      49.148  13.135  -5.840  1.00 25.00           C
ATOM    186  CA  HIS   186      52.223  11.499  -7.410  1.00 25.00           C
ATOM    187  CA  THR   187      55.356  11.150  -5.181  1.00 25.00           C
ATOM    188  CA  TYR   188      58.302  10.539  -2.827  1.00 25.00           C
ATOM    189  CA  CYS   189      60.073   8.183  -0.394  1.00 25.00           C
ATOM    190  CA  PRO   190      59.904   4.950   1.603  1.00 25.00           C
ATOM    191  CA  ASP   191      62.838   5.082   4.020  1.00 25.00           C
ATOM    192  CA  ASN   192      65.081   2.664   2.185  1.00 25.00           C
ATOM    193  CA  GLY   193      64.633   4.287  -1.175  1.00 25.00           C
ATOM    194  CA  GLU   194      67.094   6.677  -2.881  1.00 25.00           C
ATOM    195  CA  ASN   195      66.254   5.146  -6.290  1.00 25.00           C
ATOM    196  CA  TRP   196      62.514   5.561  -5.584  1.00 25.00           C
ATOM    197  CA  ILE   197      63.080   9.219  -4.603  1.00 25.00           C
ATOM    198  CA  PRO   198      65.052   9.806  -7.832  1.00 25.00           C
ATOM    199  CA  ALA   199      62.229   8.217  -9.875  1.00 25.00           C
ATOM    200  CA  ILE   200      59.666  10.455  -8.118  1.00 25.00           C
ATOM    201  CA  THR   201      61.808  13.539  -8.869  1.00 25.00           C
ATOM    202  CA  ARG   202      62.056  12.503 -12.546  1.00 25.00           C
ATOM    203  CA  LEU   203      58.256  12.051 -12.701  1.00 25.00           C
ATOM    204  CA  LEU   204      57.756  15.517 -11.151  1.00 25.00           C
ATOM    205  CA  ARG   205      60.158  17.038 -13.718  1.00 25.00           C
ATOM    206  CA  GLU   206      58.252  15.316 -16.559  1.00 25.00           C
ATOM    207  CA  GLN   207      55.093  16.388 -18.481  1.00 25.00           C
TER
END
