
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0350AL381_5-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350AL381_5-D1.T0350_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      20      M       1           -
LGA    H      21      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    S      36      S      36          2.035
LGA    Y      37      Y      37          1.410
LGA    T      38      T      38          1.231
LGA    N      39      N      39          1.067
LGA    L      40      L      40          0.746
LGA    A      41      A      41          0.385
LGA    E      42      E      42          0.954
LGA    M      43      M      43          1.052
LGA    V      44      V      44          0.977
LGA    G      45      G      45          0.808
LGA    E      46      E      46          0.640
LGA    M      47      M      47          1.289
LGA    N      48      N      48          0.761
LGA    K      49      K      49          0.445
LGA    L      50      L      50          0.801
LGA    L      51      L      51          0.903
LGA    E      52      E      52          1.012
LGA    P      53      P      53          1.478
LGA    S      54      S      54          1.428
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    Q      55      F      60          3.095
LGA    V      56      E      61          2.561
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    H      57      V      71          1.730
LGA    L      58      K      72          5.404
LGA    -       -      V      73           -
LGA    -       -      I      74           -
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      I      85           -
LGA    K      59      P      86          0.862
LGA    F      60      P      87          2.144
LGA    E      61      K      88          2.727
LGA    L      62      R      89           -
LGA    H      63      W      90           -
LGA    D      64      -       -           -
LGA    K      65      -       -           -
LGA    L      66      -       -           -
LGA    N      67      -       -           -
LGA    E      68      -       -           -
LGA    Y      69      -       -           -
LGA    Y      70      L      91          4.884
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   91    5.0     27    2.00    70.37     27.188     1.288

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.039650 * X  +   0.099208 * Y  +  -0.994276 * Z  +  11.042975
  Y_new =  -0.993071 * X  +  -0.106255 * Y  +  -0.050204 * Z  +   2.404022
  Z_new =  -0.110628 * X  +   0.989377 * Y  +   0.094308 * Z  + -53.402607 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.475763   -1.665829  [ DEG:    84.5550    -95.4450 ]
  Theta =   0.110854    3.030738  [ DEG:     6.3515    173.6485 ]
  Phi   =  -1.530890    1.610702  [ DEG:   -87.7136     92.2864 ]
 
# 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: T0350AL381_5-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_5-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   91   5.0   27   2.00   70.37  27.188
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_5-D1
REMARK Aligment from pdb entry: 1a48
ATOM      1  N   ILE    20      13.711  11.446 -38.885  1.00  0.00              
ATOM      2  CA  ILE    20      12.752  12.464 -38.492  1.00  0.00              
ATOM      3  C   ILE    20      11.336  11.937 -38.525  1.00  0.00              
ATOM      4  O   ILE    20      11.009  10.902 -39.151  1.00  0.00              
ATOM      5  N   HIS    21      10.374  12.629 -37.903  1.00  0.00              
ATOM      6  CA  HIS    21       8.978  12.259 -38.004  1.00  0.00              
ATOM      7  C   HIS    21       8.397  12.103 -39.420  1.00  0.00              
ATOM      8  O   HIS    21       7.496  11.346 -39.742  1.00  0.00              
ATOM     65  N   SER    36       0.679   7.334 -33.250  1.00  0.00              
ATOM     66  CA  SER    36       1.674   6.778 -32.366  1.00  0.00              
ATOM     67  C   SER    36       2.501   7.871 -31.648  1.00  0.00              
ATOM     68  O   SER    36       2.846   7.702 -30.500  1.00  0.00              
ATOM     69  N   TYR    37       2.852   8.959 -32.332  1.00  0.00              
ATOM     70  CA  TYR    37       3.561  10.045 -31.762  1.00  0.00              
ATOM     71  C   TYR    37       2.711  10.665 -30.662  1.00  0.00              
ATOM     72  O   TYR    37       3.277  10.957 -29.593  1.00  0.00              
ATOM     73  N   THR    38       1.439  10.913 -30.818  1.00  0.00              
ATOM     74  CA  THR    38       0.668  11.526 -29.766  1.00  0.00              
ATOM     75  C   THR    38       0.482  10.646 -28.542  1.00  0.00              
ATOM     76  O   THR    38       0.568  11.153 -27.440  1.00  0.00              
ATOM     77  N   ASN    39       0.201   9.383 -28.779  1.00  0.00              
ATOM     78  CA  ASN    39       0.035   8.422 -27.722  1.00  0.00              
ATOM     79  C   ASN    39       1.331   8.239 -26.950  1.00  0.00              
ATOM     80  O   ASN    39       1.283   8.282 -25.716  1.00  0.00              
ATOM     81  N   LEU    40       2.473   8.036 -27.549  1.00  0.00              
ATOM     82  CA  LEU    40       3.740   7.826 -26.923  1.00  0.00              
ATOM     83  C   LEU    40       4.121   8.924 -25.962  1.00  0.00              
ATOM     84  O   LEU    40       4.591   8.718 -24.883  1.00  0.00              
ATOM     85  N   ALA    41       3.967  10.186 -26.377  1.00  0.00              
ATOM     86  CA  ALA    41       4.252  11.377 -25.618  1.00  0.00              
ATOM     87  C   ALA    41       3.371  11.434 -24.386  1.00  0.00              
ATOM     88  O   ALA    41       3.876  11.737 -23.276  1.00  0.00              
ATOM     89  N   GLU    42       2.113  11.109 -24.513  1.00  0.00              
ATOM     90  CA  GLU    42       1.161  11.095 -23.404  1.00  0.00              
ATOM     91  C   GLU    42       1.545  10.044 -22.356  1.00  0.00              
ATOM     92  O   GLU    42       1.513  10.287 -21.168  1.00  0.00              
ATOM     93  N   MET    43       1.910   8.854 -22.812  1.00  0.00              
ATOM     94  CA  MET    43       2.291   7.753 -21.981  1.00  0.00              
ATOM     95  C   MET    43       3.566   8.067 -21.220  1.00  0.00              
ATOM     96  O   MET    43       3.636   7.855 -20.024  1.00  0.00              
ATOM     97  N   VAL    44       4.557   8.542 -21.901  1.00  0.00              
ATOM     98  CA  VAL    44       5.831   8.921 -21.333  1.00  0.00              
ATOM     99  C   VAL    44       5.647  10.025 -20.287  1.00  0.00              
ATOM    100  O   VAL    44       6.242   9.920 -19.198  1.00  0.00              
ATOM    101  N   GLY    45       4.898  11.088 -20.580  1.00  0.00              
ATOM    102  CA  GLY    45       4.742  12.175 -19.608  1.00  0.00              
ATOM    103  C   GLY    45       4.183  11.748 -18.275  1.00  0.00              
ATOM    104  O   GLY    45       4.629  12.177 -17.215  1.00  0.00              
ATOM    105  N   GLU    46       3.170  10.941 -18.296  1.00  0.00              
ATOM    106  CA  GLU    46       2.501  10.384 -17.139  1.00  0.00              
ATOM    107  C   GLU    46       3.446   9.584 -16.245  1.00  0.00              
ATOM    108  O   GLU    46       3.485   9.785 -15.031  1.00  0.00              
ATOM    109  N   MET    47       4.268   8.693 -16.805  1.00  0.00              
ATOM    110  CA  MET    47       5.183   7.817 -16.116  1.00  0.00              
ATOM    111  C   MET    47       6.403   8.515 -15.581  1.00  0.00              
ATOM    112  O   MET    47       6.923   8.246 -14.517  1.00  0.00              
ATOM    113  N   ASN    48       6.880   9.472 -16.383  1.00  0.00              
ATOM    114  CA  ASN    48       8.020  10.316 -16.055  1.00  0.00              
ATOM    115  C   ASN    48       7.696  11.130 -14.774  1.00  0.00              
ATOM    116  O   ASN    48       8.571  11.267 -13.907  1.00  0.00              
ATOM    117  N   LYS    49       6.513  11.687 -14.767  1.00  0.00              
ATOM    118  CA  LYS    49       6.064  12.472 -13.622  1.00  0.00              
ATOM    119  C   LYS    49       5.894  11.573 -12.391  1.00  0.00              
ATOM    120  O   LYS    49       6.337  12.016 -11.321  1.00  0.00              
ATOM    121  N   LEU    50       5.315  10.419 -12.562  1.00  0.00              
ATOM    122  CA  LEU    50       5.186   9.498 -11.452  1.00  0.00              
ATOM    123  C   LEU    50       6.537   9.145 -10.854  1.00  0.00              
ATOM    124  O   LEU    50       6.811   9.079  -9.627  1.00  0.00              
ATOM    125  N   LEU    51       7.459   8.736 -11.737  1.00  0.00              
ATOM    126  CA  LEU    51       8.763   8.298 -11.327  1.00  0.00              
ATOM    127  C   LEU    51       9.556   9.423 -10.686  1.00  0.00              
ATOM    128  O   LEU    51      10.308   9.205  -9.722  1.00  0.00              
ATOM    129  N   GLU    52       9.462  10.630 -11.199  1.00  0.00              
ATOM    130  CA  GLU    52      10.167  11.788 -10.705  1.00  0.00              
ATOM    131  C   GLU    52       9.771  12.076  -9.255  1.00  0.00              
ATOM    132  O   GLU    52      10.688  12.394  -8.489  1.00  0.00              
ATOM    133  N   PRO    53       8.583  11.873  -8.811  1.00  0.00              
ATOM    134  CA  PRO    53       8.097  12.000  -7.443  1.00  0.00              
ATOM    135  C   PRO    53       8.728  10.927  -6.541  1.00  0.00              
ATOM    136  O   PRO    53       8.852  11.120  -5.323  1.00  0.00              
ATOM    137  N   SER    54       9.153   9.799  -7.055  1.00  0.00              
ATOM    138  CA  SER    54       9.768   8.711  -6.372  1.00  0.00              
ATOM    139  C   SER    54      11.277   8.807  -6.366  1.00  0.00              
ATOM    140  O   SER    54      11.946   7.964  -5.726  1.00  0.00              
ATOM    141  N   GLN    55      14.547   9.324 -21.181  1.00  0.00              
ATOM    142  CA  GLN    55      13.998   8.920 -22.455  1.00  0.00              
ATOM    143  C   GLN    55      13.546   7.482 -22.380  1.00  0.00              
ATOM    144  O   GLN    55      13.925   6.818 -21.454  1.00  0.00              
ATOM    145  N   VAL    56      12.732   7.029 -23.345  1.00  0.00              
ATOM    146  CA  VAL    56      12.284   5.673 -23.368  1.00  0.00              
ATOM    147  C   VAL    56      12.014   5.195 -24.777  1.00  0.00              
ATOM    148  O   VAL    56      11.719   6.010 -25.608  1.00  0.00              
ATOM    149  N   HIS    57      12.034   3.936 -25.038  1.00  0.00              
ATOM    150  CA  HIS    57      11.737   3.381 -26.321  1.00  0.00              
ATOM    151  C   HIS    57      10.541   2.463 -26.212  1.00  0.00              
ATOM    152  O   HIS    57      10.629   1.442 -25.518  1.00  0.00              
ATOM    153  N   LEU    58       9.464   2.817 -26.910  1.00  0.00              
ATOM    154  CA  LEU    58       8.285   2.014 -26.992  1.00  0.00              
ATOM    155  C   LEU    58       8.226   1.276 -28.363  1.00  0.00              
ATOM    156  O   LEU    58       8.721   1.693 -29.362  1.00  0.00              
ATOM    157  N   LYS    59       7.509   0.176 -28.282  1.00  0.00              
ATOM    158  CA  LYS    59       7.152  -0.619 -29.446  1.00  0.00              
ATOM    159  C   LYS    59       5.640  -0.822 -29.405  1.00  0.00              
ATOM    160  O   LYS    59       5.086  -1.144 -28.349  1.00  0.00              
ATOM    161  N   PHE    60       4.968  -0.584 -30.522  1.00  0.00              
ATOM    162  CA  PHE    60       3.554  -0.713 -30.703  1.00  0.00              
ATOM    163  C   PHE    60       3.122  -1.682 -31.814  1.00  0.00              
ATOM    164  O   PHE    60       3.861  -1.946 -32.768  1.00  0.00              
ATOM    165  N   GLU    61       1.958  -2.221 -31.744  1.00  0.00              
ATOM    166  CA  GLU    61       1.275  -3.037 -32.698  1.00  0.00              
ATOM    167  C   GLU    61      -0.078  -2.410 -32.990  1.00  0.00              
ATOM    168  O   GLU    61      -0.461  -1.359 -32.402  1.00  0.00              
ATOM    169  N   LEU    62      -0.891  -2.936 -33.878  1.00  0.00              
ATOM    170  CA  LEU    62      -2.203  -2.465 -34.238  1.00  0.00              
ATOM    171  C   LEU    62      -3.105  -3.743 -34.340  1.00  0.00              
ATOM    172  O   LEU    62      -2.684  -4.703 -34.911  1.00  0.00              
ATOM    173  N   HIS    63      -4.276  -3.494 -33.855  1.00  0.00              
ATOM    174  CA  HIS    63      -5.359  -4.435 -33.916  1.00  0.00              
ATOM    175  C   HIS    63      -6.153  -3.789 -35.071  1.00  0.00              
ATOM    176  O   HIS    63      -6.795  -2.771 -34.944  1.00  0.00              
ATOM    177  N   ASP    64      -5.972  -4.354 -36.242  1.00  0.00              
ATOM    178  CA  ASP    64      -6.589  -3.858 -37.470  1.00  0.00              
ATOM    179  C   ASP    64      -8.097  -4.003 -37.606  1.00  0.00              
ATOM    180  O   ASP    64      -8.714  -3.397 -38.499  1.00  0.00              
ATOM    181  N   LYS    65      -8.726  -4.795 -36.772  1.00  0.00              
ATOM    182  CA  LYS    65     -10.171  -5.032 -36.703  1.00  0.00              
ATOM    183  C   LYS    65     -10.903  -3.998 -35.830  1.00  0.00              
ATOM    184  O   LYS    65     -12.121  -3.728 -35.911  1.00  0.00              
ATOM    185  N   LEU    66     -10.199  -3.320 -34.921  1.00  0.00              
ATOM    186  CA  LEU    66     -10.784  -2.335 -34.039  1.00  0.00              
ATOM    187  C   LEU    66     -10.071  -1.027 -34.372  1.00  0.00              
ATOM    188  O   LEU    66     -10.499   0.063 -34.114  1.00  0.00              
ATOM    189  N   ASN    67      -8.930  -1.226 -35.006  1.00  0.00              
ATOM    190  CA  ASN    67      -8.011  -0.162 -35.373  1.00  0.00              
ATOM    191  C   ASN    67      -7.335   0.436 -34.122  1.00  0.00              
ATOM    192  O   ASN    67      -7.109   1.654 -34.037  1.00  0.00              
ATOM    193  N   GLU    68      -6.997  -0.356 -33.121  1.00  0.00              
ATOM    194  CA  GLU    68      -6.379   0.143 -31.908  1.00  0.00              
ATOM    195  C   GLU    68      -4.881  -0.062 -31.923  1.00  0.00              
ATOM    196  O   GLU    68      -4.436  -1.095 -32.365  1.00  0.00              
ATOM    197  N   TYR    69      -4.171   0.886 -31.362  1.00  0.00              
ATOM    198  CA  TYR    69      -2.739   0.888 -31.167  1.00  0.00              
ATOM    199  C   TYR    69      -2.554   0.065 -29.853  1.00  0.00              
ATOM    200  O   TYR    69      -3.220   0.363 -28.874  1.00  0.00              
ATOM    201  N   TYR    70      -1.701  -0.903 -29.850  1.00  0.00              
ATOM    202  CA  TYR    70      -1.519  -1.773 -28.708  1.00  0.00              
ATOM    203  C   TYR    70      -0.074  -1.594 -28.240  1.00  0.00              
ATOM    204  O   TYR    70       0.825  -1.611 -29.073  1.00  0.00              
END
