
#######################################################
#                                                     #
#                        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   55 (  220),  selected   55 , name T0335TS383_1
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS383_1.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    S       3      I       2          1.684
LGA    N       4      S       3          0.911
LGA    A       5      N       4          2.820
LGA    -       -      A       5           -
LGA    K       6      K       6          2.812
LGA    I       7      I       7          2.076
LGA    A       8      A       8          1.581
LGA    R       9      R       9          2.107
LGA    I      10      I      10          1.775
LGA    N      11      N      11          0.619
LGA    E      12      E      12          1.351
LGA    L      13      L      13          1.911
LGA    A      14      A      14          1.109
LGA    A      15      A      15          1.493
LGA    K      16      K      16          2.151
LGA    A      17      A      17          1.481
LGA    K      18      K      18          1.590
LGA    A      19      A      19          3.499
LGA    -       -      G      20           -
LGA    G      20      V      21          2.654
LGA    K      27      I      22          3.442
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      -       -           -
LGA    Q      31      -       -           -
LGA    K      32      -       -           -
LGA    L      33      -       -           -
LGA    R      34      T      23          2.253
LGA    Q      35      E      24          2.292
LGA    E      36      E      25          1.946
LGA    Y      37      E      26          1.898
LGA    L      38      K      27          1.837
LGA    K      39      A      28          1.659
LGA    G      40      E      29          1.173
LGA    F      41      Q      30          1.189
LGA    R      42      Q      31          1.408
LGA    S      43      K      32          0.835
LGA    S      44      L      33          0.927
LGA    M      45      R      34          1.524
LGA    K      46      Q      35          2.456
LGA    N      47      E      36          2.417
LGA    T      48      Y      37          2.508
LGA    L      49      L      38          2.782
LGA    -       -      K      39           -
LGA    -       -      G      40           -
LGA    V      52      F      41          4.566
LGA    K      53      R      42           -
LGA    I      54      -       -           -
LGA    P      64      -       -           -
LGA    E      65      -       -           -
LGA    K      66      -       -           -
LGA    L      67      -       -           -
LGA    K      68      -       -           -
LGA    R      69      -       -           -
LGA    E      70      -       -           -
LGA    Q      71      -       -           -
LGA    R      72      -       -           -
LGA    N      73      -       -           -
LGA    N      74      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   55   42    5.0     36    2.13    44.44     73.800     1.616

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.808964 * X  +   0.106279 * Y  +  -0.578171 * Z  + -18.844782
  Y_new =   0.587722 * X  +  -0.125127 * Y  +   0.799328 * Z  +  -0.487809
  Z_new =   0.012607 * X  +  -0.986432 * Y  +  -0.163686 * Z  +  22.571001 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.735235    1.406357  [ DEG:   -99.4217     80.5783 ]
  Theta =  -0.012607   -3.128986  [ DEG:    -0.7223   -179.2777 ]
  Phi   =   0.628299   -2.513294  [ DEG:    35.9989   -144.0011 ]
 
# 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: T0335TS383_1                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS383_1.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   55   42   5.0   36   2.13   44.44  73.800
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS383_1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT 1x0tA
ATOM      1  N   SER     3       3.414  -6.704 -10.983  1.00  0.00
ATOM      2  CA  SER     3       2.819  -5.378 -10.866  1.00  0.00
ATOM      3  C   SER     3       1.374  -5.505 -10.397  1.00  0.00
ATOM      4  O   SER     3       0.911  -4.713  -9.575  1.00  0.00
ATOM      5  N   ASN     4       0.666  -6.504 -10.917  1.00  0.00
ATOM      6  CA  ASN     4      -0.720  -6.730 -10.522  1.00  0.00
ATOM      7  C   ASN     4      -0.786  -7.046  -9.033  1.00  0.00
ATOM      8  O   ASN     4      -1.668  -6.556  -8.326  1.00  0.00
ATOM      9  N   ALA     5       0.152  -7.866  -8.565  1.00  0.00
ATOM     10  CA  ALA     5       0.218  -8.242  -7.156  1.00  0.00
ATOM     11  C   ALA     5       0.448  -6.998  -6.311  1.00  0.00
ATOM     12  O   ALA     5      -0.181  -6.812  -5.269  1.00  0.00
ATOM     13  N   LYS     6       1.362  -6.150  -6.768  1.00  0.00
ATOM     14  CA  LYS     6       1.684  -4.922  -6.057  1.00  0.00
ATOM     15  C   LYS     6       0.441  -4.058  -5.910  1.00  0.00
ATOM     16  O   LYS     6       0.168  -3.527  -4.834  1.00  0.00
ATOM     17  N   ILE     7      -0.311  -3.917  -6.995  1.00  0.00
ATOM     18  CA  ILE     7      -1.524  -3.113  -6.959  1.00  0.00
ATOM     19  C   ILE     7      -2.540  -3.744  -6.012  1.00  0.00
ATOM     20  O   ILE     7      -3.231  -3.035  -5.275  1.00  0.00
ATOM     21  N   ALA     8      -2.616  -5.074  -6.024  1.00  0.00
ATOM     22  CA  ALA     8      -3.536  -5.801  -5.149  1.00  0.00
ATOM     23  C   ALA     8      -3.193  -5.519  -3.688  1.00  0.00
ATOM     24  O   ALA     8      -4.078  -5.279  -2.862  1.00  0.00
ATOM     25  N   ARG     9      -1.899  -5.557  -3.376  1.00  0.00
ATOM     26  CA  ARG     9      -1.427  -5.311  -2.018  1.00  0.00
ATOM     27  C   ARG     9      -1.720  -3.879  -1.587  1.00  0.00
ATOM     28  O   ARG     9      -2.143  -3.639  -0.455  1.00  0.00
ATOM     29  N   ILE    10      -1.491  -2.931  -2.491  1.00  0.00
ATOM     30  CA  ILE    10      -1.742  -1.522  -2.197  1.00  0.00
ATOM     31  C   ILE    10      -3.219  -1.312  -1.869  1.00  0.00
ATOM     32  O   ILE    10      -3.559  -0.609  -0.915  1.00  0.00
ATOM     33  N   ASN    11      -4.095  -1.923  -2.661  1.00  0.00
ATOM     34  CA  ASN    11      -5.532  -1.799  -2.435  1.00  0.00
ATOM     35  C   ASN    11      -5.918  -2.354  -1.064  1.00  0.00
ATOM     36  O   ASN    11      -6.729  -1.765  -0.349  1.00  0.00
ATOM     37  N   GLU    12      -5.325  -3.483  -0.698  1.00  0.00
ATOM     38  CA  GLU    12      -5.610  -4.114   0.585  1.00  0.00
ATOM     39  C   GLU    12      -5.114  -3.263   1.756  1.00  0.00
ATOM     40  O   GLU    12      -5.806  -3.114   2.766  1.00  0.00
ATOM     41  N   LEU    13      -3.916  -2.705   1.623  1.00  0.00
ATOM     42  CA  LEU    13      -3.351  -1.874   2.678  1.00  0.00
ATOM     43  C   LEU    13      -4.188  -0.620   2.921  1.00  0.00
ATOM     44  O   LEU    13      -4.367  -0.199   4.062  1.00  0.00
ATOM     45  N   ALA    14      -4.706  -0.025   1.851  1.00  0.00
ATOM     46  CA  ALA    14      -5.538   1.166   1.993  1.00  0.00
ATOM     47  C   ALA    14      -6.892   0.784   2.572  1.00  0.00
ATOM     48  O   ALA    14      -7.497   1.554   3.311  1.00  0.00
ATOM     49  N   ALA    15      -7.371  -0.407   2.229  1.00  0.00
ATOM     50  CA  ALA    15      -8.647  -0.864   2.764  1.00  0.00
ATOM     51  C   ALA    15      -8.499  -0.995   4.278  1.00  0.00
ATOM     52  O   ALA    15      -9.376  -0.581   5.036  1.00  0.00
ATOM     53  N   LYS    16      -7.381  -1.567   4.716  1.00  0.00
ATOM     54  CA  LYS    16      -7.126  -1.725   6.139  1.00  0.00
ATOM     55  C   LYS    16      -6.940  -0.355   6.784  1.00  0.00
ATOM     56  O   LYS    16      -7.435  -0.108   7.880  1.00  0.00
ATOM     57  N   ALA    17      -6.232   0.540   6.102  1.00  0.00
ATOM     58  CA  ALA    17      -6.014   1.882   6.632  1.00  0.00
ATOM     59  C   ALA    17      -7.350   2.565   6.915  1.00  0.00
ATOM     60  O   ALA    17      -7.541   3.155   7.976  1.00  0.00
ATOM     61  N   LYS    18      -8.273   2.477   5.965  1.00  0.00
ATOM     62  CA  LYS    18      -9.578   3.109   6.133  1.00  0.00
ATOM     63  C   LYS    18     -10.344   2.530   7.316  1.00  0.00
ATOM     64  O   LYS    18     -10.988   3.262   8.066  1.00  0.00
ATOM     65  N   ALA    19     -10.266   1.214   7.487  1.00  0.00
ATOM     66  CA  ALA    19     -10.965   0.552   8.581  1.00  0.00
ATOM     67  C   ALA    19     -10.431   0.914   9.962  1.00  0.00
ATOM     68  O   ALA    19     -11.198   1.005  10.920  1.00  0.00
ATOM     69  N   GLY    20      -9.125   1.144  10.068  1.00  0.00
ATOM     70  CA  GLY    20      -8.536   1.460  11.368  1.00  0.00
ATOM     71  C   GLY    20      -8.251   2.938  11.615  1.00  0.00
ATOM     72  O   GLY    20      -7.951   3.320  12.737  1.00  0.00
ATOM     73  N   LYS    27      -8.365   3.760  10.577  1.00  0.00
ATOM     74  CA  LYS    27      -8.055   5.187  10.677  1.00  0.00
ATOM     75  C   LYS    27      -8.703   6.005  11.790  1.00  0.00
ATOM     76  O   LYS    27      -8.022   6.764  12.476  1.00  0.00
ATOM     77  N   ALA    28     -10.009   5.870  11.970  1.00  0.00
ATOM     78  CA  ALA    28     -10.694   6.660  12.985  1.00  0.00
ATOM     79  C   ALA    28     -10.267   6.348  14.414  1.00  0.00
ATOM     80  O   ALA    28     -10.155   7.253  15.245  1.00  0.00
ATOM     81  N   GLU    29     -10.006   5.076  14.687  1.00  0.00
ATOM     82  CA  GLU    29      -9.615   4.630  16.021  1.00  0.00
ATOM     83  C   GLU    29      -8.100   4.601  16.227  1.00  0.00
ATOM     84  O   GLU    29      -7.605   4.925  17.311  1.00  0.00
ATOM     85  N   GLN    30      -7.370   4.211  15.186  1.00  0.00
ATOM     86  CA  GLN    30      -5.917   4.101  15.267  1.00  0.00
ATOM     87  C   GLN    30      -5.241   4.789  14.083  1.00  0.00
ATOM     88  O   GLN    30      -4.705   4.124  13.192  1.00  0.00
ATOM     89  N   GLN    31      -5.240   6.132  14.070  1.00  0.00
ATOM     90  CA  GLN    31      -4.621   6.890  12.976  1.00  0.00
ATOM     91  C   GLN    31      -3.144   6.595  12.743  1.00  0.00
ATOM     92  O   GLN    31      -2.678   6.645  11.607  1.00  0.00
ATOM     93  N   LYS    32      -2.401   6.291  13.803  1.00  0.00
ATOM     94  CA  LYS    32      -0.987   5.984  13.624  1.00  0.00
ATOM     95  C   LYS    32      -0.832   4.688  12.836  1.00  0.00
ATOM     96  O   LYS    32       0.062   4.566  11.998  1.00  0.00
ATOM     97  N   LEU    33      -1.704   3.720  13.105  1.00  0.00
ATOM     98  CA  LEU    33      -1.652   2.450  12.392  1.00  0.00
ATOM     99  C   LEU    33      -2.043   2.675  10.931  1.00  0.00
ATOM    100  O   LEU    33      -1.449   2.089  10.027  1.00  0.00
ATOM    101  N   ARG    34      -3.040   3.526  10.696  1.00  0.00
ATOM    102  CA  ARG    34      -3.464   3.803   9.326  1.00  0.00
ATOM    103  C   ARG    34      -2.314   4.443   8.557  1.00  0.00
ATOM    104  O   ARG    34      -2.089   4.128   7.390  1.00  0.00
ATOM    105  N   GLN    35      -1.583   5.334   9.219  1.00  0.00
ATOM    106  CA  GLN    35      -0.447   5.995   8.582  1.00  0.00
ATOM    107  C   GLN    35       0.604   4.939   8.217  1.00  0.00
ATOM    108  O   GLN    35       1.226   5.008   7.155  1.00  0.00
ATOM    109  N   GLU    36       0.798   3.959   9.094  1.00  0.00
ATOM    110  CA  GLU    36       1.754   2.895   8.821  1.00  0.00
ATOM    111  C   GLU    36       1.329   2.117   7.575  1.00  0.00
ATOM    112  O   GLU    36       2.156   1.817   6.713  1.00  0.00
ATOM    113  N   TYR    37       0.042   1.793   7.469  1.00  0.00
ATOM    114  CA  TYR    37      -0.431   1.054   6.303  1.00  0.00
ATOM    115  C   TYR    37      -0.262   1.863   5.027  1.00  0.00
ATOM    116  O   TYR    37       0.075   1.317   3.982  1.00  0.00
ATOM    117  N   LEU    38      -0.496   3.168   5.112  1.00  0.00
ATOM    118  CA  LEU    38      -0.338   4.028   3.948  1.00  0.00
ATOM    119  C   LEU    38       1.123   3.994   3.503  1.00  0.00
ATOM    120  O   LEU    38       1.422   3.873   2.313  1.00  0.00
ATOM    121  N   LYS    39       2.038   4.083   4.462  1.00  0.00
ATOM    122  CA  LYS    39       3.452   4.066   4.114  1.00  0.00
ATOM    123  C   LYS    39       3.890   2.729   3.525  1.00  0.00
ATOM    124  O   LYS    39       4.739   2.695   2.635  1.00  0.00
ATOM    125  N   GLY    40       3.324   1.626   4.009  1.00  0.00
ATOM    126  CA  GLY    40       3.683   0.325   3.451  1.00  0.00
ATOM    127  C   GLY    40       3.212   0.278   1.999  1.00  0.00
ATOM    128  O   GLY    40       3.890  -0.275   1.131  1.00  0.00
ATOM    129  N   PHE    41       2.053   0.875   1.734  1.00  0.00
ATOM    130  CA  PHE    41       1.516   0.906   0.381  1.00  0.00
ATOM    131  C   PHE    41       2.421   1.754  -0.510  1.00  0.00
ATOM    132  O   PHE    41       2.650   1.417  -1.671  1.00  0.00
ATOM    133  N   ARG    42       2.936   2.852   0.037  1.00  0.00
ATOM    134  CA  ARG    42       3.817   3.729  -0.724  1.00  0.00
ATOM    135  C   ARG    42       5.153   3.045  -1.011  1.00  0.00
ATOM    136  O   ARG    42       5.785   3.316  -2.030  1.00  0.00
ATOM    137  N   SER    43       5.588   2.165  -0.111  1.00  0.00
ATOM    138  CA  SER    43       6.839   1.441  -0.323  1.00  0.00
ATOM    139  C   SER    43       6.651   0.498  -1.506  1.00  0.00
ATOM    140  O   SER    43       7.508   0.406  -2.387  1.00  0.00
ATOM    141  N   SER    44       5.526  -0.210  -1.516  1.00  0.00
ATOM    142  CA  SER    44       5.234  -1.143  -2.595  1.00  0.00
ATOM    143  C   SER    44       5.168  -0.399  -3.918  1.00  0.00
ATOM    144  O   SER    44       5.703  -0.862  -4.924  1.00  0.00
ATOM    145  N   MET    45       4.521   0.762  -3.916  1.00  0.00
ATOM    146  CA  MET    45       4.412   1.556  -5.133  1.00  0.00
ATOM    147  C   MET    45       5.797   1.861  -5.689  1.00  0.00
ATOM    148  O   MET    45       6.046   1.712  -6.886  1.00  0.00
ATOM    149  N   LYS    46       6.698   2.282  -4.808  1.00  0.00
ATOM    150  CA  LYS    46       8.057   2.625  -5.207  1.00  0.00
ATOM    151  C   LYS    46       8.837   1.427  -5.738  1.00  0.00
ATOM    152  O   LYS    46       9.533   1.532  -6.747  1.00  0.00
ATOM    153  N   ASN    47       8.717   0.290  -5.058  1.00  0.00
ATOM    154  CA  ASN    47       9.425  -0.924  -5.459  1.00  0.00
ATOM    155  C   ASN    47       8.917  -1.538  -6.760  1.00  0.00
ATOM    156  O   ASN    47       9.708  -1.950  -7.611  1.00  0.00
ATOM    157  N   THR    48       7.598  -1.600  -6.913  1.00  0.00
ATOM    158  CA  THR    48       6.992  -2.193  -8.101  1.00  0.00
ATOM    159  C   THR    48       6.808  -1.220  -9.259  1.00  0.00
ATOM    160  O   THR    48       6.526  -1.636 -10.384  1.00  0.00
ATOM    161  N   LEU    49       6.963   0.070  -8.984  1.00  0.00
ATOM    162  CA  LEU    49       6.806   1.093 -10.013  1.00  0.00
ATOM    163  C   LEU    49       5.394   1.055 -10.589  1.00  0.00
ATOM    164  O   LEU    49       5.209   0.944 -11.802  1.00  0.00
ATOM    165  N   VAL    52       4.398   1.139  -9.712  1.00  0.00
ATOM    166  CA  VAL    52       3.005   1.120 -10.135  1.00  0.00
ATOM    167  C   VAL    52       2.269   2.347  -9.611  1.00  0.00
ATOM    168  O   VAL    52       2.786   3.080  -8.767  1.00  0.00
ATOM    169  N   LYS    53       1.061   2.560 -10.116  1.00  0.00
ATOM    170  CA  LYS    53       0.251   3.695  -9.700  1.00  0.00
ATOM    171  C   LYS    53      -0.749   3.277  -8.629  1.00  0.00
ATOM    172  O   LYS    53      -1.226   2.142  -8.620  1.00  0.00
ATOM    173  N   ILE    54      -1.053   4.195  -7.720  1.00  0.00
ATOM    174  CA  ILE    54      -2.017   3.919  -6.668  1.00  0.00
ATOM    175  C   ILE    54      -3.401   3.963  -7.312  1.00  0.00
ATOM    176  O   ILE    54      -3.698   4.872  -8.085  1.00  0.00
ATOM    177  N   PRO    64      -4.258   2.974  -7.016  1.00  0.00
ATOM    178  CA  PRO    64      -5.607   2.938  -7.590  1.00  0.00
ATOM    179  C   PRO    64      -6.324   4.281  -7.459  1.00  0.00
ATOM    180  O   PRO    64      -6.145   4.995  -6.473  1.00  0.00
ATOM    181  N   GLU    65      -7.130   4.619  -8.461  1.00  0.00
ATOM    182  CA  GLU    65      -7.869   5.877  -8.467  1.00  0.00
ATOM    183  C   GLU    65      -8.699   6.094  -7.200  1.00  0.00
ATOM    184  O   GLU    65      -8.809   7.216  -6.707  1.00  0.00
ATOM    185  N   LYS    66      -9.275   5.018  -6.674  1.00  0.00
ATOM    186  CA  LYS    66     -10.112   5.112  -5.483  1.00  0.00
ATOM    187  C   LYS    66      -9.344   5.441  -4.202  1.00  0.00
ATOM    188  O   LYS    66      -9.954   5.755  -3.180  1.00  0.00
ATOM    189  N   LEU    67      -8.016   5.380  -4.259  1.00  0.00
ATOM    190  CA  LEU    67      -7.191   5.661  -3.083  1.00  0.00
ATOM    191  C   LEU    67      -6.201   6.810  -3.256  1.00  0.00
ATOM    192  O   LEU    67      -5.697   7.352  -2.271  1.00  0.00
ATOM    193  N   LYS    68      -5.912   7.179  -4.497  1.00  0.00
ATOM    194  CA  LYS    68      -4.930   8.229  -4.761  1.00  0.00
ATOM    195  C   LYS    68      -5.125   9.555  -4.027  1.00  0.00
ATOM    196  O   LYS    68      -4.151  10.247  -3.743  1.00  0.00
ATOM    197  N   ARG    69      -6.368   9.908  -3.716  1.00  0.00
ATOM    198  CA  ARG    69      -6.646  11.168  -3.027  1.00  0.00
ATOM    199  C   ARG    69      -6.931  10.990  -1.541  1.00  0.00
ATOM    200  O   ARG    69      -7.195  11.968  -0.840  1.00  0.00
ATOM    201  N   GLU    70      -6.859   9.753  -1.057  1.00  0.00
ATOM    202  CA  GLU    70      -7.187   9.459   0.336  1.00  0.00
ATOM    203  C   GLU    70      -6.087   9.493   1.390  1.00  0.00
ATOM    204  O   GLU    70      -6.272   8.969   2.484  1.00  0.00
ATOM    205  N   GLN    71      -4.944  10.092   1.074  1.00  0.00
ATOM    206  CA  GLN    71      -3.870  10.201   2.057  1.00  0.00
ATOM    207  C   GLN    71      -3.133  11.502   1.808  1.00  0.00
ATOM    208  O   GLN    71      -3.138  12.021   0.691  1.00  0.00
ATOM    209  N   ARG    72      -2.512  12.038   2.851  1.00  0.00
ATOM    210  CA  ARG    72      -1.763  13.276   2.708  1.00  0.00
ATOM    211  C   ARG    72      -0.383  12.953   2.148  1.00  0.00
ATOM    212  O   ARG    72       0.341  12.130   2.702  1.00  0.00
ATOM    213  N   ASN    73      -0.020  13.600   1.049  1.00  0.00
ATOM    214  CA  ASN    73       1.273  13.340   0.441  1.00  0.00
ATOM    215  C   ASN    73       2.442  13.795   1.306  1.00  0.00
ATOM    216  O   ASN    73       3.565  13.321   1.126  1.00  0.00
ATOM    217  N   ASN    74       2.178  14.693   2.251  1.00  0.00
ATOM    218  CA  ASN    74       3.231  15.193   3.139  1.00  0.00
ATOM    219  C   ASN    74       3.418  14.364   4.411  1.00  0.00
ATOM    220  O   ASN    74       4.514  13.862   4.664  1.00  0.00
TER
END
