
#######################################################
#                                                     #
#                        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  104 (  104),  selected  104 , name T0341TS393_1-D2
# Molecule2: number of CA atoms  104 (  810),  selected  104 , name T0341_D2.pdb
# PARAMETERS: T0341TS393_1-D2.T0341_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      75      S      75          1.700
LGA    L      76      L      76          2.103
LGA    T      77      T      77          1.717
LGA    A      78      A      78          0.942
LGA    A      79      A      79          1.524
LGA    R      80      R      80          1.948
LGA    N      81      N      81          1.250
LGA    L      82      L      82          1.394
LGA    I      83      I      83          2.251
LGA    E      84      E      84          2.220
LGA    Q      85      Q      85          2.124
LGA    K      86      K      86          4.042
LGA    Q      87      -       -           -
LGA    V      88      Q      87          2.374
LGA    R      89      V      88          2.154
LGA    P      90      R      89          5.147
LGA    M      91      P      90          4.896
LGA    L      92      M      91          4.672
LGA    L      93      L      92          5.022
LGA    L      94      L      93          1.250
LGA    D      95      L      94          1.863
LGA    D      96      D      95          1.528
LGA    R      97      D      96          1.173
LGA    A      98      R      97          3.802
LGA    L      99      A      98          4.658
LGA    P     100      L      99          4.368
LGA    E     101      P     100          4.672
LGA    -       -      E     101           -
LGA    F     102      F     102          2.855
LGA    T     103      T     103          4.108
LGA    G     104      G     104           -
LGA    -       -      V     105           -
LGA    -       -      Q     106           -
LGA    V     105      T     107          2.738
LGA    Q     106      Q     108          0.897
LGA    T     107      D     109          2.140
LGA    Q     108      P     110          4.005
LGA    D     109      N     111          2.996
LGA    P     110      A     112          3.431
LGA    N     111      V     113           #
LGA    A     112      -       -           -
LGA    V     113      V     114          2.829
LGA    V     114      I     115          3.606
LGA    I     115      G     116          1.610
LGA    G     116      L     117          3.224
LGA    L     117      -       -           -
LGA    A     118      -       -           -
LGA    P     119      A     118          3.105
LGA    E     120      P     119          2.141
LGA    H     121      E     120          2.888
LGA    F     122      H     121          3.391
LGA    H     123      F     122          4.167
LGA    Y     124      H     123          1.548
LGA    -       -      Y     124           -
LGA    Q     125      Q     125          3.725
LGA    L     126      L     126          3.821
LGA    L     127      L     127          2.251
LGA    N     128      N     128          2.278
LGA    Q     129      Q     129          3.184
LGA    A     130      A     130          2.556
LGA    F     131      F     131          1.278
LGA    R     132      R     132          2.496
LGA    L     133      L     133          2.589
LGA    L     134      L     134          1.209
LGA    L     135      L     135          1.857
LGA    D     136      D     136          2.028
LGA    G     137      G     137          2.847
LGA    A     138      A     138          1.599
LGA    P     139      P     139          1.453
LGA    L     140      L     140          2.089
LGA    I     141      I     141          2.895
LGA    A     142      A     142          3.041
LGA    I     143      I     143          2.962
LGA    H     144      H     144          3.016
LGA    K     145      K     145          3.058
LGA    -       -      A     146           -
LGA    A     146      R     147          0.726
LGA    R     147      Y     148          0.831
LGA    Y     148      Y     149          1.394
LGA    Y     149      K     150          3.838
LGA    K     150      R     151          1.155
LGA    R     151      K     152          1.924
LGA    K     152      D     153          2.567
LGA    D     153      -       -           -
LGA    G     154      G     154          1.234
LGA    L     155      L     155          4.252
LGA    A     156      A     156          3.661
LGA    L     157      L     157          2.011
LGA    G     158      G     158          1.771
LGA    P     159      P     159          0.771
LGA    G     160      G     160          1.191
LGA    P     161      P     161          1.516
LGA    F     162      F     162          1.087
LGA    V     163      V     163          0.748
LGA    T     164      T     164          1.129
LGA    A     165      A     165          1.438
LGA    L     166      L     166          1.253
LGA    E     167      E     167          0.484
LGA    Y     168      Y     168          1.779
LGA    A     169      A     169          2.500
LGA    T     170      T     170          1.735
LGA    D     171      D     171          4.737
LGA    T     172      T     172          4.569
LGA    K     173      K     173          2.643
LGA    A     174      A     174          1.054
LGA    M     175      M     175          1.275
LGA    V     176      V     176          1.373
LGA    V     177      V     177          2.789
LGA    G     178      G     178          3.122

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104  104    5.0     97    2.71    68.04     57.893     3.447

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.787220 * X  +  -0.253403 * Y  +   0.562202 * Z  +  28.144171
  Y_new =  -0.614301 * X  +  -0.242375 * Y  +   0.750925 * Z  +  31.040699
  Z_new =  -0.054023 * X  +  -0.936505 * Y  +  -0.346468 * Z  +  86.028160 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.925140    1.216453  [ DEG:  -110.3024     69.6976 ]
  Theta =   0.054049    3.087544  [ DEG:     3.0968    176.9032 ]
  Phi   =  -0.662639    2.478954  [ DEG:   -37.9664    142.0336 ]
 
# 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: T0341TS393_1-D2                               
REMARK     2: T0341_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS393_1-D2.T0341_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  104  104   5.0   97   2.71   68.04  57.893
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS393_1-D2
PFRMAT TS
TARGET T0341
MODEL 1
PARENT N/A
ATOM     75  CA  SER    75      22.782  29.902  86.090  1.00 25.00           C
ATOM     76  CA  LEU    76      19.636  27.911  85.194  1.00 25.00           C
ATOM     77  CA  THR    77      17.631  29.849  87.818  1.00 25.00           C
ATOM     78  CA  ALA    78      18.932  33.161  86.401  1.00 25.00           C
ATOM     79  CA  ALA    79      17.944  32.066  82.867  1.00 25.00           C
ATOM     80  CA  ARG    80      14.445  31.127  84.110  1.00 25.00           C
ATOM     81  CA  ASN    81      14.107  34.542  85.811  1.00 25.00           C
ATOM     82  CA  LEU    82      15.182  36.288  82.576  1.00 25.00           C
ATOM     83  CA  ILE    83      12.605  34.261  80.596  1.00 25.00           C
ATOM     84  CA  GLU    84       9.884  35.212  83.117  1.00 25.00           C
ATOM     85  CA  GLN    85      10.864  38.902  82.819  1.00 25.00           C
ATOM     86  CA  LYS    86       7.794  39.181  80.639  1.00 25.00           C
ATOM     87  CA  GLN    87       5.316  37.486  78.223  1.00 25.00           C
ATOM     88  CA  VAL    88       5.372  33.740  78.847  1.00 25.00           C
ATOM     89  CA  ARG    89       8.658  33.474  76.941  1.00 25.00           C
ATOM     90  CA  PRO    90      12.111  31.817  76.505  1.00 25.00           C
ATOM     91  CA  MET    91      15.700  30.662  77.059  1.00 25.00           C
ATOM     92  CA  LEU    92      17.269  27.777  75.175  1.00 25.00           C
ATOM     93  CA  LEU    93      20.544  25.879  75.362  1.00 25.00           C
ATOM     94  CA  LEU    94      20.654  22.664  77.369  1.00 25.00           C
ATOM     95  CA  ASP    95      23.371  21.172  79.534  1.00 25.00           C
ATOM     96  CA  ASP    96      23.318  17.456  80.391  1.00 25.00           C
ATOM     97  CA  ARG    97      20.913  16.922  83.252  1.00 25.00           C
ATOM     98  CA  ALA    98      19.514  19.803  85.353  1.00 25.00           C
ATOM     99  CA  LEU    99      18.206  21.509  82.184  1.00 25.00           C
ATOM    100  CA  PRO   100      16.546  18.240  81.078  1.00 25.00           C
ATOM    101  CA  GLU   101      14.916  17.873  84.525  1.00 25.00           C
ATOM    102  CA  PHE   102      13.629  21.474  84.328  1.00 25.00           C
ATOM    103  CA  THR   103      10.042  20.414  83.410  1.00 25.00           C
ATOM    104  CA  GLY   104       8.318  17.933  81.121  1.00 25.00           C
ATOM    105  CA  VAL   105       9.455  20.400  78.405  1.00 25.00           C
ATOM    106  CA  GLN   106       6.934  21.452  75.700  1.00 25.00           C
ATOM    107  CA  THR   107       7.699  21.978  72.045  1.00 25.00           C
ATOM    108  CA  GLN   108       8.114  24.325  69.044  1.00 25.00           C
ATOM    109  CA  ASP   109       8.334  26.931  71.760  1.00 25.00           C
ATOM    110  CA  PRO   110      11.288  27.341  74.094  1.00 25.00           C
ATOM    111  CA  ASN   111      12.331  26.872  77.739  1.00 25.00           C
ATOM    112  CA  ALA   112      15.224  26.585  80.242  1.00 25.00           C
ATOM    113  CA  VAL   113      18.543  28.462  79.886  1.00 25.00           C
ATOM    114  CA  VAL   114      21.860  26.671  80.424  1.00 25.00           C
ATOM    115  CA  ILE   115      25.008  25.968  78.378  1.00 25.00           C
ATOM    116  CA  GLY   116      27.518  25.235  81.220  1.00 25.00           C
ATOM    117  CA  LEU   117      30.752  23.285  80.642  1.00 25.00           C
ATOM    118  CA  ALA   118      28.580  20.155  80.319  1.00 25.00           C
ATOM    119  CA  PRO   119      28.133  20.818  76.600  1.00 25.00           C
ATOM    120  CA  GLU   120      30.211  17.699  75.955  1.00 25.00           C
ATOM    121  CA  HIS   121      27.834  15.061  77.234  1.00 25.00           C
ATOM    122  CA  PHE   122      26.058  15.197  73.922  1.00 25.00           C
ATOM    123  CA  HIS   123      27.217  15.252  70.250  1.00 25.00           C
ATOM    124  CA  TYR   124      26.044  18.191  68.217  1.00 25.00           C
ATOM    125  CA  GLN   125      22.357  17.393  68.874  1.00 25.00           C
ATOM    126  CA  LEU   126      22.264  20.009  71.669  1.00 25.00           C
ATOM    127  CA  LEU   127      23.839  22.600  69.331  1.00 25.00           C
ATOM    128  CA  ASN   128      21.242  21.784  66.637  1.00 25.00           C
ATOM    129  CA  GLN   129      18.424  22.179  69.201  1.00 25.00           C
ATOM    130  CA  ALA   130      19.856  25.558  70.293  1.00 25.00           C
ATOM    131  CA  PHE   131      20.033  26.692  66.639  1.00 25.00           C
ATOM    132  CA  ARG   132      16.396  25.620  66.105  1.00 25.00           C
ATOM    133  CA  LEU   133      15.338  27.559  69.234  1.00 25.00           C
ATOM    134  CA  LEU   134      17.200  30.659  67.970  1.00 25.00           C
ATOM    135  CA  LEU   135      15.466  30.344  64.569  1.00 25.00           C
ATOM    136  CA  ASP   136      11.777  30.268  65.475  1.00 25.00           C
ATOM    137  CA  GLY   137      11.788  32.790  68.343  1.00 25.00           C
ATOM    138  CA  ALA   138      14.124  33.009  71.250  1.00 25.00           C
ATOM    139  CA  PRO   139      16.836  34.210  73.592  1.00 25.00           C
ATOM    140  CA  LEU   140      19.712  32.283  75.113  1.00 25.00           C
ATOM    141  CA  ILE   141      22.425  30.385  77.050  1.00 25.00           C
ATOM    142  CA  ALA   142      26.026  30.914  75.985  1.00 25.00           C
ATOM    143  CA  ILE   143      26.711  29.898  79.585  1.00 25.00           C
ATOM    144  CA  HIS   144      30.397  29.339  79.978  1.00 25.00           C
ATOM    145  CA  LYS   145      33.546  30.840  78.586  1.00 25.00           C
ATOM    146  CA  ALA   146      35.678  28.108  77.023  1.00 25.00           C
ATOM    147  CA  ARG   147      37.669  24.987  77.886  1.00 25.00           C
ATOM    148  CA  TYR   148      36.478  24.885  81.508  1.00 25.00           C
ATOM    149  CA  TYR   149      35.810  21.640  83.258  1.00 25.00           C
ATOM    150  CA  LYS   150      38.040  18.710  84.175  1.00 25.00           C
ATOM    151  CA  ARG   151      37.982  15.372  86.074  1.00 25.00           C
ATOM    152  CA  LYS   152      41.299  14.059  84.630  1.00 25.00           C
ATOM    153  CA  ASP   153      42.961  14.140  81.211  1.00 25.00           C
ATOM    154  CA  GLY   154      42.482  17.680  79.915  1.00 25.00           C
ATOM    155  CA  LEU   155      38.891  16.927  79.031  1.00 25.00           C
ATOM    156  CA  ALA   156      35.847  16.964  76.766  1.00 25.00           C
ATOM    157  CA  LEU   157      34.504  20.376  75.756  1.00 25.00           C
ATOM    158  CA  GLY   158      33.096  23.875  76.131  1.00 25.00           C
ATOM    159  CA  PRO   159      29.759  25.680  76.155  1.00 25.00           C
ATOM    160  CA  GLY   160      31.764  28.350  74.279  1.00 25.00           C
ATOM    161  CA  PRO   161      31.542  26.288  71.059  1.00 25.00           C
ATOM    162  CA  PHE   162      27.758  25.927  71.521  1.00 25.00           C
ATOM    163  CA  VAL   163      27.437  29.706  72.048  1.00 25.00           C
ATOM    164  CA  THR   164      29.476  30.348  68.870  1.00 25.00           C
ATOM    165  CA  ALA   165      27.232  27.939  66.915  1.00 25.00           C
ATOM    166  CA  LEU   166      24.116  29.727  68.239  1.00 25.00           C
ATOM    167  CA  GLU   167      25.585  33.108  67.202  1.00 25.00           C
ATOM    168  CA  TYR   168      26.334  31.738  63.705  1.00 25.00           C
ATOM    169  CA  ALA   169      22.748  30.425  63.425  1.00 25.00           C
ATOM    170  CA  THR   170      21.387  33.845  64.487  1.00 25.00           C
ATOM    171  CA  ASP   171      20.365  37.239  65.980  1.00 25.00           C
ATOM    172  CA  THR   172      18.796  35.446  68.943  1.00 25.00           C
ATOM    173  CA  LYS   173      21.896  35.888  71.121  1.00 25.00           C
ATOM    174  CA  ALA   174      23.654  35.468  74.446  1.00 25.00           C
ATOM    175  CA  MET   175      21.367  35.743  77.508  1.00 25.00           C
ATOM    176  CA  VAL   176      24.088  34.283  79.728  1.00 25.00           C
ATOM    177  CA  VAL   177      24.103  32.529  83.093  1.00 25.00           C
ATOM    178  CA  GLY   178      27.626  31.430  83.709  1.00 25.00           C
TER
END
