
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0347AL333_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL333_2-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      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    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    R      27      I      52          4.108
LGA    E      28      V      53          1.039
LGA    -       -      P      54           -
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    -       -      L      65           -
LGA    -       -      I      66           -
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    V      29      T      85          1.628
LGA    E      30      S      86          1.115
LGA    L      31      E      87          4.314
LGA    K      32      V      88           -
LGA    R      33      -       -           -
LGA    K      34      A      89          6.140
LGA    -       -      K      90           -
LGA    E      35      F      91          3.180
LGA    W      36      S      92          4.149
LGA    R      37      H      93          3.136
LGA    H      51      -       -           -
LGA    I      52      -       -           -
LGA    V      53      -       -           -
LGA    P      54      -       -           -
LGA    V      55      -       -           -
LGA    V      56      -       -           -
LGA    A      57      L      94           #
LGA    G      58      G      95          0.976
LGA    P      59      K      96          0.707
LGA    K      60      D      97          0.742
LGA    D      61      E      98          0.845
LGA    R      62      F      99          0.815
LGA    A      63      W     100          0.280
LGA    Y      64      S     101          0.577
LGA    L      65      V     102          1.018
LGA    I      66      M     103          0.832
LGA    D      67      D     104          0.479
LGA    E      87      H     105          1.078
LGA    V      88      R     106          1.300
LGA    A      89      N     107          1.128
LGA    K      90      L     108           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32   89    5.0     22    2.39     9.09     19.780     0.885

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.923088 * X  +  -0.202994 * Y  +  -0.326653 * Z  + -16.000956
  Y_new =  -0.160465 * X  +   0.568604 * Y  +  -0.806809 * Z  +  49.223305
  Z_new =   0.349513 * X  +   0.797172 * Y  +   0.492298 * Z  + -15.379625 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.017568   -2.124024  [ DEG:    58.3024   -121.6976 ]
  Theta =  -0.357051   -2.784542  [ DEG:   -20.4575   -159.5425 ]
  Phi   =  -0.172115    2.969478  [ DEG:    -9.8615    170.1385 ]
 
# 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: T0347AL333_2-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_2-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   89   5.0   22   2.39    9.09  19.780
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_2-D1
REMARK Aligment from pdb entry: 1bh9_B
ATOM     13  N   ARG    27      14.756  32.397 -10.607  1.00  0.00              
ATOM     14  CA  ARG    27      14.591  32.432  -9.150  1.00  0.00              
ATOM     15  C   ARG    27      13.434  33.270  -8.630  1.00  0.00              
ATOM     16  O   ARG    27      12.763  32.873  -7.678  1.00  0.00              
ATOM     17  N   GLU    28      13.222  34.445  -9.211  1.00  0.00              
ATOM     18  CA  GLU    28      12.114  35.265  -8.761  1.00  0.00              
ATOM     19  C   GLU    28      10.872  34.423  -8.983  1.00  0.00              
ATOM     20  O   GLU    28      10.062  34.239  -8.067  1.00  0.00              
ATOM     21  N   VAL    29      10.751  33.902 -10.205  1.00  0.00              
ATOM     22  CA  VAL    29       9.636  33.060 -10.606  1.00  0.00              
ATOM     23  C   VAL    29       9.473  31.882  -9.663  1.00  0.00              
ATOM     24  O   VAL    29       8.373  31.630  -9.171  1.00  0.00              
ATOM     25  N   GLU    30      10.558  31.155  -9.406  1.00  0.00              
ATOM     26  CA  GLU    30      10.448  30.017  -8.507  1.00  0.00              
ATOM     27  C   GLU    30      10.241  30.397  -7.061  1.00  0.00              
ATOM     28  O   GLU    30       9.645  29.633  -6.310  1.00  0.00              
ATOM     29  N   LEU    31      10.708  31.572  -6.657  1.00  0.00              
ATOM     30  CA  LEU    31      10.499  31.970  -5.286  1.00  0.00              
ATOM     31  C   LEU    31       9.002  32.278  -5.167  1.00  0.00              
ATOM     32  O   LEU    31       8.369  31.934  -4.166  1.00  0.00              
ATOM     33  N   LYS    32       3.380  31.173  -3.505  1.00  0.00              
ATOM     34  CA  LYS    32       2.002  30.982  -3.927  1.00  0.00              
ATOM     35  C   LYS    32       1.388  29.687  -3.418  1.00  0.00              
ATOM     36  O   LYS    32       0.282  29.704  -2.880  1.00  0.00              
ATOM     37  N   ARG    33       2.083  28.564  -3.562  1.00  0.00              
ATOM     38  CA  ARG    33       1.486  27.325  -3.088  1.00  0.00              
ATOM     39  C   ARG    33       1.960  26.666  -1.800  1.00  0.00              
ATOM     40  O   ARG    33       1.415  25.631  -1.403  1.00  0.00              
ATOM     41  N   LYS    34       2.952  27.234  -1.133  1.00  0.00              
ATOM     42  CA  LYS    34       3.385  26.634   0.115  1.00  0.00              
ATOM     43  C   LYS    34       2.151  26.556   1.017  1.00  0.00              
ATOM     44  O   LYS    34       1.290  27.441   0.999  1.00  0.00              
ATOM     45  N   GLU    35       2.063  25.498   1.806  1.00  0.00              
ATOM     46  CA  GLU    35       0.924  25.333   2.684  1.00  0.00              
ATOM     47  C   GLU    35       1.099  24.105   3.539  1.00  0.00              
ATOM     48  O   GLU    35       1.617  23.088   3.084  1.00  0.00              
ATOM     49  N   TRP    36       0.645  24.211   4.778  1.00  0.00              
ATOM     50  CA  TRP    36       0.730  23.125   5.725  1.00  0.00              
ATOM     51  C   TRP    36      -0.233  21.993   5.388  1.00  0.00              
ATOM     52  O   TRP    36      -1.320  22.221   4.873  1.00  0.00              
ATOM     53  N   ARG    37       0.154  20.750   5.699  1.00  0.00              
ATOM     54  CA  ARG    37      -0.718  19.608   5.424  1.00  0.00              
ATOM     55  C   ARG    37      -1.914  19.743   6.367  1.00  0.00              
ATOM     56  O   ARG    37      -1.729  20.012   7.556  1.00  0.00              
ATOM    109  N   HIS    51     -12.783  17.499  21.160  1.00  0.00              
ATOM    110  CA  HIS    51     -13.801  17.361  20.111  1.00  0.00              
ATOM    111  C   HIS    51     -13.087  17.386  18.763  1.00  0.00              
ATOM    112  O   HIS    51     -11.922  17.791  18.685  1.00  0.00              
ATOM    113  N   ILE    52     -13.783  16.964  17.706  1.00  0.00              
ATOM    114  CA  ILE    52     -13.198  17.000  16.370  1.00  0.00              
ATOM    115  C   ILE    52     -13.427  18.444  15.928  1.00  0.00              
ATOM    116  O   ILE    52     -14.034  19.230  16.664  1.00  0.00              
ATOM    117  N   VAL    53     -12.979  18.771  14.718  1.00  0.00              
ATOM    118  CA  VAL    53     -13.114  20.118  14.181  1.00  0.00              
ATOM    119  C   VAL    53     -13.450  20.121  12.687  1.00  0.00              
ATOM    120  O   VAL    53     -13.299  19.120  12.000  1.00  0.00              
ATOM    121  N   PRO    54     -13.916  21.255  12.189  1.00  0.00              
ATOM    122  CA  PRO    54     -14.326  21.360  10.798  1.00  0.00              
ATOM    123  C   PRO    54     -13.248  21.659   9.771  1.00  0.00              
ATOM    124  O   PRO    54     -12.149  22.112  10.085  1.00  0.00              
ATOM    125  N   VAL    55      -8.515  25.072   7.571  1.00  0.00              
ATOM    126  CA  VAL    55      -8.045  25.943   6.498  1.00  0.00              
ATOM    127  C   VAL    55      -7.748  27.339   7.026  1.00  0.00              
ATOM    128  O   VAL    55      -6.751  27.952   6.654  1.00  0.00              
ATOM    129  N   VAL    56      -8.620  27.824   7.897  1.00  0.00              
ATOM    130  CA  VAL    56      -8.458  29.137   8.496  1.00  0.00              
ATOM    131  C   VAL    56      -7.195  29.165   9.355  1.00  0.00              
ATOM    132  O   VAL    56      -6.422  30.114   9.313  1.00  0.00              
ATOM    133  N   ALA    57      -6.994  28.107  10.134  1.00  0.00              
ATOM    134  CA  ALA    57      -5.830  27.977  10.994  1.00  0.00              
ATOM    135  C   ALA    57      -4.560  27.910  10.136  1.00  0.00              
ATOM    136  O   ALA    57      -3.528  28.432  10.531  1.00  0.00              
ATOM    137  N   GLY    58      -4.635  27.273   8.968  1.00  0.00              
ATOM    138  CA  GLY    58      -3.481  27.176   8.074  1.00  0.00              
ATOM    139  C   GLY    58      -3.152  28.520   7.447  1.00  0.00              
ATOM    140  O   GLY    58      -1.996  28.842   7.234  1.00  0.00              
ATOM    141  N   PRO    59      -4.179  29.292   7.125  1.00  0.00              
ATOM    142  CA  PRO    59      -3.961  30.599   6.538  1.00  0.00              
ATOM    143  C   PRO    59      -3.314  31.549   7.529  1.00  0.00              
ATOM    144  O   PRO    59      -2.402  32.291   7.167  1.00  0.00              
ATOM    145  N   LYS    60      -3.784  31.524   8.774  1.00  0.00              
ATOM    146  CA  LYS    60      -3.256  32.378   9.837  1.00  0.00              
ATOM    147  C   LYS    60      -1.826  31.991  10.222  1.00  0.00              
ATOM    148  O   LYS    60      -1.001  32.846  10.543  1.00  0.00              
ATOM    149  N   ASP    61      -1.526  30.702  10.168  1.00  0.00              
ATOM    150  CA  ASP    61      -0.202  30.225  10.520  1.00  0.00              
ATOM    151  C   ASP    61       0.778  30.548   9.416  1.00  0.00              
ATOM    152  O   ASP    61       1.957  30.768   9.672  1.00  0.00              
ATOM    153  N   ARG    62       0.300  30.588   8.183  1.00  0.00              
ATOM    154  CA  ARG    62       1.189  30.921   7.088  1.00  0.00              
ATOM    155  C   ARG    62       1.604  32.381   7.271  1.00  0.00              
ATOM    156  O   ARG    62       2.773  32.710   7.150  1.00  0.00              
ATOM    157  N   ALA    63       0.649  33.246   7.587  1.00  0.00              
ATOM    158  CA  ALA    63       0.946  34.657   7.816  1.00  0.00              
ATOM    159  C   ALA    63       1.957  34.840   8.956  1.00  0.00              
ATOM    160  O   ALA    63       2.862  35.670   8.865  1.00  0.00              
ATOM    161  N   TYR    64       1.786  34.069  10.026  1.00  0.00              
ATOM    162  CA  TYR    64       2.693  34.087  11.171  1.00  0.00              
ATOM    163  C   TYR    64       4.094  33.747  10.669  1.00  0.00              
ATOM    164  O   TYR    64       5.051  34.486  10.921  1.00  0.00              
ATOM    165  N   LEU    65       4.204  32.617   9.971  1.00  0.00              
ATOM    166  CA  LEU    65       5.477  32.187   9.420  1.00  0.00              
ATOM    167  C   LEU    65       6.043  33.338   8.617  1.00  0.00              
ATOM    168  O   LEU    65       7.209  33.681   8.759  1.00  0.00              
ATOM    169  N   ILE    66       5.197  33.945   7.793  1.00  0.00              
ATOM    170  CA  ILE    66       5.615  35.058   6.961  1.00  0.00              
ATOM    171  C   ILE    66       6.200  36.227   7.713  1.00  0.00              
ATOM    172  O   ILE    66       7.180  36.819   7.286  1.00  0.00              
ATOM    173  N   ASP    67       5.588  36.562   8.841  1.00  0.00              
ATOM    174  CA  ASP    67       6.055  37.665   9.651  1.00  0.00              
ATOM    175  C   ASP    67       7.362  37.342  10.369  1.00  0.00              
ATOM    176  O   ASP    67       8.188  38.224  10.568  1.00  0.00              
ATOM    177  N   GLU    87       7.568  36.083  10.740  1.00  0.00              
ATOM    178  CA  GLU    87       8.799  35.706  11.419  1.00  0.00              
ATOM    179  C   GLU    87       9.982  35.692  10.444  1.00  0.00              
ATOM    180  O   GLU    87      11.040  36.229  10.747  1.00  0.00              
ATOM    181  N   VAL    88       9.804  35.081   9.274  1.00  0.00              
ATOM    182  CA  VAL    88      10.874  35.033   8.278  1.00  0.00              
ATOM    183  C   VAL    88      11.196  36.446   7.801  1.00  0.00              
ATOM    184  O   VAL    88      12.356  36.819   7.689  1.00  0.00              
ATOM    185  N   ALA    89      10.168  37.239   7.536  1.00  0.00              
ATOM    186  CA  ALA    89      10.378  38.614   7.090  1.00  0.00              
ATOM    187  C   ALA    89      11.092  39.451   8.149  1.00  0.00              
ATOM    188  O   ALA    89      11.899  40.319   7.813  1.00  0.00              
ATOM    189  N   LYS    90      10.813  39.182   9.424  1.00  0.00              
ATOM    190  CA  LYS    90      11.460  39.912  10.507  1.00  0.00              
ATOM    191  C   LYS    90      12.894  39.420  10.735  1.00  0.00              
ATOM    192  O   LYS    90      13.791  40.214  11.003  1.00  0.00              
END
