
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0335TS307_3u
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS307_3u.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          3.845
LGA    I       2      I       2          2.530
LGA    S       3      S       3          3.241
LGA    N       4      N       4          1.913
LGA    A       5      A       5          2.143
LGA    K       6      K       6          1.761
LGA    I       7      I       7          1.112
LGA    A       8      A       8          1.282
LGA    R       9      R       9          1.642
LGA    I      10      I      10          1.266
LGA    N      11      N      11          0.510
LGA    E      12      E      12          1.233
LGA    L      13      L      13          1.515
LGA    A      14      A      14          0.908
LGA    A      15      A      15          0.437
LGA    K      16      K      16          1.258
LGA    A      17      A      17          1.727
LGA    K      18      K      18          2.201
LGA    A      19      A      19          2.760
LGA    G      20      G      20          2.102
LGA    I      22      V      21          1.837
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    E      25      -       -           -
LGA    E      26      -       -           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      I      22          3.625
LGA    Q      31      T      23          1.255
LGA    K      32      E      24          3.570
LGA    -       -      E      25           -
LGA    L      33      E      26          1.489
LGA    R      34      K      27          0.599
LGA    Q      35      A      28          0.498
LGA    E      36      E      29          1.242
LGA    L      38      Q      30          1.502
LGA    K      39      Q      31          1.275
LGA    G      40      K      32          1.129
LGA    F      41      L      33          0.761
LGA    R      42      R      34          0.966
LGA    S      43      Q      35          1.276
LGA    S      44      E      36          1.227
LGA    M      45      Y      37          1.250
LGA    K      46      L      38          3.247
LGA    -       -      K      39           -
LGA    N      47      G      40          2.386
LGA    T      48      F      41          6.422
LGA    -       -      R      42           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   42    5.0     39    2.15    56.41     81.760     1.731

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.339712 * X  +   0.715108 * Y  +   0.610914 * Z  +  -6.955250
  Y_new =  -0.452949 * X  +  -0.693648 * Y  +   0.560080 * Z  +   7.478924
  Z_new =   0.824277 * X  +  -0.086447 * Y  +   0.559548 * Z  +  10.763756 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.153282    2.988310  [ DEG:    -8.7824    171.2176 ]
  Theta =  -0.968924   -2.172669  [ DEG:   -55.5153   -124.4847 ]
  Phi   =  -2.214298    0.927295  [ DEG:  -126.8699     53.1301 ]
 
# 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_3u                                 
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_3u.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   42   5.0   39   2.15   56.41  81.760
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_3u
PFRMAT   TS
TARGET   T0335
MODEL    3  UNREFINED
PARENT   1e52_A
ATOM     1   N   MET     1       0.301  -6.235 -17.441  1.00                    
ATOM     1   CA  MET     1      -0.297  -4.934 -17.027  1.00                    
ATOM     1   C   MET     1       0.194  -4.549 -15.629  1.00                    
ATOM     1   O   MET     1       0.478  -3.400 -15.355  1.00                    
ATOM     1   N   ILE     2       0.297  -5.502 -14.743  1.00                    
ATOM     1   CA  ILE     2       0.771  -5.190 -13.364  1.00                    
ATOM     1   C   ILE     2       1.353  -6.449 -12.708  1.00                    
ATOM     1   O   ILE     2       1.130  -7.547 -13.179  1.00                    
ATOM     1   N   SER     3       2.082  -6.251 -11.637  1.00                    
ATOM     1   CA  SER     3       2.698  -7.397 -10.918  1.00                    
ATOM     1   C   SER     3       1.640  -8.247 -10.205  1.00                    
ATOM     1   O   SER     3       1.934  -9.303  -9.683  1.00                    
ATOM     1   N   ASN     4       0.414  -7.800 -10.192  1.00                    
ATOM     1   CA  ASN     4      -0.684  -8.574  -9.524  1.00                    
ATOM     1   C   ASN     4      -0.433  -8.692  -8.015  1.00                    
ATOM     1   O   ASN     4      -1.127  -8.091  -7.219  1.00                    
ATOM     1   N   ALA     5       0.547  -9.456  -7.609  1.00                    
ATOM     1   CA  ALA     5       0.825  -9.599  -6.148  1.00                    
ATOM     1   C   ALA     5       0.961  -8.216  -5.507  1.00                    
ATOM     1   O   ALA     5       0.209  -7.851  -4.625  1.00                    
ATOM     1   N   LYS     6       1.907  -7.441  -5.957  1.00                    
ATOM     1   CA  LYS     6       2.086  -6.076  -5.389  1.00                    
ATOM     1   C   LYS     6       0.774  -5.291  -5.535  1.00                    
ATOM     1   O   LYS     6       0.172  -4.880  -4.563  1.00                    
ATOM     1   N   ILE     7       0.331  -5.087  -6.746  1.00                    
ATOM     1   CA  ILE     7      -0.940  -4.335  -6.967  1.00                    
ATOM     1   C   ILE     7      -2.055  -4.896  -6.078  1.00                    
ATOM     1   O   ILE     7      -2.912  -4.173  -5.612  1.00                    
ATOM     1   N   ALA     8      -2.046  -6.179  -5.838  1.00                    
ATOM     1   CA  ALA     8      -3.103  -6.780  -4.977  1.00                    
ATOM     1   C   ALA     8      -2.876  -6.387  -3.515  1.00                    
ATOM     1   O   ALA     8      -3.809  -6.159  -2.771  1.00                    
ATOM     1   N   ARG     9      -1.641  -6.307  -3.099  1.00                    
ATOM     1   CA  ARG     9      -1.354  -5.928  -1.687  1.00                    
ATOM     1   C   ARG     9      -1.658  -4.444  -1.469  1.00                    
ATOM     1   O   ARG     9      -2.278  -4.063  -0.496  1.00                    
ATOM     1   N   ILE    10      -1.226  -3.603  -2.368  1.00                    
ATOM     1   CA  ILE    10      -1.491  -2.143  -2.213  1.00                    
ATOM     1   C   ILE    10      -2.990  -1.896  -2.041  1.00                    
ATOM     1   O   ILE    10      -3.422  -1.281  -1.085  1.00                    
ATOM     1   N   ASN    11      -3.787  -2.368  -2.959  1.00                    
ATOM     1   CA  ASN    11      -5.260  -2.158  -2.846  1.00                    
ATOM     1   C   ASN    11      -5.791  -2.801  -1.562  1.00                    
ATOM     1   O   ASN    11      -6.836  -2.436  -1.061  1.00                    
ATOM     1   N   GLU    12      -5.080  -3.756  -1.028  1.00                    
ATOM     1   CA  GLU    12      -5.545  -4.423   0.222  1.00                    
ATOM     1   C   GLU    12      -5.202  -3.565   1.444  1.00                    
ATOM     1   O   GLU    12      -6.003  -3.399   2.342  1.00                    
ATOM     1   N   LEU    13      -4.016  -3.022   1.486  1.00                    
ATOM     1   CA  LEU    13      -3.621  -2.180   2.653  1.00                    
ATOM     1   C   LEU    13      -4.376  -0.847   2.632  1.00                    
ATOM     1   O   LEU    13      -4.854  -0.380   3.646  1.00                    
ATOM     1   N   ALA    14      -4.486  -0.233   1.486  1.00                    
ATOM     1   CA  ALA    14      -5.210   1.069   1.406  1.00                    
ATOM     1   C   ALA    14      -6.671   0.893   1.832  1.00                    
ATOM     1   O   ALA    14      -7.217   1.697   2.559  1.00                    
ATOM     1   N   ALA    15      -7.307  -0.154   1.380  1.00                    
ATOM     1   CA  ALA    15      -8.731  -0.380   1.757  1.00                    
ATOM     1   C   ALA    15      -8.831  -0.654   3.259  1.00                    
ATOM     1   O   ALA    15      -9.870  -0.479   3.863  1.00                    
ATOM     1   N   LYS    16      -7.760  -1.083   3.869  1.00                    
ATOM     1   CA  LYS    16      -7.799  -1.368   5.333  1.00                    
ATOM     1   C   LYS    16      -7.826  -0.059   6.128  1.00                    
ATOM     1   O   LYS    16      -8.520   0.061   7.119  1.00                    
ATOM     1   N   ALA    17      -7.077   0.922   5.704  1.00                    
ATOM     1   CA  ALA    17      -7.061   2.220   6.437  1.00                    
ATOM     1   C   ALA    17      -8.487   2.749   6.615  1.00                    
ATOM     1   O   ALA    17      -8.902   3.091   7.704  1.00                    
ATOM     1   N   LYS    18      -9.238   2.826   5.548  1.00                    
ATOM     1   CA  LYS    18     -10.637   3.339   5.647  1.00                    
ATOM     1   C   LYS    18     -11.390   2.640   6.783  1.00                    
ATOM     1   O   LYS    18     -12.075   3.268   7.565  1.00                    
ATOM     1   N   ALA    19     -11.273   1.344   6.877  1.00                    
ATOM     1   CA  ALA    19     -11.984   0.606   7.961  1.00                    
ATOM     1   C   ALA    19     -11.678   1.233   9.326  1.00                    
ATOM     1   O   ALA    19     -12.502   1.909   9.908  1.00                    
ATOM     1   N   GLY    20     -10.502   1.006   9.842  1.00                    
ATOM     1   CA  GLY    20     -10.144   1.580  11.171  1.00                    
ATOM     1   C   GLY    20     -10.341   3.099  11.177  1.00                    
ATOM     1   O   GLY    20     -11.043   3.635  12.011  1.00                    
ATOM     1   N   ILE    22      -9.726   3.797  10.254  1.00                    
ATOM     1   CA  ILE    22      -9.878   5.286  10.204  1.00                    
ATOM     1   C   ILE    22     -11.357   5.670  10.335  1.00                    
ATOM     1   O   ILE    22     -11.697   6.706  10.870  1.00                    
ATOM     1   N   THR    23     -12.237   4.827   9.864  1.00                    
ATOM     1   CA  THR    23     -13.692   5.128   9.978  1.00                    
ATOM     1   C   THR    23     -14.171   4.780  11.390  1.00                    
ATOM     1   O   THR    23     -15.022   5.440  11.951  1.00                    
ATOM     1   N   GLU    24     -13.613   3.752  11.971  1.00                    
ATOM     1   CA  GLU    24     -14.016   3.362  13.352  1.00                    
ATOM     1   C   GLU    24     -13.050   3.982  14.364  1.00                    
ATOM     1   O   GLU    24     -12.879   3.490  15.462  1.00                    
ATOM     1   N   GLU    25     -12.416   5.062  13.996  1.00                    
ATOM     1   CA  GLU    25     -11.456   5.732  14.920  1.00                    
ATOM     1   C   GLU    25     -10.384   4.748  15.396  1.00                    
ATOM     1   O   GLU    25      -9.856   4.869  16.484  1.00                    
ATOM     1   N   GLU    26     -10.045   3.785  14.585  1.00                    
ATOM     1   CA  GLU    26      -8.993   2.806  14.988  1.00                    
ATOM     1   C   GLU    26      -7.729   3.026  14.149  1.00                    
ATOM     1   O   GLU    26      -6.896   2.152  14.019  1.00                    
ATOM     1   N   LYS    27      -7.591   4.194  13.575  1.00                    
ATOM     1   CA  LYS    27      -6.401   4.499  12.731  1.00                    
ATOM     1   C   LYS    27      -5.095   4.412  13.526  1.00                    
ATOM     1   O   LYS    27      -4.029   4.475  12.953  1.00                    
ATOM     1   N   ALA    28      -5.146   4.269  14.828  1.00                    
ATOM     1   CA  ALA    28      -3.874   4.181  15.611  1.00                    
ATOM     1   C   ALA    28      -2.944   3.156  14.956  1.00                    
ATOM     1   O   ALA    28      -1.927   3.495  14.382  1.00                    
ATOM     1   N   GLU    29      -3.308   1.911  15.014  1.00                    
ATOM     1   CA  GLU    29      -2.476   0.859  14.367  1.00                    
ATOM     1   C   GLU    29      -2.788   0.806  12.865  1.00                    
ATOM     1   O   GLU    29      -2.029   0.275  12.079  1.00                    
ATOM     1   N   GLN    30      -3.918   1.339  12.468  1.00                    
ATOM     1   CA  GLN    30      -4.306   1.308  11.026  1.00                    
ATOM     1   C   GLN    30      -3.540   2.357  10.213  1.00                    
ATOM     1   O   GLN    30      -2.961   2.055   9.189  1.00                    
ATOM     1   N   GLN    31      -3.541   3.589  10.646  1.00                    
ATOM     1   CA  GLN    31      -2.823   4.647   9.877  1.00                    
ATOM     1   C   GLN    31      -1.387   4.214   9.582  1.00                    
ATOM     1   O   GLN    31      -0.773   4.678   8.644  1.00                    
ATOM     1   N   LYS    32      -0.846   3.319  10.364  1.00                    
ATOM     1   CA  LYS    32       0.549   2.862  10.100  1.00                    
ATOM     1   C   LYS    32       0.659   2.358   8.661  1.00                    
ATOM     1   O   LYS    32       1.684   2.492   8.021  1.00                    
ATOM     1   N   LEU    33      -0.398   1.792   8.140  1.00                    
ATOM     1   CA  LEU    33      -0.362   1.293   6.736  1.00                    
ATOM     1   C   LEU    33       0.079   2.425   5.808  1.00                    
ATOM     1   O   LEU    33       0.675   2.202   4.773  1.00                    
ATOM     1   N   ARG    34      -0.201   3.645   6.185  1.00                    
ATOM     1   CA  ARG    34       0.209   4.810   5.344  1.00                    
ATOM     1   C   ARG    34       1.686   4.671   4.951  1.00                    
ATOM     1   O   ARG    34       2.090   5.056   3.872  1.00                    
ATOM     1   N   GLN    35       2.487   4.115   5.816  1.00                    
ATOM     1   CA  GLN    35       3.931   3.943   5.488  1.00                    
ATOM     1   C   GLN    35       4.096   2.845   4.434  1.00                    
ATOM     1   O   GLN    35       4.923   2.939   3.550  1.00                    
ATOM     1   N   GLU    36       3.307   1.808   4.519  1.00                    
ATOM     1   CA  GLU    36       3.411   0.708   3.519  1.00                    
ATOM     1   C   GLU    36       2.678   1.098   2.233  1.00                    
ATOM     1   O   GLU    36       3.088   0.753   1.142  1.00                    
ATOM     1   N   LEU    38       1.595   1.818   2.353  1.00                    
ATOM     1   CA  LEU    38       0.834   2.232   1.140  1.00                    
ATOM     1   C   LEU    38       1.663   3.211   0.304  1.00                    
ATOM     1   O   LEU    38       1.631   3.187  -0.910  1.00                    
ATOM     1   N   LYS    39       2.405   4.071   0.946  1.00                    
ATOM     1   CA  LYS    39       3.235   5.052   0.188  1.00                    
ATOM     1   C   LYS    39       4.486   4.367  -0.368  1.00                    
ATOM     1   O   LYS    39       4.856   4.560  -1.509  1.00                    
ATOM     1   N   GLY    40       5.142   3.570   0.430  1.00                    
ATOM     1   CA  GLY    40       6.370   2.875  -0.054  1.00                    
ATOM     1   C   GLY    40       6.018   1.906  -1.186  1.00                    
ATOM     1   O   GLY    40       6.694   1.842  -2.194  1.00                    
ATOM     1   N   PHE    41       4.966   1.151  -1.029  1.00                    
ATOM     1   CA  PHE    41       4.574   0.187  -2.097  1.00                    
ATOM     1   C   PHE    41       4.159   0.942  -3.363  1.00                    
ATOM     1   O   PHE    41       4.221   0.418  -4.458  1.00                    
ATOM     1   N   ARG    42       3.737   2.169  -3.223  1.00                    
ATOM     1   CA  ARG    42       3.319   2.955  -4.419  1.00                    
ATOM     1   C   ARG    42       4.497   3.115  -5.384  1.00                    
ATOM     1   O   ARG    42       4.456   2.659  -6.509  1.00                    
ATOM     1   N   SER    43       5.547   3.758  -4.953  1.00                    
ATOM     1   CA  SER    43       6.726   3.946  -5.847  1.00                    
ATOM     1   C   SER    43       7.203   2.593  -6.382  1.00                    
ATOM     1   O   SER    43       7.605   2.472  -7.521  1.00                    
ATOM     1   N   SER    44       7.160   1.575  -5.566  1.00                    
ATOM     1   CA  SER    44       7.610   0.230  -6.027  1.00                    
ATOM     1   C   SER    44       6.693  -0.283  -7.142  1.00                    
ATOM     1   O   SER    44       7.055  -1.161  -7.900  1.00                    
ATOM     1   N   MET    45       5.508   0.256  -7.248  1.00                    
ATOM     1   CA  MET    45       4.570  -0.202  -8.314  1.00                    
ATOM     1   C   MET    45       5.263  -0.182  -9.680  1.00                    
ATOM     1   O   MET    45       5.154  -1.110 -10.456  1.00                    
ATOM     1   N   LYS    46       5.976   0.869  -9.979  1.00                    
ATOM     1   CA  LYS    46       6.674   0.946 -11.294  1.00                    
ATOM     1   C   LYS    46       7.933   0.076 -11.274  1.00                    
ATOM     1   O   LYS    46       8.166  -0.716 -12.166  1.00                    
ATOM     1   N   ASN    47       8.747   0.215 -10.263  1.00                    
ATOM     1   CA  ASN    47       9.989  -0.606 -10.187  1.00                    
ATOM     1   C   ASN    47       9.646  -2.093 -10.315  1.00                    
ATOM     1   O   ASN    47      10.466  -2.897 -10.715  1.00                    
ATOM     1   N   THR    48       8.442  -2.465  -9.980  1.00                    
ATOM     1   CA  THR    48       8.048  -3.899 -10.083  1.00                    
ATOM     1   C   THR    48       7.588  -4.219 -11.508  1.00                    
ATOM     1   O   THR    48       8.292  -4.852 -12.270  1.00                    
TER
END
