
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0378AL509_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL509_1-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    N       5      A       4          1.617
LGA    Q       6      N       5          2.960
LGA    -       -      Q       6           -
LGA    I       7      I       7          0.358
LGA    K       8      K       8          1.243
LGA    F       9      F       9          1.584
LGA    L      10      L      10          1.165
LGA    R      11      R      11          0.317
LGA    S      12      S      12          0.510
LGA    L      13      L      13          0.570
LGA    R      14      R      14          0.610
LGA    E      15      E      15          0.384
LGA    R      16      R      16          0.519
LGA    K      17      K      17          0.911
LGA    Y      18      Y      18          0.406
LGA    R      19      R      19          0.194
LGA    L      20      L      20          0.857
LGA    R      21      R      21          1.295
LGA    E      22      E      22          0.815
LGA    Q      23      Q      23          0.348
LGA    A      24      A      24          0.691
LGA    F      25      F      25          0.887
LGA    A      26      A      26          0.688
LGA    V      27      V      27          0.597
LGA    E      28      E      28          0.481
LGA    G      29      G      29          1.439
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25   89    5.0     25    1.04    92.00     27.311     2.194

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.685092 * X  +  -0.728431 * Y  +   0.006100 * Z  +  18.467520
  Y_new =   0.704177 * X  +   0.660092 * Y  +  -0.261559 * Z  +   4.084925
  Z_new =   0.186501 * X  +   0.183488 * Y  +   0.965168 * Z  +  26.563175 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.187868   -2.953725  [ DEG:    10.7640   -169.2360 ]
  Theta =  -0.187600   -2.953993  [ DEG:   -10.7487   -169.2513 ]
  Phi   =   0.799135   -2.342458  [ DEG:    45.7870   -134.2130 ]
 
# 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: T0378AL509_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL509_1-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25   89   5.0   25   1.04   92.00  27.311
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL509_1-D1
REMARK Aligment from pdb entry: 1ipaA_
ATOM      1  N   ASN     5       6.949  37.976  53.420  1.00  0.00              
ATOM      2  CA  ASN     5       7.900  37.296  54.314  1.00  0.00              
ATOM      3  C   ASN     5       7.824  35.770  54.322  1.00  0.00              
ATOM      4  O   ASN     5       8.845  35.095  54.456  1.00  0.00              
ATOM      5  N   GLN     6       6.619  35.230  54.176  1.00  0.00              
ATOM      6  CA  GLN     6       6.455  33.787  54.154  1.00  0.00              
ATOM      7  C   GLN     6       7.097  33.217  52.900  1.00  0.00              
ATOM      8  O   GLN     6       7.698  32.145  52.930  1.00  0.00              
ATOM      9  N   ILE     7       6.966  33.945  51.799  1.00  0.00              
ATOM     10  CA  ILE     7       7.525  33.520  50.532  1.00  0.00              
ATOM     11  C   ILE     7       9.039  33.713  50.503  1.00  0.00              
ATOM     12  O   ILE     7       9.757  32.978  49.827  1.00  0.00              
ATOM     13  N   LYS     8       9.530  34.701  51.235  1.00  0.00              
ATOM     14  CA  LYS     8      10.964  34.933  51.286  1.00  0.00              
ATOM     15  C   LYS     8      11.627  33.801  52.070  1.00  0.00              
ATOM     16  O   LYS     8      12.758  33.406  51.775  1.00  0.00              
ATOM     17  N   PHE     9      10.914  33.270  53.059  1.00  0.00              
ATOM     18  CA  PHE     9      11.442  32.180  53.869  1.00  0.00              
ATOM     19  C   PHE     9      11.481  30.881  53.067  1.00  0.00              
ATOM     20  O   PHE     9      12.433  30.120  53.157  1.00  0.00              
ATOM     21  N   LEU    10      10.450  30.630  52.274  1.00  0.00              
ATOM     22  CA  LEU    10      10.421  29.417  51.470  1.00  0.00              
ATOM     23  C   LEU    10      11.444  29.455  50.322  1.00  0.00              
ATOM     24  O   LEU    10      12.047  28.434  49.988  1.00  0.00              
ATOM     25  N   ARG    11      11.655  30.632  49.738  1.00  0.00              
ATOM     26  CA  ARG    11      12.609  30.777  48.630  1.00  0.00              
ATOM     27  C   ARG    11      14.036  30.381  49.023  1.00  0.00              
ATOM     28  O   ARG    11      14.808  29.904  48.189  1.00  0.00              
ATOM     29  N   SER    12      14.388  30.583  50.287  1.00  0.00              
ATOM     30  CA  SER    12      15.716  30.233  50.767  1.00  0.00              
ATOM     31  C   SER    12      15.974  28.735  50.616  1.00  0.00              
ATOM     32  O   SER    12      17.119  28.296  50.521  1.00  0.00              
ATOM     33  N   LEU    13      14.903  27.951  50.594  1.00  0.00              
ATOM     34  CA  LEU    13      15.035  26.509  50.473  1.00  0.00              
ATOM     35  C   LEU    13      15.556  26.085  49.099  1.00  0.00              
ATOM     36  O   LEU    13      15.829  24.904  48.873  1.00  0.00              
ATOM     37  N   ARG    14      15.703  27.040  48.180  1.00  0.00              
ATOM     38  CA  ARG    14      16.230  26.701  46.859  1.00  0.00              
ATOM     39  C   ARG    14      17.729  26.437  46.953  1.00  0.00              
ATOM     40  O   ARG    14      18.313  25.808  46.075  1.00  0.00              
ATOM     41  N   GLU    15      18.340  26.900  48.041  1.00  0.00              
ATOM     42  CA  GLU    15      19.764  26.692  48.258  1.00  0.00              
ATOM     43  C   GLU    15      19.986  25.558  49.265  1.00  0.00              
ATOM     44  O   GLU    15      19.224  25.411  50.223  1.00  0.00              
ATOM     45  N   ARG    16      21.024  24.751  49.048  1.00  0.00              
ATOM     46  CA  ARG    16      21.277  23.609  49.921  1.00  0.00              
ATOM     47  C   ARG    16      21.540  23.871  51.397  1.00  0.00              
ATOM     48  O   ARG    16      20.955  23.206  52.242  1.00  0.00              
ATOM     49  N   LYS    17      22.423  24.807  51.716  1.00  0.00              
ATOM     50  CA  LYS    17      22.726  25.086  53.118  1.00  0.00              
ATOM     51  C   LYS    17      21.466  25.373  53.942  1.00  0.00              
ATOM     52  O   LYS    17      21.351  24.933  55.082  1.00  0.00              
ATOM     53  N   TYR    18      20.530  26.112  53.356  1.00  0.00              
ATOM     54  CA  TYR    18      19.289  26.462  54.028  1.00  0.00              
ATOM     55  C   TYR    18      18.371  25.270  54.238  1.00  0.00              
ATOM     56  O   TYR    18      17.667  25.199  55.240  1.00  0.00              
ATOM     57  N   ARG    19      18.375  24.330  53.301  1.00  0.00              
ATOM     58  CA  ARG    19      17.547  23.144  53.439  1.00  0.00              
ATOM     59  C   ARG    19      18.106  22.276  54.552  1.00  0.00              
ATOM     60  O   ARG    19      17.365  21.737  55.371  1.00  0.00              
ATOM     61  N   LEU    20      19.426  22.146  54.579  1.00  0.00              
ATOM     62  CA  LEU    20      20.078  21.311  55.575  1.00  0.00              
ATOM     63  C   LEU    20      19.955  21.821  57.002  1.00  0.00              
ATOM     64  O   LEU    20      19.685  21.047  57.918  1.00  0.00              
ATOM     65  N   ARG    21      20.135  23.120  57.198  1.00  0.00              
ATOM     66  CA  ARG    21      20.069  23.655  58.542  1.00  0.00              
ATOM     67  C   ARG    21      18.651  23.644  59.081  1.00  0.00              
ATOM     68  O   ARG    21      18.444  23.391  60.261  1.00  0.00              
ATOM     69  N   GLU    22      17.672  23.894  58.220  1.00  0.00              
ATOM     70  CA  GLU    22      16.275  23.911  58.658  1.00  0.00              
ATOM     71  C   GLU    22      15.567  22.574  58.493  1.00  0.00              
ATOM     72  O   GLU    22      14.424  22.424  58.910  1.00  0.00              
ATOM     73  N   GLN    23      16.247  21.609  57.888  1.00  0.00              
ATOM     74  CA  GLN    23      15.667  20.293  57.663  1.00  0.00              
ATOM     75  C   GLN    23      14.333  20.358  56.933  1.00  0.00              
ATOM     76  O   GLN    23      13.387  19.648  57.278  1.00  0.00              
ATOM     77  N   ALA    24      14.264  21.205  55.915  1.00  0.00              
ATOM     78  CA  ALA    24      13.051  21.339  55.123  1.00  0.00              
ATOM     79  C   ALA    24      13.383  21.549  53.648  1.00  0.00              
ATOM     80  O   ALA    24      14.477  22.011  53.308  1.00  0.00              
ATOM     81  N   PHE    25      12.452  21.181  52.777  1.00  0.00              
ATOM     82  CA  PHE    25      12.658  21.331  51.346  1.00  0.00              
ATOM     83  C   PHE    25      11.324  21.405  50.618  1.00  0.00              
ATOM     84  O   PHE    25      10.294  20.962  51.132  1.00  0.00              
ATOM     85  N   ALA    26      11.361  21.982  49.421  1.00  0.00              
ATOM     86  CA  ALA    26      10.175  22.160  48.615  1.00  0.00              
ATOM     87  C   ALA    26       9.991  21.014  47.645  1.00  0.00              
ATOM     88  O   ALA    26      10.960  20.434  47.146  1.00  0.00              
ATOM     89  N   VAL    27       8.734  20.682  47.390  1.00  0.00              
ATOM     90  CA  VAL    27       8.422  19.619  46.465  1.00  0.00              
ATOM     91  C   VAL    27       7.410  20.136  45.445  1.00  0.00              
ATOM     92  O   VAL    27       6.220  20.246  45.736  1.00  0.00              
ATOM     93  N   GLU    28       7.904  20.465  44.255  1.00  0.00              
ATOM     94  CA  GLU    28       7.076  20.974  43.157  1.00  0.00              
ATOM     95  C   GLU    28       6.500  19.851  42.276  1.00  0.00              
ATOM     96  O   GLU    28       7.234  18.982  41.801  1.00  0.00              
ATOM     97  N   GLY    29       5.185  19.874  42.072  1.00  0.00              
ATOM     98  CA  GLY    29       4.550  18.872  41.239  1.00  0.00              
ATOM     99  C   GLY    29       3.691  17.881  41.995  1.00  0.00              
ATOM    100  O   GLY    29       4.119  17.311  43.004  1.00  0.00              
END
