
#######################################################
#                                                     #
#                        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  148 (  148),  selected  148 , name T0298TS393_5-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS393_5-D1.T0298_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Q       3      Q       3          2.955
LGA    P       4      P       4          1.325
LGA    L       5      L       5          1.074
LGA    N       6      N       6          2.182
LGA    V       7      V       7          1.784
LGA    A       8      A       8          1.481
LGA    V       9      V       9          0.449
LGA    V      10      V      10          1.093
LGA    G      11      G      11          1.281
LGA    A      12      A      12          1.635
LGA    T      13      T      13          4.131
LGA    G      14      G      14          3.337
LGA    S      15      S      15          3.559
LGA    V      16      V      16          2.413
LGA    G      17      G      17          1.043
LGA    E      18      E      18          3.060
LGA    A      19      A      19          3.636
LGA    L      20      L      20          1.947
LGA    V      21      V      21          1.492
LGA    G      22      G      22          3.440
LGA    L      23      L      23          3.245
LGA    L      24      L      24          1.219
LGA    D      25      D      25          1.675
LGA    E      26      E      26          3.578
LGA    R      27      R      27          3.046
LGA    D      28      D      28          3.406
LGA    F      29      F      29          2.918
LGA    P      30      P      30          3.389
LGA    L      31      L      31          2.978
LGA    H      32      H      32          2.157
LGA    R      33      R      33          2.991
LGA    L      34      L      34          3.334
LGA    H      35      H      35          3.411
LGA    L      36      L      36          1.137
LGA    L      37      L      37          1.505
LGA    A      38      A      38          2.054
LGA    S      39      S      39          2.771
LGA    A      40      A      40          3.108
LGA    -       -      E      41           -
LGA    E      41      S      42           #
LGA    S      42      A      43           #
LGA    A      43      -       -           -
LGA    G      44      -       -           -
LGA    Q      45      -       -           -
LGA    R      46      G      44          3.362
LGA    M      47      Q      45          4.438
LGA    G      48      R      46          2.082
LGA    F      49      M      47          2.269
LGA    A      50      G      48          3.872
LGA    -       -      F      49           -
LGA    -       -      A      50           -
LGA    E      51      E      51          3.317
LGA    S      52      S      52          1.013
LGA    S      53      S      53          2.150
LGA    L      54      L      54          2.353
LGA    R      55      R      55          3.876
LGA    V      56      V      56          5.405
LGA    G      57      G      57          4.108
LGA    D      58      D      58          5.284
LGA    -       -      V      59           -
LGA    -       -      D      60           -
LGA    V      59      S      61           #
LGA    D      60      F      62          5.715
LGA    S      61      D      63          4.553
LGA    F      62      -       -           -
LGA    D      63      -       -           -
LGA    F      64      F      64          0.595
LGA    S      65      S      65          0.726
LGA    S      66      S      66          4.230
LGA    V      67      V      67          2.100
LGA    -       -      G      68           -
LGA    G      68      L      69          0.448
LGA    L      69      A      70          3.447
LGA    A      70      F      71          1.632
LGA    F      71      F      72          3.626
LGA    F      72      A      73          0.574
LGA    A      73      A      74          2.958
LGA    A      74      A      75          1.408
LGA    A      75      A      76          2.921
LGA    A      76      E      77          3.590
LGA    E      77      -       -           -
LGA    V      78      V      78          3.943
LGA    S      79      S      79          3.400
LGA    R      80      R      80          1.653
LGA    A      81      A      81          1.705
LGA    H      82      H      82          2.271
LGA    A      83      A      83          2.908
LGA    E      84      E      84          4.656
LGA    R      85      R      85          3.420
LGA    A      86      A      86          2.814
LGA    R      87      -       -           -
LGA    A      88      -       -           -
LGA    A      89      -       -           -
LGA    G      90      -       -           -
LGA    C      91      R      87          0.345
LGA    S      92      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    -       -      S      92           -
LGA    V      93      V      93          1.048
LGA    I      94      I      94          3.827
LGA    D      95      D      95          2.307
LGA    L      96      L      96          2.376
LGA    S      97      S      97          2.122
LGA    G      98      G      98          2.848
LGA    -       -      A      99           -
LGA    A      99      L     100          0.685
LGA    L     100      E     101          3.427
LGA    E     101      P     102          1.092
LGA    P     102      S     103          0.837
LGA    S     103      V     104          2.668
LGA    V     104      -       -           -
LGA    A     105      -       -           -
LGA    P     106      A     105          3.327
LGA    P     107      P     106          2.871
LGA    V     108      P     107           #
LGA    M     109      V     108          1.598
LGA    V     110      M     109          2.753
LGA    S     111      V     110          4.323
LGA    V     112      S     111           #
LGA    N     113      V     112          3.066
LGA    A     114      N     113          4.389
LGA    E     115      A     114          3.499
LGA    R     116      E     115          1.516
LGA    L     117      R     116          5.579
LGA    A     118      -       -           -
LGA    S     119      L     117          4.893
LGA    Q     120      A     118          2.625
LGA    A     121      S     119          4.437
LGA    A     122      Q     120          0.664
LGA    P     123      A     121          4.554
LGA    -       -      A     122           -
LGA    -       -      P     123           -
LGA    F     124      F     124          3.107
LGA    L     125      L     125           #
LGA    L     126      L     126          4.007
LGA    S     127      S     127          4.768
LGA    S     128      S     128          2.410
LGA    P     129      P     129          4.311
LGA    V     316      V     316           -
LGA    R     317      R     317           -
LGA    K     318      K     318           -
LGA    G     319      G     319           -
LGA    A     320      A     320           -
LGA    A     321      A     321           -
LGA    L     322      L     322           -
LGA    N     323      N     323           -
LGA    A     324      A     324           -
LGA    V     325      V     325           -
LGA    L     326      L     326           -
LGA    L     327      L     327           -
LGA    G     328      G     328           -
LGA    E     329      E     329           -
LGA    L     330      L     330           -
LGA    L     331      L     331           -
LGA    I     332      I     332           -
LGA    K     333      K     333           -
LGA    H     334      H     334           -
LGA    Y     335      Y     335           -
LGA    L     336      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    107    3.02    70.09     41.131     3.434

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.478830 * X  +  -0.234457 * Y  +   0.846021 * Z  +  -9.098997
  Y_new =   0.043303 * X  +   0.968814 * Y  +   0.243978 * Z  +  73.952354
  Z_new =  -0.876839 * X  +  -0.080188 * Y  +   0.474050 * Z  +  -1.746589 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.167569    2.974023  [ DEG:    -9.6010    170.3990 ]
  Theta =   1.069247    2.072345  [ DEG:    61.2633    118.7367 ]
  Phi   =   0.090190   -3.051402  [ DEG:     5.1675   -174.8325 ]
 
# 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: T0298TS393_5-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS393_5-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  148  148   5.0  107   3.02   70.09  41.131
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS393_5-D1
PFRMAT TS
TARGET T0298
MODEL 5
PARENT N/A
ATOM      3  CA  GLN     3     -39.258  69.234 -15.724  1.00 25.00           C
ATOM      4  CA  PRO     4     -36.276  67.181 -14.514  1.00 25.00           C
ATOM      5  CA  LEU     5     -32.780  67.866 -13.190  1.00 25.00           C
ATOM      6  CA  ASN     6     -29.196  67.104 -12.360  1.00 25.00           C
ATOM      7  CA  VAL     7     -25.962  65.575 -13.540  1.00 25.00           C
ATOM      8  CA  ALA     8     -22.287  64.590 -13.635  1.00 25.00           C
ATOM      9  CA  VAL     9     -20.754  63.999 -10.203  1.00 25.00           C
ATOM     10  CA  VAL    10     -17.375  65.022 -11.483  1.00 25.00           C
ATOM     11  CA  GLY    11     -14.522  62.465 -11.147  1.00 25.00           C
ATOM     12  CA  ALA    12     -16.122  60.072  -8.621  1.00 25.00           C
ATOM     13  CA  THR    13     -12.816  60.529  -6.707  1.00 25.00           C
ATOM     14  CA  GLY    14     -11.598  61.955  -3.430  1.00 25.00           C
ATOM     15  CA  SER    15     -13.152  63.356  -0.187  1.00 25.00           C
ATOM     16  CA  VAL    16     -14.672  65.956  -2.554  1.00 25.00           C
ATOM     17  CA  GLY    17     -16.544  63.189  -4.428  1.00 25.00           C
ATOM     18  CA  GLU    18     -17.872  61.807  -1.112  1.00 25.00           C
ATOM     19  CA  ALA    19     -19.038  65.310  -0.092  1.00 25.00           C
ATOM     20  CA  LEU    20     -20.804  65.732  -3.464  1.00 25.00           C
ATOM     21  CA  VAL    21     -22.524  62.340  -3.016  1.00 25.00           C
ATOM     22  CA  GLY    22     -23.660  63.353   0.498  1.00 25.00           C
ATOM     23  CA  LEU    23     -25.044  66.650  -0.872  1.00 25.00           C
ATOM     24  CA  LEU    24     -26.926  64.749  -3.613  1.00 25.00           C
ATOM     25  CA  ASP    25     -28.388  62.369  -0.992  1.00 25.00           C
ATOM     26  CA  GLU    26     -29.497  65.354   1.136  1.00 25.00           C
ATOM     27  CA  ARG    27     -33.226  65.558   0.262  1.00 25.00           C
ATOM     28  CA  ASP    28     -32.874  67.194  -3.092  1.00 25.00           C
ATOM     29  CA  PHE    29     -31.662  64.535  -5.594  1.00 25.00           C
ATOM     30  CA  PRO    30     -35.361  63.997  -6.291  1.00 25.00           C
ATOM     31  CA  LEU    31     -35.527  65.206  -9.894  1.00 25.00           C
ATOM     32  CA  HIS    32     -33.162  62.456 -10.835  1.00 25.00           C
ATOM     33  CA  ARG    33     -30.335  59.999 -11.384  1.00 25.00           C
ATOM     34  CA  LEU    34     -27.586  60.306  -8.734  1.00 25.00           C
ATOM     35  CA  HIS    35     -24.287  60.007 -10.639  1.00 25.00           C
ATOM     36  CA  LEU    36     -20.975  58.635 -12.076  1.00 25.00           C
ATOM     37  CA  LEU    37     -19.552  60.457 -15.107  1.00 25.00           C
ATOM     38  CA  ALA    38     -15.779  60.035 -15.368  1.00 25.00           C
ATOM     39  CA  SER    39     -13.383  57.280 -14.375  1.00 25.00           C
ATOM     40  CA  ALA    40     -11.153  54.330 -15.325  1.00 25.00           C
ATOM     41  CA  GLU    41     -11.973  53.035 -18.791  1.00 25.00           C
ATOM     42  CA  SER    42     -12.845  49.621 -17.315  1.00 25.00           C
ATOM     43  CA  ALA    43     -15.972  48.220 -19.074  1.00 25.00           C
ATOM     44  CA  GLY    44     -18.115  49.644 -21.923  1.00 25.00           C
ATOM     45  CA  GLN    45     -20.222  51.513 -19.350  1.00 25.00           C
ATOM     46  CA  ARG    46     -20.677  51.038 -15.564  1.00 25.00           C
ATOM     47  CA  MET    47     -20.752  53.267 -12.483  1.00 25.00           C
ATOM     48  CA  GLY    48     -22.521  51.769  -9.458  1.00 25.00           C
ATOM     49  CA  PHE    49     -23.932  52.160  -5.978  1.00 25.00           C
ATOM     50  CA  ALA    50     -24.754  48.929  -4.233  1.00 25.00           C
ATOM     51  CA  GLU    51     -28.326  49.716  -3.243  1.00 25.00           C
ATOM     52  CA  SER    52     -30.797  50.703  -5.913  1.00 25.00           C
ATOM     53  CA  SER    53     -28.755  51.500  -9.071  1.00 25.00           C
ATOM     54  CA  LEU    54     -27.248  52.780 -12.360  1.00 25.00           C
ATOM     55  CA  ARG    55     -25.660  53.980 -15.602  1.00 25.00           C
ATOM     56  CA  VAL    56     -23.761  57.182 -16.509  1.00 25.00           C
ATOM     57  CA  GLY    57     -22.190  56.495 -19.912  1.00 25.00           C
ATOM     58  CA  ASP    58     -20.864  60.030 -19.978  1.00 25.00           C
ATOM     59  CA  VAL    59     -23.924  62.035 -21.189  1.00 25.00           C
ATOM     60  CA  ASP    60     -24.931  62.655 -24.798  1.00 25.00           C
ATOM     61  CA  SER    61     -21.693  61.870 -26.640  1.00 25.00           C
ATOM     62  CA  PHE    62     -19.106  64.691 -26.504  1.00 25.00           C
ATOM     63  CA  ASP    63     -20.620  65.955 -23.221  1.00 25.00           C
ATOM     64  CA  PHE    64     -23.168  67.076 -20.556  1.00 25.00           C
ATOM     65  CA  SER    65     -25.614  68.575 -23.064  1.00 25.00           C
ATOM     66  CA  SER    66     -27.554  70.368 -20.351  1.00 25.00           C
ATOM     67  CA  VAL    67     -26.842  69.511 -16.728  1.00 25.00           C
ATOM     68  CA  GLY    68     -25.668  70.744 -13.340  1.00 25.00           C
ATOM     69  CA  LEU    69     -24.069  70.788  -9.913  1.00 25.00           C
ATOM     70  CA  ALA    70     -20.519  69.730 -10.820  1.00 25.00           C
ATOM     71  CA  PHE    71     -18.966  68.423  -7.636  1.00 25.00           C
ATOM     72  CA  PHE    72     -15.362  67.066  -7.736  1.00 25.00           C
ATOM     73  CA  ALA    73     -13.146  67.744 -10.736  1.00 25.00           C
ATOM     74  CA  ALA    74      -9.856  65.979  -9.829  1.00 25.00           C
ATOM     75  CA  ALA    75      -6.303  67.384 -10.261  1.00 25.00           C
ATOM     76  CA  ALA    76      -4.297  69.635 -12.526  1.00 25.00           C
ATOM     77  CA  GLU    77      -3.750  68.626 -16.181  1.00 25.00           C
ATOM     78  CA  VAL    78      -6.691  66.260 -16.830  1.00 25.00           C
ATOM     79  CA  SER    79      -8.952  68.426 -14.623  1.00 25.00           C
ATOM     80  CA  ARG    80      -7.850  71.560 -16.529  1.00 25.00           C
ATOM     81  CA  ALA    81      -8.597  69.827 -19.862  1.00 25.00           C
ATOM     82  CA  HIS    82     -12.063  68.815 -18.588  1.00 25.00           C
ATOM     83  CA  ALA    83     -12.737  72.420 -17.486  1.00 25.00           C
ATOM     84  CA  GLU    84     -11.661  73.701 -20.931  1.00 25.00           C
ATOM     85  CA  ARG    85     -13.985  71.171 -22.624  1.00 25.00           C
ATOM     86  CA  ALA    86     -16.879  72.289 -20.379  1.00 25.00           C
ATOM     87  CA  ARG    87     -16.174  75.951 -21.253  1.00 25.00           C
ATOM     88  CA  ALA    88     -16.150  75.081 -24.984  1.00 25.00           C
ATOM     89  CA  ALA    89     -19.746  74.091 -25.536  1.00 25.00           C
ATOM     90  CA  GLY    90     -21.730  75.147 -22.490  1.00 25.00           C
ATOM     91  CA  CYS    91     -20.750  75.498 -18.815  1.00 25.00           C
ATOM     92  CA  SER    92     -20.259  73.059 -15.896  1.00 25.00           C
ATOM     93  CA  VAL    93     -20.041  74.480 -12.346  1.00 25.00           C
ATOM     94  CA  ILE    94     -16.682  72.832 -11.639  1.00 25.00           C
ATOM     95  CA  ASP    95     -13.571  73.050  -9.433  1.00 25.00           C
ATOM     96  CA  LEU    96     -12.130  70.903  -6.567  1.00 25.00           C
ATOM     97  CA  SER    97      -8.917  71.788  -8.435  1.00 25.00           C
ATOM     98  CA  GLY    98      -8.395  75.296  -9.861  1.00 25.00           C
ATOM     99  CA  ALA    99     -10.498  77.523 -12.116  1.00 25.00           C
ATOM    100  CA  LEU   100     -13.104  79.925 -10.736  1.00 25.00           C
ATOM    101  CA  GLU   101     -10.511  82.535  -9.900  1.00 25.00           C
ATOM    102  CA  PRO   102     -12.224  85.364 -11.687  1.00 25.00           C
ATOM    103  CA  SER   103     -11.526  84.153 -15.276  1.00 25.00           C
ATOM    104  CA  VAL   104     -14.910  85.289 -16.461  1.00 25.00           C
ATOM    105  CA  ALA   105     -18.365  84.451 -15.117  1.00 25.00           C
ATOM    106  CA  PRO   106     -17.475  81.920 -12.399  1.00 25.00           C
ATOM    107  CA  PRO   107     -17.726  82.384  -8.701  1.00 25.00           C
ATOM    108  CA  VAL   108     -20.119  81.523  -5.906  1.00 25.00           C
ATOM    109  CA  MET   109     -17.893  79.505  -3.609  1.00 25.00           C
ATOM    110  CA  VAL   110     -17.617  78.294   0.019  1.00 25.00           C
ATOM    111  CA  SER   111     -19.634  79.804   2.854  1.00 25.00           C
ATOM    112  CA  VAL   112     -18.196  83.174   1.832  1.00 25.00           C
ATOM    113  CA  ASN   113     -21.102  85.514   1.462  1.00 25.00           C
ATOM    114  CA  ALA   114     -23.582  82.701   1.677  1.00 25.00           C
ATOM    115  CA  GLU   115     -26.320  85.153   0.603  1.00 25.00           C
ATOM    116  CA  ARG   116     -24.374  85.964  -2.595  1.00 25.00           C
ATOM    117  CA  LEU   117     -23.991  82.225  -3.337  1.00 25.00           C
ATOM    118  CA  ALA   118     -27.749  81.711  -2.809  1.00 25.00           C
ATOM    119  CA  SER   119     -28.506  84.623  -5.178  1.00 25.00           C
ATOM    120  CA  GLN   120     -25.626  85.028  -7.627  1.00 25.00           C
ATOM    121  CA  ALA   121     -27.271  86.131 -10.871  1.00 25.00           C
ATOM    122  CA  ALA   122     -23.705  86.269 -12.216  1.00 25.00           C
ATOM    123  CA  PRO   123     -23.640  82.536 -11.883  1.00 25.00           C
ATOM    124  CA  PHE   124     -22.601  79.141 -10.546  1.00 25.00           C
ATOM    125  CA  LEU   125     -22.636  76.410  -7.844  1.00 25.00           C
ATOM    126  CA  LEU   126     -18.975  75.377  -7.271  1.00 25.00           C
ATOM    127  CA  SER   127     -16.889  73.141  -5.012  1.00 25.00           C
ATOM    128  CA  SER   128     -13.913  75.394  -4.296  1.00 25.00           C
ATOM    129  CA  PRO   129     -10.680  77.166  -5.104  1.00 25.00           C
ATOM    316  CA  VAL   316       2.742  70.242   5.644  1.00 25.00           C
ATOM    317  CA  ARG   317       0.467  72.837   3.982  1.00 25.00           C
ATOM    318  CA  LYS   318       0.498  74.946   7.178  1.00 25.00           C
ATOM    319  CA  GLY   319       4.320  74.748   7.302  1.00 25.00           C
ATOM    320  CA  ALA   320       4.520  75.836   3.635  1.00 25.00           C
ATOM    321  CA  ALA   321       2.185  78.784   4.357  1.00 25.00           C
ATOM    322  CA  LEU   322       4.355  79.801   7.345  1.00 25.00           C
ATOM    323  CA  ASN   323       7.493  79.627   5.158  1.00 25.00           C
ATOM    324  CA  ALA   324       5.793  81.799   2.502  1.00 25.00           C
ATOM    325  CA  VAL   325       4.802  84.347   5.184  1.00 25.00           C
ATOM    326  CA  LEU   326       8.404  84.418   6.481  1.00 25.00           C
ATOM    327  CA  LEU   327       9.701  84.974   2.921  1.00 25.00           C
ATOM    328  CA  GLY   328       7.206  87.838   2.433  1.00 25.00           C
ATOM    329  CA  GLU   329       8.333  89.417   5.736  1.00 25.00           C
ATOM    330  CA  LEU   330      11.996  89.132   4.649  1.00 25.00           C
ATOM    331  CA  LEU   331      11.154  90.782   1.297  1.00 25.00           C
ATOM    332  CA  ILE   332       9.343  93.621   3.120  1.00 25.00           C
ATOM    333  CA  LYS   333      12.371  94.115   5.412  1.00 25.00           C
ATOM    334  CA  HIS   334      14.689  94.233   2.365  1.00 25.00           C
ATOM    335  CA  TYR   335      14.659  97.380   0.197  1.00 25.00           C
ATOM    336  CA  LEU   336      12.183  99.558   2.004  1.00 25.00           C
TER
END
