
#######################################################
#                                                     #
#                        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 T0317TS168_3-D1
# Molecule2: number of CA atoms  149 ( 1129),  selected  149 , name T0317_D1.pdb
# PARAMETERS: T0317TS168_3-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      -       -           -
LGA    V      14      -       -           -
LGA    A      15      R      13           #
LGA    -       -      V      14           -
LGA    -       -      A      15           -
LGA    P      16      P      16          2.647
LGA    A      17      A      17          3.104
LGA    L      18      L      18          2.724
LGA    F      19      F      19          1.056
LGA    I      20      I      20          0.959
LGA    G      21      G      21          0.975
LGA    N      22      N      22          1.592
LGA    A      23      A      23           #
LGA    R      24      R      24          1.873
LGA    A      25      A      25          1.719
LGA    A      26      A      26          1.629
LGA    G      27      G      27          0.129
LGA    A      28      A      28          2.054
LGA    T      29      T      29          4.921
LGA    E      30      E      30          2.546
LGA    L      31      L      31          1.981
LGA    L      32      L      32          1.447
LGA    V      33      V      33          2.570
LGA    R      34      R      34          2.008
LGA    A      35      A      35          4.223
LGA    G      36      G      36          2.702
LGA    I      37      I      37          1.419
LGA    T      38      T      38          1.799
LGA    L      39      L      39          1.056
LGA    C      40      C      40          0.499
LGA    V      41      V      41          0.691
LGA    N      42      N      42          0.790
LGA    V      43      V      43          0.809
LGA    S      44      S      44          0.178
LGA    R      45      R      45          2.939
LGA    Q      46      Q      46          2.274
LGA    Q      47      Q      47          2.067
LGA    P      48      P      48          2.311
LGA    G      49      G      49          5.537
LGA    P      50      P      50          4.802
LGA    R      51      R      51          3.783
LGA    A      52      A      52          3.034
LGA    P      53      P      53          1.939
LGA    G      54      G      54          1.612
LGA    V      55      V      55          2.039
LGA    A      56      A      56          2.025
LGA    E      57      E      57          1.601
LGA    L      58      L      58          1.850
LGA    R      59      R      59          2.019
LGA    V      60      V      60          1.066
LGA    P      61      P      61          1.456
LGA    V      62      V      62          0.855
LGA    F      63      F      63          3.326
LGA    -       -      D      64           -
LGA    -       -      D      65           -
LGA    -       -      P      66           -
LGA    -       -      A      67           -
LGA    D      64      E      68          1.841
LGA    D      65      D      69          3.636
LGA    P      66      L      70          4.930
LGA    A      67      L      71          4.959
LGA    E      68      T      72          3.903
LGA    D      69      -       -           -
LGA    L      70      H      73          1.782
LGA    L      71      L      74          4.244
LGA    T      72      -       -           -
LGA    H      73      -       -           -
LGA    L      74      E      75          3.501
LGA    E      75      P      76          1.211
LGA    P      76      T      77          3.125
LGA    T      77      C      78          3.171
LGA    C      78      A      79          1.862
LGA    A      79      A      80          2.080
LGA    A      80      M      81          2.657
LGA    M      81      E      82          2.144
LGA    E      82      A      83          2.088
LGA    A      83      A      84          2.222
LGA    A      84      V      85          1.930
LGA    V      85      R      86          1.968
LGA    R      86      D      87          2.156
LGA    D      87      G      88          1.677
LGA    G      88      -       -           -
LGA    G      89      G      89          2.822
LGA    S      90      S      90          1.244
LGA    C      91      C      91          1.909
LGA    L      92      L      92          2.172
LGA    V      93      V      93          2.281
LGA    Y      94      Y      94          2.110
LGA    C      95      C      95          0.940
LGA    K      96      K      96          1.077
LGA    N      97      N      97          1.584
LGA    G      98      G      98          0.691
LGA    R      99      R      99          2.007
LGA    S     100      S     100          1.011
LGA    R     101      R     101          1.081
LGA    S     102      S     102          0.826
LGA    A     103      A     103          1.161
LGA    A     104      A     104          0.725
LGA    V     105      V     105          0.414
LGA    C     106      C     106          0.605
LGA    T     107      T     107          0.803
LGA    A     108      A     108          0.720
LGA    Y     109      Y     109          0.841
LGA    L     110      L     110          1.223
LGA    M     111      M     111          1.549
LGA    R     112      R     112          1.395
LGA    H     113      H     113          0.935
LGA    R     114      R     114          2.609
LGA    G     115      G     115          1.882
LGA    H     116      H     116          1.576
LGA    S     117      S     117          1.930
LGA    L     118      L     118          2.443
LGA    D     119      D     119          1.780
LGA    R     120      R     120          1.618
LGA    A     121      A     121          1.708
LGA    F     122      F     122          0.415
LGA    Q     123      Q     123          0.273
LGA    M     124      M     124          1.346
LGA    V     125      V     125          1.851
LGA    K     126      K     126          1.795
LGA    S     127      S     127          1.679
LGA    A     128      A     128          2.438
LGA    R     129      R     129          3.053
LGA    P     130      P     130          2.563
LGA    V     131      V     131          3.106
LGA    A     132      A     132          2.533
LGA    E     133      E     133          4.232
LGA    P     134      P     134           #
LGA    N     135      N     135          2.886
LGA    L     136      L     136          2.859
LGA    G     137      G     137          3.070
LGA    F     138      F     138          3.209
LGA    W     139      W     139          2.494
LGA    A     140      A     140          1.974
LGA    Q     141      Q     141          2.037
LGA    L     142      L     142          1.737
LGA    Q     143      Q     143          1.236
LGA    K     144      K     144          1.276
LGA    Y     145      Y     145          0.980
LGA    E     146      E     146          1.268
LGA    Q     147      Q     147          1.676
LGA    T     148      T     148          1.914
LGA    L     149      L     149          2.279
LGA    Q     150      Q     150          2.733
LGA    A     151      A     151           #
LGA    Q     152      Q     152           -
LGA    A     153      A     153           -
LGA    I     154      I     154           -
LGA    L     155      L     155           -
LGA    P     156      P     156           -
LGA    R     157      R     157           -
LGA    E     158      E     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  149    5.0    129    2.28    86.82     61.091     5.419

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.584921 * X  +  -0.202943 * Y  +   0.785290 * Z  +  32.165501
  Y_new =   0.810855 * X  +  -0.123026 * Y  +   0.572170 * Z  +  31.350826
  Z_new =  -0.019507 * X  +   0.971431 * Y  +   0.236518 * Z  +   5.986472 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.331969   -1.809623  [ DEG:    76.3162   -103.6838 ]
  Theta =   0.019508    3.122084  [ DEG:     1.1177    178.8823 ]
  Phi   =   2.195717   -0.945876  [ DEG:   125.8053    -54.1947 ]
 
# 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: T0317TS168_3-D1                               
REMARK     2: T0317_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0317TS168_3-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  129   2.28   86.82  61.091
REMARK  ---------------------------------------------------------- 
MOLECULE T0317TS168_3-D1
PFRMAT TS
TARGET T0317
MODEL 3
PARENT N/A
ATOM     10  CA  PRO    10      37.428  41.685 -15.684  1.00 25.00           C
ATOM     11  CA  PHE    11      36.327  39.646 -12.628  1.00 25.00           C
ATOM     12  CA  ALA    12      37.989  36.794 -14.404  1.00 25.00           C
ATOM     13  CA  ARG    13      40.789  36.247 -11.823  1.00 25.00           C
ATOM     14  CA  VAL    14      41.238  34.264  -8.611  1.00 25.00           C
ATOM     15  CA  ALA    15      39.130  33.466  -5.545  1.00 25.00           C
ATOM     16  CA  PRO    16      38.566  31.720  -2.278  1.00 25.00           C
ATOM     17  CA  ALA    17      37.963  28.870   0.138  1.00 25.00           C
ATOM     18  CA  LEU    18      35.356  28.878   2.945  1.00 25.00           C
ATOM     19  CA  PHE    19      32.832  27.454   0.452  1.00 25.00           C
ATOM     20  CA  ILE    20      29.208  27.908   1.704  1.00 25.00           C
ATOM     21  CA  GLY    21      27.498  25.096  -0.220  1.00 25.00           C
ATOM     22  CA  ASN    22      24.505  22.783   0.203  1.00 25.00           C
ATOM     23  CA  ALA    23      21.879  22.440  -2.499  1.00 25.00           C
ATOM     24  CA  ARG    24      21.306  18.671  -2.310  1.00 25.00           C
ATOM     25  CA  ALA    25      25.091  18.569  -2.467  1.00 25.00           C
ATOM     26  CA  ALA    26      27.068  16.511   0.073  1.00 25.00           C
ATOM     27  CA  GLY    27      25.639  13.189  -1.247  1.00 25.00           C
ATOM     28  CA  ALA    28      28.431  13.048  -3.878  1.00 25.00           C
ATOM     29  CA  THR    29      28.096  16.037  -6.222  1.00 25.00           C
ATOM     30  CA  GLU    30      30.972  15.028  -8.542  1.00 25.00           C
ATOM     31  CA  LEU    31      32.731  18.359  -7.854  1.00 25.00           C
ATOM     32  CA  LEU    32      32.311  17.830  -4.083  1.00 25.00           C
ATOM     33  CA  VAL    33      33.763  14.300  -4.392  1.00 25.00           C
ATOM     34  CA  ARG    34      36.745  15.673  -6.366  1.00 25.00           C
ATOM     35  CA  ALA    35      40.041  17.643  -6.241  1.00 25.00           C
ATOM     36  CA  GLY    36      40.497  16.404  -2.674  1.00 25.00           C
ATOM     37  CA  ILE    37      37.830  18.974  -1.778  1.00 25.00           C
ATOM     38  CA  THR    38      39.366  18.805   1.666  1.00 25.00           C
ATOM     39  CA  LEU    39      36.713  19.328   4.283  1.00 25.00           C
ATOM     40  CA  CYS    40      33.068  19.023   5.279  1.00 25.00           C
ATOM     41  CA  VAL    41      31.371  21.041   7.976  1.00 25.00           C
ATOM     42  CA  ASN    42      27.759  20.949   9.288  1.00 25.00           C
ATOM     43  CA  VAL    43      26.293  23.917  11.231  1.00 25.00           C
ATOM     44  CA  SER    44      23.221  21.698  11.574  1.00 25.00           C
ATOM     45  CA  ARG    45      22.384  17.961  11.471  1.00 25.00           C
ATOM     46  CA  GLN    46      19.585  16.134   9.640  1.00 25.00           C
ATOM     47  CA  GLN    47      21.816  15.901   6.603  1.00 25.00           C
ATOM     48  CA  PRO    48      22.985  12.565   8.138  1.00 25.00           C
ATOM     49  CA  GLY    49      25.407   9.773   9.009  1.00 25.00           C
ATOM     50  CA  PRO    50      27.587   9.430   5.905  1.00 25.00           C
ATOM     51  CA  ARG    51      31.287   8.374   6.133  1.00 25.00           C
ATOM     52  CA  ALA    52      32.013  10.636   3.153  1.00 25.00           C
ATOM     53  CA  PRO    53      34.827   9.726   0.789  1.00 25.00           C
ATOM     54  CA  GLY    54      37.775  10.957   2.825  1.00 25.00           C
ATOM     55  CA  VAL    55      36.872  13.859   5.093  1.00 25.00           C
ATOM     56  CA  ALA    56      36.371  15.815   8.289  1.00 25.00           C
ATOM     57  CA  GLU    57      32.969  16.553   9.846  1.00 25.00           C
ATOM     58  CA  LEU    58      33.855  19.400  12.164  1.00 25.00           C
ATOM     59  CA  ARG    59      30.627  19.007  14.230  1.00 25.00           C
ATOM     60  CA  VAL    60      28.623  21.963  15.501  1.00 25.00           C
ATOM     61  CA  PRO    61      25.278  21.733  17.376  1.00 25.00           C
ATOM     62  CA  VAL    62      23.966  24.960  15.747  1.00 25.00           C
ATOM     63  CA  PHE    63      21.509  26.060  18.388  1.00 25.00           C
ATOM     64  CA  ASP    64      22.958  28.972  20.415  1.00 25.00           C
ATOM     65  CA  ASP    65      25.080  27.465  23.144  1.00 25.00           C
ATOM     66  CA  PRO    66      27.426  30.374  22.530  1.00 25.00           C
ATOM     67  CA  ALA    67      31.039  30.877  23.667  1.00 25.00           C
ATOM     68  CA  GLU    68      31.191  27.077  24.173  1.00 25.00           C
ATOM     69  CA  ASP    69      29.703  25.003  21.318  1.00 25.00           C
ATOM     70  CA  LEU    70      30.110  27.963  18.922  1.00 25.00           C
ATOM     71  CA  LEU    71      33.756  28.381  20.018  1.00 25.00           C
ATOM     72  CA  THR    72      34.382  24.647  19.442  1.00 25.00           C
ATOM     73  CA  HIS    73      32.818  24.897  15.955  1.00 25.00           C
ATOM     74  CA  LEU    74      35.033  27.915  15.151  1.00 25.00           C
ATOM     75  CA  GLU    75      38.128  25.988  16.326  1.00 25.00           C
ATOM     76  CA  PRO    76      37.136  23.011  14.131  1.00 25.00           C
ATOM     77  CA  THR    77      36.687  25.343  11.127  1.00 25.00           C
ATOM     78  CA  CYS    78      40.133  26.882  11.774  1.00 25.00           C
ATOM     79  CA  ALA    79      41.686  23.386  11.961  1.00 25.00           C
ATOM     80  CA  ALA    80      39.999  22.432   8.658  1.00 25.00           C
ATOM     81  CA  MET    81      41.331  25.631   7.027  1.00 25.00           C
ATOM     82  CA  GLU    82      44.855  24.845   8.306  1.00 25.00           C
ATOM     83  CA  ALA    83      44.597  21.291   6.902  1.00 25.00           C
ATOM     84  CA  ALA    84      43.463  22.683   3.519  1.00 25.00           C
ATOM     85  CA  VAL    85      46.414  25.124   3.506  1.00 25.00           C
ATOM     86  CA  ARG    86      48.824  22.255   4.302  1.00 25.00           C
ATOM     87  CA  ASP    87      47.581  20.839   0.967  1.00 25.00           C
ATOM     88  CA  GLY    88      46.108  20.008  -2.443  1.00 25.00           C
ATOM     89  CA  GLY    89      42.818  21.644  -1.398  1.00 25.00           C
ATOM     90  CA  SER    90      39.725  23.657  -0.264  1.00 25.00           C
ATOM     91  CA  CYS    91      36.206  23.615   1.222  1.00 25.00           C
ATOM     92  CA  LEU    92      32.784  22.025   0.608  1.00 25.00           C
ATOM     93  CA  VAL    93      30.555  23.211   3.453  1.00 25.00           C
ATOM     94  CA  TYR    94      27.145  21.813   4.392  1.00 25.00           C
ATOM     95  CA  CYS    95      24.263  23.225   6.376  1.00 25.00           C
ATOM     96  CA  LYS    96      20.660  22.153   6.389  1.00 25.00           C
ATOM     97  CA  ASN    97      19.653  25.427   4.629  1.00 25.00           C
ATOM     98  CA  GLY    98      22.813  26.956   3.276  1.00 25.00           C
ATOM     99  CA  ARG    99      23.288  30.725   3.345  1.00 25.00           C
ATOM    100  CA  SER   100      22.196  31.718   6.867  1.00 25.00           C
ATOM    101  CA  ARG   101      24.605  29.504   8.670  1.00 25.00           C
ATOM    102  CA  SER   102      27.304  28.416   6.179  1.00 25.00           C
ATOM    103  CA  ALA   103      27.927  32.071   5.219  1.00 25.00           C
ATOM    104  CA  ALA   104      28.231  33.017   8.918  1.00 25.00           C
ATOM    105  CA  VAL   105      30.721  30.160   9.468  1.00 25.00           C
ATOM    106  CA  CYS   106      32.772  31.333   6.453  1.00 25.00           C
ATOM    107  CA  THR   107      32.788  34.909   7.824  1.00 25.00           C
ATOM    108  CA  ALA   108      33.951  33.620  11.238  1.00 25.00           C
ATOM    109  CA  TYR   109      36.750  31.619   9.556  1.00 25.00           C
ATOM    110  CA  LEU   110      37.834  34.729   7.602  1.00 25.00           C
ATOM    111  CA  MET   111      37.878  36.777  10.837  1.00 25.00           C
ATOM    112  CA  ARG   112      39.998  34.082  12.542  1.00 25.00           C
ATOM    113  CA  HIS   113      42.437  34.096   9.589  1.00 25.00           C
ATOM    114  CA  ARG   114      43.732  36.888   7.396  1.00 25.00           C
ATOM    115  CA  GLY   115      43.021  40.291   8.885  1.00 25.00           C
ATOM    116  CA  HIS   116      39.388  40.979   7.870  1.00 25.00           C
ATOM    117  CA  SER   117      36.739  42.325  10.226  1.00 25.00           C
ATOM    118  CA  LEU   118      34.530  39.777   8.466  1.00 25.00           C
ATOM    119  CA  ASP   119      32.963  42.596   6.403  1.00 25.00           C
ATOM    120  CA  ARG   120      34.682  41.276   3.246  1.00 25.00           C
ATOM    121  CA  ALA   121      33.379  37.750   3.982  1.00 25.00           C
ATOM    122  CA  PHE   122      29.839  39.132   4.460  1.00 25.00           C
ATOM    123  CA  GLN   123      30.098  41.012   1.134  1.00 25.00           C
ATOM    124  CA  MET   124      31.275  37.814  -0.613  1.00 25.00           C
ATOM    125  CA  VAL   125      28.333  35.880   0.897  1.00 25.00           C
ATOM    126  CA  LYS   126      25.906  38.586  -0.306  1.00 25.00           C
ATOM    127  CA  SER   127      27.417  38.416  -3.820  1.00 25.00           C
ATOM    128  CA  ALA   128      27.046  34.605  -3.821  1.00 25.00           C
ATOM    129  CA  ARG   129      23.331  34.155  -4.040  1.00 25.00           C
ATOM    130  CA  PRO   130      22.401  37.789  -4.244  1.00 25.00           C
ATOM    131  CA  VAL   131      20.946  37.201  -0.781  1.00 25.00           C
ATOM    132  CA  ALA   132      22.441  36.289   2.592  1.00 25.00           C
ATOM    133  CA  GLU   133      22.854  39.809   4.003  1.00 25.00           C
ATOM    134  CA  PRO   134      19.862  38.993   6.106  1.00 25.00           C
ATOM    135  CA  ASN   135      18.694  37.067   9.159  1.00 25.00           C
ATOM    136  CA  LEU   136      21.070  39.725  10.590  1.00 25.00           C
ATOM    137  CA  GLY   137      21.983  37.385  13.481  1.00 25.00           C
ATOM    138  CA  PHE   138      25.130  36.261  11.609  1.00 25.00           C
ATOM    139  CA  TRP   139      26.103  39.914  11.001  1.00 25.00           C
ATOM    140  CA  ALA   140      25.598  40.693  14.716  1.00 25.00           C
ATOM    141  CA  GLN   141      27.779  37.693  15.667  1.00 25.00           C
ATOM    142  CA  LEU   142      30.506  38.879  13.253  1.00 25.00           C
ATOM    143  CA  GLN   143      30.359  42.390  14.774  1.00 25.00           C
ATOM    144  CA  LYS   144      30.663  40.908  18.292  1.00 25.00           C
ATOM    145  CA  TYR   145      33.685  38.834  17.182  1.00 25.00           C
ATOM    146  CA  GLU   146      35.311  41.961  15.682  1.00 25.00           C
ATOM    147  CA  GLN   147      34.704  43.871  18.945  1.00 25.00           C
ATOM    148  CA  THR   148      36.270  41.004  20.944  1.00 25.00           C
ATOM    149  CA  LEU   149      39.312  41.012  18.619  1.00 25.00           C
ATOM    150  CA  GLN   150      39.670  44.799  19.060  1.00 25.00           C
ATOM    151  CA  ALA   151      38.000  47.217  21.544  1.00 25.00           C
ATOM    152  CA  GLN   152      36.698  49.829  23.981  1.00 25.00           C
ATOM    153  CA  ALA   153      35.312  52.947  22.309  1.00 25.00           C
ATOM    154  CA  ILE   154      32.580  55.114  20.862  1.00 25.00           C
ATOM    155  CA  LEU   155      32.885  56.403  17.306  1.00 25.00           C
ATOM    156  CA  PRO   156      30.458  58.939  15.841  1.00 25.00           C
ATOM    157  CA  ARG   157      27.156  58.097  14.182  1.00 25.00           C
ATOM    158  CA  GLU   158      26.610  58.550  10.456  1.00 25.00           C
TER
END
