
#######################################################
#                                                     #
#                        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   75 (   75),  selected   75 , name T0330TS168_4-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330TS168_4-D2.T0330_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      -       -           -
LGA    E      18      -       -           -
LGA    S      19      V      17           #
LGA    M      20      E      18           #
LGA    N      21      S      19          4.894
LGA    R      22      M      20          4.250
LGA    R      23      N      21          4.734
LGA    V      24      R      22          2.320
LGA    L      25      R      23          1.201
LGA    A      26      V      24          3.904
LGA    D      27      L      25          2.192
LGA    A      28      A      26          4.104
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      I      30           -
LGA    -       -      E      31           -
LGA    -       -      V      32           -
LGA    -       -      Y      33           -
LGA    -       -      G      34           -
LGA    L      29      T      35           #
LGA    I      30      E      36          1.367
LGA    E      31      G      37          3.244
LGA    V      32      S      38          2.179
LGA    Y      33      T      39          2.958
LGA    G      34      -       -           -
LGA    T      35      -       -           -
LGA    E      36      -       -           -
LGA    G      37      D      43          4.583
LGA    S      38      F      44           #
LGA    T      39      S      45           #
LGA    G      40      -       -           -
LGA    S      41      -       -           -
LGA    H      42      -       -           -
LGA    D      43      G      46           #
LGA    F      44      -       -           -
LGA    S      45      -       -           -
LGA    G      46      -       -           -
LGA    K      47      -       -           -
LGA    M      48      K      47           #
LGA    -       -      M      48           -
LGA    D      49      D      49          1.418
LGA    G      50      G      50          1.730
LGA    A      51      A      51          1.347
LGA    I      52      I      52          0.740
LGA    I      53      I      53          0.670
LGA    Y      54      Y      54          1.261
LGA    E      55      E      55          1.858
LGA    V      56      V      56          1.908
LGA    L      57      L      57          2.120
LGA    S      58      S      58          2.334
LGA    N      59      N      59          2.525
LGA    V      60      V      60          2.913
LGA    G      61      G      61          2.852
LGA    L      62      L      62          1.734
LGA    E      63      E      63           #
LGA    R      64      R      64           -
LGA    -       -      A      65           -
LGA    A      65      E      66          1.922
LGA    -       -      I      67           -
LGA    E      66      A      68          3.860
LGA    I      67      D      69          4.739
LGA    A      68      K      70          4.170
LGA    D      69      F      71          0.996
LGA    K      70      D      72          3.633
LGA    F      71      K      73          4.710
LGA    D      72      A      74          2.867
LGA    K      73      K      75          0.624
LGA    A      74      E      76          2.942
LGA    K      75      T      77          4.165
LGA    E      76      Y      78          3.343
LGA    T      77      I      79          1.177
LGA    Y      78      A      80          2.858
LGA    I      79      L      81           #
LGA    A      80      F      82          4.841
LGA    L      81      R      83          1.220
LGA    -       -      E      84           -
LGA    F      82      R      85          4.431
LGA    R      83      A      86          5.118
LGA    E      84      -       -           -
LGA    R      85      -       -           -
LGA    A      86      R      87          3.167
LGA    R      87      -       -           -
LGA    R      88      -       -           -
LGA    E      89      -       -           -
LGA    D      90      R      88          3.246
LGA    I      91      E      89          3.066
LGA    -       -      D      90           -
LGA    -       -      I      91           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   72    5.0     48    3.09    33.33     42.398     1.505

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.233672 * X  +  -0.535862 * Y  +  -0.811326 * Z  +   5.698067
  Y_new =  -0.962727 * X  +  -0.010614 * Y  +  -0.270268 * Z  +  29.432989
  Z_new =   0.136215 * X  +   0.844239 * Y  +  -0.518369 * Z  +  -3.610094 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.121452   -1.020141  [ DEG:   121.5502    -58.4498 ]
  Theta =  -0.136640   -3.004953  [ DEG:    -7.8289   -172.1711 ]
  Phi   =  -1.332682    1.808911  [ DEG:   -76.3570    103.6430 ]
 
# 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: T0330TS168_4-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS168_4-D2.T0330_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   75   72   5.0   48   3.09   33.33  42.398
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS168_4-D2
PFRMAT TS
TARGET T0330
MODEL 4
PARENT N/A
ATOM     17  CA  VAL    17       5.140  32.733   1.936  1.00 25.00           C
ATOM     18  CA  GLU    18       8.105  33.127   4.326  1.00 25.00           C
ATOM     19  CA  SER    19       8.781  36.617   2.900  1.00 25.00           C
ATOM     20  CA  MET    20      11.795  37.012   5.231  1.00 25.00           C
ATOM     21  CA  ASN    21      13.132  33.599   4.120  1.00 25.00           C
ATOM     22  CA  ARG    22      12.714  34.603   0.448  1.00 25.00           C
ATOM     23  CA  ARG    23      14.583  37.880   1.105  1.00 25.00           C
ATOM     24  CA  VAL    24      17.413  35.952   2.821  1.00 25.00           C
ATOM     25  CA  LEU    25      17.622  33.558  -0.161  1.00 25.00           C
ATOM     26  CA  ALA    26      17.780  36.532  -2.568  1.00 25.00           C
ATOM     27  CA  ASP    27      20.576  38.107  -0.478  1.00 25.00           C
ATOM     28  CA  ALA    28      22.507  34.799  -0.524  1.00 25.00           C
ATOM     29  CA  LEU    29      22.101  34.587  -4.326  1.00 25.00           C
ATOM     30  CA  ILE    30      23.371  38.182  -4.688  1.00 25.00           C
ATOM     31  CA  GLU    31      26.397  37.360  -2.487  1.00 25.00           C
ATOM     32  CA  VAL    32      27.136  34.264  -4.618  1.00 25.00           C
ATOM     33  CA  TYR    33      26.950  31.946  -1.614  1.00 25.00           C
ATOM     34  CA  GLY    34      29.115  29.106  -0.200  1.00 25.00           C
ATOM     35  CA  THR    35      26.944  27.569   2.537  1.00 25.00           C
ATOM     36  CA  GLU    36      29.102  29.397   5.076  1.00 25.00           C
ATOM     37  CA  GLY    37      26.505  32.103   5.278  1.00 25.00           C
ATOM     38  CA  SER    38      24.394  29.405   6.847  1.00 25.00           C
ATOM     39  CA  THR    39      23.780  31.721   9.804  1.00 25.00           C
ATOM     40  CA  GLY    40      23.217  28.413  11.649  1.00 25.00           C
ATOM     41  CA  SER    41      19.580  29.390  12.343  1.00 25.00           C
ATOM     42  CA  HIS    42      18.272  32.932  12.827  1.00 25.00           C
ATOM     43  CA  ASP    43      20.720  35.459  14.141  1.00 25.00           C
ATOM     44  CA  PHE    44      20.796  36.656  10.487  1.00 25.00           C
ATOM     45  CA  SER    45      17.283  37.902   9.602  1.00 25.00           C
ATOM     46  CA  GLY    46      18.355  41.487  10.496  1.00 25.00           C
ATOM     47  CA  LYS    47      19.778  44.932  11.096  1.00 25.00           C
ATOM     48  CA  MET    48      23.157  45.375   9.287  1.00 25.00           C
ATOM     49  CA  ASP    49      24.004  43.733   5.924  1.00 25.00           C
ATOM     50  CA  GLY    50      24.879  46.659   3.612  1.00 25.00           C
ATOM     51  CA  ALA    51      28.572  46.348   4.576  1.00 25.00           C
ATOM     52  CA  ILE    52      28.469  42.588   3.854  1.00 25.00           C
ATOM     53  CA  ILE    53      26.866  43.262   0.442  1.00 25.00           C
ATOM     54  CA  TYR    54      29.580  45.844  -0.351  1.00 25.00           C
ATOM     55  CA  GLU    55      32.296  43.330   0.638  1.00 25.00           C
ATOM     56  CA  VAL    56      30.693  40.678  -1.613  1.00 25.00           C
ATOM     57  CA  LEU    57      30.589  43.170  -4.519  1.00 25.00           C
ATOM     58  CA  SER    58      34.282  44.013  -3.958  1.00 25.00           C
ATOM     59  CA  ASN    59      35.158  40.286  -3.947  1.00 25.00           C
ATOM     60  CA  VAL    60      33.718  40.302  -7.406  1.00 25.00           C
ATOM     61  CA  GLY    61      35.266  43.259  -9.318  1.00 25.00           C
ATOM     62  CA  LEU    62      32.075  45.303  -9.006  1.00 25.00           C
ATOM     63  CA  GLU    63      30.670  46.138 -12.442  1.00 25.00           C
ATOM     64  CA  ARG    64      28.323  48.990 -11.813  1.00 25.00           C
ATOM     65  CA  ALA    65      29.190  49.857  -8.185  1.00 25.00           C
ATOM     66  CA  GLU    66      26.223  52.273  -8.027  1.00 25.00           C
ATOM     67  CA  ILE    67      23.908  49.560  -9.423  1.00 25.00           C
ATOM     68  CA  ALA    68      25.200  47.078  -6.807  1.00 25.00           C
ATOM     69  CA  ASP    69      24.588  49.646  -4.032  1.00 25.00           C
ATOM     70  CA  LYS    70      21.029  50.228  -5.323  1.00 25.00           C
ATOM     71  CA  PHE    71      20.398  46.451  -5.361  1.00 25.00           C
ATOM     72  CA  ASP    72      21.697  46.172  -1.769  1.00 25.00           C
ATOM     73  CA  LYS    73      19.398  49.039  -0.690  1.00 25.00           C
ATOM     74  CA  ALA    74      16.418  47.314  -2.368  1.00 25.00           C
ATOM     75  CA  LYS    75      17.274  44.040  -0.576  1.00 25.00           C
ATOM     76  CA  GLU    76      17.477  45.894   2.768  1.00 25.00           C
ATOM     77  CA  THR    77      14.072  47.517   2.103  1.00 25.00           C
ATOM     78  CA  TYR    78      12.573  44.092   1.278  1.00 25.00           C
ATOM     79  CA  ILE    79      14.019  42.650   4.518  1.00 25.00           C
ATOM     80  CA  ALA    80      12.538  45.569   6.506  1.00 25.00           C
ATOM     81  CA  LEU    81       9.127  44.988   4.864  1.00 25.00           C
ATOM     82  CA  PHE    82       9.314  41.264   5.735  1.00 25.00           C
ATOM     83  CA  ARG    83      10.181  42.131   9.362  1.00 25.00           C
ATOM     84  CA  GLU    84       7.214  44.547   9.521  1.00 25.00           C
ATOM     85  CA  ARG    85       4.898  41.834   8.126  1.00 25.00           C
ATOM     86  CA  ALA    86       6.191  39.352  10.740  1.00 25.00           C
ATOM     87  CA  ARG    87       5.578  41.919  13.516  1.00 25.00           C
ATOM     88  CA  ARG    88       6.191  38.952  15.785  1.00 25.00           C
ATOM     89  CA  GLU    89       5.290  35.406  14.648  1.00 25.00           C
ATOM     90  CA  ASP    90       7.880  34.125  12.148  1.00 25.00           C
ATOM     91  CA  ILE    91       6.223  32.576   9.023  1.00 25.00           C
TER
END
