
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0309AL381_5
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309AL381_5.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       2           -
LGA    -       -      S       3           -
LGA    -       -      K       4           -
LGA    -       -      K       5           -
LGA    -       -      V       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      V      11           -
LGA    -       -      K      12           -
LGA    -       -      G      13           -
LGA    F      35      F      14           #
LGA    K      36      F      15          4.029
LGA    E      37      -       -           -
LGA    I      38      D      16           #
LGA    L      39      M      17           -
LGA    -       -      D      18           -
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      V      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      A      29           -
LGA    -       -      E      30           -
LGA    -       -      Y      31           -
LGA    S      40      T      32          5.009
LGA    E      41      Y      33          3.925
LGA    F      42      D      34          4.459
LGA    N      43      F      35          4.483
LGA    G      44      K      36          3.581
LGA    K      45      E      37          1.157
LGA    N      46      I      38          1.625
LGA    V      47      L      39          1.269
LGA    S      48      S      40          2.935
LGA    I      49      E      41          2.930
LGA    T      50      F      42          0.524
LGA    V      51      N      43          2.848
LGA    K      52      G      44          2.806
LGA    E      53      K      45          3.636
LGA    E      54      N      46          3.557
LGA    -       -      V      47           -
LGA    N      55      S      48           #
LGA    E      56      I      49           -
LGA    L      57      T      50          4.281
LGA    P      58      V      51          3.820
LGA    V      59      -       -           -
LGA    K      60      K      52          1.503
LGA    G      61      E      53           #
LGA    V      62      -       -           -
LGA    E      63      -       -           -
LGA    M      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    D      67      -       -           -
LGA    P      68      E      54          3.560
LGA    -       -      N      55           -
LGA    -       -      E      56           -
LGA    -       -      L      57           -
LGA    -       -      P      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    -       -      V      62           -
LGA    -       -      E      63           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34   62    5.0     20    3.33    10.00     22.634     0.582

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.523120 * X  +   0.832214 * Y  +   0.183750 * Z  +   5.739346
  Y_new =  -0.852254 * X  +  -0.510092 * Y  +  -0.116059 * Z  +   1.098140
  Z_new =  -0.002857 * X  +  -0.217314 * Y  +   0.976097 * Z  +   1.880674 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.219063    2.922529  [ DEG:   -12.5514    167.4486 ]
  Theta =   0.002857    3.138736  [ DEG:     0.1637    179.8363 ]
  Phi   =  -2.121307    1.020286  [ DEG:  -121.5419     58.4581 ]
 
# 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: T0309AL381_5                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309AL381_5.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   62   5.0   20   3.33   10.00  22.634
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL381_5
REMARK Aligment from pdb entry: 1pn5A
ATOM      1  N   PHE    35       7.330 -10.264  -4.330  1.00  0.00              
ATOM      2  CA  PHE    35       6.160 -11.143  -4.277  1.00  0.00              
ATOM      3  C   PHE    35       4.980 -10.378  -4.885  1.00  0.00              
ATOM      4  O   PHE    35       4.273 -10.878  -5.759  1.00  0.00              
ATOM      5  N   LYS    36       4.826  -9.115  -4.474  1.00  0.00              
ATOM      6  CA  LYS    36       3.778  -8.214  -4.942  1.00  0.00              
ATOM      7  C   LYS    36       4.070  -7.630  -6.334  1.00  0.00              
ATOM      8  O   LYS    36       3.495  -6.602  -6.693  1.00  0.00              
ATOM      9  N   GLU    37       4.988  -8.208  -7.111  1.00  0.00              
ATOM     10  CA  GLU    37       5.169  -7.884  -8.526  1.00  0.00              
ATOM     11  C   GLU    37       4.548  -8.973  -9.403  1.00  0.00              
ATOM     12  O   GLU    37       4.188  -8.697 -10.547  1.00  0.00              
ATOM     13  N   ILE    38       4.403 -10.202  -8.892  1.00  0.00              
ATOM     14  CA  ILE    38       3.826 -11.302  -9.655  1.00  0.00              
ATOM     15  C   ILE    38       2.338 -11.016  -9.919  1.00  0.00              
ATOM     16  O   ILE    38       1.903 -11.073 -11.074  1.00  0.00              
ATOM     17  N   LEU    39       1.582 -10.654  -8.874  1.00  0.00              
ATOM     18  CA  LEU    39       0.152 -10.380  -8.968  1.00  0.00              
ATOM     19  C   LEU    39      -0.133  -8.890  -9.108  1.00  0.00              
ATOM     20  O   LEU    39       0.605  -8.033  -8.617  1.00  0.00              
ATOM     21  N   SER    40      -1.249  -8.602  -9.763  1.00  0.00              
ATOM     22  CA  SER    40      -1.766  -7.288 -10.154  1.00  0.00              
ATOM     23  C   SER    40      -3.196  -7.193  -9.627  1.00  0.00              
ATOM     24  O   SER    40      -3.575  -8.007  -8.781  1.00  0.00              
ATOM     25  N   GLU    41      -4.003  -6.196 -10.021  1.00  0.00              
ATOM     26  CA  GLU    41      -5.315  -5.970  -9.385  1.00  0.00              
ATOM     27  C   GLU    41      -6.197  -7.218  -9.386  1.00  0.00              
ATOM     28  O   GLU    41      -7.006  -7.340  -8.468  1.00  0.00              
ATOM     29  N   PHE    42      -6.028  -8.123 -10.356  1.00  0.00              
ATOM     30  CA  PHE    42      -6.789  -9.362 -10.520  1.00  0.00              
ATOM     31  C   PHE    42      -6.930 -10.125  -9.202  1.00  0.00              
ATOM     32  O   PHE    42      -7.992 -10.700  -8.958  1.00  0.00              
ATOM     33  N   ASN    43      -5.919 -10.095  -8.327  1.00  0.00              
ATOM     34  CA  ASN    43      -6.051 -10.612  -6.976  1.00  0.00              
ATOM     35  C   ASN    43      -5.285  -9.795  -5.918  1.00  0.00              
ATOM     36  O   ASN    43      -5.535  -9.993  -4.739  1.00  0.00              
ATOM     37  N   GLY    44      -4.428  -8.820  -6.259  1.00  0.00              
ATOM     38  CA  GLY    44      -3.817  -7.896  -5.282  1.00  0.00              
ATOM     39  C   GLY    44      -4.878  -7.064  -4.543  1.00  0.00              
ATOM     40  O   GLY    44      -4.743  -6.753  -3.356  1.00  0.00              
ATOM     41  N   LYS    45      -5.928  -6.660  -5.261  1.00  0.00              
ATOM     42  CA  LYS    45      -7.121  -6.057  -4.657  1.00  0.00              
ATOM     43  C   LYS    45      -7.782  -7.055  -3.725  1.00  0.00              
ATOM     44  O   LYS    45      -7.985  -6.709  -2.569  1.00  0.00              
ATOM     45  N   ASN    46      -8.086  -8.266  -4.169  1.00  0.00              
ATOM     46  CA  ASN    46      -8.699  -9.249  -3.284  1.00  0.00              
ATOM     47  C   ASN    46      -7.826  -9.504  -2.059  1.00  0.00              
ATOM     48  O   ASN    46      -8.348  -9.555  -0.956  1.00  0.00              
ATOM     49  N   VAL    47      -6.505  -9.527  -2.202  1.00  0.00              
ATOM     50  CA  VAL    47      -5.587  -9.682  -1.094  1.00  0.00              
ATOM     51  C   VAL    47      -5.805  -8.595  -0.042  1.00  0.00              
ATOM     52  O   VAL    47      -6.107  -8.905   1.107  1.00  0.00              
ATOM     53  N   SER    48      -5.669  -7.313  -0.414  1.00  0.00              
ATOM     54  CA  SER    48      -5.816  -6.215   0.546  1.00  0.00              
ATOM     55  C   SER    48      -7.236  -6.148   1.143  1.00  0.00              
ATOM     56  O   SER    48      -7.408  -5.578   2.222  1.00  0.00              
ATOM     57  N   ILE    49      -8.237  -6.688   0.441  1.00  0.00              
ATOM     58  CA  ILE    49      -9.625  -6.796   0.823  1.00  0.00              
ATOM     59  C   ILE    49      -9.790  -7.888   1.888  1.00  0.00              
ATOM     60  O   ILE    49     -10.117  -7.574   3.028  1.00  0.00              
ATOM     61  N   THR    50      -9.538  -9.151   1.529  1.00  0.00              
ATOM     62  CA  THR    50      -9.673 -10.350   2.361  1.00  0.00              
ATOM     63  C   THR    50      -8.962 -10.178   3.705  1.00  0.00              
ATOM     64  O   THR    50      -9.535 -10.463   4.758  1.00  0.00              
ATOM     65  N   VAL    51      -7.742  -9.630   3.665  1.00  0.00              
ATOM     66  CA  VAL    51      -6.958  -9.138   4.781  1.00  0.00              
ATOM     67  C   VAL    51      -7.837  -8.384   5.774  1.00  0.00              
ATOM     68  O   VAL    51      -7.895  -8.746   6.951  1.00  0.00              
ATOM     69  N   LYS    52      -8.500  -7.322   5.322  1.00  0.00              
ATOM     70  CA  LYS    52      -9.225  -6.413   6.192  1.00  0.00              
ATOM     71  C   LYS    52     -10.463  -7.068   6.809  1.00  0.00              
ATOM     72  O   LYS    52     -10.962  -6.590   7.826  1.00  0.00              
ATOM     73  N   GLU    53     -10.954  -8.153   6.205  1.00  0.00              
ATOM     74  CA  GLU    53     -12.051  -8.941   6.752  1.00  0.00              
ATOM     75  C   GLU    53     -11.525  -9.829   7.879  1.00  0.00              
ATOM     76  O   GLU    53     -12.055  -9.814   8.992  1.00  0.00              
ATOM     77  N   GLU    54     -10.451 -10.584   7.605  1.00  0.00              
ATOM     78  CA  GLU    54      -9.815 -11.495   8.535  1.00  0.00              
ATOM     79  C   GLU    54      -9.342 -10.719   9.762  1.00  0.00              
ATOM     80  O   GLU    54      -9.630 -11.138  10.882  1.00  0.00              
ATOM     81  N   ASN    55      -0.803 -21.051  -2.696  1.00  0.00              
ATOM     82  CA  ASN    55       0.137 -21.935  -2.020  1.00  0.00              
ATOM     83  C   ASN    55       1.556 -21.683  -2.509  1.00  0.00              
ATOM     84  O   ASN    55       2.484 -21.802  -1.720  1.00  0.00              
ATOM     85  N   GLU    56       1.728 -21.304  -3.780  1.00  0.00              
ATOM     86  CA  GLU    56       3.029 -20.946  -4.320  1.00  0.00              
ATOM     87  C   GLU    56       3.650 -19.810  -3.512  1.00  0.00              
ATOM     88  O   GLU    56       4.822 -19.892  -3.175  1.00  0.00              
ATOM     89  N   LEU    57       2.872 -18.794  -3.133  1.00  0.00              
ATOM     90  CA  LEU    57       3.388 -17.627  -2.426  1.00  0.00              
ATOM     91  C   LEU    57       3.748 -18.020  -1.006  1.00  0.00              
ATOM     92  O   LEU    57       4.847 -17.737  -0.543  1.00  0.00              
ATOM     93  N   PRO    58       2.831 -18.704  -0.324  1.00  0.00              
ATOM     94  CA  PRO    58       3.052 -19.281   0.992  1.00  0.00              
ATOM     95  C   PRO    58       4.268 -20.220   1.024  1.00  0.00              
ATOM     96  O   PRO    58       4.872 -20.396   2.087  1.00  0.00              
ATOM     97  N   VAL    59       4.616 -20.841  -0.106  1.00  0.00              
ATOM     98  CA  VAL    59       5.825 -21.621  -0.294  1.00  0.00              
ATOM     99  C   VAL    59       7.019 -20.677  -0.466  1.00  0.00              
ATOM    100  O   VAL    59       7.908 -20.684   0.375  1.00  0.00              
ATOM    101  N   LYS    60       7.035 -19.831  -1.500  1.00  0.00              
ATOM    102  CA  LYS    60       8.095 -18.875  -1.840  1.00  0.00              
ATOM    103  C   LYS    60       8.515 -18.030  -0.627  1.00  0.00              
ATOM    104  O   LYS    60       9.709 -17.830  -0.385  1.00  0.00              
ATOM    105  N   GLY    61       7.541 -17.574   0.164  1.00  0.00              
ATOM    106  CA  GLY    61       7.712 -16.804   1.391  1.00  0.00              
ATOM    107  C   GLY    61       8.532 -17.536   2.456  1.00  0.00              
ATOM    108  O   GLY    61       9.060 -16.880   3.349  1.00  0.00              
ATOM    109  N   VAL    62       8.650 -18.863   2.372  1.00  0.00              
ATOM    110  CA  VAL    62       9.262 -19.722   3.378  1.00  0.00              
ATOM    111  C   VAL    62      10.348 -20.631   2.785  1.00  0.00              
ATOM    112  O   VAL    62      11.071 -21.283   3.530  1.00  0.00              
ATOM    113  N   GLU    63      10.501 -20.664   1.461  1.00  0.00              
ATOM    114  CA  GLU    63      11.343 -21.571   0.679  1.00  0.00              
ATOM    115  C   GLU    63      12.850 -21.374   0.902  1.00  0.00              
ATOM    116  O   GLU    63      13.657 -22.037   0.251  1.00  0.00              
ATOM    117  N   MET    64      13.253 -20.444   1.767  1.00  0.00              
ATOM    118  CA  MET    64      14.654 -20.099   1.972  1.00  0.00              
ATOM    119  C   MET    64      15.278 -19.439   0.738  1.00  0.00              
ATOM    120  O   MET    64      16.502 -19.351   0.654  1.00  0.00              
ATOM    121  N   ALA    65      14.469 -18.996  -0.232  1.00  0.00              
ATOM    122  CA  ALA    65      14.911 -18.784  -1.609  1.00  0.00              
ATOM    123  C   ALA    65      14.866 -17.332  -2.077  1.00  0.00              
ATOM    124  O   ALA    65      15.599 -16.981  -2.998  1.00  0.00              
ATOM    125  N   GLY    66      14.008 -16.510  -1.470  1.00  0.00              
ATOM    126  CA  GLY    66      13.829 -15.116  -1.856  1.00  0.00              
ATOM    127  C   GLY    66      13.189 -14.962  -3.239  1.00  0.00              
ATOM    128  O   GLY    66      13.595 -14.078  -3.991  1.00  0.00              
ATOM    129  N   ASP    67      12.172 -15.782  -3.549  1.00  0.00              
ATOM    130  CA  ASP    67      11.643 -16.026  -4.895  1.00  0.00              
ATOM    131  C   ASP    67      12.685 -16.773  -5.744  1.00  0.00              
ATOM    132  O   ASP    67      13.645 -17.309  -5.199  1.00  0.00              
ATOM    133  N   PRO    68      12.448 -16.928  -7.050  1.00  0.00              
ATOM    134  CA  PRO    68      13.379 -17.591  -7.952  1.00  0.00              
ATOM    135  C   PRO    68      13.103 -17.125  -9.386  1.00  0.00              
ATOM    136  O   PRO    68      13.970 -16.510 -10.006  1.00  0.00              
END
