
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0307AL044_5-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307AL044_5-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      18      -       -           -
LGA    T      19      -       -           -
LGA    A      20      I      10          4.913
LGA    I      21      M      11          2.596
LGA    I      22      T      12          2.950
LGA    K      23      F      13          4.014
LGA    M      24      S      14           #
LGA    A      25      G      15          3.964
LGA    -       -      Q      16           -
LGA    -       -      E      17           -
LGA    K      26      L      18          1.024
LGA    S      27      T      19          1.841
LGA    G      33      A      20          1.020
LGA    K      34      I      21          0.824
LGA    K      36      I      22          1.233
LGA    P      37      K      23          1.196
LGA    A      38      M      24          0.837
LGA    E      39      A      25          2.043
LGA    I      40      K      26          2.419
LGA    A      41      S      27          1.471
LGA    M      48      M      28          1.360
LGA    R      49      V      29          2.038
LGA    F      50      M      30          1.447
LGA    G      51      A      31          1.091
LGA    I      52      D      32          4.936
LGA    Q      54      G      33          4.925
LGA    -       -      K      34           -
LGA    -       -      I      35           -
LGA    -       -      K      36           -
LGA    -       -      P      37           -
LGA    -       -      A      38           -
LGA    D      55      E      39           #
LGA    Q      56      I      40           -
LGA    V      57      A      41           -
LGA    D      58      -       -           -
LGA    L      60      -       -           -
LGA    L      61      V      42          1.381
LGA    -       -      M      43           -
LGA    -       -      T      44           -
LGA    -       -      R      45           -
LGA    K      62      E      46          3.664
LGA    -       -      F      47           -
LGA    -       -      M      48           -
LGA    -       -      R      49           -
LGA    -       -      F      50           -
LGA    -       -      G      51           -
LGA    -       -      I      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    -       -      L      60           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    -       -      E      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    -       -      Y      86           -
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    A      63      V      93          2.511
LGA    S      64      I      94          2.564
LGA    D      65      M      95          4.045
LGA    -       -      A      96           -
LGA    -       -      S      97           -
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    S      66      I     101           #
LGA    -       -      D     102           -
LGA    -       -      D     103           -
LGA    -       -      N     104           -
LGA    -       -      E     105           -
LGA    I      67      L     106          0.938
LGA    E      68      A     107          0.935
LGA    -       -      L     108           -
LGA    -       -      W     109           -
LGA    K      85      T     110          4.951
LGA    Y      86      L     111          4.633
LGA    V      87      I     112           -
LGA    A      88      S     113           -
LGA    S      89      T     114           -
LGA    D     103      L     115           -
LGA    N     104      C     116           -
LGA    -       -      G     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      T     120           -
LGA    -       -      M     121           -
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  123    5.0     30    2.85     3.33     16.982     1.017

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.087287 * X  +   0.424959 * Y  +   0.900994 * Z  +  11.506976
  Y_new =   0.292450 * X  +  -0.853663 * Y  +   0.430967 * Z  +   5.220559
  Z_new =   0.952289 * X  +   0.301113 * Y  +  -0.049766 * Z  +  21.549234 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.734589   -1.407004  [ DEG:    99.3846    -80.6154 ]
  Theta =  -1.260650   -1.880943  [ DEG:   -72.2299   -107.7701 ]
  Phi   =   1.860847   -1.280746  [ DEG:   106.6187    -73.3813 ]
 
# 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: T0307AL044_5-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307AL044_5-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  123   5.0   30   2.85    3.33  16.982
REMARK  ---------------------------------------------------------- 
MOLECULE T0307AL044_5-D1
REMARK Aligment from pdb entry: 1y41_A
ATOM      1  N   LEU    18      16.932  20.884  31.655  1.00  0.00              
ATOM      2  CA  LEU    18      16.424  22.204  31.973  1.00  0.00              
ATOM      3  C   LEU    18      14.952  22.159  32.329  1.00  0.00              
ATOM      4  O   LEU    18      14.458  22.993  33.087  1.00  0.00              
ATOM      5  N   THR    19      13.391  21.479  37.091  1.00  0.00              
ATOM      6  CA  THR    19      12.299  22.094  37.839  1.00  0.00              
ATOM      7  C   THR    19      11.085  21.169  37.904  1.00  0.00              
ATOM      8  O   THR    19      10.270  21.266  38.822  1.00  0.00              
ATOM      9  N   ALA    20      10.973  20.265  36.933  1.00  0.00              
ATOM     10  CA  ALA    20       9.860  19.319  36.893  1.00  0.00              
ATOM     11  C   ALA    20      10.157  18.145  37.812  1.00  0.00              
ATOM     12  O   ALA    20       9.294  17.680  38.556  1.00  0.00              
ATOM     13  N   ILE    21      11.401  17.694  37.762  1.00  0.00              
ATOM     14  CA  ILE    21      11.863  16.594  38.592  1.00  0.00              
ATOM     15  C   ILE    21      13.246  16.923  39.144  1.00  0.00              
ATOM     16  O   ILE    21      14.226  16.243  38.842  1.00  0.00              
ATOM     17  N   ILE    22      13.343  17.991  39.956  1.00  0.00              
ATOM     18  CA  ILE    22      14.614  18.423  40.538  1.00  0.00              
ATOM     19  C   ILE    22      15.218  17.366  41.458  1.00  0.00              
ATOM     20  O   ILE    22      16.420  17.374  41.721  1.00  0.00              
ATOM     21  N   LYS    23      14.376  16.460  41.947  1.00  0.00              
ATOM     22  CA  LYS    23      14.832  15.400  42.840  1.00  0.00              
ATOM     23  C   LYS    23      15.094  14.106  42.073  1.00  0.00              
ATOM     24  O   LYS    23      15.830  13.237  42.542  1.00  0.00              
ATOM     25  N   MET    24      14.486  13.979  40.898  1.00  0.00              
ATOM     26  CA  MET    24      14.655  12.786  40.076  1.00  0.00              
ATOM     27  C   MET    24      15.565  13.054  38.876  1.00  0.00              
ATOM     28  O   MET    24      15.948  12.125  38.164  1.00  0.00              
ATOM     29  N   ALA    25      18.532  14.761  39.196  1.00  0.00              
ATOM     30  CA  ALA    25      19.907  14.705  39.689  1.00  0.00              
ATOM     31  C   ALA    25      20.668  13.515  39.099  1.00  0.00              
ATOM     32  O   ALA    25      21.764  13.677  38.563  1.00  0.00              
ATOM     33  N   LYS    26      21.154  14.014  35.226  1.00  0.00              
ATOM     34  CA  LYS    26      22.137  15.014  34.827  1.00  0.00              
ATOM     35  C   LYS    26      23.558  14.494  35.027  1.00  0.00              
ATOM     36  O   LYS    26      24.487  14.921  34.341  1.00  0.00              
ATOM     37  N   SER    27      23.723  13.572  35.971  1.00  0.00              
ATOM     38  CA  SER    27      25.032  12.998  36.259  1.00  0.00              
ATOM     39  C   SER    27      25.139  11.576  35.717  1.00  0.00              
ATOM     40  O   SER    27      26.200  11.156  35.252  1.00  0.00              
ATOM     41  N   GLY    33      24.036  10.838  35.780  1.00  0.00              
ATOM     42  CA  GLY    33      24.027   9.471  35.293  1.00  0.00              
ATOM     43  C   GLY    33      23.569   9.374  33.852  1.00  0.00              
ATOM     44  O   GLY    33      24.343   8.997  32.972  1.00  0.00              
ATOM     45  N   LYS    34      22.307   9.717  33.607  1.00  0.00              
ATOM     46  CA  LYS    34      21.753   9.668  32.258  1.00  0.00              
ATOM     47  C   LYS    34      22.628  10.446  31.283  1.00  0.00              
ATOM     48  O   LYS    34      22.883   9.996  30.167  1.00  0.00              
ATOM     49  N   LYS    36      23.097  11.613  31.717  1.00  0.00              
ATOM     50  CA  LYS    36      23.956  12.444  30.886  1.00  0.00              
ATOM     51  C   LYS    36      25.233  11.696  30.526  1.00  0.00              
ATOM     52  O   LYS    36      25.808  11.903  29.458  1.00  0.00              
ATOM     53  N   PRO    37      25.663  10.816  31.425  1.00  0.00              
ATOM     54  CA  PRO    37      26.863  10.022  31.204  1.00  0.00              
ATOM     55  C   PRO    37      26.586   8.917  30.193  1.00  0.00              
ATOM     56  O   PRO    37      27.420   8.615  29.340  1.00  0.00              
ATOM     57  N   ALA    38      25.399   8.324  30.290  1.00  0.00              
ATOM     58  CA  ALA    38      24.996   7.259  29.379  1.00  0.00              
ATOM     59  C   ALA    38      25.152   7.711  27.930  1.00  0.00              
ATOM     60  O   ALA    38      25.484   6.916  27.052  1.00  0.00              
ATOM     61  N   GLU    39      24.916   8.998  27.694  1.00  0.00              
ATOM     62  CA  GLU    39      25.034   9.570  26.357  1.00  0.00              
ATOM     63  C   GLU    39      26.397   9.258  25.742  1.00  0.00              
ATOM     64  O   GLU    39      26.485   8.691  24.655  1.00  0.00              
ATOM     65  N   ILE    40      27.454   9.639  26.447  1.00  0.00              
ATOM     66  CA  ILE    40      28.816   9.412  25.974  1.00  0.00              
ATOM     67  C   ILE    40      29.104   7.925  25.793  1.00  0.00              
ATOM     68  O   ILE    40      29.981   7.545  25.018  1.00  0.00              
ATOM     69  N   ALA    41      28.364   7.088  26.511  1.00  0.00              
ATOM     70  CA  ALA    41      28.548   5.644  26.426  1.00  0.00              
ATOM     71  C   ALA    41      27.756   5.057  25.262  1.00  0.00              
ATOM     72  O   ALA    41      28.121   4.017  24.714  1.00  0.00              
ATOM     73  N   MET    48      26.668   5.725  24.890  1.00  0.00              
ATOM     74  CA  MET    48      25.827   5.258  23.793  1.00  0.00              
ATOM     75  C   MET    48      26.199   5.930  22.476  1.00  0.00              
ATOM     76  O   MET    48      26.193   5.293  21.423  1.00  0.00              
ATOM     77  N   ARG    49      26.525   7.217  22.540  1.00  0.00              
ATOM     78  CA  ARG    49      26.901   7.967  21.349  1.00  0.00              
ATOM     79  C   ARG    49      28.065   7.284  20.648  1.00  0.00              
ATOM     80  O   ARG    49      28.154   7.282  19.421  1.00  0.00              
ATOM     81  N   PHE    50      28.940   6.681  21.443  1.00  0.00              
ATOM     82  CA  PHE    50      30.085   5.963  20.907  1.00  0.00              
ATOM     83  C   PHE    50      29.623   4.773  20.071  1.00  0.00              
ATOM     84  O   PHE    50      30.384   4.225  19.275  1.00  0.00              
ATOM     85  N   GLY    51      28.363   4.383  20.261  1.00  0.00              
ATOM     86  CA  GLY    51      27.786   3.262  19.528  1.00  0.00              
ATOM     87  C   GLY    51      26.643   3.726  18.625  1.00  0.00              
ATOM     88  O   GLY    51      26.216   2.996  17.732  1.00  0.00              
ATOM     89  N   ILE    52      26.153   4.944  18.859  1.00  0.00              
ATOM     90  CA  ILE    52      25.065   5.503  18.062  1.00  0.00              
ATOM     91  C   ILE    52      25.346   5.333  16.574  1.00  0.00              
ATOM     92  O   ILE    52      24.464   4.969  15.797  1.00  0.00              
ATOM     93  N   GLN    54      26.587   5.601  16.189  1.00  0.00              
ATOM     94  CA  GLN    54      27.001   5.482  14.797  1.00  0.00              
ATOM     95  C   GLN    54      26.841   4.049  14.294  1.00  0.00              
ATOM     96  O   GLN    54      26.796   3.807  13.087  1.00  0.00              
ATOM     97  N   ASP    55      19.693   4.156  14.945  1.00  0.00              
ATOM     98  CA  ASP    55      19.026   5.369  15.405  1.00  0.00              
ATOM     99  C   ASP    55      18.441   6.141  14.225  1.00  0.00              
ATOM    100  O   ASP    55      19.156   6.487  13.285  1.00  0.00              
ATOM    101  N   GLN    56      17.140   6.404  14.277  1.00  0.00              
ATOM    102  CA  GLN    56      16.470   7.131  13.206  1.00  0.00              
ATOM    103  C   GLN    56      15.138   7.704  13.678  1.00  0.00              
ATOM    104  O   GLN    56      14.359   7.024  14.347  1.00  0.00              
ATOM    105  N   VAL    57      14.884   8.961  13.324  1.00  0.00              
ATOM    106  CA  VAL    57      13.648   9.635  13.705  1.00  0.00              
ATOM    107  C   VAL    57      13.392  10.849  12.817  1.00  0.00              
ATOM    108  O   VAL    57      14.179  11.149  11.918  1.00  0.00              
ATOM    109  N   ASP    58       9.916  11.549  11.717  1.00  0.00              
ATOM    110  CA  ASP    58       8.521  11.428  11.307  1.00  0.00              
ATOM    111  C   ASP    58       7.573  11.835  12.435  1.00  0.00              
ATOM    112  O   ASP    58       6.366  11.960  12.223  1.00  0.00              
ATOM    113  N   LEU    60       8.121  12.040  13.630  1.00  0.00              
ATOM    114  CA  LEU    60       7.311  12.431  14.781  1.00  0.00              
ATOM    115  C   LEU    60       8.178  12.655  16.017  1.00  0.00              
ATOM    116  O   LEU    60       7.894  13.532  16.832  1.00  0.00              
ATOM    117  N   LEU    61      16.427  16.298  18.933  1.00  0.00              
ATOM    118  CA  LEU    61      16.904  16.758  20.232  1.00  0.00              
ATOM    119  C   LEU    61      15.922  16.384  21.344  1.00  0.00              
ATOM    120  O   LEU    61      16.189  16.623  22.521  1.00  0.00              
ATOM    121  N   LYS    62      14.787  15.798  20.965  1.00  0.00              
ATOM    122  CA  LYS    62      13.793  15.406  21.946  1.00  0.00              
ATOM    123  C   LYS    62      13.946  13.967  22.387  1.00  0.00              
ATOM    124  O   LYS    62      14.162  13.691  23.567  1.00  0.00              
ATOM    125  N   ALA    63      13.820  13.046  21.439  1.00  0.00              
ATOM    126  CA  ALA    63      13.933  11.627  21.742  1.00  0.00              
ATOM    127  C   ALA    63      14.119  10.806  20.467  1.00  0.00              
ATOM    128  O   ALA    63      13.371  10.962  19.502  1.00  0.00              
ATOM    129  N   SER    64      15.122   9.933  20.474  1.00  0.00              
ATOM    130  CA  SER    64      15.409   9.085  19.321  1.00  0.00              
ATOM    131  C   SER    64      15.324   7.608  19.694  1.00  0.00              
ATOM    132  O   SER    64      15.625   7.226  20.825  1.00  0.00              
ATOM    133  N   ASP    65      14.912   6.781  18.738  1.00  0.00              
ATOM    134  CA  ASP    65      14.788   5.348  18.973  1.00  0.00              
ATOM    135  C   ASP    65      16.050   4.605  18.544  1.00  0.00              
ATOM    136  O   ASP    65      16.526   4.770  17.422  1.00  0.00              
ATOM    137  N   SER    66      16.586   3.788  19.445  1.00  0.00              
ATOM    138  CA  SER    66      17.793   3.018  19.161  1.00  0.00              
ATOM    139  C   SER    66      17.503   1.522  19.192  1.00  0.00              
ATOM    140  O   SER    66      17.540   0.893  20.250  1.00  0.00              
ATOM    141  N   ILE    67      17.216   0.960  18.025  1.00  0.00              
ATOM    142  CA  ILE    67      16.918  -0.463  17.912  1.00  0.00              
ATOM    143  C   ILE    67      18.195  -1.297  17.960  1.00  0.00              
ATOM    144  O   ILE    67      18.902  -1.422  16.960  1.00  0.00              
ATOM    145  N   GLU    68      18.484  -1.869  19.125  1.00  0.00              
ATOM    146  CA  GLU    68      19.677  -2.691  19.295  1.00  0.00              
ATOM    147  C   GLU    68      19.629  -3.470  20.606  1.00  0.00              
ATOM    148  O   GLU    68      19.177  -2.956  21.629  1.00  0.00              
ATOM    149  N   LYS    85      20.104  -4.711  20.567  1.00  0.00              
ATOM    150  CA  LYS    85      20.124  -5.562  21.753  1.00  0.00              
ATOM    151  C   LYS    85      21.551  -5.983  22.089  1.00  0.00              
ATOM    152  O   LYS    85      22.444  -5.913  21.245  1.00  0.00              
ATOM    153  N   TYR    86      21.757  -6.425  23.325  1.00  0.00              
ATOM    154  CA  TYR    86      23.076  -6.862  23.773  1.00  0.00              
ATOM    155  C   TYR    86      23.638  -7.934  22.842  1.00  0.00              
ATOM    156  O   TYR    86      23.028  -8.271  21.828  1.00  0.00              
ATOM    157  N   VAL    87      24.804  -8.467  23.195  1.00  0.00              
ATOM    158  CA  VAL    87      25.448  -9.500  22.391  1.00  0.00              
ATOM    159  C   VAL    87      24.521 -10.697  22.182  1.00  0.00              
ATOM    160  O   VAL    87      24.687 -11.462  21.232  1.00  0.00              
ATOM    161  N   ALA    88      23.546 -10.853  23.075  1.00  0.00              
ATOM    162  CA  ALA    88      22.596 -11.958  22.987  1.00  0.00              
ATOM    163  C   ALA    88      21.912 -11.992  21.622  1.00  0.00              
ATOM    164  O   ALA    88      21.792 -13.050  21.003  1.00  0.00              
ATOM    165  N   SER    89      21.460 -10.831  21.161  1.00  0.00              
ATOM    166  CA  SER    89      20.787 -10.755  19.878  1.00  0.00              
ATOM    167  C   SER    89      19.485 -11.526  19.872  1.00  0.00              
ATOM    168  O   SER    89      19.191 -12.262  18.930  1.00  0.00              
ATOM    169  N   ASP   103      18.705 -11.363  20.936  1.00  0.00              
ATOM    170  CA  ASP   103      17.429 -12.054  21.065  1.00  0.00              
ATOM    171  C   ASP   103      16.283 -11.228  20.485  1.00  0.00              
ATOM    172  O   ASP   103      15.417 -11.759  19.788  1.00  0.00              
ATOM    173  N   ASN   104      16.277  -9.930  20.777  1.00  0.00              
ATOM    174  CA  ASN   104      15.227  -9.047  20.280  1.00  0.00              
ATOM    175  C   ASN   104      15.616  -7.578  20.446  1.00  0.00              
ATOM    176  O   ASN   104      15.547  -7.034  21.548  1.00  0.00              
END
