
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0363TS125_3u-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS125_3u-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    Q      12      Q      12          1.174
LGA    I      13      I      13          1.785
LGA    N      14      N      14          0.717
LGA    I      15      I      15          0.641
LGA    E      16      E      16          2.208
LGA    I      17      I      17          2.269
LGA    A      18      A      18          2.651
LGA    Y      19      Y      19          2.482
LGA    A      20      A      20          3.047
LGA    F      21      F      21          1.841
LGA    P      22      P      22           #
LGA    -       -      E      23           -
LGA    E      23      R      24          4.153
LGA    R      24      Y      25          4.767
LGA    Y      25      -       -           -
LGA    Y      26      Y      26          3.630
LGA    L      27      L      27          1.770
LGA    K      28      K      28          1.352
LGA    S      29      S      29          0.660
LGA    F      30      F      30          1.307
LGA    Q      31      Q      31          1.370
LGA    V      32      V      32          1.379
LGA    D      33      D      33          1.397
LGA    E      34      E      34          2.320
LGA    G      35      G      35          0.773
LGA    I      36      I      36          0.493
LGA    T      37      T      37          0.551
LGA    V      38      V      38          0.582
LGA    Q      39      Q      39          0.938
LGA    T      40      T      40          0.809
LGA    A      41      A      41          1.120
LGA    I      42      I      42          1.255
LGA    T      43      T      43          0.708
LGA    Q      44      Q      44          2.016
LGA    I      47      S      45          2.797
LGA    L      48      G      46          2.819
LGA    S      49      -       -           -
LGA    Q      50      I      47          5.316
LGA    F      51      L      48          5.842
LGA    P      52      S      49          1.692
LGA    E      53      Q      50          2.147
LGA    I      54      F      51          2.981
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    D      55      D      55           #
LGA    L      56      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     38    2.39    76.32     60.736     1.524

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.487482 * X  +  -0.847359 * Y  +  -0.210582 * Z  +  26.928467
  Y_new =   0.817158 * X  +   0.357797 * Y  +   0.451923 * Z  +  15.681185
  Z_new =  -0.307595 * X  +  -0.392383 * Y  +   0.866845 * Z  +   7.489945 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.425060    2.716532  [ DEG:   -24.3542    155.6458 ]
  Theta =   0.312664    2.828928  [ DEG:    17.9144    162.0856 ]
  Phi   =   1.032912   -2.108681  [ DEG:    59.1815   -120.8185 ]
 
# 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: T0363TS125_3u-D1                              
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS125_3u-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   38   2.39   76.32  60.736
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS125_3u-D1
PFRMAT   TS
TARGET   T0363
MODEL    3  UNREFINED
PARENT   1vjka   
ATOM      1  N   GLN    12      17.724   1.189   9.048    1.00  0.50
ATOM      2  CA  GLN    12      18.443   2.327   8.372    1.00  0.50
ATOM      3  C   GLN    12      17.939   3.708   8.825    1.00  0.50
ATOM      4  O   GLN    12      16.759   3.881   9.179    1.00  0.50
ATOM      7  N   ILE    13      18.850   4.681   8.821    1.00  0.50
ATOM      8  CA  ILE    13      18.544   6.079   9.136    1.00  0.50
ATOM      9  C   ILE    13      18.911   6.889   7.879    1.00  0.50
ATOM     10  O   ILE    13      20.072   6.867   7.462    1.00  0.50
ATOM     14  N   ASN    14      17.940   7.569   7.271    1.00  0.50
ATOM     15  CA  ASN    14      18.211   8.350   6.073    1.00  0.50
ATOM     16  C   ASN    14      18.227   9.819   6.421    1.00  0.50
ATOM     17  O   ASN    14      17.214  10.359   6.920    1.00  0.50
ATOM     23  N   ILE    15      19.359  10.469   6.186    1.00  0.50
ATOM     24  CA  ILE    15      19.500  11.889   6.489    1.00  0.50
ATOM     25  C   ILE    15      19.651  12.673   5.201    1.00  0.50
ATOM     26  O   ILE    15      20.148  12.149   4.176    1.00  0.50
ATOM     30  N   GLU    16      19.229  13.920   5.218    1.00  0.50
ATOM     31  CA  GLU    16      19.363  14.812   4.095    1.00  0.50
ATOM     32  C   GLU    16      20.543  15.701   4.376    1.00  0.50
ATOM     33  O   GLU    16      20.517  16.478   5.341    1.00  0.50
ATOM     39  N   ILE    17      21.575  15.613   3.559    1.00  0.50
ATOM     40  CA  ILE    17      22.763  16.438   3.703    1.00  0.50
ATOM     41  C   ILE    17      22.694  17.617   2.765    1.00  0.50
ATOM     42  O   ILE    17      22.467  17.421   1.570    1.00  0.50
ATOM     46  N   ALA    18      22.854  18.834   3.302    1.00  0.50
ATOM     47  CA  ALA    18      22.848  20.051   2.485    1.00  0.50
ATOM     48  C   ALA    18      24.239  20.641   2.529    1.00  0.50
ATOM     49  O   ALA    18      24.756  20.972   3.611    1.00  0.50
ATOM     54  N   TYR    19      24.854  20.771   1.365    1.00  0.50
ATOM     55  CA  TYR    19      26.180  21.383   1.247    1.00  0.50
ATOM     56  C   TYR    19      26.054  22.842   0.922    1.00  0.50
ATOM     57  O   TYR    19      25.144  23.257   0.183    1.00  0.50
ATOM     77  N   ALA    20      28.211  26.645  -0.097    1.00  0.50
ATOM     78  CA  ALA    20      29.381  27.362  -0.598    1.00  0.50
ATOM     79  C   ALA    20      30.323  26.400  -1.339    1.00  0.50
ATOM     80  O   ALA    20      29.854  25.633  -2.190    1.00  0.50
ATOM     82  N   PHE    21      31.628  26.421  -1.042    1.00  0.50
ATOM     83  CA  PHE    21      32.540  25.630  -1.893    1.00  0.50
ATOM     84  C   PHE    21      32.321  24.141  -1.755    1.00  0.50
ATOM     85  O   PHE    21      32.716  23.374  -2.629    1.00  0.50
ATOM     93  N   PRO    22      31.659  23.717  -0.679    1.00  0.50
ATOM     94  CA  PRO    22      31.417  22.279  -0.467    1.00  0.50
ATOM     95  C   PRO    22      30.394  21.721  -1.427    1.00  0.50
ATOM     96  O   PRO    22      30.351  20.507  -1.630    1.00  0.50
ATOM    104  N   GLU    23      29.614  22.597  -2.057    1.00  0.50
ATOM    105  CA  GLU    23      28.748  22.177  -3.163    1.00  0.50
ATOM    106  C   GLU    23      29.584  21.690  -4.334    1.00  0.50
ATOM    107  O   GLU    23      29.171  20.751  -5.030    1.00  0.50
ATOM    115  N   ARG    24      30.732  22.332  -4.598    1.00  0.50
ATOM    116  CA  ARG    24      31.608  21.850  -5.647    1.00  0.50
ATOM    117  C   ARG    24      32.338  20.613  -5.270    1.00  0.50
ATOM    118  O   ARG    24      32.514  19.748  -6.113    1.00  0.50
ATOM    124  N   TYR    25      32.782  20.507  -4.013    1.00  0.50
ATOM    125  CA  TYR    25      33.470  19.284  -3.597    1.00  0.50
ATOM    126  C   TYR    25      32.552  18.067  -3.635    1.00  0.50
ATOM    127  O   TYR    25      32.985  16.974  -3.999    1.00  0.50
ATOM    132  N   TYR    26      31.293  18.240  -3.217    1.00  0.50
ATOM    133  CA  TYR    26      30.345  17.134  -3.243    1.00  0.50
ATOM    134  C   TYR    26      29.799  16.869  -4.640    1.00  0.50
ATOM    135  O   TYR    26      29.309  15.766  -4.921    1.00  0.50
ATOM    156  N   LEU    27      22.773  18.924  -2.452    1.00  0.50
ATOM    157  CA  LEU    27      22.214  18.129  -1.369    1.00  0.50
ATOM    158  C   LEU    27      22.200  16.684  -1.777    1.00  0.50
ATOM    159  O   LEU    27      22.229  16.358  -2.969    1.00  0.50
ATOM    165  N   LYS    28      22.151  15.802  -0.787    1.00  0.50
ATOM    166  CA  LYS    28      22.100  14.377  -1.039    1.00  0.50
ATOM    167  C   LYS    28      21.538  13.650   0.150    1.00  0.50
ATOM    168  O   LYS    28      21.756  14.062   1.296    1.00  0.50
ATOM    174  N   SER    29      20.797  12.593  -0.111    1.00  0.50
ATOM    175  CA  SER    29      20.289  11.722   0.920    1.00  0.50
ATOM    176  C   SER    29      21.290  10.646   1.209    1.00  0.50
ATOM    177  O   SER    29      21.759   9.957   0.277    1.00  0.50
ATOM    183  N   PHE    30      21.602  10.438   2.476    1.00  0.50
ATOM    184  CA  PHE    30      22.556   9.428   2.862    1.00  0.50
ATOM    185  C   PHE    30      21.916   8.453   3.838    1.00  0.50
ATOM    186  O   PHE    30      21.488   8.830   4.947    1.00  0.50
ATOM    191  N   GLN    31      21.820   7.203   3.418    1.00  0.50
ATOM    192  CA  GLN    31      21.312   6.126   4.258    1.00  0.50
ATOM    193  C   GLN    31      22.457   5.585   5.114    1.00  0.50
ATOM    194  O   GLN    31      23.531   5.259   4.601    1.00  0.50
ATOM    200  N   VAL    32      22.218   5.515   6.421    1.00  0.50
ATOM    201  CA  VAL    32      23.213   5.107   7.389    1.00  0.50
ATOM    202  C   VAL    32      22.665   3.954   8.208    1.00  0.50
ATOM    203  O   VAL    32      21.457   3.837   8.357    1.00  0.50
ATOM    208  N   ASP    33      23.531   3.084   8.739    1.00  0.50
ATOM    209  CA  ASP    33      23.065   1.986   9.582    1.00  0.50
ATOM    210  C   ASP    33      22.469   2.479  10.891    1.00  0.50
ATOM    211  O   ASP    33      22.795   3.568  11.377    1.00  0.50
ATOM    215  N   GLU    34      21.590   1.659  11.449    1.00  0.50
ATOM    216  CA  GLU    34      21.046   1.867  12.773    1.00  0.50
ATOM    217  C   GLU    34      22.150   2.281  13.753    1.00  0.50
ATOM    218  O   GLU    34      23.230   1.698  13.759    1.00  0.50
ATOM    224  N   GLY    35      21.860   3.304  14.555    1.00  0.50
ATOM    225  CA  GLY    35      22.782   3.764  15.586    1.00  0.50
ATOM    226  C   GLY    35      23.794   4.781  15.090    1.00  0.50
ATOM    227  O   GLY    35      24.670   5.227  15.850    1.00  0.50
ATOM    228  N   ILE    36      23.694   5.162  13.824    1.00  0.50
ATOM    229  CA  ILE    36      24.663   6.089  13.268    1.00  0.50
ATOM    230  C   ILE    36      24.728   7.376  14.033    1.00  0.50
ATOM    231  O   ILE    36      23.703   7.928  14.466    1.00  0.50
ATOM    233  N   THR    37      25.959   7.868  14.157    1.00  0.50
ATOM    234  CA  THR    37      26.254   9.122  14.824    1.00  0.50
ATOM    235  C   THR    37      26.779  10.149  13.825    1.00  0.50
ATOM    236  O   THR    37      27.184   9.813  12.701    1.00  0.50
ATOM    244  N   VAL    38      26.830  11.414  14.228    1.00  0.50
ATOM    245  CA  VAL    38      27.410  12.458  13.383    1.00  0.50
ATOM    246  C   VAL    38      28.796  12.058  12.839    1.00  0.50
ATOM    247  O   VAL    38      29.082  12.224  11.632    1.00  0.50
ATOM    251  N   GLN    39      29.659  11.493  13.696    1.00  0.50
ATOM    252  CA  GLN    39      30.986  11.108  13.211    1.00  0.50
ATOM    253  C   GLN    39      30.920  10.060  12.069    1.00  0.50
ATOM    254  O   GLN    39      31.775  10.063  11.168    1.00  0.50
ATOM    262  N   THR    40      29.917   9.175  12.114    1.00  0.50
ATOM    263  CA  THR    40      29.772   8.150  11.056    1.00  0.50
ATOM    264  C   THR    40      29.342   8.800   9.776    1.00  0.50
ATOM    265  O   THR    40      29.806   8.407   8.698    1.00  0.50
ATOM    270  N   ALA    41      28.479   9.798   9.872    1.00  0.50
ATOM    271  CA  ALA    41      28.069  10.540   8.680    1.00  0.50
ATOM    272  C   ALA    41      29.252  11.281   8.045    1.00  0.50
ATOM    273  O   ALA    41      29.416  11.237   6.812    1.00  0.50
ATOM    278  N   ILE    42      30.096  11.904   8.866    1.00  0.50
ATOM    279  CA  ILE    42      31.278  12.579   8.345    1.00  0.50
ATOM    280  C   ILE    42      32.167  11.583   7.605    1.00  0.50
ATOM    281  O   ILE    42      32.664  11.876   6.487    1.00  0.50
ATOM    286  N   THR    43      32.379  10.389   8.186    1.00  0.50
ATOM    287  CA  THR    43      33.168   9.382   7.465    1.00  0.50
ATOM    288  C   THR    43      32.554   8.952   6.154    1.00  0.50
ATOM    289  O   THR    43      33.293   8.702   5.176    1.00  0.50
ATOM    295  N   GLN    44      31.234   8.865   6.102    1.00  0.50
ATOM    296  CA  GLN    44      30.569   8.486   4.869    1.00  0.50
ATOM    297  C   GLN    44      30.677   9.592   3.819    1.00  0.50
ATOM    298  O   GLN    44      30.852   9.280   2.636    1.00  0.50
ATOM    304  N   ILE    47      30.597  10.874   4.224    1.00  0.50
ATOM    305  CA  ILE    47      30.786  11.973   3.267    1.00  0.50
ATOM    306  C   ILE    47      32.175  11.875   2.633    1.00  0.50
ATOM    307  O   ILE    47      32.311  11.988   1.396    1.00  0.50
ATOM    312  N   LEU    48      33.178  11.618   3.467    1.00  0.50
ATOM    313  CA  LEU    48      34.557  11.465   2.987    1.00  0.50
ATOM    314  C   LEU    48      34.723  10.255   2.056    1.00  0.50
ATOM    315  O   LEU    48      35.515  10.315   1.087    1.00  0.50
ATOM    321  N   SER    49      33.989   9.180   2.329    1.00  0.50
ATOM    322  CA  SER    49      34.040   7.990   1.496    1.00  0.50
ATOM    323  C   SER    49      33.399   8.245   0.135    1.00  0.50
ATOM    324  O   SER    49      33.890   7.749  -0.890    1.00  0.50
ATOM    330  N   GLN    50      32.297   8.990   0.102    1.00  0.50
ATOM    331  CA  GLN    50      31.612   9.262  -1.150    1.00  0.50
ATOM    332  C   GLN    50      32.333  10.304  -1.991    1.00  0.50
ATOM    333  O   GLN    50      32.250  10.304  -3.218    1.00  0.50
ATOM    341  N   PHE    51      32.969  11.244  -1.308    1.00  0.50
ATOM    342  CA  PHE    51      33.540  12.417  -1.958    1.00  0.50
ATOM    343  C   PHE    51      34.934  12.634  -1.430    1.00  0.50
ATOM    344  O   PHE    51      35.136  13.365  -0.428    1.00  0.50
ATOM    351  N   PRO    52      35.906  12.028  -2.111    1.00  0.50
ATOM    352  CA  PRO    52      37.272  11.961  -1.587    1.00  0.50
ATOM    353  C   PRO    52      37.912  13.319  -1.339    1.00  0.50
ATOM    354  O   PRO    52      38.823  13.413  -0.521    1.00  0.50
ATOM    360  N   GLU    53      37.436  14.363  -2.013    1.00  0.50
ATOM    361  CA  GLU    53      38.011  15.709  -1.788    1.00  0.50
ATOM    362  C   GLU    53      37.761  16.202  -0.363    1.00  0.50
ATOM    363  O   GLU    53      38.463  17.107   0.112    1.00  0.50
ATOM    369  N   ILE    54      36.793  15.604   0.350    1.00  0.50
ATOM    370  CA  ILE    54      36.563  15.970   1.748    1.00  0.50
ATOM    371  C   ILE    54      37.554  15.338   2.724    1.00  0.50
ATOM    372  O   ILE    54      37.602  15.726   3.899    1.00  0.50
ATOM    461  N   ASP    55      35.726  27.848  14.411    1.00  0.50
ATOM    462  CA  ASP    55      36.123  28.751  13.323    1.00  0.50
ATOM    463  C   ASP    55      37.441  28.346  12.671    1.00  0.50
ATOM    464  O   ASP    55      37.750  28.792  11.558    1.00  0.50
ATOM    466  N   LEU    56      38.207  27.484  13.339    1.00  0.50
ATOM    467  CA  LEU    56      39.524  27.082  12.818    1.00  0.50
ATOM    468  C   LEU    56      39.456  25.878  11.867    1.00  0.50
ATOM    469  O   LEU    56      40.413  25.593  11.144    1.00  0.50
TER
END
