
#######################################################
#                                                     #
#                        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 T0357AL381_2
# Molecule2: number of CA atoms  132 ( 2030),  selected  132 , name T0357.pdb
# PARAMETERS: T0357AL381_2.T0357.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      V       2           -
LGA    -       -      K       3           -
LGA    -       -      F       4           -
LGA    -       -      A       5           -
LGA    -       -      C       6           -
LGA    -       -      R       7           -
LGA    -       -      A       8           -
LGA    -       -      I       9           -
LGA    -       -      T      10           -
LGA    -       -      R      11           -
LGA    -       -      G      12           -
LGA    -       -      R      13           -
LGA    -       -      A      14           -
LGA    -       -      E      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      A      18           -
LGA    -       -      L      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      K      22           -
LGA    -       -      E      23           -
LGA    -       -      Y      24           -
LGA    -       -      I      25           -
LGA    -       -      S      26           -
LGA    -       -      F      27           -
LGA    -       -      L      28           -
LGA    -       -      G      29           -
LGA    -       -      G      30           -
LGA    -       -      I      31           -
LGA    -       -      D      32           -
LGA    -       -      K      33           -
LGA    -       -      E      34           -
LGA    -       -      T      35           -
LGA    -       -      G      36           -
LGA    -       -      I      37           -
LGA    -       -      V      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      D      41           -
LGA    -       -      C      42           -
LGA    V       2      E      43          2.247
LGA    K       3      I      44          5.156
LGA    F       4      K      45          3.276
LGA    A       5      G      46          2.807
LGA    C       6      E      47          1.582
LGA    R       7      -       -           -
LGA    A       8      S      48          5.438
LGA    I       9      V      49           -
LGA    T      10      A      50           #
LGA    R      11      G      51           -
LGA    G      12      R      52           -
LGA    -       -      I      53           -
LGA    -       -      L      54           -
LGA    -       -      V      55           -
LGA    -       -      F      56           -
LGA    -       -      P      57           -
LGA    -       -      G      58           -
LGA    -       -      G      59           -
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    -       -      S      62           -
LGA    -       -      T      63           -
LGA    -       -      V      64           -
LGA    -       -      G      65           -
LGA    -       -      S      66           -
LGA    -       -      Y      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      N      71           -
LGA    -       -      L      72           -
LGA    -       -      R      73           -
LGA    R      13      K      74           #
LGA    A      14      N      75          2.633
LGA    E      15      G      76          2.958
LGA    G      16      V      77           #
LGA    -       -      A      78           -
LGA    -       -      P      79           -
LGA    E      17      K      80          3.742
LGA    A      18      A      81          1.373
LGA    L      19      I      82          1.973
LGA    V      20      I      83          1.159
LGA    T      21      N      84          1.503
LGA    K      22      K      85          2.672
LGA    E      23      K      86          2.620
LGA    Y      24      T      87          3.047
LGA    I      25      E      88          0.915
LGA    S      26      T      89          3.027
LGA    F      27      I      90          2.573
LGA    L      28      I      91          1.122
LGA    G      29      A      92          3.432
LGA    G      30      V      93          2.824
LGA    I      31      G      94          3.678
LGA    D      32      A      95          3.445
LGA    K      33      A      96           #
LGA    E      34      M      97           -
LGA    -       -      A      98           -
LGA    -       -      E      99           -
LGA    T      35      I     100          3.310
LGA    G      36      P     101           -
LGA    -       -      L     102           -
LGA    -       -      V     103           -
LGA    -       -      E     104           -
LGA    -       -      V     105           -
LGA    -       -      R     106           -
LGA    -       -      D     107           -
LGA    -       -      E     108           -
LGA    -       -      K     109           -
LGA    -       -      F     110           -
LGA    -       -      F     111           -
LGA    -       -      E     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      K     115           -
LGA    -       -      T     116           -
LGA    -       -      G     117           -
LGA    -       -      D     118           -
LGA    -       -      R     119           -
LGA    -       -      V     120           -
LGA    -       -      V     121           -
LGA    -       -      V     122           -
LGA    -       -      N     123           -
LGA    -       -      A     124           -
LGA    -       -      D     125           -
LGA    -       -      E     126           -
LGA    -       -      G     127           -
LGA    -       -      Y     128           -
LGA    -       -      V     129           -
LGA    -       -      E     130           -
LGA    -       -      L     131           -
LGA    -       -      I     132           -
LGA    -       -      E     133           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35  132    5.0     25    2.96     8.00     12.558     0.818

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.499970 * X  +  -0.649524 * Y  +   0.572842 * Z  + -37.926670
  Y_new =  -0.504995 * X  +  -0.756007 * Y  +  -0.416454 * Z  +  75.257851
  Z_new =   0.703570 * X  +  -0.081068 * Y  +  -0.705987 * Z  +  19.985947 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.027264    0.114329  [ DEG:  -173.4494      6.5506 ]
  Theta =  -0.780408   -2.361184  [ DEG:   -44.7141   -135.2859 ]
  Phi   =  -0.790399    2.351194  [ DEG:   -45.2865    134.7135 ]
 
# 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: T0357AL381_2                                  
REMARK     2: T0357.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0357AL381_2.T0357.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35  132   5.0   25   2.96    8.00  12.558
REMARK  ---------------------------------------------------------- 
MOLECULE T0357AL381_2
REMARK Aligment from pdb entry: 1qdlB
ATOM      1  N   VAL     2     -15.926  -1.205  -7.281  1.00  0.00              
ATOM      2  CA  VAL     2     -16.358  -2.006  -8.415  1.00  0.00              
ATOM      3  C   VAL     2     -15.539  -3.291  -8.511  1.00  0.00              
ATOM      4  O   VAL     2     -14.363  -3.324  -8.150  1.00  0.00              
ATOM      5  N   LYS     3     -16.175  -4.352  -8.985  1.00  0.00              
ATOM      6  CA  LYS     3     -15.508  -5.635  -9.144  1.00  0.00              
ATOM      7  C   LYS     3     -15.337  -5.882 -10.643  1.00  0.00              
ATOM      8  O   LYS     3     -16.302  -5.800 -11.405  1.00  0.00              
ATOM      9  N   PHE     4     -14.114  -6.174 -11.069  1.00  0.00              
ATOM     10  CA  PHE     4     -13.856  -6.435 -12.484  1.00  0.00              
ATOM     11  C   PHE     4     -12.777  -7.482 -12.661  1.00  0.00              
ATOM     12  O   PHE     4     -12.109  -7.868 -11.701  1.00  0.00              
ATOM     13  N   ALA     5     -12.616  -7.957 -13.892  1.00  0.00              
ATOM     14  CA  ALA     5     -11.578  -8.935 -14.175  1.00  0.00              
ATOM     15  C   ALA     5     -10.260  -8.172 -14.105  1.00  0.00              
ATOM     16  O   ALA     5     -10.218  -6.950 -14.325  1.00  0.00              
ATOM     17  N   CYS     6      -9.191  -8.884 -13.771  1.00  0.00              
ATOM     18  CA  CYS     6      -7.874  -8.274 -13.671  1.00  0.00              
ATOM     19  C   CYS     6      -7.270  -8.228 -15.060  1.00  0.00              
ATOM     20  O   CYS     6      -7.634  -9.025 -15.929  1.00  0.00              
ATOM     21  N   ARG     7      -6.353  -7.297 -15.284  1.00  0.00              
ATOM     22  CA  ARG     7      -5.733  -7.226 -16.587  1.00  0.00              
ATOM     23  C   ARG     7      -4.913  -8.496 -16.778  1.00  0.00              
ATOM     24  O   ARG     7      -4.944  -9.103 -17.849  1.00  0.00              
ATOM     25  N   ALA     8      -4.213  -8.916 -15.726  1.00  0.00              
ATOM     26  CA  ALA     8      -3.412 -10.134 -15.775  1.00  0.00              
ATOM     27  C   ALA     8      -3.926 -11.163 -14.757  1.00  0.00              
ATOM     28  O   ALA     8      -4.352 -10.800 -13.660  1.00  0.00              
ATOM     29  N   ILE     9      -3.887 -12.443 -15.124  1.00  0.00              
ATOM     30  CA  ILE     9      -4.367 -13.522 -14.257  1.00  0.00              
ATOM     31  C   ILE     9      -3.287 -14.228 -13.433  1.00  0.00              
ATOM     32  O   ILE     9      -2.492 -15.019 -13.955  1.00  0.00              
ATOM     33  N   THR    10      -3.279 -13.947 -12.134  1.00  0.00              
ATOM     34  CA  THR    10      -2.324 -14.558 -11.225  1.00  0.00              
ATOM     35  C   THR    10      -2.968 -15.710 -10.497  1.00  0.00              
ATOM     36  O   THR    10      -3.744 -15.521  -9.566  1.00  0.00              
ATOM     37  N   ARG    11      -2.649 -16.914 -10.930  1.00  0.00              
ATOM     38  CA  ARG    11      -3.205 -18.084 -10.294  1.00  0.00              
ATOM     39  C   ARG    11      -2.036 -18.873  -9.751  1.00  0.00              
ATOM     40  O   ARG    11      -1.466 -19.707 -10.450  1.00  0.00              
ATOM     41  N   GLY    12      -1.672 -18.601  -8.504  1.00  0.00              
ATOM     42  CA  GLY    12      -0.554 -19.300  -7.904  1.00  0.00              
ATOM     43  C   GLY    12       0.742 -18.598  -8.250  1.00  0.00              
ATOM     44  O   GLY    12       1.822 -19.133  -8.026  1.00  0.00              
ATOM     45  N   ARG    13       0.629 -17.401  -8.813  1.00  0.00              
ATOM     46  CA  ARG    13       1.800 -16.615  -9.185  1.00  0.00              
ATOM     47  C   ARG    13       2.136 -15.628  -8.069  1.00  0.00              
ATOM     48  O   ARG    13       1.244 -15.090  -7.411  1.00  0.00              
ATOM     49  N   ALA    14       3.430 -15.405  -7.862  1.00  0.00              
ATOM     50  CA  ALA    14       3.914 -14.498  -6.827  1.00  0.00              
ATOM     51  C   ALA    14       4.079 -13.085  -7.362  1.00  0.00              
ATOM     52  O   ALA    14       4.778 -12.868  -8.351  1.00  0.00              
ATOM     53  N   GLU    15       3.443 -12.125  -6.701  1.00  0.00              
ATOM     54  CA  GLU    15       3.512 -10.734  -7.124  1.00  0.00              
ATOM     55  C   GLU    15       4.261  -9.887  -6.103  1.00  0.00              
ATOM     56  O   GLU    15       4.430 -10.286  -4.950  1.00  0.00              
ATOM     57  N   GLY    16       4.719  -8.718  -6.537  1.00  0.00              
ATOM     58  CA  GLY    16       5.428  -7.802  -5.660  1.00  0.00              
ATOM     59  C   GLY    16       4.436  -6.769  -5.205  1.00  0.00              
ATOM     60  O   GLY    16       4.039  -5.897  -5.974  1.00  0.00              
ATOM     61  N   GLU    17       4.022  -6.883  -3.952  1.00  0.00              
ATOM     62  CA  GLU    17       3.070  -5.950  -3.400  1.00  0.00              
ATOM     63  C   GLU    17       3.817  -4.691  -2.998  1.00  0.00              
ATOM     64  O   GLU    17       4.893  -4.747  -2.394  1.00  0.00              
ATOM     65  N   ALA    18       3.252  -3.549  -3.357  1.00  0.00              
ATOM     66  CA  ALA    18       3.867  -2.288  -3.002  1.00  0.00              
ATOM     67  C   ALA    18       2.913  -1.531  -2.107  1.00  0.00              
ATOM     68  O   ALA    18       1.840  -1.094  -2.537  1.00  0.00              
ATOM     69  N   LEU    19       3.299  -1.408  -0.847  1.00  0.00              
ATOM     70  CA  LEU    19       2.491  -0.687   0.105  1.00  0.00              
ATOM     71  C   LEU    19       2.511   0.754  -0.359  1.00  0.00              
ATOM     72  O   LEU    19       3.566   1.305  -0.672  1.00  0.00              
ATOM     73  N   VAL    20       1.335   1.355  -0.430  1.00  0.00              
ATOM     74  CA  VAL    20       1.218   2.733  -0.864  1.00  0.00              
ATOM     75  C   VAL    20       0.403   3.499   0.162  1.00  0.00              
ATOM     76  O   VAL    20      -0.314   4.438  -0.184  1.00  0.00              
ATOM     77  N   THR    21       0.505   3.086   1.422  1.00  0.00              
ATOM     78  CA  THR    21      -0.233   3.758   2.481  1.00  0.00              
ATOM     79  C   THR    21       0.450   5.080   2.817  1.00  0.00              
ATOM     80  O   THR    21       1.661   5.136   3.031  1.00  0.00              
ATOM     81  N   LYS    22      -0.340   6.147   2.820  1.00  0.00              
ATOM     82  CA  LYS    22       0.161   7.481   3.118  1.00  0.00              
ATOM     83  C   LYS    22       0.432   7.581   4.605  1.00  0.00              
ATOM     84  O   LYS    22       1.438   8.141   5.031  1.00  0.00              
ATOM     85  N   GLU    23      -0.493   7.045   5.389  1.00  0.00              
ATOM     86  CA  GLU    23      -0.361   7.042   6.835  1.00  0.00              
ATOM     87  C   GLU    23      -0.234   5.592   7.278  1.00  0.00              
ATOM     88  O   GLU    23      -0.890   4.703   6.728  1.00  0.00              
ATOM     89  N   TYR    24       0.620   5.336   8.281  1.00  0.00              
ATOM     90  CA  TYR    24       0.899   4.013   8.854  1.00  0.00              
ATOM     91  C   TYR    24      -0.321   3.187   9.256  1.00  0.00              
ATOM     92  O   TYR    24      -1.313   3.725   9.752  1.00  0.00              
ATOM     93  N   ILE    25      -0.230   1.875   9.042  1.00  0.00              
ATOM     94  CA  ILE    25      -1.312   0.957   9.370  1.00  0.00              
ATOM     95  C   ILE    25      -0.845  -0.105  10.358  1.00  0.00              
ATOM     96  O   ILE    25       0.295  -0.566  10.291  1.00  0.00              
ATOM     97  N   SER    26      -1.734  -0.495  11.271  1.00  0.00              
ATOM     98  CA  SER    26      -1.410  -1.516  12.263  1.00  0.00              
ATOM     99  C   SER    26      -1.143  -2.830  11.548  1.00  0.00              
ATOM    100  O   SER    26      -0.152  -3.512  11.813  1.00  0.00              
ATOM    101  N   PHE    27      -2.038  -3.170  10.629  1.00  0.00              
ATOM    102  CA  PHE    27      -1.927  -4.400   9.874  1.00  0.00              
ATOM    103  C   PHE    27      -0.583  -4.571   9.170  1.00  0.00              
ATOM    104  O   PHE    27      -0.128  -5.700   8.971  1.00  0.00              
ATOM    105  N   LEU    28       0.054  -3.462   8.799  1.00  0.00              
ATOM    106  CA  LEU    28       1.332  -3.529   8.091  1.00  0.00              
ATOM    107  C   LEU    28       2.543  -3.113   8.913  1.00  0.00              
ATOM    108  O   LEU    28       3.579  -2.710   8.374  1.00  0.00              
ATOM    109  N   GLY    29       2.405  -3.231  10.227  1.00  0.00              
ATOM    110  CA  GLY    29       3.477  -2.895  11.144  1.00  0.00              
ATOM    111  C   GLY    29       4.690  -3.801  10.923  1.00  0.00              
ATOM    112  O   GLY    29       4.572  -5.025  10.928  1.00  0.00              
ATOM    113  N   GLY    30       5.859  -3.199  10.739  1.00  0.00              
ATOM    114  CA  GLY    30       7.059  -3.984  10.524  1.00  0.00              
ATOM    115  C   GLY    30       7.113  -4.677   9.172  1.00  0.00              
ATOM    116  O   GLY    30       7.972  -5.527   8.948  1.00  0.00              
ATOM    117  N   ILE    31       6.204  -4.324   8.265  1.00  0.00              
ATOM    118  CA  ILE    31       6.188  -4.935   6.937  1.00  0.00              
ATOM    119  C   ILE    31       6.971  -4.086   5.931  1.00  0.00              
ATOM    120  O   ILE    31       6.781  -2.864   5.864  1.00  0.00              
ATOM    121  N   ASP    32       7.846  -4.737   5.157  1.00  0.00              
ATOM    122  CA  ASP    32       8.667  -4.068   4.143  1.00  0.00              
ATOM    123  C   ASP    32       7.801  -3.266   3.169  1.00  0.00              
ATOM    124  O   ASP    32       6.709  -3.708   2.810  1.00  0.00              
ATOM    125  N   LYS    33       8.296  -2.107   2.730  1.00  0.00              
ATOM    126  CA  LYS    33       7.562  -1.233   1.802  1.00  0.00              
ATOM    127  C   LYS    33       7.003  -1.985   0.595  1.00  0.00              
ATOM    128  O   LYS    33       5.992  -1.593   0.016  1.00  0.00              
ATOM    129  N   GLU    34       7.686  -3.050   0.198  1.00  0.00              
ATOM    130  CA  GLU    34       7.217  -3.903  -0.880  1.00  0.00              
ATOM    131  C   GLU    34       7.754  -5.278  -0.558  1.00  0.00              
ATOM    132  O   GLU    34       8.920  -5.432  -0.184  1.00  0.00              
ATOM    133  N   THR    35       6.879  -6.267  -0.670  1.00  0.00              
ATOM    134  CA  THR    35       7.221  -7.642  -0.363  1.00  0.00              
ATOM    135  C   THR    35       6.624  -8.531  -1.434  1.00  0.00              
ATOM    136  O   THR    35       5.954  -8.052  -2.353  1.00  0.00              
ATOM    137  N   GLY    36       6.866  -9.829  -1.309  1.00  0.00              
ATOM    138  CA  GLY    36       6.345 -10.787  -2.262  1.00  0.00              
ATOM    139  C   GLY    36       5.183 -11.550  -1.641  1.00  0.00              
ATOM    140  O   GLY    36       5.224 -11.914  -0.467  1.00  0.00              
END
