
#######################################################
#                                                     #
#                        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   36 (  178),  selected   36 , name T0335TS121_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS121_3-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          3.458
LGA    K       6      K       6          2.277
LGA    I       7      I       7          1.649
LGA    A       8      A       8          1.500
LGA    R       9      R       9          2.013
LGA    I      10      I      10          1.749
LGA    N      11      N      11          1.266
LGA    E      12      E      12          1.268
LGA    L      13      L      13          2.142
LGA    A      14      A      14          1.810
LGA    A      15      A      15          2.411
LGA    K      16      K      16          2.615
LGA    A      17      A      17          2.131
LGA    K      18      K      18          2.090
LGA    A      19      A      19          4.549
LGA    G      20      G      20          4.398
LGA    V      21      V      21          4.934
LGA    I      22      I      22          3.286
LGA    T      23      T      23          1.651
LGA    E      24      E      24          1.837
LGA    E      25      E      25          1.637
LGA    E      26      E      26          1.908
LGA    K      27      K      27          1.827
LGA    A      28      A      28          1.241
LGA    E      29      E      29          1.603
LGA    Q      30      Q      30          2.166
LGA    Q      31      Q      31          1.240
LGA    K      32      K      32          2.006
LGA    L      33      L      33          1.864
LGA    R      34      R      34          1.593
LGA    Q      35      Q      35          1.871
LGA    E      36      E      36          2.624
LGA    Y      37      Y      37          2.150
LGA    L      38      L      38          1.130
LGA    K      39      K      39          2.826
LGA    G      40      G      40          3.202

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     36    2.40   100.00     74.716     1.439

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.330332 * X  +  -0.291673 * Y  +   0.897668 * Z  +  -1.037679
  Y_new =   0.321491 * X  +   0.928956 * Y  +   0.183535 * Z  +   3.080628
  Z_new =  -0.887426 * X  +   0.227964 * Y  +   0.400634 * Z  +  -6.584823 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.517320   -2.624272  [ DEG:    29.6403   -150.3597 ]
  Theta =   1.091730    2.049862  [ DEG:    62.5515    117.4485 ]
  Phi   =   0.771835   -2.369758  [ DEG:    44.2229   -135.7771 ]
 
# 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: T0335TS121_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS121_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   36   2.40  100.00  74.716
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS121_3-D1
PFRMAT    TS
TARGET    T0335
MODEL     3
PARENT    N/A
ATOM      5  N   ALA     5      -0.668  -9.545 -10.165  1.00  0.00          
ATOM      5  CA  ALA     5      -0.688 -10.100  -8.801  1.00  0.00          
ATOM      5  C   ALA     5      -0.344  -9.033  -7.760  1.00  0.00          
ATOM      5  O   ALA     5      -1.004  -8.892  -6.720  1.00  0.00          
ATOM      5  CB  ALA     5       0.390 -11.198  -8.718  1.00  0.00          
ATOM      6  N   LYS     6       0.705  -8.294  -8.075  1.00  0.00          
ATOM      6  CA  LYS     6       1.210  -7.213  -7.217  1.00  0.00          
ATOM      6  C   LYS     6       0.138  -6.139  -7.013  1.00  0.00          
ATOM      6  O   LYS     6      -0.069  -5.620  -5.907  1.00  0.00          
ATOM      6  CB  LYS     6       2.414  -6.550  -7.909  1.00  0.00          
ATOM      7  N   ILE     7      -0.528  -5.828  -8.109  1.00  0.00          
ATOM      7  CA  ILE     7      -1.601  -4.822  -8.138  1.00  0.00          
ATOM      7  C   ILE     7      -2.711  -5.206  -7.158  1.00  0.00          
ATOM      7  O   ILE     7      -3.255  -4.372  -6.422  1.00  0.00          
ATOM      7  CB  ILE     7      -2.198  -4.826  -9.559  1.00  0.00          
ATOM      8  N   ALA     8      -3.023  -6.490  -7.175  1.00  0.00          
ATOM      8  CA  ALA     8      -4.062  -7.074  -6.314  1.00  0.00          
ATOM      8  C   ALA     8      -3.666  -6.834  -4.856  1.00  0.00          
ATOM      8  O   ALA     8      -4.493  -6.492  -3.997  1.00  0.00          
ATOM      8  CB  ALA     8      -4.093  -8.597  -6.560  1.00  0.00          
ATOM      9  N   ARG     9      -2.383  -7.026  -4.610  1.00  0.00          
ATOM      9  CA  ARG     9      -1.788  -6.852  -3.278  1.00  0.00          
ATOM      9  C   ARG     9      -1.980  -5.414  -2.793  1.00  0.00          
ATOM      9  O   ARG     9      -2.332  -5.154  -1.633  1.00  0.00          
ATOM      9  CB  ARG     9      -0.267  -7.086  -3.392  1.00  0.00          
ATOM     10  N   ILE    10      -1.738  -4.500  -3.714  1.00  0.00          
ATOM     10  CA  ILE    10      -1.861  -3.057  -3.461  1.00  0.00          
ATOM     10  C   ILE    10      -3.296  -2.726  -3.048  1.00  0.00          
ATOM     10  O   ILE    10      -3.549  -1.951  -2.113  1.00  0.00          
ATOM     10  CB  ILE    10      -1.571  -2.311  -4.780  1.00  0.00          
ATOM     11  N   ASN    11      -4.217  -3.336  -3.771  1.00  0.00          
ATOM     11  CA  ASN    11      -5.658  -3.161  -3.544  1.00  0.00          
ATOM     11  C   ASN    11      -6.053  -3.585  -2.128  1.00  0.00          
ATOM     11  O   ASN    11      -6.807  -2.898  -1.422  1.00  0.00          
ATOM     11  CB  ASN    11      -6.396  -4.065  -4.551  1.00  0.00          
ATOM     12  N   GLU    12      -5.524  -4.730  -1.741  1.00  0.00          
ATOM     12  CA  GLU    12      -5.771  -5.323  -0.419  1.00  0.00          
ATOM     12  C   GLU    12      -5.295  -4.324   0.637  1.00  0.00          
ATOM     12  O   GLU    12      -5.932  -4.118   1.682  1.00  0.00          
ATOM     12  CB  GLU    12      -4.939  -6.614  -0.274  1.00  0.00          
ATOM     13  N   LEU    13      -4.162  -3.720   0.331  1.00  0.00          
ATOM     13  CA  LEU    13      -3.527  -2.724   1.205  1.00  0.00          
ATOM     13  C   LEU    13      -4.517  -1.584   1.454  1.00  0.00          
ATOM     13  O   LEU    13      -4.628  -1.041   2.563  1.00  0.00          
ATOM     13  CB  LEU    13      -2.295  -2.145   0.478  1.00  0.00          
ATOM     14  N   ALA    14      -5.225  -1.247   0.392  1.00  0.00          
ATOM     14  CA  ALA    14      -6.234  -0.178   0.410  1.00  0.00          
ATOM     14  C   ALA    14      -7.300  -0.476   1.466  1.00  0.00          
ATOM     14  O   ALA    14      -7.749   0.404   2.213  1.00  0.00          
ATOM     14  CB  ALA    14      -6.931  -0.171  -0.966  1.00  0.00          
ATOM     15  N   ALA    15      -7.686  -1.738   1.502  1.00  0.00          
ATOM     15  CA  ALA    15      -8.700  -2.242   2.441  1.00  0.00          
ATOM     15  C   ALA    15      -8.243  -2.040   3.887  1.00  0.00          
ATOM     15  O   ALA    15      -8.999  -1.582   4.757  1.00  0.00          
ATOM     15  CB  ALA    15      -8.841  -3.764   2.228  1.00  0.00          
ATOM     16  N   LYS    16      -6.991  -2.394   4.108  1.00  0.00          
ATOM     16  CA  LYS    16      -6.349  -2.284   5.426  1.00  0.00          
ATOM     16  C   LYS    16      -6.364  -0.806   5.823  1.00  0.00          
ATOM     16  O   LYS    16      -6.583  -0.441   6.986  1.00  0.00          
ATOM     16  CB  LYS    16      -4.872  -2.715   5.305  1.00  0.00          
ATOM     17  N   ALA    17      -6.124   0.023   4.824  1.00  0.00          
ATOM     17  CA  ALA    17      -6.092   1.485   4.983  1.00  0.00          
ATOM     17  C   ALA    17      -7.432   1.984   5.525  1.00  0.00          
ATOM     17  O   ALA    17      -7.502   2.861   6.399  1.00  0.00          
ATOM     17  CB  ALA    17      -5.932   2.068   3.564  1.00  0.00          
ATOM     18  N   LYS    18      -8.483   1.401   4.980  1.00  0.00          
ATOM     18  CA  LYS    18      -9.866   1.730   5.354  1.00  0.00          
ATOM     18  C   LYS    18     -10.063   1.491   6.852  1.00  0.00          
ATOM     18  O   LYS    18     -10.733   2.259   7.558  1.00  0.00          
ATOM     18  CB  LYS    18     -10.813   0.781   4.593  1.00  0.00          
ATOM     19  N   ALA    19      -9.462   0.408   7.309  1.00  0.00          
ATOM     19  CA  ALA    19      -9.521  -0.009   8.718  1.00  0.00          
ATOM     19  C   ALA    19      -8.579   0.812   9.601  1.00  0.00          
ATOM     19  O   ALA    19      -8.803   0.998  10.807  1.00  0.00          
ATOM     19  CB  ALA    19      -9.068  -1.478   8.789  1.00  0.00          
ATOM     20  N   GLY    20      -7.527   1.292   8.963  1.00  0.00          
ATOM     20  CA  GLY    20      -6.496   2.108   9.620  1.00  0.00          
ATOM     20  C   GLY    20      -5.667   2.896   8.601  1.00  0.00          
ATOM     20  O   GLY    20      -4.432   2.813   8.555  1.00  0.00          
ATOM     21  N   VAL    21      -6.385   3.656   7.796  1.00  0.00          
ATOM     21  CA  VAL    21      -5.790   4.496   6.743  1.00  0.00          
ATOM     21  C   VAL    21      -5.374   5.823   7.381  1.00  0.00          
ATOM     21  O   VAL    21      -4.499   6.545   6.882  1.00  0.00          
ATOM     21  CB  VAL    21      -6.889   4.812   5.712  1.00  0.00          
ATOM     22  N   ILE    22      -6.027   6.114   8.491  1.00  0.00          
ATOM     22  CA  ILE    22      -5.784   7.341   9.264  1.00  0.00          
ATOM     22  C   ILE    22      -4.658   7.177  10.290  1.00  0.00          
ATOM     22  O   ILE    22      -4.122   8.150  10.835  1.00  0.00          
ATOM     22  CB  ILE    22      -7.086   7.624  10.035  1.00  0.00          
ATOM     23  N   THR    23      -4.326   5.922  10.528  1.00  0.00          
ATOM     23  CA  THR    23      -3.270   5.538  11.478  1.00  0.00          
ATOM     23  C   THR    23      -1.943   5.974  10.850  1.00  0.00          
ATOM     23  O   THR    23      -1.640   5.677   9.687  1.00  0.00          
ATOM     23  CB  THR    23      -3.269   4.012  11.661  1.00  0.00          
ATOM     24  N   GLU    24      -1.171   6.680  11.655  1.00  0.00          
ATOM     24  CA  GLU    24       0.146   7.199  11.254  1.00  0.00          
ATOM     24  C   GLU    24       1.083   6.086  10.776  1.00  0.00          
ATOM     24  O   GLU    24       1.777   6.205   9.757  1.00  0.00          
ATOM     24  CB  GLU    24       0.792   7.834  12.501  1.00  0.00          
ATOM     25  N   GLU    25       1.079   5.011  11.541  1.00  0.00          
ATOM     25  CA  GLU    25       1.904   3.824  11.266  1.00  0.00          
ATOM     25  C   GLU    25       1.486   3.281   9.899  1.00  0.00          
ATOM     25  O   GLU    25       2.315   2.870   9.073  1.00  0.00          
ATOM     25  CB  GLU    25       1.569   2.755  12.327  1.00  0.00          
ATOM     26  N   GLU    26       0.182   3.296   9.694  1.00  0.00          
ATOM     26  CA  GLU    26      -0.436   2.819   8.449  1.00  0.00          
ATOM     26  C   GLU    26       0.102   3.623   7.263  1.00  0.00          
ATOM     26  O   GLU    26       0.380   3.087   6.181  1.00  0.00          
ATOM     26  CB  GLU    26      -1.947   3.102   8.569  1.00  0.00          
ATOM     27  N   LYS    27       0.236   4.913   7.504  1.00  0.00          
ATOM     27  CA  LYS    27       0.736   5.867   6.503  1.00  0.00          
ATOM     27  C   LYS    27       2.128   5.455   6.020  1.00  0.00          
ATOM     27  O   LYS    27       2.445   5.491   4.823  1.00  0.00          
ATOM     27  CB  LYS    27       0.854   7.242   7.192  1.00  0.00          
ATOM     28  N   ALA    28       2.939   5.066   6.987  1.00  0.00          
ATOM     28  CA  ALA    28       4.322   4.628   6.745  1.00  0.00          
ATOM     28  C   ALA    28       4.330   3.387   5.850  1.00  0.00          
ATOM     28  O   ALA    28       5.068   3.299   4.857  1.00  0.00          
ATOM     28  CB  ALA    28       4.939   4.241   8.107  1.00  0.00          
ATOM     29  N   GLU    29       3.490   2.443   6.233  1.00  0.00          
ATOM     29  CA  GLU    29       3.338   1.169   5.516  1.00  0.00          
ATOM     29  C   GLU    29       2.852   1.471   4.097  1.00  0.00          
ATOM     29  O   GLU    29       3.311   0.884   3.108  1.00  0.00          
ATOM     29  CB  GLU    29       2.260   0.327   6.232  1.00  0.00          
ATOM     30  N   GLN    30       1.916   2.398   4.036  1.00  0.00          
ATOM     30  CA  GLN    30       1.308   2.842   2.773  1.00  0.00          
ATOM     30  C   GLN    30       2.379   3.366   1.813  1.00  0.00          
ATOM     30  O   GLN    30       2.366   3.096   0.604  1.00  0.00          
ATOM     30  CB  GLN    30       0.390   4.034   3.103  1.00  0.00          
ATOM     31  N   GLN    31       3.298   4.117   2.390  1.00  0.00          
ATOM     31  CA  GLN    31       4.418   4.722   1.654  1.00  0.00          
ATOM     31  C   GLN    31       5.261   3.650   0.959  1.00  0.00          
ATOM     31  O   GLN    31       5.670   3.787  -0.202  1.00  0.00          
ATOM     31  CB  GLN    31       5.322   5.430   2.680  1.00  0.00          
ATOM     32  N   LYS    32       5.504   2.589   1.705  1.00  0.00          
ATOM     32  CA  LYS    32       6.294   1.441   1.235  1.00  0.00          
ATOM     32  C   LYS    32       5.656   0.774   0.014  1.00  0.00          
ATOM     32  O   LYS    32       6.315   0.484  -0.996  1.00  0.00          
ATOM     32  CB  LYS    32       6.308   0.409   2.381  1.00  0.00          
ATOM     33  N   LEU    33       4.363   0.543   0.141  1.00  0.00          
ATOM     33  CA  LEU    33       3.554  -0.088  -0.912  1.00  0.00          
ATOM     33  C   LEU    33       3.558   0.738  -2.200  1.00  0.00          
ATOM     33  O   LEU    33       3.716   0.217  -3.314  1.00  0.00          
ATOM     33  CB  LEU    33       2.100  -0.138  -0.402  1.00  0.00          
ATOM     34  N   ARG    34       3.381   2.032  -2.009  1.00  0.00          
ATOM     34  CA  ARG    34       3.351   3.007  -3.110  1.00  0.00          
ATOM     34  C   ARG    34       4.648   2.968  -3.921  1.00  0.00          
ATOM     34  O   ARG    34       4.649   3.019  -5.160  1.00  0.00          
ATOM     34  CB  ARG    34       3.258   4.423  -2.508  1.00  0.00          
ATOM     35  N   GLN    35       5.740   2.875  -3.186  1.00  0.00          
ATOM     35  CA  GLN    35       7.092   2.822  -3.763  1.00  0.00          
ATOM     35  C   GLN    35       7.228   1.634  -4.717  1.00  0.00          
ATOM     35  O   GLN    35       7.785   1.737  -5.820  1.00  0.00          
ATOM     35  CB  GLN    35       8.092   2.620  -2.608  1.00  0.00          
ATOM     36  N   GLU    36       6.704   0.513  -4.257  1.00  0.00          
ATOM     36  CA  GLU    36       6.725  -0.749  -5.011  1.00  0.00          
ATOM     36  C   GLU    36       5.985  -0.679  -6.348  1.00  0.00          
ATOM     36  O   GLU    36       6.513  -1.039  -7.411  1.00  0.00          
ATOM     36  CB  GLU    36       6.024  -1.809  -4.135  1.00  0.00          
ATOM     37  N   TYR    37       4.756  -0.208  -6.258  1.00  0.00          
ATOM     37  CA  TYR    37       3.868  -0.056  -7.420  1.00  0.00          
ATOM     37  C   TYR    37       4.470   0.907  -8.443  1.00  0.00          
ATOM     37  O   TYR    37       4.449   0.670  -9.660  1.00  0.00          
ATOM     37  CB  TYR    37       2.520   0.533  -6.955  1.00  0.00          
ATOM     38  N   LEU    38       5.003   1.993  -7.912  1.00  0.00          
ATOM     38  CA  LEU    38       5.636   3.049  -8.713  1.00  0.00          
ATOM     38  C   LEU    38       6.786   2.497  -9.560  1.00  0.00          
ATOM     38  O   LEU    38       6.973   2.861 -10.729  1.00  0.00          
ATOM     38  CB  LEU    38       6.225   4.078  -7.731  1.00  0.00          
ATOM     39  N   LYS    39       7.541   1.614  -8.934  1.00  0.00          
ATOM     39  CA  LYS    39       8.700   0.960  -9.561  1.00  0.00          
ATOM     39  C   LYS    39       8.351   0.194 -10.841  1.00  0.00          
ATOM     39  O   LYS    39       9.071   0.238 -11.849  1.00  0.00          
ATOM     39  CB  LYS    39       9.229  -0.086  -8.563  1.00  0.00          
ATOM     40  N   GLY    40       7.231  -0.500 -10.765  1.00  0.00          
ATOM     40  CA  GLY    40       6.711  -1.307 -11.879  1.00  0.00          
ATOM     40  C   GLY    40       6.112  -0.338 -12.898  1.00  0.00          
ATOM     40  O   GLY    40       6.367  -0.417 -14.110  1.00  0.00          
TER
END
