
#######################################################
#                                                     #
#                        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  128 (  128),  selected  128 , name T0322TS393_5-D1
# Molecule2: number of CA atoms  128 (  980),  selected  128 , name T0322_D1.pdb
# PARAMETERS: T0322TS393_5-D1.T0322_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      16      G      16           -
LGA    F      17      F      17           -
LGA    S      18      S      18           -
LGA    Q      19      Q      19           -
LGA    L      20      L      20           -
LGA    N      21      N      21           -
LGA    W      22      -       -           -
LGA    S      23      W      22           #
LGA    R      24      S      23          2.215
LGA    G      25      R      24          3.304
LGA    -       -      G      25           -
LGA    F      26      F      26           #
LGA    G      27      G      27          4.259
LGA    R      28      R      28          3.709
LGA    Q      29      Q      29          2.716
LGA    I      30      I      30          2.262
LGA    G      31      G      31          2.294
LGA    -       -      P      32           -
LGA    P      32      L      33          1.368
LGA    L      33      F      34          1.994
LGA    F      34      E      35          2.680
LGA    E      35      H      36           #
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    H      36      P      40           #
LGA    R      37      G      41          2.547
LGA    E      38      Q      42           #
LGA    G      39      -       -           -
LGA    P      40      -       -           -
LGA    G      41      -       -           -
LGA    Q      42      -       -           -
LGA    A      43      A      43          1.932
LGA    R      44      R      44          1.656
LGA    L      45      L      45          2.532
LGA    A      46      A      46          2.851
LGA    F      47      F      47          2.771
LGA    R      48      R      48          2.045
LGA    V      49      V      49          0.917
LGA    E      50      E      50          1.623
LGA    E      51      E      51          3.118
LGA    H      52      H      52          2.850
LGA    H      53      H      53          1.595
LGA    T      54      T      54          1.160
LGA    N      55      N      55          2.674
LGA    G      56      G      56          4.240
LGA    L      57      L      57          1.963
LGA    G      58      G      58          3.160
LGA    N      59      N      59          3.320
LGA    C      60      C      60          1.496
LGA    H      61      H      61          2.880
LGA    G      62      G      62          2.393
LGA    G      63      G      63          0.516
LGA    M      64      M      64          1.208
LGA    L      65      L      65          1.946
LGA    M      66      M      66          1.620
LGA    S      67      S      67          0.793
LGA    F      68      F      68          0.699
LGA    A      69      A      69          2.173
LGA    D      70      D      70          2.484
LGA    M      71      M      71          1.632
LGA    A      72      A      72          2.369
LGA    W      73      W      73          4.990
LGA    G      74      G      74          5.097
LGA    R      75      R      75          2.884
LGA    I      76      I      76          3.431
LGA    I      77      I      77          4.144
LGA    S      78      S      78          3.047
LGA    L      79      L      79          2.459
LGA    Q      80      Q      80          4.207
LGA    K      81      K      81          4.293
LGA    S      82      S      82          5.167
LGA    Y      83      Y      83          2.987
LGA    S      84      S      84          1.879
LGA    W      85      W      85          0.635
LGA    V      86      V      86          1.518
LGA    T      87      T      87          0.831
LGA    V      88      V      88          1.216
LGA    R      89      R      89          0.472
LGA    L      90      L      90          0.780
LGA    M      91      M      91          1.321
LGA    C      92      C      92          1.521
LGA    D      93      D      93          2.056
LGA    F      94      F      94          2.343
LGA    L      95      L      95          2.280
LGA    S      96      S      96          1.307
LGA    G      97      G      97          0.742
LGA    A      98      A      98          0.707
LGA    K      99      K      99          1.740
LGA    L     100      L     100          1.732
LGA    G     101      G     101          2.925
LGA    D     102      D     102          1.698
LGA    W     103      W     103          2.945
LGA    V     104      V     104          1.254
LGA    E     105      E     105          1.004
LGA    G     106      G     106          0.624
LGA    E     107      E     107          0.804
LGA    G     108      G     108          2.870
LGA    E     109      E     109          2.325
LGA    L     110      L     110          1.755
LGA    I     111      I     111          2.013
LGA    S     112      S     112          2.755
LGA    E     113      E     113          3.377
LGA    E     114      E     114          4.968
LGA    D     115      D     115          5.504
LGA    -       -      M     116           -
LGA    M     116      L     117          2.678
LGA    L     117      F     118          2.154
LGA    F     118      T     119          4.401
LGA    T     119      V     120          0.760
LGA    V     120      R     121          3.731
LGA    R     121      G     122          1.475
LGA    G     122      R     123          0.526
LGA    R     123      I     124          3.951
LGA    I     124      W     125          1.039
LGA    W     125      -       -           -
LGA    A     126      A     126          1.900
LGA    G     127      G     127          1.664
LGA    E     128      E     128          1.151
LGA    R     129      R     129          2.115
LGA    T     130      T     130          1.197
LGA    L     131      L     131          1.123
LGA    I     132      I     132          2.359
LGA    T     133      T     133          2.658
LGA    G     134      G     134          2.207
LGA    T     135      T     135          1.377
LGA    G     136      G     136          1.583
LGA    V     137      V     137          1.899
LGA    F     138      F     138          2.173
LGA    K     139      K     139          2.379
LGA    A     140      A     140          2.919
LGA    L     141      L     141          4.176
LGA    S     142      S     142          6.013
LGA    A     143      A     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  128  128    5.0    110    2.60    86.36     54.859     4.067

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.701354 * X  +  -0.658216 * Y  +   0.273596 * Z  +   9.484044
  Y_new =  -0.542977 * X  +  -0.244653 * Y  +   0.803319 * Z  +  -9.445344
  Z_new =  -0.461821 * X  +  -0.711967 * Y  +  -0.528984 * Z  + -15.399154 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.209796    0.931796  [ DEG:  -126.6120     53.3880 ]
  Theta =   0.480048    2.661545  [ DEG:    27.5047    152.4953 ]
  Phi   =  -0.658800    2.482792  [ DEG:   -37.7465    142.2535 ]
 
# 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: T0322TS393_5-D1                               
REMARK     2: T0322_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS393_5-D1.T0322_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  128  128   5.0  110   2.60   86.36  54.859
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS393_5-D1
PFRMAT TS
TARGET T0322
MODEL 5
PARENT N/A
ATOM     16  CA  GLY    16      18.133 -15.845   8.976  1.00 25.00           C
ATOM     17  CA  PHE    17      14.442 -16.653   8.514  1.00 25.00           C
ATOM     18  CA  SER    18      13.355 -13.191   7.370  1.00 25.00           C
ATOM     19  CA  GLN    19      16.042 -10.591   7.718  1.00 25.00           C
ATOM     20  CA  LEU    20      13.115  -8.097   7.779  1.00 25.00           C
ATOM     21  CA  ASN    21      13.529  -4.334   7.201  1.00 25.00           C
ATOM     22  CA  TRP    22      11.555  -3.527   3.998  1.00 25.00           C
ATOM     23  CA  SER    23      14.316  -1.459   2.462  1.00 25.00           C
ATOM     24  CA  ARG    24      12.980  -2.517  -1.001  1.00 25.00           C
ATOM     25  CA  GLY    25       9.406  -1.508  -1.957  1.00 25.00           C
ATOM     26  CA  PHE    26       8.893  -1.943  -5.644  1.00 25.00           C
ATOM     27  CA  GLY    27       8.622  -5.737  -6.088  1.00 25.00           C
ATOM     28  CA  ARG    28       6.509  -5.984  -2.904  1.00 25.00           C
ATOM     29  CA  GLN    29       4.221  -3.189  -4.176  1.00 25.00           C
ATOM     30  CA  ILE    30       4.046  -4.419  -7.817  1.00 25.00           C
ATOM     31  CA  GLY    31       4.322  -8.145  -7.109  1.00 25.00           C
ATOM     32  CA  PRO    32       7.106 -10.004  -8.917  1.00 25.00           C
ATOM     33  CA  LEU    33       7.288 -13.687  -9.579  1.00 25.00           C
ATOM     34  CA  PHE    34       9.949 -15.009 -11.927  1.00 25.00           C
ATOM     35  CA  GLU    35       8.863 -18.543 -12.929  1.00 25.00           C
ATOM     36  CA  HIS    36      11.038 -17.909 -16.008  1.00 25.00           C
ATOM     37  CA  ARG    37      12.318 -17.041 -19.546  1.00 25.00           C
ATOM     38  CA  GLU    38      12.830 -20.068 -21.807  1.00 25.00           C
ATOM     39  CA  GLY    39      16.238 -19.714 -23.464  1.00 25.00           C
ATOM     40  CA  PRO    40      18.520 -17.521 -21.392  1.00 25.00           C
ATOM     41  CA  GLY    41      17.225 -14.786 -23.721  1.00 25.00           C
ATOM     42  CA  GLN    42      15.330 -12.924 -21.018  1.00 25.00           C
ATOM     43  CA  ALA    43      14.213 -11.839 -17.529  1.00 25.00           C
ATOM     44  CA  ARG    44      10.655 -12.736 -16.360  1.00 25.00           C
ATOM     45  CA  LEU    45       9.463  -9.965 -13.987  1.00 25.00           C
ATOM     46  CA  ALA    46       5.835 -11.089 -13.649  1.00 25.00           C
ATOM     47  CA  PHE    47       2.681 -10.383 -11.570  1.00 25.00           C
ATOM     48  CA  ARG    48       0.842 -12.927  -9.422  1.00 25.00           C
ATOM     49  CA  VAL    49      -2.762 -11.763  -8.997  1.00 25.00           C
ATOM     50  CA  GLU    50      -3.196 -11.907  -5.249  1.00 25.00           C
ATOM     51  CA  GLU    51      -6.897 -11.269  -5.018  1.00 25.00           C
ATOM     52  CA  HIS    52      -6.243  -7.721  -3.731  1.00 25.00           C
ATOM     53  CA  HIS    53      -3.876  -7.065  -6.669  1.00 25.00           C
ATOM     54  CA  THR    54      -7.016  -6.257  -8.633  1.00 25.00           C
ATOM     55  CA  ASN    55      -8.927  -3.058  -9.211  1.00 25.00           C
ATOM     56  CA  GLY    56     -12.706  -3.051  -9.915  1.00 25.00           C
ATOM     57  CA  LEU    57     -14.254  -6.370  -8.765  1.00 25.00           C
ATOM     58  CA  GLY    58     -12.795  -9.313 -10.684  1.00 25.00           C
ATOM     59  CA  ASN    59     -10.996  -7.835 -13.727  1.00 25.00           C
ATOM     60  CA  CYS    60      -7.231  -8.388 -13.520  1.00 25.00           C
ATOM     61  CA  HIS    61      -6.946  -5.547 -15.990  1.00 25.00           C
ATOM     62  CA  GLY    62      -5.291  -3.265 -18.617  1.00 25.00           C
ATOM     63  CA  GLY    63      -3.641  -1.314 -15.764  1.00 25.00           C
ATOM     64  CA  MET    64      -2.197  -4.564 -14.344  1.00 25.00           C
ATOM     65  CA  LEU    65      -0.831  -5.496 -17.798  1.00 25.00           C
ATOM     66  CA  MET    66       0.769  -2.032 -18.127  1.00 25.00           C
ATOM     67  CA  SER    67       2.364  -2.414 -14.666  1.00 25.00           C
ATOM     68  CA  PHE    68       3.728  -5.855 -15.647  1.00 25.00           C
ATOM     69  CA  ALA    69       5.176  -4.388 -18.875  1.00 25.00           C
ATOM     70  CA  ASP    70       6.827  -1.565 -16.881  1.00 25.00           C
ATOM     71  CA  MET    71       8.323  -4.123 -14.454  1.00 25.00           C
ATOM     72  CA  ALA    72       9.670  -6.166 -17.399  1.00 25.00           C
ATOM     73  CA  TRP    73      11.224  -3.010 -18.912  1.00 25.00           C
ATOM     74  CA  GLY    74      12.855  -2.171 -15.549  1.00 25.00           C
ATOM     75  CA  ARG    75      14.253  -5.729 -15.312  1.00 25.00           C
ATOM     76  CA  ILE    76      15.654  -5.441 -18.865  1.00 25.00           C
ATOM     77  CA  ILE    77      17.287  -2.093 -17.976  1.00 25.00           C
ATOM     78  CA  SER    78      18.836  -3.654 -14.840  1.00 25.00           C
ATOM     79  CA  LEU    79      20.182  -6.570 -16.926  1.00 25.00           C
ATOM     80  CA  GLN    80      21.708  -4.270 -19.536  1.00 25.00           C
ATOM     81  CA  LYS    81      23.441  -2.500 -16.643  1.00 25.00           C
ATOM     82  CA  SER    82      23.376   1.348 -16.413  1.00 25.00           C
ATOM     83  CA  TYR    83      21.955   1.970 -19.893  1.00 25.00           C
ATOM     84  CA  SER    84      18.950   3.267 -17.990  1.00 25.00           C
ATOM     85  CA  TRP    85      15.738   2.315 -19.761  1.00 25.00           C
ATOM     86  CA  VAL    86      13.122   4.594 -21.289  1.00 25.00           C
ATOM     87  CA  THR    87       9.743   2.916 -21.039  1.00 25.00           C
ATOM     88  CA  VAL    88       9.344   3.650 -24.760  1.00 25.00           C
ATOM     89  CA  ARG    89       6.196   2.308 -26.356  1.00 25.00           C
ATOM     90  CA  LEU    90       3.310   0.261 -24.832  1.00 25.00           C
ATOM     91  CA  MET    91       0.179  -1.094 -26.483  1.00 25.00           C
ATOM     92  CA  CYS    92      -1.952  -3.650 -24.562  1.00 25.00           C
ATOM     93  CA  ASP    93      -5.047  -5.851 -25.157  1.00 25.00           C
ATOM     94  CA  PHE    94      -6.503  -7.084 -21.905  1.00 25.00           C
ATOM     95  CA  LEU    95      -8.231 -10.123 -23.472  1.00 25.00           C
ATOM     96  CA  SER    96      -9.605 -12.745 -21.136  1.00 25.00           C
ATOM     97  CA  GLY    97      -8.582 -12.616 -17.492  1.00 25.00           C
ATOM     98  CA  ALA    98      -6.936 -13.729 -14.229  1.00 25.00           C
ATOM     99  CA  LYS    99      -9.655 -15.251 -11.991  1.00 25.00           C
ATOM    100  CA  LEU   100      -7.800 -15.135  -8.643  1.00 25.00           C
ATOM    101  CA  GLY   101      -6.283 -18.613  -8.336  1.00 25.00           C
ATOM    102  CA  ASP   102      -4.664 -17.965 -11.735  1.00 25.00           C
ATOM    103  CA  TRP   103      -1.948 -15.420 -12.763  1.00 25.00           C
ATOM    104  CA  VAL   104       1.042 -14.126 -14.759  1.00 25.00           C
ATOM    105  CA  GLU   105       4.147 -15.456 -16.548  1.00 25.00           C
ATOM    106  CA  GLY   106       4.724 -12.235 -18.487  1.00 25.00           C
ATOM    107  CA  GLU   107       7.647 -12.999 -20.797  1.00 25.00           C
ATOM    108  CA  GLY   108      10.744 -10.852 -21.002  1.00 25.00           C
ATOM    109  CA  GLU   109      11.236 -12.370 -24.406  1.00 25.00           C
ATOM    110  CA  LEU   110      13.537 -10.270 -26.672  1.00 25.00           C
ATOM    111  CA  ILE   111      12.869 -10.107 -30.370  1.00 25.00           C
ATOM    112  CA  SER   112      16.012  -8.392 -31.642  1.00 25.00           C
ATOM    113  CA  GLU   113      16.287  -4.886 -33.130  1.00 25.00           C
ATOM    114  CA  GLU   114      16.052  -2.456 -35.958  1.00 25.00           C
ATOM    115  CA  ASP   115      16.668   0.123 -33.264  1.00 25.00           C
ATOM    116  CA  MET   116      16.238  -0.955 -29.665  1.00 25.00           C
ATOM    117  CA  LEU   117      16.062  -4.164 -27.573  1.00 25.00           C
ATOM    118  CA  PHE   118      13.201  -5.384 -25.402  1.00 25.00           C
ATOM    119  CA  THR   119       9.984  -6.613 -27.016  1.00 25.00           C
ATOM    120  CA  VAL   120       7.656  -8.374 -24.663  1.00 25.00           C
ATOM    121  CA  ARG   121       5.546 -11.007 -26.314  1.00 25.00           C
ATOM    122  CA  GLY   122       3.340 -11.874 -23.343  1.00 25.00           C
ATOM    123  CA  ARG   123       3.239 -15.505 -22.222  1.00 25.00           C
ATOM    124  CA  ILE   124       0.251 -14.847 -19.944  1.00 25.00           C
ATOM    125  CA  TRP   125       0.337 -18.238 -18.352  1.00 25.00           C
ATOM    126  CA  ALA   126      -2.966 -19.119 -16.703  1.00 25.00           C
ATOM    127  CA  GLY   127      -1.957 -22.785 -17.250  1.00 25.00           C
ATOM    128  CA  GLU   128      -3.644 -22.559 -20.700  1.00 25.00           C
ATOM    129  CA  ARG   129      -2.928 -19.331 -22.577  1.00 25.00           C
ATOM    130  CA  THR   130      -3.312 -15.783 -23.885  1.00 25.00           C
ATOM    131  CA  LEU   131      -4.642 -13.528 -21.167  1.00 25.00           C
ATOM    132  CA  ILE   132      -2.483 -10.412 -20.971  1.00 25.00           C
ATOM    133  CA  THR   133      -1.200  -9.225 -24.347  1.00 25.00           C
ATOM    134  CA  GLY   134       1.922  -7.230 -25.146  1.00 25.00           C
ATOM    135  CA  THR   135       4.371  -4.960 -26.948  1.00 25.00           C
ATOM    136  CA  GLY   136       6.874  -3.280 -24.556  1.00 25.00           C
ATOM    137  CA  VAL   137      10.046  -1.399 -25.487  1.00 25.00           C
ATOM    138  CA  PHE   138      12.799  -0.960 -22.882  1.00 25.00           C
ATOM    139  CA  LYS   139      15.509   0.843 -24.813  1.00 25.00           C
ATOM    140  CA  ALA   140      19.236   0.051 -24.415  1.00 25.00           C
ATOM    141  CA  LEU   141      20.721   3.551 -24.548  1.00 25.00           C
ATOM    142  CA  SER   142      21.691   7.197 -24.157  1.00 25.00           C
ATOM    143  CA  ALA   143      23.341   9.947 -22.230  1.00 25.00           C
TER
END
