
#######################################################
#                                                     #
#                        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 T0335TS261_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS261_1-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          2.300
LGA    K       6      K       6          1.203
LGA    I       7      I       7          1.716
LGA    A       8      A       8          1.158
LGA    R       9      R       9          0.260
LGA    I      10      I      10          1.217
LGA    N      11      N      11          0.735
LGA    E      12      E      12          0.833
LGA    L      13      L      13          0.959
LGA    A      14      A      14          2.144
LGA    A      15      A      15          2.698
LGA    K      16      K      16          2.106
LGA    A      17      A      17          1.597
LGA    K      18      K      18          1.542
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    A      19      V      21          2.661
LGA    G      20      I      22          3.556
LGA    V      21      T      23          1.022
LGA    -       -      E      24           -
LGA    I      22      E      25          2.651
LGA    T      23      E      26          1.518
LGA    E      24      K      27          1.260
LGA    E      25      A      28          1.174
LGA    E      26      E      29          1.287
LGA    K      27      Q      30          0.846
LGA    A      28      Q      31          0.698
LGA    E      29      K      32          0.864
LGA    Q      30      L      33          1.121
LGA    Q      31      R      34          0.755
LGA    K      32      Q      35          0.984
LGA    L      33      E      36          0.626
LGA    R      34      Y      37          0.125
LGA    Q      35      L      38          0.655
LGA    E      36      K      39          1.467
LGA    Y      37      G      40          1.601
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     33    1.57    45.45     85.197     1.980

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.263096 * X  +  -0.337419 * Y  +  -0.903841 * Z  +   7.414331
  Y_new =  -0.939400 * X  +  -0.303023 * Y  +  -0.160323 * Z  + -25.274708
  Z_new =  -0.219789 * X  +   0.891249 * Y  +  -0.396696 * Z  + -29.346365 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.989568   -1.152024  [ DEG:   113.9939    -66.0061 ]
  Theta =   0.221598    2.919994  [ DEG:    12.6966    167.3034 ]
  Phi   =  -1.297725    1.843868  [ DEG:   -74.3541    105.6459 ]
 
# 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: T0335TS261_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS261_1-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   33   1.57   45.45  85.197
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS261_1-D1
PFRMAT TS
TARGET T0335
MODEL  1
PARENT 2c5k_T
ATOM     21  N   ALA     5      -0.385  -8.368  -8.208  1.00 10.00
ATOM     22  CA  ALA     5      -0.486  -8.986  -6.889  1.00 10.00
ATOM     23  C   ALA     5      -0.124  -7.988  -5.774  1.00 10.00
ATOM     24  O   ALA     5      -0.815  -7.886  -4.776  1.00 10.00
ATOM     25  CB  ALA     5       0.416 -10.229  -6.821  1.00 10.00
ATOM     26  N   LYS     6       0.976  -7.267  -5.961  1.00  6.28
ATOM     27  CA  LYS     6       1.438  -6.292  -4.961  1.00  6.28
ATOM     28  C   LYS     6       0.419  -5.159  -4.759  1.00  6.28
ATOM     29  O   LYS     6       0.106  -4.773  -3.640  1.00  6.28
ATOM     30  CB  LYS     6       2.785  -5.706  -5.391  1.00  6.28
ATOM     31  N   ILE     7      -0.115  -4.649  -5.859  1.00  5.28
ATOM     32  CA  ILE     7      -1.162  -3.648  -5.776  1.00  5.28
ATOM     33  C   ILE     7      -2.421  -4.206  -5.135  1.00  5.28
ATOM     34  O   ILE     7      -2.994  -3.571  -4.274  1.00  5.28
ATOM     35  CB  ILE     7      -1.447  -3.060  -7.161  1.00  5.28
ATOM     36  N   ALA     8      -2.826  -5.405  -5.531  1.00 10.00
ATOM     37  CA  ALA     8      -3.981  -6.035  -4.949  1.00 10.00
ATOM     38  C   ALA     8      -3.849  -6.231  -3.434  1.00 10.00
ATOM     39  O   ALA     8      -4.810  -6.012  -2.690  1.00 10.00
ATOM     40  CB  ALA     8      -4.273  -7.362  -5.647  1.00 10.00
ATOM     41  N   ARG     9      -2.672  -6.650  -2.984  1.00  5.78
ATOM     42  CA  ARG     9      -2.410  -6.822  -1.541  1.00  5.78
ATOM     43  C   ARG     9      -2.591  -5.519  -0.724  1.00  5.78
ATOM     44  O   ARG     9      -3.232  -5.515   0.328  1.00  5.78
ATOM     45  CB  ARG     9      -1.002  -7.385  -1.350  1.00  5.78
ATOM     46  N   ILE    10      -2.050  -4.407  -1.214  1.00  6.39
ATOM     47  CA  ILE    10      -2.299  -3.119  -0.565  1.00  6.39
ATOM     48  C   ILE    10      -3.775  -2.708  -0.606  1.00  6.39
ATOM     49  O   ILE    10      -4.298  -2.127   0.359  1.00  6.39
ATOM     50  CB  ILE    10      -1.436  -2.018  -1.171  1.00  6.39
ATOM     51  N   ASN    11      -4.429  -2.980  -1.731  1.00  2.91
ATOM     52  CA  ASN    11      -5.833  -2.678  -1.897  1.00  2.91
ATOM     53  C   ASN    11      -6.706  -3.397  -0.863  1.00  2.91
ATOM     54  O   ASN    11      -7.547  -2.766  -0.228  1.00  2.91
ATOM     55  CB  ASN    11      -6.299  -2.994  -3.330  1.00  2.91
ATOM     56  N   GLU    12      -6.469  -4.692  -0.677  1.00  9.19
ATOM     57  CA  GLU    12      -7.146  -5.484   0.356  1.00  9.19
ATOM     58  C   GLU    12      -6.892  -4.914   1.766  1.00  9.19
ATOM     59  O   GLU    12      -7.798  -4.846   2.616  1.00  9.19
ATOM     60  CB  GLU    12      -6.698  -6.961   0.267  1.00  9.19
ATOM     61  N   LEU    13      -5.648  -4.502   2.005  1.00  8.81
ATOM     62  CA  LEU    13      -5.262  -3.906   3.275  1.00  8.81
ATOM     63  C   LEU    13      -6.038  -2.619   3.539  1.00  8.81
ATOM     64  O   LEU    13      -6.534  -2.405   4.639  1.00  8.81
ATOM     65  CB  LEU    13      -3.754  -3.649   3.331  1.00  8.81
ATOM     66  N   ALA    14      -6.134  -1.767   2.526  1.00  8.79
ATOM     67  CA  ALA    14      -6.815  -0.477   2.646  1.00  8.79
ATOM     68  C   ALA    14      -8.291  -0.668   2.977  1.00  8.79
ATOM     69  O   ALA    14      -8.824   0.045   3.811  1.00  8.79
ATOM     70  CB  ALA    14      -6.629   0.418   1.363  1.00  8.79
ATOM     71  N   ALA    15      -8.933  -1.634   2.335  1.00  7.69
ATOM     72  CA  ALA    15     -10.322  -1.974   2.633  1.00  7.69
ATOM     73  C   ALA    15     -10.487  -2.242   4.141  1.00  7.69
ATOM     74  O   ALA    15     -11.412  -1.726   4.770  1.00  7.69
ATOM     75  CB  ALA    15     -10.792  -3.189   1.788  1.00  7.69
ATOM     76  N   LYS    16      -9.564  -3.007   4.719  1.00  6.95
ATOM     77  CA  LYS    16      -9.644  -3.369   6.129  1.00  6.95
ATOM     78  C   LYS    16      -9.166  -2.287   7.095  1.00  6.95
ATOM     79  O   LYS    16      -9.513  -2.332   8.261  1.00  6.95
ATOM     80  CB  LYS    16      -8.892  -4.668   6.391  1.00  6.95
ATOM     81  N   ALA    17      -8.375  -1.325   6.625  1.00  5.49
ATOM     82  CA  ALA    17      -7.906  -0.219   7.476  1.00  5.49
ATOM     83  C   ALA    17      -8.105   1.130   6.755  1.00  5.49
ATOM     84  O   ALA    17      -7.126   1.827   6.439  1.00  5.49
ATOM     85  CB  ALA    17      -6.423  -0.390   7.846  1.00  5.49
ATOM     86  N   LYS    18      -9.371   1.488   6.508  1.00  5.14
ATOM     87  CA  LYS    18      -9.742   2.652   5.670  1.00  5.14
ATOM     88  C   LYS    18      -9.792   3.989   6.447  1.00  5.14
ATOM     89  O   LYS    18     -10.456   4.952   6.031  1.00  5.14
ATOM     90  CB  LYS    18     -11.089   2.378   4.961  1.00  5.14
ATOM     91  N   ALA    19      -9.098   4.033   7.584  1.00  4.52
ATOM     92  CA  ALA    19      -8.989   5.248   8.398  1.00  4.52
ATOM     93  C   ALA    19      -7.525   5.702   8.403  1.00  4.52
ATOM     94  O   ALA    19      -6.616   4.871   8.308  1.00  4.52
ATOM     95  CB  ALA    19      -9.531   5.048   9.861  1.00  4.52
ATOM     96  N   GLY    20      -7.293   7.009   8.507  1.00  5.75
ATOM     97  CA  GLY    20      -5.938   7.552   8.341  1.00  5.75
ATOM     98  C   GLY    20      -5.039   7.418   9.578  1.00  5.75
ATOM     99  O   GLY    20      -5.331   7.965  10.643  1.00  5.75
ATOM    100  N   VAL    21      -1.601   5.051  11.251  1.00  5.27
ATOM    101  CA  VAL    21      -1.617   3.736  10.614  1.00  5.27
ATOM    102  C   VAL    21      -0.214   3.136  10.508  1.00  5.27
ATOM    103  O   VAL    21       0.734   3.798  10.069  1.00  5.27
ATOM    104  CB  VAL    21      -2.262   3.813   9.226  1.00  5.27
ATOM    105  N   ILE    22      -0.112   1.871  10.907  1.00  5.32
ATOM    106  CA  ILE    22       1.145   1.124  10.981  1.00  5.32
ATOM    107  C   ILE    22       1.895   0.999   9.660  1.00  5.32
ATOM    108  O   ILE    22       3.126   1.019   9.644  1.00  5.32
ATOM    109  CB  ILE    22       0.882  -0.283  11.537  1.00  5.32
ATOM    110  N   THR    23       1.151   0.868   8.563  1.00  5.30
ATOM    111  CA  THR    23       1.733   0.560   7.256  1.00  5.30
ATOM    112  C   THR    23       1.838   1.761   6.315  1.00  5.30
ATOM    113  O   THR    23       2.100   1.593   5.121  1.00  5.30
ATOM    114  CB  THR    23       0.918  -0.545   6.572  1.00  5.30
ATOM    115  N   GLU    24       1.647   2.960   6.851  1.00  6.28
ATOM    116  CA  GLU    24       1.608   4.161   6.035  1.00  6.28
ATOM    117  C   GLU    24       2.916   4.443   5.265  1.00  6.28
ATOM    118  O   GLU    24       2.868   4.704   4.073  1.00  6.28
ATOM    119  CB  GLU    24       1.211   5.372   6.886  1.00  6.28
ATOM    120  N   GLU    25       4.062   4.401   5.955  1.00  6.69
ATOM    121  CA  GLU    25       5.378   4.562   5.312  1.00  6.69
ATOM    122  C   GLU    25       5.621   3.415   4.343  1.00  6.69
ATOM    123  O   GLU    25       6.112   3.612   3.237  1.00  6.69
ATOM    124  CB  GLU    25       6.534   4.580   6.341  1.00  6.69
ATOM    125  N   GLU    26       5.304   2.206   4.790  1.00  7.02
ATOM    126  CA  GLU    26       5.530   1.025   3.997  1.00  7.02
ATOM    127  C   GLU    26       4.796   1.097   2.655  1.00  7.02
ATOM    128  O   GLU    26       5.393   0.867   1.596  1.00  7.02
ATOM    129  CB  GLU    26       5.116  -0.194   4.807  1.00  7.02
ATOM    130  N   LYS    27       3.514   1.454   2.711  1.00  9.40
ATOM    131  CA  LYS    27       2.688   1.573   1.500  1.00  9.40
ATOM    132  C   LYS    27       3.239   2.625   0.525  1.00  9.40
ATOM    133  O   LYS    27       3.346   2.365  -0.671  1.00  9.40
ATOM    134  CB  LYS    27       1.187   1.814   1.850  1.00  9.40
ATOM    135  N   ALA    28       3.637   3.785   1.044  1.00 10.00
ATOM    136  CA  ALA    28       4.294   4.792   0.217  1.00 10.00
ATOM    137  C   ALA    28       5.552   4.264  -0.469  1.00 10.00
ATOM    138  O   ALA    28       5.751   4.509  -1.659  1.00 10.00
ATOM    139  CB  ALA    28       4.602   6.065   1.018  1.00 10.00
ATOM    140  N   GLU    29       6.391   3.537   0.278  1.00  8.34
ATOM    141  CA  GLU    29       7.601   2.952  -0.296  1.00  8.34
ATOM    142  C   GLU    29       7.283   1.950  -1.393  1.00  8.34
ATOM    143  O   GLU    29       7.883   1.996  -2.452  1.00  8.34
ATOM    144  CB  GLU    29       8.449   2.270   0.785  1.00  8.34
ATOM    145  N   GLN    30       6.338   1.051  -1.144  1.00 10.00
ATOM    146  CA  GLN    30       6.003   0.044  -2.143  1.00 10.00
ATOM    147  C   GLN    30       5.362   0.681  -3.388  1.00 10.00
ATOM    148  O   GLN    30       5.683   0.302  -4.498  1.00 10.00
ATOM    149  CB  GLN    30       5.098  -1.051  -1.562  1.00 10.00
ATOM    150  N   GLN    31       4.476   1.650  -3.202  1.00 10.00
ATOM    151  CA  GLN    31       3.861   2.350  -4.359  1.00 10.00
ATOM    152  C   GLN    31       4.888   3.056  -5.235  1.00 10.00
ATOM    153  O   GLN    31       4.747   3.083  -6.461  1.00 10.00
ATOM    154  CB  GLN    31       2.787   3.368  -3.934  1.00 10.00
ATOM    155  N   LYS    32       5.902   3.649  -4.601  1.00  8.39
ATOM    156  CA  LYS    32       6.979   4.299  -5.359  1.00  8.39
ATOM    157  C   LYS    32       7.797   3.265  -6.103  1.00  8.39
ATOM    158  O   LYS    32       8.165   3.479  -7.258  1.00  8.39
ATOM    159  CB  LYS    32       7.878   5.158  -4.441  1.00  8.39
ATOM    160  N   LEU    33       8.092   2.141  -5.454  1.00 10.00
ATOM    161  CA  LEU    33       8.768   1.037  -6.157  1.00 10.00
ATOM    162  C   LEU    33       7.946   0.551  -7.364  1.00 10.00
ATOM    163  O   LEU    33       8.503   0.268  -8.421  1.00 10.00
ATOM    164  CB  LEU    33       9.046  -0.161  -5.234  1.00 10.00
ATOM    165  N   ARG    34       6.627   0.446  -7.198  1.00  9.97
ATOM    166  CA  ARG    34       5.723   0.080  -8.305  1.00  9.97
ATOM    167  C   ARG    34       5.766   1.084  -9.475  1.00  9.97
ATOM    168  O   ARG    34       5.862   0.682 -10.628  1.00  9.97
ATOM    169  CB  ARG    34       4.253  -0.132  -7.800  1.00  9.97
ATOM    170  N   GLN    35       5.714   2.385  -9.179  1.00  9.41
ATOM    171  CA  GLN    35       5.964   3.426 -10.188  1.00  9.41
ATOM    172  C   GLN    35       7.204   3.166 -11.048  1.00  9.41
ATOM    173  O   GLN    35       7.177   3.309 -12.263  1.00  9.41
ATOM    174  CB  GLN    35       6.217   4.763  -9.497  1.00  9.41
ATOM    175  N   GLU    36       8.315   2.865 -10.380  1.00  6.30
ATOM    176  CA  GLU    36       9.590   2.668 -11.039  1.00  6.30
ATOM    177  C   GLU    36       9.626   1.318 -11.759  1.00  6.30
ATOM    178  O   GLU    36      10.265   1.168 -12.792  1.00  6.30
ATOM    179  CB  GLU    36      10.716   2.812 -10.005  1.00  6.30
ATOM    180  N   TYR    37       8.915   0.341 -11.216  1.00  5.90
ATOM    181  CA  TYR    37       8.722  -0.933 -11.922  1.00  5.90
ATOM    182  C   TYR    37       7.993  -0.777 -13.253  1.00  5.90
ATOM    183  O   TYR    37       8.358  -1.416 -14.235  1.00  5.90
ATOM    184  CB  TYR    37       7.940  -1.926 -11.074  1.00  5.90
ATOM    185  N   LEU    38       6.953   0.059 -13.275  1.00  7.45
ATOM    186  CA  LEU    38       6.173   0.303 -14.490  1.00  7.45
ATOM    187  C   LEU    38       7.049   0.990 -15.547  1.00  7.45
ATOM    188  O   LEU    38       6.937   0.707 -16.731  1.00  7.45
ATOM    189  CB  LEU    38       4.918   1.167 -14.163  1.00  7.45
ATOM    190  N   LYS    39       7.926   1.893 -15.100  1.00  8.86
ATOM    191  CA  LYS    39       8.912   2.529 -15.989  1.00  8.86
ATOM    192  C   LYS    39       9.769   1.438 -16.642  1.00  8.86
ATOM    193  O   LYS    39       9.989   1.468 -17.856  1.00  8.86
ATOM    194  CB  LYS    39       9.780   3.613 -15.241  1.00  8.86
ATOM    195  N   GLY    40      10.211   0.463 -15.844  1.00  1.35
ATOM    196  CA  GLY    40      11.000  -0.665 -16.379  1.00  1.35
ATOM    197  C   GLY    40      10.223  -1.502 -17.393  1.00  1.35
ATOM    198  O   GLY    40      10.780  -1.903 -18.432  1.00  1.35
TER
END
