
#######################################################
#                                                     #
#                        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  149 (  149),  selected  149 , name T0317TS393_4-D1
# Molecule2: number of CA atoms  149 ( 1129),  selected  149 , name T0317_D1.pdb
# PARAMETERS: T0317TS393_4-D1.T0317_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P      10      P      10           -
LGA    F      11      F      11           -
LGA    A      12      A      12           -
LGA    R      13      R      13           -
LGA    V      14      V      14           -
LGA    A      15      A      15          4.122
LGA    P      16      P      16          2.998
LGA    A      17      A      17          3.321
LGA    L      18      L      18          3.028
LGA    F      19      F      19          2.454
LGA    I      20      I      20          1.576
LGA    G      21      G      21          2.058
LGA    N      22      N      22          2.262
LGA    A      23      A      23           #
LGA    R      24      R      24           #
LGA    A      25      A      25          4.022
LGA    A      26      A      26          3.707
LGA    G      27      G      27          2.032
LGA    A      28      A      28          1.365
LGA    T      29      T      29          1.129
LGA    E      30      E      30          0.998
LGA    L      31      L      31          1.036
LGA    L      32      L      32          1.055
LGA    V      33      V      33          1.034
LGA    R      34      R      34          1.011
LGA    A      35      A      35          1.755
LGA    G      36      G      36          0.569
LGA    I      37      I      37          1.246
LGA    T      38      T      38          1.100
LGA    L      39      L      39          1.117
LGA    C      40      C      40          1.402
LGA    V      41      V      41          1.176
LGA    N      42      N      42          1.764
LGA    V      43      V      43          1.912
LGA    S      44      S      44          2.158
LGA    R      45      R      45          2.387
LGA    Q      46      Q      46          1.234
LGA    Q      47      Q      47          3.462
LGA    P      48      P      48          3.549
LGA    G      49      G      49          4.986
LGA    P      50      P      50          5.998
LGA    R      51      R      51          3.330
LGA    A      52      A      52          3.253
LGA    P      53      P      53          2.820
LGA    G      54      G      54          2.462
LGA    V      55      V      55          1.893
LGA    A      56      A      56          1.721
LGA    E      57      E      57          1.642
LGA    L      58      L      58          1.522
LGA    R      59      R      59          2.275
LGA    V      60      V      60          1.294
LGA    P      61      P      61          1.416
LGA    V      62      V      62          1.576
LGA    F      63      F      63          2.309
LGA    D      64      D      64           #
LGA    -       -      D      65           -
LGA    -       -      P      66           -
LGA    D      65      A      67          4.181
LGA    P      66      E      68          2.791
LGA    A      67      -       -           -
LGA    E      68      -       -           -
LGA    D      69      D      69          3.411
LGA    L      70      L      70          1.397
LGA    L      71      L      71          2.145
LGA    T      72      T      72          2.655
LGA    H      73      H      73          1.888
LGA    L      74      L      74          1.280
LGA    E      75      E      75          1.561
LGA    P      76      P      76          2.601
LGA    T      77      T      77          2.209
LGA    C      78      C      78          1.137
LGA    A      79      A      79          1.548
LGA    A      80      A      80          1.679
LGA    M      81      M      81          1.593
LGA    E      82      E      82          1.941
LGA    A      83      A      83          1.743
LGA    A      84      A      84          1.017
LGA    V      85      V      85          2.277
LGA    R      86      R      86          3.113
LGA    D      87      D      87          1.766
LGA    G      88      G      88          1.177
LGA    G      89      G      89          1.939
LGA    S      90      S      90          1.682
LGA    C      91      C      91          0.537
LGA    L      92      L      92          0.901
LGA    V      93      V      93          0.838
LGA    Y      94      Y      94          0.894
LGA    C      95      C      95          2.536
LGA    K      96      K      96          1.079
LGA    N      97      N      97          0.833
LGA    G      98      G      98          1.457
LGA    R      99      R      99          2.710
LGA    S     100      S     100          2.512
LGA    R     101      R     101          0.965
LGA    S     102      S     102          1.341
LGA    A     103      A     103          1.412
LGA    A     104      A     104          0.851
LGA    V     105      V     105          0.710
LGA    C     106      C     106          0.707
LGA    T     107      T     107          0.530
LGA    A     108      A     108          0.453
LGA    Y     109      Y     109          0.587
LGA    L     110      L     110          0.532
LGA    M     111      M     111          0.697
LGA    R     112      R     112          0.421
LGA    H     113      H     113          1.421
LGA    R     114      R     114          3.535
LGA    G     115      G     115          3.342
LGA    H     116      H     116          2.527
LGA    S     117      S     117          1.445
LGA    L     118      L     118          1.227
LGA    D     119      D     119          1.167
LGA    R     120      R     120          0.472
LGA    A     121      A     121          0.722
LGA    F     122      F     122          1.363
LGA    Q     123      Q     123          1.235
LGA    M     124      M     124          1.395
LGA    V     125      V     125          2.027
LGA    K     126      K     126          2.062
LGA    S     127      S     127          1.838
LGA    A     128      A     128          2.400
LGA    R     129      R     129          1.882
LGA    P     130      -       -           -
LGA    V     131      P     130          2.364
LGA    A     132      V     131          1.519
LGA    E     133      A     132          3.509
LGA    P     134      E     133          4.755
LGA    N     135      -       -           -
LGA    L     136      -       -           -
LGA    G     137      P     134           #
LGA    F     138      N     135          1.899
LGA    W     139      L     136          4.642
LGA    A     140      G     137          4.887
LGA    Q     141      F     138          2.139
LGA    L     142      W     139          1.978
LGA    Q     143      A     140          4.235
LGA    K     144      Q     141          4.535
LGA    Y     145      L     142          2.554
LGA    E     146      Q     143          1.510
LGA    Q     147      K     144          5.006
LGA    T     148      Y     145           #
LGA    L     149      E     146          3.189
LGA    Q     150      Q     147          3.226
LGA    A     151      T     148           -
LGA    Q     152      L     149           -
LGA    A     153      Q     150           -
LGA    I     154      A     151           -
LGA    L     155      Q     152           -
LGA    P     156      A     153           -
LGA    R     157      I     154           -
LGA    E     158      L     155           -
LGA    -       -      P     156           -
LGA    -       -      R     157           -
LGA    -       -      E     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  149    5.0    126    2.34    86.51     59.905     5.163

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.361022 * X  +  -0.030716 * Y  +  -0.932051 * Z  +  30.576317
  Y_new =  -0.885129 * X  +   0.325964 * Y  +   0.332105 * Z  +  31.267776
  Z_new =   0.293614 * X  +   0.944883 * Y  +  -0.144868 * Z  +   5.518499 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.722930   -1.418663  [ DEG:    98.7166    -81.2834 ]
  Theta =  -0.298006   -2.843587  [ DEG:   -17.0745   -162.9255 ]
  Phi   =  -1.958073    1.183520  [ DEG:  -112.1893     67.8107 ]
 
# 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: T0317TS393_4-D1                               
REMARK     2: T0317_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0317TS393_4-D1.T0317_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  149  149   5.0  126   2.34   86.51  59.905
REMARK  ---------------------------------------------------------- 
MOLECULE T0317TS393_4-D1
PFRMAT TS
TARGET T0317
MODEL 4
PARENT N/A
ATOM     10  CA  PRO    10      37.013  38.785 -16.695  1.00 25.00           C
ATOM     11  CA  PHE    11      35.739  36.356 -14.067  1.00 25.00           C
ATOM     12  CA  ALA    12      39.278  35.705 -12.723  1.00 25.00           C
ATOM     13  CA  ARG    13      42.715  34.487 -11.592  1.00 25.00           C
ATOM     14  CA  VAL    14      41.799  33.593  -8.013  1.00 25.00           C
ATOM     15  CA  ALA    15      40.016  33.735  -4.710  1.00 25.00           C
ATOM     16  CA  PRO    16      39.160  32.497  -1.257  1.00 25.00           C
ATOM     17  CA  ALA    17      38.189  29.236   0.448  1.00 25.00           C
ATOM     18  CA  LEU    18      35.152  29.637   2.705  1.00 25.00           C
ATOM     19  CA  PHE    19      32.045  27.855   1.577  1.00 25.00           C
ATOM     20  CA  ILE    20      28.227  27.389   1.522  1.00 25.00           C
ATOM     21  CA  GLY    21      28.146  24.208  -0.610  1.00 25.00           C
ATOM     22  CA  ASN    22      24.685  22.538  -0.417  1.00 25.00           C
ATOM     23  CA  ALA    23      21.739  22.663  -2.774  1.00 25.00           C
ATOM     24  CA  ARG    24      23.107  20.666  -5.781  1.00 25.00           C
ATOM     25  CA  ALA    25      26.609  19.281  -5.052  1.00 25.00           C
ATOM     26  CA  ALA    26      26.972  17.931  -1.574  1.00 25.00           C
ATOM     27  CA  GLY    27      24.980  14.753  -2.430  1.00 25.00           C
ATOM     28  CA  ALA    28      27.394  14.044  -5.281  1.00 25.00           C
ATOM     29  CA  THR    29      30.899  13.530  -3.894  1.00 25.00           C
ATOM     30  CA  GLU    30      32.053  14.086  -7.504  1.00 25.00           C
ATOM     31  CA  LEU    31      32.151  17.869  -6.916  1.00 25.00           C
ATOM     32  CA  LEU    32      34.210  17.345  -3.729  1.00 25.00           C
ATOM     33  CA  VAL    33      36.642  15.089  -5.643  1.00 25.00           C
ATOM     34  CA  ARG    34      36.985  17.743  -8.383  1.00 25.00           C
ATOM     35  CA  ALA    35      38.360  20.555  -6.324  1.00 25.00           C
ATOM     36  CA  GLY    36      39.787  18.802  -3.288  1.00 25.00           C
ATOM     37  CA  ILE    37      38.150  18.936   0.174  1.00 25.00           C
ATOM     38  CA  THR    38      38.338  16.690   3.260  1.00 25.00           C
ATOM     39  CA  LEU    39      37.218  19.152   6.015  1.00 25.00           C
ATOM     40  CA  CYS    40      33.460  19.559   6.514  1.00 25.00           C
ATOM     41  CA  VAL    41      30.982  21.122   8.942  1.00 25.00           C
ATOM     42  CA  ASN    42      27.527  20.453  10.330  1.00 25.00           C
ATOM     43  CA  VAL    43      24.581  22.880  10.461  1.00 25.00           C
ATOM     44  CA  SER    44      21.200  21.271  11.041  1.00 25.00           C
ATOM     45  CA  ARG    45      22.816  18.016  12.220  1.00 25.00           C
ATOM     46  CA  GLN    46      20.104  15.424  11.348  1.00 25.00           C
ATOM     47  CA  GLN    47      21.541  13.743   8.210  1.00 25.00           C
ATOM     48  CA  PRO    48      22.323  10.994   5.684  1.00 25.00           C
ATOM     49  CA  GLY    49      25.741   9.463   6.544  1.00 25.00           C
ATOM     50  CA  PRO    50      29.137   9.722   8.236  1.00 25.00           C
ATOM     51  CA  ARG    51      31.165   8.003   5.505  1.00 25.00           C
ATOM     52  CA  ALA    52      30.844  10.540   2.728  1.00 25.00           C
ATOM     53  CA  PRO    53      33.722   8.936   0.910  1.00 25.00           C
ATOM     54  CA  GLY    54      36.795  11.143   1.125  1.00 25.00           C
ATOM     55  CA  VAL    55      35.371  12.648   4.276  1.00 25.00           C
ATOM     56  CA  ALA    56      34.905  13.984   7.850  1.00 25.00           C
ATOM     57  CA  GLU    57      32.374  15.984   9.930  1.00 25.00           C
ATOM     58  CA  LEU    58      33.009  18.186  12.966  1.00 25.00           C
ATOM     59  CA  ARG    59      29.834  19.168  14.874  1.00 25.00           C
ATOM     60  CA  VAL    60      28.251  22.558  15.597  1.00 25.00           C
ATOM     61  CA  PRO    61      24.795  22.096  17.047  1.00 25.00           C
ATOM     62  CA  VAL    62      22.308  24.414  15.234  1.00 25.00           C
ATOM     63  CA  PHE    63      20.297  26.666  17.536  1.00 25.00           C
ATOM     64  CA  ASP    64      22.501  26.063  20.582  1.00 25.00           C
ATOM     65  CA  ASP    65      20.916  29.293  21.964  1.00 25.00           C
ATOM     66  CA  PRO    66      23.779  31.546  20.845  1.00 25.00           C
ATOM     67  CA  ALA    67      26.704  33.730  21.850  1.00 25.00           C
ATOM     68  CA  GLU    68      29.211  31.476  23.583  1.00 25.00           C
ATOM     69  CA  ASP    69      28.023  28.452  21.556  1.00 25.00           C
ATOM     70  CA  LEU    70      28.281  30.487  18.322  1.00 25.00           C
ATOM     71  CA  LEU    71      31.830  31.577  19.263  1.00 25.00           C
ATOM     72  CA  THR    72      32.790  27.935  19.961  1.00 25.00           C
ATOM     73  CA  HIS    73      31.359  26.883  16.568  1.00 25.00           C
ATOM     74  CA  LEU    74      33.348  29.661  14.839  1.00 25.00           C
ATOM     75  CA  GLU    75      36.539  28.522  16.623  1.00 25.00           C
ATOM     76  CA  PRO    76      35.893  24.910  15.522  1.00 25.00           C
ATOM     77  CA  THR    77      35.378  26.077  11.911  1.00 25.00           C
ATOM     78  CA  CYS    78      38.653  28.055  12.056  1.00 25.00           C
ATOM     79  CA  ALA    79      40.483  24.975  13.407  1.00 25.00           C
ATOM     80  CA  ALA    80      39.023  22.838  10.584  1.00 25.00           C
ATOM     81  CA  MET    81      40.151  25.433   8.003  1.00 25.00           C
ATOM     82  CA  GLU    82      43.671  25.440   9.515  1.00 25.00           C
ATOM     83  CA  ALA    83      43.771  21.615   9.360  1.00 25.00           C
ATOM     84  CA  ALA    84      42.668  21.709   5.694  1.00 25.00           C
ATOM     85  CA  VAL    85      45.402  24.275   4.911  1.00 25.00           C
ATOM     86  CA  ARG    86      48.007  22.062   6.640  1.00 25.00           C
ATOM     87  CA  ASP    87      47.894  20.065   3.418  1.00 25.00           C
ATOM     88  CA  GLY    88      45.344  20.749   0.711  1.00 25.00           C
ATOM     89  CA  GLY    89      41.897  22.378   0.658  1.00 25.00           C
ATOM     90  CA  SER    90      38.624  24.184   0.115  1.00 25.00           C
ATOM     91  CA  CYS    91      36.256  23.041   2.930  1.00 25.00           C
ATOM     92  CA  LEU    92      32.691  22.788   1.669  1.00 25.00           C
ATOM     93  CA  VAL    93      30.636  24.133   4.624  1.00 25.00           C
ATOM     94  CA  TYR    94      26.950  23.060   4.393  1.00 25.00           C
ATOM     95  CA  CYS    95      23.587  21.733   5.465  1.00 25.00           C
ATOM     96  CA  LYS    96      19.782  21.937   5.065  1.00 25.00           C
ATOM     97  CA  ASN    97      18.798  25.105   3.272  1.00 25.00           C
ATOM     98  CA  GLY    98      22.392  25.970   2.450  1.00 25.00           C
ATOM     99  CA  ARG    99      23.782  29.416   3.336  1.00 25.00           C
ATOM    100  CA  SER   100      22.409  29.352   6.917  1.00 25.00           C
ATOM    101  CA  ARG   101      24.932  28.432   9.648  1.00 25.00           C
ATOM    102  CA  SER   102      27.585  27.356   7.104  1.00 25.00           C
ATOM    103  CA  ALA   103      27.723  30.918   5.704  1.00 25.00           C
ATOM    104  CA  ALA   104      28.134  32.320   9.244  1.00 25.00           C
ATOM    105  CA  VAL   105      30.968  29.835   9.925  1.00 25.00           C
ATOM    106  CA  CYS   106      32.685  30.860   6.659  1.00 25.00           C
ATOM    107  CA  THR   107      32.368  34.553   7.623  1.00 25.00           C
ATOM    108  CA  ALA   108      33.875  33.808  11.064  1.00 25.00           C
ATOM    109  CA  TYR   109      36.781  31.937   9.416  1.00 25.00           C
ATOM    110  CA  LEU   110      37.379  34.894   7.057  1.00 25.00           C
ATOM    111  CA  MET   111      37.378  37.303  10.035  1.00 25.00           C
ATOM    112  CA  ARG   112      39.894  35.072  11.870  1.00 25.00           C
ATOM    113  CA  HIS   113      42.134  35.002   8.764  1.00 25.00           C
ATOM    114  CA  ARG   114      43.776  38.246   7.635  1.00 25.00           C
ATOM    115  CA  GLY   115      43.535  41.474   9.664  1.00 25.00           C
ATOM    116  CA  HIS   116      40.931  42.126   6.889  1.00 25.00           C
ATOM    117  CA  SER   117      37.900  42.672   9.147  1.00 25.00           C
ATOM    118  CA  LEU   118      34.300  41.426   9.461  1.00 25.00           C
ATOM    119  CA  ASP   119      32.443  43.872   7.172  1.00 25.00           C
ATOM    120  CA  ARG   120      34.345  42.516   4.138  1.00 25.00           C
ATOM    121  CA  ALA   121      33.451  38.932   5.148  1.00 25.00           C
ATOM    122  CA  PHE   122      29.768  39.925   5.500  1.00 25.00           C
ATOM    123  CA  GLN   123      29.851  41.555   2.036  1.00 25.00           C
ATOM    124  CA  MET   124      31.414  38.388   0.555  1.00 25.00           C
ATOM    125  CA  VAL   125      28.697  36.248   2.201  1.00 25.00           C
ATOM    126  CA  LYS   126      25.987  38.549   0.779  1.00 25.00           C
ATOM    127  CA  SER   127      27.554  38.282  -2.706  1.00 25.00           C
ATOM    128  CA  ALA   128      27.630  34.464  -2.405  1.00 25.00           C
ATOM    129  CA  ARG   129      24.918  32.518  -4.230  1.00 25.00           C
ATOM    130  CA  PRO   130      22.392  34.570  -6.198  1.00 25.00           C
ATOM    131  CA  VAL   131      20.949  36.226  -3.129  1.00 25.00           C
ATOM    132  CA  ALA   132      22.123  34.763   0.130  1.00 25.00           C
ATOM    133  CA  GLU   133      21.428  36.610   3.438  1.00 25.00           C
ATOM    134  CA  PRO   134      17.768  35.762   3.249  1.00 25.00           C
ATOM    135  CA  ASN   135      15.719  35.421   6.430  1.00 25.00           C
ATOM    136  CA  LEU   136      17.975  37.826   8.357  1.00 25.00           C
ATOM    137  CA  GLY   137      18.419  36.495  11.921  1.00 25.00           C
ATOM    138  CA  PHE   138      21.796  34.970  10.957  1.00 25.00           C
ATOM    139  CA  TRP   139      22.892  38.304   9.423  1.00 25.00           C
ATOM    140  CA  ALA   140      21.846  40.144  12.614  1.00 25.00           C
ATOM    141  CA  GLN   141      23.826  37.643  14.735  1.00 25.00           C
ATOM    142  CA  LEU   142      26.896  38.145  12.502  1.00 25.00           C
ATOM    143  CA  GLN   143      26.562  41.944  12.851  1.00 25.00           C
ATOM    144  CA  LYS   144      26.320  41.597  16.658  1.00 25.00           C
ATOM    145  CA  TYR   145      29.450  39.391  16.680  1.00 25.00           C
ATOM    146  CA  GLU   146      31.317  41.976  14.561  1.00 25.00           C
ATOM    147  CA  GLN   147      30.250  44.757  16.970  1.00 25.00           C
ATOM    148  CA  THR   148      31.466  42.678  19.948  1.00 25.00           C
ATOM    149  CA  LEU   149      34.823  42.093  18.200  1.00 25.00           C
ATOM    150  CA  GLN   150      35.153  45.848  17.523  1.00 25.00           C
ATOM    151  CA  ALA   151      34.083  49.320  18.392  1.00 25.00           C
ATOM    152  CA  GLN   152      31.677  51.362  20.472  1.00 25.00           C
ATOM    153  CA  ALA   153      28.422  53.239  20.055  1.00 25.00           C
ATOM    154  CA  ILE   154      26.754  55.478  17.426  1.00 25.00           C
ATOM    155  CA  LEU   155      23.057  56.227  17.816  1.00 25.00           C
ATOM    156  CA  PRO   156      20.547  57.634  15.328  1.00 25.00           C
ATOM    157  CA  ARG   157      21.148  56.003  12.006  1.00 25.00           C
ATOM    158  CA  GLU   158      22.390  58.100   9.147  1.00 25.00           C
TER
END
