
#######################################################
#                                                     #
#                        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 T0335TS307_1u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS307_1u-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.516
LGA    K       6      K       6          2.163
LGA    I       7      I       7          1.635
LGA    A       8      A       8          1.305
LGA    R       9      R       9          1.697
LGA    I      10      I      10          1.824
LGA    N      11      N      11          1.314
LGA    E      12      E      12          0.982
LGA    L      13      L      13          1.523
LGA    A      14      A      14          1.485
LGA    A      15      A      15          1.158
LGA    K      16      K      16          1.614
LGA    A      17      A      17          2.360
LGA    K      18      K      18          1.223
LGA    A      19      A      19          2.993
LGA    G      20      G      20          4.088
LGA    V      21      V      21          2.538
LGA    I      22      I      22          3.346
LGA    T      23      T      23          2.609
LGA    A      28      -       -           -
LGA    E      29      E      24          1.454
LGA    Q      30      E      25          2.028
LGA    Q      31      E      26          3.483
LGA    K      32      K      27          2.386
LGA    L      33      A      28          0.567
LGA    R      34      E      29          2.170
LGA    Q      35      Q      30          2.252
LGA    E      36      Q      31          0.654
LGA    Y      37      K      32          2.117
LGA    L      38      L      33          2.201
LGA    K      39      R      34          1.116
LGA    G      40      Q      35          2.346
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32   36    5.0     31    2.13    74.19     65.982     1.390

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.993444 * X  +  -0.112039 * Y  +  -0.022732 * Z  +   1.701891
  Y_new =  -0.077297 * X  +  -0.804796 * Y  +   0.588498 * Z  +  -2.663950
  Z_new =  -0.084229 * X  +  -0.582882 * Y  +  -0.808179 * Z  +   1.152828 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.516761    0.624832  [ DEG:  -144.1998     35.8002 ]
  Theta =   0.084329    3.057263  [ DEG:     4.8317    175.1683 ]
  Phi   =  -0.077651    3.063942  [ DEG:    -4.4491    175.5509 ]
 
# 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: T0335TS307_1u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_1u-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   36   5.0   31   2.13   74.19  65.982
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_1u-D1
PFRMAT   TS
TARGET   T0335
MODEL    1  UNREFINED
PARENT   1ywm_A
ATOM    814  N   ALA     5      -1.619 -11.440  -8.896  1.00 18.74           N  
ATOM    815  CA  ALA     5      -1.900 -11.670  -7.472  1.00 23.45           C  
ATOM    816  C   ALA     5      -1.244 -10.602  -6.590  1.00 20.91           C  
ATOM    817  O   ALA     5      -1.840 -10.136  -5.606  1.00 18.80           O  
ATOM    821  N   LYS     6      -0.005 -10.237  -6.922  1.00 16.56           N  
ATOM    822  CA  LYS     6       0.643  -9.118  -6.248  1.00 15.55           C  
ATOM    823  C   LYS     6      -0.224  -7.875  -6.318  1.00 17.28           C  
ATOM    824  O   LYS     6      -0.434  -7.195  -5.294  1.00 16.00           O  
ATOM    829  N   ILE     7      -0.751  -7.567  -7.502  1.00 14.20           N  
ATOM    830  CA  ILE     7      -1.532  -6.332  -7.642  1.00 16.86           C  
ATOM    831  C   ILE     7      -2.825  -6.384  -6.816  1.00 17.32           C  
ATOM    832  O   ILE     7      -3.223  -5.395  -6.209  1.00 16.45           O  
ATOM    840  N   ALA     8      -3.457  -7.557  -6.774  1.00 14.80           N  
ATOM    841  CA  ALA     8      -4.642  -7.758  -5.942  1.00 17.33           C  
ATOM    842  C   ALA     8      -4.281  -7.595  -4.482  1.00 17.72           C  
ATOM    843  O   ALA     8      -4.999  -6.934  -3.740  1.00 15.55           O  
ATOM    848  N   ARG     9      -3.192  -8.229  -4.070  1.00 13.75           N  
ATOM    849  CA  ARG     9      -2.719  -8.106  -2.686  1.00 20.31           C  
ATOM    850  C   ARG     9      -2.461  -6.649  -2.301  1.00 16.34           C  
ATOM    851  O   ARG     9      -2.821  -6.188  -1.196  1.00 13.68           O  
ATOM    857  N   ILE    10      -1.794  -5.925  -3.184  1.00 14.00           N  
ATOM    858  CA  ILE    10      -1.542  -4.528  -2.932  1.00 15.11           C  
ATOM    859  C   ILE    10      -2.837  -3.753  -2.722  1.00 16.46           C  
ATOM    860  O   ILE    10      -2.917  -2.924  -1.806  1.00 14.51           O  
ATOM    865  N   ASN    11      -3.855  -4.011  -3.552  1.00 13.04           N  
ATOM    866  CA  ASN    11      -5.131  -3.277  -3.414  1.00 12.82           C  
ATOM    867  C   ASN    11      -5.847  -3.668  -2.122  1.00 14.24           C  
ATOM    868  O   ASN    11      -6.483  -2.828  -1.491  1.00 13.15           O  
ATOM    874  N   GLU    12      -5.710  -4.923  -1.717  1.00 16.54           N  
ATOM    875  CA  GLU    12      -6.326  -5.377  -0.455  1.00 16.86           C  
ATOM    876  C   GLU    12      -5.693  -4.687   0.761  1.00 16.71           C  
ATOM    877  O   GLU    12      -6.415  -4.240   1.686  1.00 14.00           O  
ATOM    883  N   LEU    13      -4.366  -4.556   0.757  1.00 14.44           N  
ATOM    884  CA  LEU    13      -3.676  -3.881   1.875  1.00 17.60           C  
ATOM    885  C   LEU    13      -3.991  -2.385   1.841  1.00 16.18           C  
ATOM    886  O   LEU    13      -4.168  -1.756   2.882  1.00 14.16           O  
ATOM    890  N   ALA    14      -4.036  -1.800   0.646  1.00 10.98           N  
ATOM    891  CA  ALA    14      -4.403  -0.402   0.505  1.00 11.62           C  
ATOM    892  C   ALA    14      -5.782  -0.151   1.128  1.00 15.73           C  
ATOM    893  O   ALA    14      -5.989   0.823   1.883  1.00 17.35           O  
ATOM    901  N   ALA    15      -6.733  -1.029   0.806  1.00 13.16           N  
ATOM    902  CA  ALA    15      -8.104  -0.865   1.283  1.00 15.03           C  
ATOM    903  C   ALA    15      -8.113  -0.962   2.819  1.00 17.22           C  
ATOM    904  O   ALA    15      -8.703  -0.140   3.507  1.00 15.39           O  
ATOM    908  N   LYS    16      -7.434  -1.974   3.327  1.00 10.96           N  
ATOM    909  CA  LYS    16      -7.287  -2.139   4.767  1.00 15.18           C  
ATOM    910  C   LYS    16      -6.651  -0.897   5.420  1.00 17.06           C  
ATOM    911  O   LYS    16      -7.190  -0.356   6.407  1.00 13.18           O  
ATOM    916  N   ALA    17      -5.519  -0.449   4.873  1.00 15.43           N  
ATOM    917  CA  ALA    17      -4.770   0.666   5.446  1.00 17.89           C  
ATOM    918  C   ALA    17      -5.616   1.942   5.524  1.00 18.60           C  
ATOM    919  O   ALA    17      -5.413   2.745   6.426  1.00 13.87           O  
ATOM    921  N   LYS    18      -6.556   2.108   4.594  1.00 13.05           N  
ATOM    922  CA  LYS    18      -7.395   3.311   4.546  1.00 14.24           C  
ATOM    923  C   LYS    18      -8.509   3.361   5.588  1.00 11.86           C  
ATOM    924  O   LYS    18      -9.163   4.390   5.758  1.00 12.63           O  
ATOM    929  N   ALA    19      -8.666   2.275   6.328  1.00 12.04           N  
ATOM    930  CA  ALA    19      -9.640   2.244   7.424  1.00 14.23           C  
ATOM    931  C   ALA    19      -9.214   3.267   8.517  1.00 11.95           C  
ATOM    932  O   ALA    19      -8.085   3.195   8.998  1.00 12.62           O  
ATOM    937  N   GLY    20     -10.079   4.203   8.908  1.00 13.05           N  
ATOM    938  CA  GLY    20      -9.714   5.168   9.944  1.00 15.08           C  
ATOM    939  C   GLY    20      -9.400   4.573  11.305  1.00 13.92           C  
ATOM    940  O   GLY    20      -8.913   5.336  12.146  1.00 16.96           O  
ATOM    944  N   VAL    21      -9.579   3.267  11.524  1.00 10.20           N  
ATOM    945  CA  VAL    21      -9.195   2.709  12.833  1.00 10.33           C  
ATOM    946  C   VAL    21      -7.652   2.680  13.059  1.00 14.81           C  
ATOM    947  O   VAL    21      -7.183   2.564  14.200  1.00 11.35           O  
ATOM    953  N   ILE    22      -6.884   2.764  11.963  1.00 12.20           N  
ATOM    954  CA  ILE    22      -5.419   2.757  11.999  1.00 11.20           C  
ATOM    955  C   ILE    22      -4.879   4.164  12.179  1.00  7.51           C  
ATOM    956  O   ILE    22      -5.468   5.129  11.696  1.00 12.56           O  
ATOM    967  N   THR    23      -3.767   4.299  12.899  1.00  8.21           N  
ATOM    968  CA  THR    23      -3.125   5.603  13.020  1.00 13.83           C  
ATOM    969  C   THR    23      -2.789   6.165  11.638  1.00 12.74           C  
ATOM    970  O   THR    23      -2.425   5.417  10.723  1.00 13.22           O  
ATOM    974  N   ALA    28      -2.873   7.481  11.496  1.00 11.34           N  
ATOM    975  CA  ALA    28      -2.467   8.076  10.218  1.00 15.90           C  
ATOM    976  C   ALA    28      -0.976   7.798   9.919  1.00 13.75           C  
ATOM    977  O   ALA    28      -0.593   7.529   8.777  1.00 17.03           O  
ATOM    983  N   GLU    29      -0.144   7.832  10.946  1.00 15.38           N  
ATOM    984  CA  GLU    29       1.292   7.629  10.771  1.00 15.35           C  
ATOM    985  C   GLU    29       1.594   6.213  10.232  1.00 20.44           C  
ATOM    986  O   GLU    29       2.436   6.044   9.328  1.00 18.18           O  
ATOM    992  N   GLN    30       0.929   5.195  10.782  1.00 13.69           N  
ATOM    993  CA  GLN    30       1.133   3.847  10.236  1.00 15.09           C  
ATOM    994  C   GLN    30       0.532   3.676   8.816  1.00 13.36           C  
ATOM    995  O   GLN    30       1.168   3.049   7.934  1.00 13.06           O  
ATOM    998  N   GLN    31      -0.660   4.222   8.593  1.00 10.56           N  
ATOM    999  CA  GLN    31      -1.262   4.185   7.253  1.00 13.00           C  
ATOM   1000  C   GLN    31      -0.269   4.743   6.226  1.00 12.17           C  
ATOM   1001  O   GLN    31      -0.061   4.165   5.153  1.00  9.95           O  
ATOM   1009  N   LYS    32       0.304   5.893   6.546  1.00 10.59           N  
ATOM   1010  CA  LYS    32       1.159   6.589   5.600  1.00 14.09           C  
ATOM   1011  C   LYS    32       2.408   5.770   5.295  1.00 12.93           C  
ATOM   1012  O   LYS    32       2.848   5.698   4.143  1.00  9.40           O  
ATOM   1016  N   LEU    33       2.983   5.150   6.320  1.00  8.69           N  
ATOM   1017  CA  LEU    33       4.177   4.338   6.107  1.00 10.85           C  
ATOM   1018  C   LEU    33       3.853   3.137   5.236  1.00 12.13           C  
ATOM   1019  O   LEU    33       4.625   2.779   4.341  1.00 11.96           O  
ATOM   1025  N   ARG    34       2.708   2.511   5.496  1.00  6.96           N  
ATOM   1026  CA  ARG    34       2.294   1.347   4.713  1.00 10.84           C  
ATOM   1027  C   ARG    34       2.010   1.755   3.250  1.00 10.17           C  
ATOM   1028  O   ARG    34       2.506   1.114   2.296  1.00 13.04           O  
ATOM   1032  N   GLN    35       1.262   2.834   3.063  1.00  8.99           N  
ATOM   1033  CA  GLN    35       0.959   3.264   1.672  1.00  8.55           C  
ATOM   1034  C   GLN    35       2.203   3.665   0.913  1.00 11.03           C  
ATOM   1035  O   GLN    35       2.294   3.487  -0.335  1.00 11.70           O  
ATOM   1040  N   GLU    36       3.180   4.230   1.622  1.00  8.16           N  
ATOM   1041  CA  GLU    36       4.433   4.613   0.973  1.00  9.85           C  
ATOM   1042  C   GLU    36       5.134   3.380   0.387  1.00 12.98           C  
ATOM   1043  O   GLU    36       5.669   3.405  -0.741  1.00 13.99           O  
ATOM   1047  N   TYR    37       5.147   2.307   1.165  1.00 12.14           N  
ATOM   1048  CA  TYR    37       5.793   1.072   0.726  1.00 16.99           C  
ATOM   1049  C   TYR    37       5.033   0.437  -0.439  1.00 15.30           C  
ATOM   1050  O   TYR    37       5.634  -0.068  -1.425  1.00 14.35           O  
ATOM   1051  N   LEU    38       3.713   0.417  -0.331  1.00 10.68           N  
ATOM   1052  CA  LEU    38       2.908  -0.072  -1.455  1.00 12.08           C  
ATOM   1053  C   LEU    38       3.137   0.748  -2.739  1.00 12.54           C  
ATOM   1054  O   LEU    38       3.196   0.175  -3.839  1.00 10.82           O  
ATOM   1059  N   LYS    39       3.181   2.077  -2.624  1.00 13.30           N  
ATOM   1060  CA  LYS    39       3.434   2.938  -3.779  1.00 15.42           C  
ATOM   1061  C   LYS    39       4.775   2.670  -4.436  1.00 13.38           C  
ATOM   1062  O   LYS    39       4.881   2.703  -5.662  1.00 11.76           O  
ATOM   1067  N   GLY    40       5.786   2.407  -3.626  1.00 14.43           N  
ATOM   1068  CA  GLY    40       7.118   2.104  -4.145  1.00 17.65           C  
ATOM   1069  C   GLY    40       7.099   0.802  -4.981  1.00 14.53           C  
ATOM   1070  O   GLY    40       7.619   0.753  -6.121  1.00 15.01           O  
TER
END
