
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0327AL044_1
# Molecule2: number of CA atoms   73 ( 1169),  selected   73 , name T0327.pdb
# PARAMETERS: T0327AL044_1.T0327.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K       5           -
LGA    Y      45      L       6          2.265
LGA    I      46      R       7          2.669
LGA    I      47      Y       8          2.214
LGA    -       -      A       9           -
LGA    -       -      I      10           -
LGA    Y      51      L      11          2.692
LGA    S      52      K      12          3.650
LGA    -       -      E      13           -
LGA    D      53      I      14          3.185
LGA    D      54      F      15          2.566
LGA    -       -      E      16           -
LGA    R      55      G      17          3.681
LGA    -       -      N      18           -
LGA    H      57      T      19          4.787
LGA    L      58      P      20          2.641
LGA    Y      59      L      21          2.777
LGA    K      60      S      22          3.880
LGA    L      61      E      23          1.750
LGA    G      62      N      24          3.158
LGA    P      63      D      25          3.312
LGA    -       -      I      26           -
LGA    -       -      G      27           -
LGA    E      64      V      28          5.345
LGA    L      65      T      29          1.068
LGA    T      66      E      30          2.499
LGA    E      67      D      31          1.863
LGA    K      68      Q      32          3.701
LGA    -       -      F      33           -
LGA    -       -      D      34           -
LGA    -       -      D      35           -
LGA    G      69      A      36          0.692
LGA    E      70      V      37          1.856
LGA    -       -      N      38           -
LGA    -       -      F      39           -
LGA    N      71      L      40          1.960
LGA    Y      72      K      41          3.471
LGA    -       -      R      42           -
LGA    -       -      E      43           -
LGA    -       -      G      44           -
LGA    L      73      Y      45          2.547
LGA    G      77      I      46          2.116
LGA    T      78      I      47          2.044
LGA    -       -      G      48           -
LGA    W      79      V      49          2.807
LGA    S      80      H      50          1.935
LGA    K      81      Y      51           -
LGA    -       -      S      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    A      82      R      55           #
LGA    Y      83      P      56          1.889
LGA    K      84      H      57          2.462
LGA    T      85      L      58          0.866
LGA    I      86      Y      59           #
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      G      62           -
LGA    -       -      P      63           -
LGA    -       -      E      64           -
LGA    -       -      L      65           -
LGA    -       -      T      66           -
LGA    -       -      E      67           -
LGA    -       -      K      68           -
LGA    -       -      G      69           -
LGA    -       -      E      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      E      75           -
LGA    -       -      N      76           -
LGA    -       -      G      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   73    5.0     32    2.82     0.00     26.448     1.095

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.932272 * X  +  -0.360766 * Y  +  -0.026776 * Z  + -100.398453
  Y_new =   0.316542 * X  +   0.849341 * Y  +  -0.422400 * Z  + -35.803490
  Z_new =   0.175129 * X  +   0.385316 * Y  +   0.906014 * Z  + -25.368063 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.402113   -2.739479  [ DEG:    23.0394   -156.9606 ]
  Theta =  -0.176037   -2.965555  [ DEG:   -10.0862   -169.9138 ]
  Phi   =   0.327325   -2.814268  [ DEG:    18.7543   -161.2457 ]
 
# 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: T0327AL044_1                                  
REMARK     2: T0327.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0327AL044_1.T0327.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   73   5.0   32   2.82    0.00  26.448
REMARK  ---------------------------------------------------------- 
MOLECULE T0327AL044_1
REMARK Aligment from pdb entry: 1j93_A
ATOM      1  N   TYR    45      -5.879   3.780   5.440  1.00  0.00              
ATOM      2  CA  TYR    45      -6.066   2.481   4.828  1.00  0.00              
ATOM      3  C   TYR    45      -6.493   2.743   3.403  1.00  0.00              
ATOM      4  O   TYR    45      -7.460   3.457   3.147  1.00  0.00              
ATOM      5  N   ILE    46      -5.756   2.167   2.471  1.00  0.00              
ATOM      6  CA  ILE    46      -6.050   2.335   1.064  1.00  0.00              
ATOM      7  C   ILE    46      -5.381   1.170   0.350  1.00  0.00              
ATOM      8  O   ILE    46      -4.173   1.191   0.133  1.00  0.00              
ATOM      9  N   ILE    47      -6.148   0.140   0.004  1.00  0.00              
ATOM     10  CA  ILE    47      -5.561  -1.006  -0.674  1.00  0.00              
ATOM     11  C   ILE    47      -5.149  -0.620  -2.086  1.00  0.00              
ATOM     12  O   ILE    47      -5.747   0.263  -2.697  1.00  0.00              
ATOM     13  N   TYR    51      -4.118  -1.282  -2.596  1.00  0.00              
ATOM     14  CA  TYR    51      -3.646  -0.977  -3.927  1.00  0.00              
ATOM     15  C   TYR    51      -2.847   0.308  -3.917  1.00  0.00              
ATOM     16  O   TYR    51      -2.917   1.093  -4.861  1.00  0.00              
ATOM     17  N   SER    52      -2.081   0.520  -2.848  1.00  0.00              
ATOM     18  CA  SER    52      -1.274   1.727  -2.706  1.00  0.00              
ATOM     19  C   SER    52       0.184   1.486  -3.080  1.00  0.00              
ATOM     20  O   SER    52       1.037   2.356  -2.895  1.00  0.00              
ATOM     21  N   ASP    53       0.453   0.302  -3.619  1.00  0.00              
ATOM     22  CA  ASP    53       1.798  -0.064  -4.022  1.00  0.00              
ATOM     23  C   ASP    53       2.590   0.974  -4.797  1.00  0.00              
ATOM     24  O   ASP    53       3.816   1.016  -4.706  1.00  0.00              
ATOM     25  N   ASP    54       1.912   1.817  -5.564  1.00  0.00              
ATOM     26  CA  ASP    54       2.628   2.823  -6.328  1.00  0.00              
ATOM     27  C   ASP    54       2.582   4.201  -5.697  1.00  0.00              
ATOM     28  O   ASP    54       3.169   5.152  -6.224  1.00  0.00              
ATOM     29  N   ARG    55       1.897   4.305  -4.559  1.00  0.00              
ATOM     30  CA  ARG    55       1.750   5.572  -3.852  1.00  0.00              
ATOM     31  C   ARG    55       2.468   5.637  -2.517  1.00  0.00              
ATOM     32  O   ARG    55       2.445   6.663  -1.844  1.00  0.00              
ATOM     33  N   HIS    57       3.100   4.543  -2.126  1.00  0.00              
ATOM     34  CA  HIS    57       3.769   4.491  -0.838  1.00  0.00              
ATOM     35  C   HIS    57       4.518   5.746  -0.437  1.00  0.00              
ATOM     36  O   HIS    57       4.242   6.324   0.612  1.00  0.00              
ATOM     37  N   LEU    58       5.447   6.186  -1.268  1.00  0.00              
ATOM     38  CA  LEU    58       6.235   7.364  -0.941  1.00  0.00              
ATOM     39  C   LEU    58       5.436   8.617  -0.617  1.00  0.00              
ATOM     40  O   LEU    58       5.922   9.473   0.122  1.00  0.00              
ATOM     41  N   TYR    59       4.219   8.744  -1.143  1.00  0.00              
ATOM     42  CA  TYR    59       3.447   9.941  -0.842  1.00  0.00              
ATOM     43  C   TYR    59       2.500   9.807   0.337  1.00  0.00              
ATOM     44  O   TYR    59       2.046  10.814   0.874  1.00  0.00              
ATOM     45  N   LYS    60       2.200   8.587   0.762  1.00  0.00              
ATOM     46  CA  LYS    60       1.276   8.426   1.883  1.00  0.00              
ATOM     47  C   LYS    60       1.719   9.192   3.138  1.00  0.00              
ATOM     48  O   LYS    60       0.930   9.915   3.756  1.00  0.00              
ATOM     49  N   LEU    61       2.994   9.055   3.525  1.00  0.00              
ATOM     50  CA  LEU    61       3.473   9.767   4.715  1.00  0.00              
ATOM     51  C   LEU    61       3.261  11.273   4.637  1.00  0.00              
ATOM     52  O   LEU    61       3.072  11.937   5.652  1.00  0.00              
ATOM     53  N   GLY    62       3.288  11.818   3.430  1.00  0.00              
ATOM     54  CA  GLY    62       3.115  13.252   3.270  1.00  0.00              
ATOM     55  C   GLY    62       1.748  13.741   3.743  1.00  0.00              
ATOM     56  O   GLY    62       1.541  14.939   3.900  1.00  0.00              
ATOM     57  N   PRO    63       0.819  12.816   3.976  1.00  0.00              
ATOM     58  CA  PRO    63      -0.518  13.188   4.446  1.00  0.00              
ATOM     59  C   PRO    63      -0.412  13.565   5.909  1.00  0.00              
ATOM     60  O   PRO    63      -1.229  14.322   6.420  1.00  0.00              
ATOM     61  N   GLU    64       0.601  13.020   6.578  1.00  0.00              
ATOM     62  CA  GLU    64       0.795  13.309   7.983  1.00  0.00              
ATOM     63  C   GLU    64       0.191  12.259   8.900  1.00  0.00              
ATOM     64  O   GLU    64       0.304  12.359  10.118  1.00  0.00              
ATOM     65  N   LEU    65      -0.447  11.247   8.322  1.00  0.00              
ATOM     66  CA  LEU    65      -1.066  10.200   9.123  1.00  0.00              
ATOM     67  C   LEU    65      -0.021   9.512   9.982  1.00  0.00              
ATOM     68  O   LEU    65       1.116   9.354   9.567  1.00  0.00              
ATOM     69  N   THR    66      -0.413   9.106  11.186  1.00  0.00              
ATOM     70  CA  THR    66       0.498   8.433  12.107  1.00  0.00              
ATOM     71  C   THR    66       0.806   7.002  11.690  1.00  0.00              
ATOM     72  O   THR    66       1.896   6.493  11.961  1.00  0.00              
ATOM     73  N   GLU    67      -0.149   6.341  11.048  1.00  0.00              
ATOM     74  CA  GLU    67       0.079   4.972  10.614  1.00  0.00              
ATOM     75  C   GLU    67      -0.536   4.660   9.252  1.00  0.00              
ATOM     76  O   GLU    67      -1.634   5.112   8.927  1.00  0.00              
ATOM     77  N   LYS    68       0.206   3.911   8.445  1.00  0.00              
ATOM     78  CA  LYS    68      -0.240   3.526   7.114  1.00  0.00              
ATOM     79  C   LYS    68      -0.513   2.033   7.075  1.00  0.00              
ATOM     80  O   LYS    68       0.339   1.214   7.426  1.00  0.00              
ATOM     81  N   GLY    69      -1.721   1.688   6.655  1.00  0.00              
ATOM     82  CA  GLY    69      -2.117   0.298   6.559  1.00  0.00              
ATOM     83  C   GLY    69      -1.671  -0.172   5.187  1.00  0.00              
ATOM     84  O   GLY    69      -2.153   0.325   4.175  1.00  0.00              
ATOM     85  N   GLU    70      -0.734  -1.113   5.162  1.00  0.00              
ATOM     86  CA  GLU    70      -0.210  -1.655   3.912  1.00  0.00              
ATOM     87  C   GLU    70      -1.001  -2.888   3.478  1.00  0.00              
ATOM     88  O   GLU    70      -1.406  -3.683   4.329  1.00  0.00              
ATOM     89  N   ASN    71      -1.223  -3.058   2.170  1.00  0.00              
ATOM     90  CA  ASN    71      -1.947  -4.234   1.699  1.00  0.00              
ATOM     91  C   ASN    71      -0.909  -5.321   1.492  1.00  0.00              
ATOM     92  O   ASN    71       0.275  -5.067   1.642  1.00  0.00              
ATOM     93  N   TYR    72      -1.338  -6.530   1.167  1.00  0.00              
ATOM     94  CA  TYR    72      -0.405  -7.634   1.006  1.00  0.00              
ATOM     95  C   TYR    72       0.440  -7.654  -0.275  1.00  0.00              
ATOM     96  O   TYR    72       1.373  -8.461  -0.378  1.00  0.00              
ATOM     97  N   LEU    73       0.133  -6.792  -1.246  1.00  0.00              
ATOM     98  CA  LEU    73       0.897  -6.785  -2.490  1.00  0.00              
ATOM     99  C   LEU    73       2.271  -6.125  -2.339  1.00  0.00              
ATOM    100  O   LEU    73       3.149  -6.298  -3.187  1.00  0.00              
ATOM    101  N   GLY    77       2.452  -5.370  -1.260  1.00  0.00              
ATOM    102  CA  GLY    77       3.720  -4.712  -0.988  1.00  0.00              
ATOM    103  C   GLY    77       4.424  -5.509   0.106  1.00  0.00              
ATOM    104  O   GLY    77       3.839  -5.769   1.153  1.00  0.00              
ATOM    105  N   THR    78       5.669  -5.909  -0.129  1.00  0.00              
ATOM    106  CA  THR    78       6.406  -6.659   0.878  1.00  0.00              
ATOM    107  C   THR    78       6.652  -5.772   2.091  1.00  0.00              
ATOM    108  O   THR    78       6.911  -4.579   1.949  1.00  0.00              
ATOM    109  N   TRP    79       6.567  -6.357   3.286  1.00  0.00              
ATOM    110  CA  TRP    79       6.749  -5.596   4.511  1.00  0.00              
ATOM    111  C   TRP    79       8.063  -4.844   4.534  1.00  0.00              
ATOM    112  O   TRP    79       8.094  -3.661   4.873  1.00  0.00              
ATOM    113  N   SER    80       9.150  -5.521   4.185  1.00  0.00              
ATOM    114  CA  SER    80      10.444  -4.873   4.187  1.00  0.00              
ATOM    115  C   SER    80      10.437  -3.698   3.221  1.00  0.00              
ATOM    116  O   SER    80      10.896  -2.608   3.554  1.00  0.00              
ATOM    117  N   LYS    81       9.898  -3.914   2.027  1.00  0.00              
ATOM    118  CA  LYS    81       9.847  -2.858   1.015  1.00  0.00              
ATOM    119  C   LYS    81       9.034  -1.676   1.504  1.00  0.00              
ATOM    120  O   LYS    81       9.442  -0.520   1.365  1.00  0.00              
ATOM    121  N   ALA    82       7.860  -1.980   2.049  1.00  0.00              
ATOM    122  CA  ALA    82       6.978  -0.945   2.550  1.00  0.00              
ATOM    123  C   ALA    82       7.604  -0.172   3.686  1.00  0.00              
ATOM    124  O   ALA    82       7.497   1.058   3.728  1.00  0.00              
ATOM    125  N   TYR    83       8.255  -0.882   4.605  1.00  0.00              
ATOM    126  CA  TYR    83       8.899  -0.238   5.743  1.00  0.00              
ATOM    127  C   TYR    83       9.972   0.726   5.248  1.00  0.00              
ATOM    128  O   TYR    83      10.191   1.796   5.832  1.00  0.00              
ATOM    129  N   LYS    84      10.634   0.353   4.156  1.00  0.00              
ATOM    130  CA  LYS    84      11.676   1.200   3.591  1.00  0.00              
ATOM    131  C   LYS    84      11.103   2.376   2.807  1.00  0.00              
ATOM    132  O   LYS    84      11.465   3.526   3.051  1.00  0.00              
ATOM    133  N   THR    85      10.195   2.080   1.876  1.00  0.00              
ATOM    134  CA  THR    85       9.582   3.093   1.018  1.00  0.00              
ATOM    135  C   THR    85       8.746   4.128   1.743  1.00  0.00              
ATOM    136  O   THR    85       8.568   5.240   1.246  1.00  0.00              
ATOM    137  N   ILE    86       8.234   3.778   2.917  1.00  0.00              
ATOM    138  CA  ILE    86       7.413   4.719   3.674  1.00  0.00              
ATOM    139  C   ILE    86       8.240   5.679   4.528  1.00  0.00              
ATOM    140  O   ILE    86       7.745   6.712   4.976  1.00  0.00              
END
