
#######################################################
#                                                     #
#                        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 T0341TS168_2-D2
# Molecule2: number of CA atoms  104 (  810),  selected  104 , name T0341_D2.pdb
# PARAMETERS: T0341TS168_2-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          2.848
LGA    L      76      L      76          2.940
LGA    T      77      T      77          2.426
LGA    A      78      A      78          1.626
LGA    A      79      A      79          1.564
LGA    R      80      R      80          2.002
LGA    N      81      N      81          1.429
LGA    L      82      L      82          0.620
LGA    I      83      I      83          1.485
LGA    E      84      E      84          1.992
LGA    Q      85      Q      85          1.647
LGA    K      86      K      86          4.429
LGA    Q      87      -       -           -
LGA    V      88      Q      87          3.244
LGA    R      89      V      88          1.420
LGA    P      90      R      89          2.203
LGA    M      91      P      90          2.154
LGA    L      92      M      91          3.997
LGA    L      93      L      92          3.639
LGA    L      94      L      93          2.669
LGA    D      95      L      94          2.709
LGA    D      96      D      95          1.625
LGA    R      97      D      96          2.581
LGA    A      98      R      97          3.651
LGA    L      99      A      98          4.123
LGA    P     100      L      99          4.320
LGA    E     101      P     100          5.128
LGA    -       -      E     101           -
LGA    F     102      F     102          2.353
LGA    T     103      T     103          3.703
LGA    -       -      G     104           -
LGA    G     104      V     105           #
LGA    V     105      Q     106          3.317
LGA    Q     106      T     107          3.606
LGA    T     107      Q     108          2.123
LGA    Q     108      D     109          2.596
LGA    D     109      P     110          2.222
LGA    P     110      N     111          1.934
LGA    N     111      A     112          1.778
LGA    A     112      V     113          4.696
LGA    V     113      V     114          3.162
LGA    V     114      I     115          4.858
LGA    I     115      G     116          2.146
LGA    G     116      -       -           -
LGA    L     117      L     117          4.663
LGA    A     118      A     118          4.574
LGA    P     119      P     119          4.593
LGA    E     120      E     120          4.587
LGA    H     121      H     121           #
LGA    F     122      F     122          3.421
LGA    H     123      H     123          2.973
LGA    Y     124      Y     124           -
LGA    Q     125      Q     125           -
LGA    L     126      -       -           -
LGA    L     127      -       -           -
LGA    N     128      L     126          2.274
LGA    Q     129      -       -           -
LGA    A     130      L     127          4.814
LGA    F     131      N     128          3.825
LGA    R     132      Q     129          2.622
LGA    L     133      A     130          2.969
LGA    L     134      F     131          2.505
LGA    L     135      R     132          1.374
LGA    D     136      L     133          2.656
LGA    G     137      L     134          4.143
LGA    -       -      L     135           -
LGA    -       -      D     136           -
LGA    -       -      G     137           -
LGA    A     138      A     138          1.989
LGA    P     139      P     139          2.867
LGA    L     140      L     140          1.479
LGA    I     141      I     141          3.346
LGA    A     142      A     142          2.629
LGA    I     143      I     143          3.560
LGA    H     144      H     144          1.875
LGA    K     145      K     145          1.021
LGA    A     146      A     146          2.237
LGA    R     147      R     147          1.296
LGA    Y     148      Y     148          1.506
LGA    Y     149      Y     149          1.020
LGA    K     150      K     150          2.576
LGA    R     151      R     151          2.698
LGA    K     152      K     152          4.631
LGA    D     153      D     153          4.293
LGA    G     154      G     154          1.765
LGA    L     155      L     155          3.497
LGA    A     156      A     156          2.571
LGA    L     157      L     157          1.481
LGA    G     158      G     158          3.179
LGA    P     159      P     159          3.138
LGA    G     160      G     160          2.601
LGA    P     161      P     161          1.492
LGA    F     162      F     162          1.681
LGA    V     163      V     163          2.091
LGA    T     164      T     164          1.984
LGA    A     165      A     165          1.595
LGA    L     166      L     166          1.742
LGA    E     167      E     167          2.125
LGA    Y     168      Y     168          2.109
LGA    A     169      A     169          1.645
LGA    T     170      T     170          2.237
LGA    D     171      D     171          2.316
LGA    T     172      T     172          2.662
LGA    K     173      K     173          1.519
LGA    A     174      A     174          1.430
LGA    M     175      M     175          1.872
LGA    V     176      V     176          2.380
LGA    V     177      V     177          2.467
LGA    G     178      G     178          1.650

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104  104    5.0     95    2.85    68.42     53.065     3.222

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.967392 * X  +  -0.205150 * Y  +   0.148545 * Z  +  29.051712
  Y_new =  -0.231982 * X  +  -0.953072 * Y  +   0.194519 * Z  +  30.836542
  Z_new =   0.101668 * X  +  -0.222636 * Y  +  -0.969586 * Z  +  85.764648 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.915886    0.225707  [ DEG:  -167.0679     12.9321 ]
  Theta =  -0.101844   -3.039748  [ DEG:    -5.8352   -174.1647 ]
  Phi   =  -0.235357    2.906235  [ DEG:   -13.4850    166.5150 ]
 
# 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: T0341TS168_2-D2                               
REMARK     2: T0341_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS168_2-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   95   2.85   68.42  53.065
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS168_2-D2
PFRMAT TS
TARGET T0341
MODEL 2
PARENT N/A
ATOM     75  CA  SER    75      21.393  28.776  87.507  1.00 25.00           C
ATOM     76  CA  LEU    76      18.091  26.974  86.786  1.00 25.00           C
ATOM     77  CA  THR    77      16.214  29.476  88.997  1.00 25.00           C
ATOM     78  CA  ALA    78      17.878  32.391  87.153  1.00 25.00           C
ATOM     79  CA  ALA    79      16.888  30.860  83.786  1.00 25.00           C
ATOM     80  CA  ARG    80      13.279  30.457  85.003  1.00 25.00           C
ATOM     81  CA  ASN    81      13.233  34.110  86.150  1.00 25.00           C
ATOM     82  CA  LEU    82      14.569  35.225  82.739  1.00 25.00           C
ATOM     83  CA  ILE    83      11.861  33.167  80.979  1.00 25.00           C
ATOM     84  CA  GLU    84       9.176  34.749  83.206  1.00 25.00           C
ATOM     85  CA  GLN    85      10.528  38.240  82.396  1.00 25.00           C
ATOM     86  CA  LYS    86       7.977  39.963  80.189  1.00 25.00           C
ATOM     87  CA  GLN    87       6.631  38.222  77.103  1.00 25.00           C
ATOM     88  CA  VAL    88       5.403  34.653  77.465  1.00 25.00           C
ATOM     89  CA  ARG    89       7.917  31.833  77.622  1.00 25.00           C
ATOM     90  CA  PRO    90      10.055  28.795  78.486  1.00 25.00           C
ATOM     91  CA  MET    91      13.632  27.586  78.457  1.00 25.00           C
ATOM     92  CA  LEU    92      16.950  25.869  77.518  1.00 25.00           C
ATOM     93  CA  LEU    93      19.942  24.503  79.402  1.00 25.00           C
ATOM     94  CA  LEU    94      22.393  23.858  76.514  1.00 25.00           C
ATOM     95  CA  ASP    95      23.818  20.824  78.398  1.00 25.00           C
ATOM     96  CA  ASP    96      24.662  18.474  81.224  1.00 25.00           C
ATOM     97  CA  ARG    97      20.911  18.495  82.003  1.00 25.00           C
ATOM     98  CA  ALA    98      19.627  19.704  85.403  1.00 25.00           C
ATOM     99  CA  LEU    99      18.100  22.804  83.751  1.00 25.00           C
ATOM    100  CA  PRO   100      16.400  20.596  81.123  1.00 25.00           C
ATOM    101  CA  GLU   101      15.003  18.342  83.886  1.00 25.00           C
ATOM    102  CA  PHE   102      13.674  21.411  85.752  1.00 25.00           C
ATOM    103  CA  THR   103      10.570  20.772  83.707  1.00 25.00           C
ATOM    104  CA  GLY   104       8.069  19.509  81.160  1.00 25.00           C
ATOM    105  CA  VAL   105       9.056  22.311  78.759  1.00 25.00           C
ATOM    106  CA  GLN   106       5.893  21.941  76.621  1.00 25.00           C
ATOM    107  CA  THR   107       8.301  22.077  73.647  1.00 25.00           C
ATOM    108  CA  GLN   108       8.368  23.036  69.962  1.00 25.00           C
ATOM    109  CA  ASP   109       8.371  26.636  71.242  1.00 25.00           C
ATOM    110  CA  PRO   110      11.350  28.236  73.105  1.00 25.00           C
ATOM    111  CA  ASN   111      13.292  31.163  74.608  1.00 25.00           C
ATOM    112  CA  ALA   112      16.560  31.881  76.454  1.00 25.00           C
ATOM    113  CA  VAL   113      19.161  30.426  78.819  1.00 25.00           C
ATOM    114  CA  VAL   114      21.877  28.889  80.992  1.00 25.00           C
ATOM    115  CA  ILE   115      24.686  26.382  81.264  1.00 25.00           C
ATOM    116  CA  GLY   116      28.249  27.428  80.674  1.00 25.00           C
ATOM    117  CA  LEU   117      31.064  24.882  81.329  1.00 25.00           C
ATOM    118  CA  ALA   118      28.225  22.694  80.188  1.00 25.00           C
ATOM    119  CA  PRO   119      29.532  19.126  80.229  1.00 25.00           C
ATOM    120  CA  GLU   120      28.741  15.733  78.664  1.00 25.00           C
ATOM    121  CA  HIS   121      28.026  13.556  75.713  1.00 25.00           C
ATOM    122  CA  PHE   122      28.224  16.330  73.155  1.00 25.00           C
ATOM    123  CA  HIS   123      25.805  14.601  70.818  1.00 25.00           C
ATOM    124  CA  TYR   124      22.950  13.348  73.051  1.00 25.00           C
ATOM    125  CA  GLN   125      19.475  14.388  74.276  1.00 25.00           C
ATOM    126  CA  LEU   126      20.897  17.696  75.580  1.00 25.00           C
ATOM    127  CA  LEU   127      22.605  18.319  72.209  1.00 25.00           C
ATOM    128  CA  ASN   128      19.314  17.606  70.383  1.00 25.00           C
ATOM    129  CA  GLN   129      17.475  20.043  72.696  1.00 25.00           C
ATOM    130  CA  ALA   130      20.129  22.721  72.026  1.00 25.00           C
ATOM    131  CA  PHE   131      19.772  22.166  68.253  1.00 25.00           C
ATOM    132  CA  ARG   132      15.967  22.493  68.541  1.00 25.00           C
ATOM    133  CA  LEU   133      16.371  25.746  70.520  1.00 25.00           C
ATOM    134  CA  LEU   134      18.761  27.101  67.853  1.00 25.00           C
ATOM    135  CA  LEU   135      16.252  26.190  65.106  1.00 25.00           C
ATOM    136  CA  ASP   136      12.890  27.881  64.637  1.00 25.00           C
ATOM    137  CA  GLY   137      12.624  31.089  66.664  1.00 25.00           C
ATOM    138  CA  ALA   138      15.058  30.968  69.512  1.00 25.00           C
ATOM    139  CA  PRO   139      17.726  33.552  70.073  1.00 25.00           C
ATOM    140  CA  LEU   140      19.350  30.971  72.344  1.00 25.00           C
ATOM    141  CA  ILE   141      22.174  30.377  74.818  1.00 25.00           C
ATOM    142  CA  ALA   142      25.053  29.036  76.930  1.00 25.00           C
ATOM    143  CA  ILE   143      26.192  31.988  78.938  1.00 25.00           C
ATOM    144  CA  HIS   144      29.673  32.071  80.444  1.00 25.00           C
ATOM    145  CA  LYS   145      30.723  31.289  76.833  1.00 25.00           C
ATOM    146  CA  ALA   146      34.424  30.365  77.341  1.00 25.00           C
ATOM    147  CA  ARG   147      36.530  27.233  76.877  1.00 25.00           C
ATOM    148  CA  TYR   148      38.249  24.432  78.786  1.00 25.00           C
ATOM    149  CA  TYR   149      37.281  22.831  82.063  1.00 25.00           C
ATOM    150  CA  LYS   150      38.168  19.278  83.060  1.00 25.00           C
ATOM    151  CA  ARG   151      38.903  15.692  82.030  1.00 25.00           C
ATOM    152  CA  LYS   152      41.770  13.282  81.452  1.00 25.00           C
ATOM    153  CA  ASP   153      43.429  14.720  78.358  1.00 25.00           C
ATOM    154  CA  GLY   154      43.175  18.296  79.757  1.00 25.00           C
ATOM    155  CA  LEU   155      41.771  19.200  76.339  1.00 25.00           C
ATOM    156  CA  ALA   156      38.112  18.200  75.947  1.00 25.00           C
ATOM    157  CA  LEU   157      36.078  21.181  74.809  1.00 25.00           C
ATOM    158  CA  GLY   158      33.628  21.055  77.752  1.00 25.00           C
ATOM    159  CA  PRO   159      30.592  22.690  76.146  1.00 25.00           C
ATOM    160  CA  GLY   160      31.340  26.428  76.503  1.00 25.00           C
ATOM    161  CA  PRO   161      33.055  26.437  73.080  1.00 25.00           C
ATOM    162  CA  PHE   162      30.029  24.671  71.532  1.00 25.00           C
ATOM    163  CA  VAL   163      27.684  27.252  73.115  1.00 25.00           C
ATOM    164  CA  THR   164      29.842  30.099  71.733  1.00 25.00           C
ATOM    165  CA  ALA   165      29.757  28.506  68.251  1.00 25.00           C
ATOM    166  CA  LEU   166      25.946  28.190  68.462  1.00 25.00           C
ATOM    167  CA  GLU   167      25.672  31.868  69.491  1.00 25.00           C
ATOM    168  CA  TYR   168      27.896  32.884  66.544  1.00 25.00           C
ATOM    169  CA  ALA   169      25.715  30.829  64.158  1.00 25.00           C
ATOM    170  CA  THR   170      22.567  32.503  65.556  1.00 25.00           C
ATOM    171  CA  ASP   171      22.063  35.979  64.119  1.00 25.00           C
ATOM    172  CA  THR   172      20.059  37.009  67.105  1.00 25.00           C
ATOM    173  CA  LYS   173      23.109  36.982  69.354  1.00 25.00           C
ATOM    174  CA  ALA   174      22.179  35.281  72.584  1.00 25.00           C
ATOM    175  CA  MET   175      20.427  35.689  76.006  1.00 25.00           C
ATOM    176  CA  VAL   176      22.150  34.960  79.282  1.00 25.00           C
ATOM    177  CA  VAL   177      21.438  33.203  82.515  1.00 25.00           C
ATOM    178  CA  GLY   178      25.096  33.932  83.460  1.00 25.00           C
TER
END
