
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0347AL381_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL381_2-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    H      51      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    I      52      K      16           #
LGA    V      53      L      17          4.302
LGA    P      54      R      18          1.972
LGA    V      55      P      19          0.888
LGA    V      56      T      20          3.474
LGA    A      57      Q      21          3.424
LGA    -       -      I      22           -
LGA    G      58      A      23          1.337
LGA    I      66      V      24          1.533
LGA    D      67      G      25          1.264
LGA    H      68      F      26          2.911
LGA    H      69      R      27          2.606
LGA    H      70      E      28          0.370
LGA    L      71      V      29          2.178
LGA    V      72      E      30          2.678
LGA    L      73      L      31          1.230
LGA    A      74      K      32          1.590
LGA    L      75      R      33          2.888
LGA    S      76      K      34          1.576
LGA    K      77      -       -           -
LGA    E      78      E      35          2.158
LGA    G      79      W      36          1.291
LGA    V      80      R      37           #
LGA    E      81      H      51          4.309
LGA    H      82      I      52          4.139
LGA    V      83      V      53          2.981
LGA    L      84      P      54          3.498
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    T      85      L      65          2.560
LGA    S      86      I      66          1.287
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    E      87      M     103           #
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   30   89    5.0     25    2.58    12.00     21.353     0.933

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.950960 * X  +   0.229218 * Y  +   0.207690 * Z  + -60.139763
  Y_new =   0.306489 * X  +  -0.788835 * Y  +  -0.532733 * Z  + 131.753555
  Z_new =   0.041721 * X  +   0.570262 * Y  +  -0.820403 * Z  +  29.418310 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.534163   -0.607430  [ DEG:   145.1968    -34.8032 ]
  Theta =  -0.041733   -3.099859  [ DEG:    -2.3911   -177.6089 ]
  Phi   =   0.311783   -2.829810  [ DEG:    17.8638   -162.1362 ]
 
# 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: T0347AL381_2-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_2-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30   89   5.0   25   2.58   12.00  21.353
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_2-D1
REMARK Aligment from pdb entry: 1c30B
ATOM     33  N   HIS    51      -7.585  33.568  -2.948  1.00  0.00              
ATOM     34  CA  HIS    51      -7.136  33.093  -4.240  1.00  0.00              
ATOM     35  C   HIS    51      -5.737  32.569  -4.198  1.00  0.00              
ATOM     36  O   HIS    51      -5.176  32.206  -5.230  1.00  0.00              
ATOM     37  N   ILE    52      -5.209  32.595  -2.972  1.00  0.00              
ATOM     38  CA  ILE    52      -3.868  32.171  -2.665  1.00  0.00              
ATOM     39  C   ILE    52      -2.813  32.916  -3.449  1.00  0.00              
ATOM     40  O   ILE    52      -1.889  32.297  -3.990  1.00  0.00              
ATOM     41  N   VAL    53      -2.968  34.242  -3.497  1.00  0.00              
ATOM     42  CA  VAL    53      -2.028  35.057  -4.230  1.00  0.00              
ATOM     43  C   VAL    53      -0.971  35.702  -3.343  1.00  0.00              
ATOM     44  O   VAL    53      -1.310  36.340  -2.352  1.00  0.00              
ATOM     45  N   PRO    54       0.300  35.567  -3.720  1.00  0.00              
ATOM     46  CA  PRO    54       1.399  36.201  -2.993  1.00  0.00              
ATOM     47  C   PRO    54       1.401  37.657  -3.435  1.00  0.00              
ATOM     48  O   PRO    54       1.486  37.910  -4.635  1.00  0.00              
ATOM     49  N   VAL    55       1.234  38.607  -2.503  1.00  0.00              
ATOM     50  CA  VAL    55       1.221  40.015  -2.875  1.00  0.00              
ATOM     51  C   VAL    55       2.090  40.845  -1.941  1.00  0.00              
ATOM     52  O   VAL    55       2.285  40.545  -0.763  1.00  0.00              
ATOM     53  N   VAL    56       2.599  41.936  -2.469  1.00  0.00              
ATOM     54  CA  VAL    56       3.427  42.788  -1.663  1.00  0.00              
ATOM     55  C   VAL    56       2.960  44.228  -1.814  1.00  0.00              
ATOM     56  O   VAL    56       2.552  44.673  -2.891  1.00  0.00              
ATOM     57  N   ALA    57       2.990  44.967  -0.723  1.00  0.00              
ATOM     58  CA  ALA    57       2.600  46.369  -0.776  1.00  0.00              
ATOM     59  C   ALA    57       3.709  47.174  -0.153  1.00  0.00              
ATOM     60  O   ALA    57       4.639  46.588   0.415  1.00  0.00              
ATOM     61  N   GLY    58       3.624  48.496  -0.268  1.00  0.00              
ATOM     62  CA  GLY    58       4.580  49.409   0.338  1.00  0.00              
ATOM     63  C   GLY    58       5.956  49.546  -0.283  1.00  0.00              
ATOM     64  O   GLY    58       6.901  49.966   0.390  1.00  0.00              
ATOM     65  N   ILE    66       6.072  49.246  -1.564  1.00  0.00              
ATOM     66  CA  ILE    66       7.316  49.374  -2.255  1.00  0.00              
ATOM     67  C   ILE    66       7.282  50.530  -3.268  1.00  0.00              
ATOM     68  O   ILE    66       6.236  50.985  -3.715  1.00  0.00              
ATOM     69  N   ASP    67       8.466  51.002  -3.611  1.00  0.00              
ATOM     70  CA  ASP    67       8.617  52.065  -4.570  1.00  0.00              
ATOM     71  C   ASP    67       8.275  51.551  -5.975  1.00  0.00              
ATOM     72  O   ASP    67       9.135  51.209  -6.798  1.00  0.00              
ATOM     73  N   HIS    68       6.999  51.507  -6.253  1.00  0.00              
ATOM     74  CA  HIS    68       6.564  51.060  -7.565  1.00  0.00              
ATOM     75  C   HIS    68       7.031  51.909  -8.729  1.00  0.00              
ATOM     76  O   HIS    68       7.175  51.414  -9.862  1.00  0.00              
ATOM     77  N   HIS    69       7.271  53.171  -8.479  1.00  0.00              
ATOM     78  CA  HIS    69       7.708  54.013  -9.567  1.00  0.00              
ATOM     79  C   HIS    69       9.131  53.655  -9.960  1.00  0.00              
ATOM     80  O   HIS    69       9.537  53.671 -11.126  1.00  0.00              
ATOM     81  N   HIS    70       9.901  53.302  -8.951  1.00  0.00              
ATOM     82  CA  HIS    70      11.289  52.918  -9.185  1.00  0.00              
ATOM     83  C   HIS    70      11.295  51.675 -10.047  1.00  0.00              
ATOM     84  O   HIS    70      11.997  51.591 -11.068  1.00  0.00              
ATOM     85  N   LEU    71      10.459  50.733  -9.593  1.00  0.00              
ATOM     86  CA  LEU    71      10.248  49.462 -10.265  1.00  0.00              
ATOM     87  C   LEU    71       9.860  49.681 -11.731  1.00  0.00              
ATOM     88  O   LEU    71      10.487  49.168 -12.657  1.00  0.00              
ATOM     89  N   VAL    72       8.831  50.482 -11.944  1.00  0.00              
ATOM     90  CA  VAL    72       8.354  50.825 -13.279  1.00  0.00              
ATOM     91  C   VAL    72       9.446  51.425 -14.145  1.00  0.00              
ATOM     92  O   VAL    72       9.598  51.078 -15.303  1.00  0.00              
ATOM     93  N   LEU    73      10.208  52.360 -13.604  1.00  0.00              
ATOM     94  CA  LEU    73      11.240  52.997 -14.388  1.00  0.00              
ATOM     95  C   LEU    73      12.339  52.032 -14.785  1.00  0.00              
ATOM     96  O   LEU    73      13.004  52.167 -15.802  1.00  0.00              
ATOM     97  N   ALA    74      12.532  51.047 -13.953  1.00  0.00              
ATOM     98  CA  ALA    74      13.536  50.038 -14.200  1.00  0.00              
ATOM     99  C   ALA    74      13.165  49.128 -15.387  1.00  0.00              
ATOM    100  O   ALA    74      13.977  48.856 -16.277  1.00  0.00              
ATOM    101  N   LEU    75      11.905  48.680 -15.386  1.00  0.00              
ATOM    102  CA  LEU    75      11.305  47.840 -16.406  1.00  0.00              
ATOM    103  C   LEU    75      11.280  48.575 -17.747  1.00  0.00              
ATOM    104  O   LEU    75      11.527  48.028 -18.826  1.00  0.00              
ATOM    105  N   SER    76      10.950  49.860 -17.694  1.00  0.00              
ATOM    106  CA  SER    76      10.876  50.659 -18.891  1.00  0.00              
ATOM    107  C   SER    76      12.244  50.820 -19.519  1.00  0.00              
ATOM    108  O   SER    76      12.511  50.545 -20.676  1.00  0.00              
ATOM    109  N   LYS    77      13.137  51.258 -18.688  1.00  0.00              
ATOM    110  CA  LYS    77      14.468  51.469 -19.136  1.00  0.00              
ATOM    111  C   LYS    77      15.194  50.203 -19.489  1.00  0.00              
ATOM    112  O   LYS    77      15.788  50.094 -20.537  1.00  0.00              
ATOM    113  N   GLU    78      15.182  49.263 -18.583  1.00  0.00              
ATOM    114  CA  GLU    78      15.910  48.052 -18.841  1.00  0.00              
ATOM    115  C   GLU    78      15.144  46.828 -19.379  1.00  0.00              
ATOM    116  O   GLU    78      15.718  45.767 -19.582  1.00  0.00              
ATOM    117  N   GLY    79      13.845  46.977 -19.643  1.00  0.00              
ATOM    118  CA  GLY    79      12.987  45.909 -20.156  1.00  0.00              
ATOM    119  C   GLY    79      12.459  44.962 -19.083  1.00  0.00              
ATOM    120  O   GLY    79      12.925  44.979 -17.953  1.00  0.00              
ATOM    121  N   VAL    80      11.486  44.112 -19.449  1.00  0.00              
ATOM    122  CA  VAL    80      10.908  43.119 -18.554  1.00  0.00              
ATOM    123  C   VAL    80      12.000  42.271 -17.926  1.00  0.00              
ATOM    124  O   VAL    80      13.057  42.052 -18.509  1.00  0.00              
ATOM    125  N   GLU    81      11.725  41.817 -16.712  1.00  0.00              
ATOM    126  CA  GLU    81      12.644  41.021 -15.975  1.00  0.00              
ATOM    127  C   GLU    81      11.821  40.062 -15.186  1.00  0.00              
ATOM    128  O   GLU    81      10.686  40.363 -14.862  1.00  0.00              
ATOM    129  N   HIS    82      12.391  38.923 -14.889  1.00  0.00              
ATOM    130  CA  HIS    82      11.727  37.903 -14.135  1.00  0.00              
ATOM    131  C   HIS    82      11.957  38.197 -12.682  1.00  0.00              
ATOM    132  O   HIS    82      12.988  38.775 -12.315  1.00  0.00              
ATOM    133  N   VAL    83      11.010  37.778 -11.861  1.00  0.00              
ATOM    134  CA  VAL    83      11.225  38.074 -10.487  1.00  0.00              
ATOM    135  C   VAL    83      10.591  37.105  -9.525  1.00  0.00              
ATOM    136  O   VAL    83       9.898  36.158  -9.899  1.00  0.00              
ATOM    137  N   LEU    84      10.856  37.380  -8.262  1.00  0.00              
ATOM    138  CA  LEU    84      10.310  36.560  -7.241  1.00  0.00              
ATOM    139  C   LEU    84       9.888  37.389  -6.063  1.00  0.00              
ATOM    140  O   LEU    84      10.580  38.296  -5.619  1.00  0.00              
ATOM    141  N   THR    85       8.712  37.058  -5.574  1.00  0.00              
ATOM    142  CA  THR    85       8.210  37.739  -4.421  1.00  0.00              
ATOM    143  C   THR    85       8.155  36.687  -3.336  1.00  0.00              
ATOM    144  O   THR    85       7.644  35.600  -3.582  1.00  0.00              
ATOM    145  N   SER    86       8.694  36.990  -2.151  1.00  0.00              
ATOM    146  CA  SER    86       8.623  36.065  -1.049  1.00  0.00              
ATOM    147  C   SER    86       7.948  36.729   0.120  1.00  0.00              
ATOM    148  O   SER    86       8.430  37.726   0.667  1.00  0.00              
ATOM    149  N   GLU    87       6.839  36.151   0.521  1.00  0.00              
ATOM    150  CA  GLU    87       6.102  36.709   1.625  1.00  0.00              
ATOM    151  C   GLU    87       6.111  35.753   2.809  1.00  0.00              
ATOM    152  O   GLU    87       5.544  34.667   2.739  1.00  0.00              
END
