
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0335AL381_5
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335AL381_5.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    E      26      M       1           -
LGA    K      27      I       2           -
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      -       -           -
LGA    Q      31      -       -           -
LGA    K      32      S       3          5.270
LGA    L      33      N       4          2.329
LGA    R      34      A       5          4.475
LGA    Q      35      K       6          2.674
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    E      36      R       9          1.530
LGA    Y      37      I      10          1.440
LGA    L      38      N      11          2.950
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    K      39      A      14          3.930
LGA    G      40      A      15          3.034
LGA    F      41      K      16          1.521
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    R      42      A      19          4.233
LGA    S      43      G      20           #
LGA    S      44      -       -           -
LGA    M      45      -       -           -
LGA    K      46      V      21          4.185
LGA    N      47      -       -           -
LGA    T      48      -       -           -
LGA    L      49      I      22          3.035
LGA    K      50      T      23          2.503
LGA    -       -      E      24           -
LGA    S      51      E      25          2.577
LGA    V      52      E      26          2.201
LGA    K      53      K      27          1.584
LGA    I      54      A      28          0.725
LGA    I      55      E      29          1.391
LGA    D      56      Q      30          2.711
LGA    P      57      Q      31          1.361
LGA    -       -      K      32           -
LGA    -       -      L      33           -
LGA    E      58      R      34          2.903
LGA    G      59      Q      35           #
LGA    N      60      -       -           -
LGA    D      61      -       -           -
LGA    V      62      E      36          3.403
LGA    T      63      Y      37          2.502
LGA    P      64      L      38          4.096
LGA    E      65      K      39          1.891
LGA    K      66      G      40          5.058
LGA    L      67      F      41           -
LGA    K      68      R      42           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   42    5.0     27    3.04     3.70     40.433     0.860

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.403800 * X  +  -0.416528 * Y  +   0.814524 * Z  + -35.212814
  Y_new =   0.705994 * X  +   0.424359 * Y  +   0.567003 * Z  + -23.672539
  Z_new =  -0.581823 * X  +   0.804005 * Y  +   0.122710 * Z  +  29.520098 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.419341   -1.722251  [ DEG:    81.3223    -98.6777 ]
  Theta =   0.620969    2.520624  [ DEG:    35.5789    144.4211 ]
  Phi   =   2.090343   -1.051250  [ DEG:   119.7678    -60.2322 ]
 
# 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: T0335AL381_5                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_5.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   42   5.0   27   3.04    3.70  40.433
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_5
REMARK Aligment from pdb entry: 1qw7A
ATOM      1  N   GLU    26      11.345 -21.138 -15.518  1.00  0.00              
ATOM      2  CA  GLU    26      10.688 -21.201 -16.809  1.00  0.00              
ATOM      3  C   GLU    26       9.203 -20.965 -16.808  1.00  0.00              
ATOM      4  O   GLU    26       8.530 -21.403 -17.726  1.00  0.00              
ATOM      5  N   LYS    27       8.680 -20.245 -15.820  1.00  0.00              
ATOM      6  CA  LYS    27       7.243 -20.003 -15.776  1.00  0.00              
ATOM      7  C   LYS    27       6.834 -18.557 -15.885  1.00  0.00              
ATOM      8  O   LYS    27       5.854 -18.153 -15.291  1.00  0.00              
ATOM      9  N   ALA    28       7.573 -17.764 -16.651  1.00  0.00              
ATOM     10  CA  ALA    28       7.225 -16.351 -16.769  1.00  0.00              
ATOM     11  C   ALA    28       5.774 -16.143 -17.159  1.00  0.00              
ATOM     12  O   ALA    28       5.146 -15.228 -16.678  1.00  0.00              
ATOM     13  N   GLU    29       5.230 -17.014 -18.007  1.00  0.00              
ATOM     14  CA  GLU    29       3.841 -16.880 -18.461  1.00  0.00              
ATOM     15  C   GLU    29       2.779 -17.135 -17.401  1.00  0.00              
ATOM     16  O   GLU    29       1.613 -16.789 -17.605  1.00  0.00              
ATOM     17  N   GLN    30       3.193 -17.707 -16.269  1.00  0.00              
ATOM     18  CA  GLN    30       2.280 -18.092 -15.188  1.00  0.00              
ATOM     19  C   GLN    30       2.233 -17.107 -14.042  1.00  0.00              
ATOM     20  O   GLN    30       1.494 -17.314 -13.093  1.00  0.00              
ATOM     21  N   GLN    31       3.047 -16.073 -14.117  1.00  0.00              
ATOM     22  CA  GLN    31       3.132 -15.097 -13.029  1.00  0.00              
ATOM     23  C   GLN    31       2.237 -13.881 -13.190  1.00  0.00              
ATOM     24  O   GLN    31       2.131 -13.332 -14.284  1.00  0.00              
ATOM     25  N   LYS    32       1.599 -13.468 -12.091  1.00  0.00              
ATOM     26  CA  LYS    32       0.772 -12.260 -12.069  1.00  0.00              
ATOM     27  C   LYS    32       1.283 -11.511 -10.826  1.00  0.00              
ATOM     28  O   LYS    32       1.490 -12.097  -9.765  1.00  0.00              
ATOM     29  N   LEU    33       1.505 -10.217 -10.967  1.00  0.00              
ATOM     30  CA  LEU    33       2.070  -9.452  -9.873  1.00  0.00              
ATOM     31  C   LEU    33       1.144  -8.349  -9.416  1.00  0.00              
ATOM     32  O   LEU    33       0.438  -7.746 -10.234  1.00  0.00              
ATOM     33  N   ARG    34       1.147  -8.066  -8.115  1.00  0.00              
ATOM     34  CA  ARG    34       0.312  -6.984  -7.604  1.00  0.00              
ATOM     35  C   ARG    34       0.796  -6.485  -6.236  1.00  0.00              
ATOM     36  O   ARG    34       1.812  -6.971  -5.739  1.00  0.00              
ATOM     37  N   GLN    35       0.091  -5.510  -5.658  1.00  0.00              
ATOM     38  CA  GLN    35       0.476  -4.882  -4.380  1.00  0.00              
ATOM     39  C   GLN    35      -0.493  -5.258  -3.278  1.00  0.00              
ATOM     40  O   GLN    35      -0.165  -5.143  -2.105  1.00  0.00              
ATOM     41  N   GLU    36      -1.702  -5.683  -3.640  1.00  0.00              
ATOM     42  CA  GLU    36      -2.710  -5.985  -2.621  1.00  0.00              
ATOM     43  C   GLU    36      -2.808  -4.752  -1.710  1.00  0.00              
ATOM     44  O   GLU    36      -2.757  -4.850  -0.484  1.00  0.00              
ATOM     45  N   TYR    37      -2.928  -3.586  -2.340  1.00  0.00              
ATOM     46  CA  TYR    37      -3.056  -2.322  -1.636  1.00  0.00              
ATOM     47  C   TYR    37      -4.530  -1.899  -1.489  1.00  0.00              
ATOM     48  O   TYR    37      -5.437  -2.576  -1.952  1.00  0.00              
ATOM     49  N   LEU    38      -4.749  -0.771  -0.829  1.00  0.00              
ATOM     50  CA  LEU    38      -6.084  -0.219  -0.621  1.00  0.00              
ATOM     51  C   LEU    38      -5.925   1.228  -0.154  1.00  0.00              
ATOM     52  O   LEU    38      -4.800   1.683   0.091  1.00  0.00              
ATOM     53  N   LYS    39      -7.036   1.943  -0.045  1.00  0.00              
ATOM     54  CA  LYS    39      -6.989   3.345   0.325  1.00  0.00              
ATOM     55  C   LYS    39      -7.814   3.569   1.569  1.00  0.00              
ATOM     56  O   LYS    39      -7.764   4.634   2.175  1.00  0.00              
ATOM     57  N   GLY    40      -8.545   2.522   1.948  1.00  0.00              
ATOM     58  CA  GLY    40      -9.361   2.521   3.158  1.00  0.00              
ATOM     59  C   GLY    40      -9.306   1.080   3.666  1.00  0.00              
ATOM     60  O   GLY    40      -9.345   0.163   2.847  1.00  0.00              
ATOM     61  N   PHE    41      -9.248   0.861   4.979  1.00  0.00              
ATOM     62  CA  PHE    41      -9.137  -0.502   5.533  1.00  0.00              
ATOM     63  C   PHE    41      -9.824  -0.565   6.924  1.00  0.00              
ATOM     64  O   PHE    41      -9.273  -0.109   7.935  1.00  0.00              
ATOM     65  N   ARG    42     -11.035  -1.115   6.979  1.00  0.00              
ATOM     66  CA  ARG    42     -11.794  -1.158   8.232  1.00  0.00              
ATOM     67  C   ARG    42     -11.912  -2.544   8.864  1.00  0.00              
ATOM     68  O   ARG    42     -12.306  -2.669  10.015  1.00  0.00              
ATOM     69  N   SER    43     -11.581  -3.576   8.102  1.00  0.00              
ATOM     70  CA  SER    43     -11.701  -4.944   8.581  1.00  0.00              
ATOM     71  C   SER    43     -10.550  -5.395   9.458  1.00  0.00              
ATOM     72  O   SER    43     -10.372  -6.596   9.696  1.00  0.00              
ATOM     73  N   SER    44      -9.783  -4.431   9.964  1.00  0.00              
ATOM     74  CA  SER    44      -8.663  -4.746  10.843  1.00  0.00              
ATOM     75  C   SER    44      -8.585  -3.734  11.986  1.00  0.00              
ATOM     76  O   SER    44      -9.582  -3.051  12.286  1.00  0.00              
ATOM     77  N   MET    45      -7.429  -3.625  12.641  1.00  0.00              
ATOM     78  CA  MET    45      -7.352  -2.672  13.745  1.00  0.00              
ATOM     79  C   MET    45      -7.483  -1.233  13.195  1.00  0.00              
ATOM     80  O   MET    45      -7.242  -0.980  12.017  1.00  0.00              
ATOM     81  N   LYS    46      -7.882  -0.309  14.052  1.00  0.00              
ATOM     82  CA  LYS    46      -8.053   1.078  13.642  1.00  0.00              
ATOM     83  C   LYS    46      -6.694   1.685  13.318  1.00  0.00              
ATOM     84  O   LYS    46      -5.693   1.374  13.951  1.00  0.00              
ATOM     85  N   ASN    47      -6.665   2.529  12.306  1.00  0.00              
ATOM     86  CA  ASN    47      -5.430   3.181  11.918  1.00  0.00              
ATOM     87  C   ASN    47      -4.380   2.291  11.238  1.00  0.00              
ATOM     88  O   ASN    47      -3.235   2.699  11.066  1.00  0.00              
ATOM     89  N   THR    48      -4.775   1.086  10.833  1.00  0.00              
ATOM     90  CA  THR    48      -3.851   0.192  10.137  1.00  0.00              
ATOM     91  C   THR    48      -3.488   0.809   8.773  1.00  0.00              
ATOM     92  O   THR    48      -2.374   0.617   8.271  1.00  0.00              
ATOM     93  N   LEU    49      -4.425   1.541   8.176  1.00  0.00              
ATOM     94  CA  LEU    49      -4.174   2.180   6.878  1.00  0.00              
ATOM     95  C   LEU    49      -3.000   3.137   7.027  1.00  0.00              
ATOM     96  O   LEU    49      -2.131   3.209   6.156  1.00  0.00              
ATOM     97  N   LYS    50      -2.953   3.864   8.138  1.00  0.00              
ATOM     98  CA  LYS    50      -1.847   4.800   8.364  1.00  0.00              
ATOM     99  C   LYS    50      -0.503   4.114   8.489  1.00  0.00              
ATOM    100  O   LYS    50       0.513   4.654   8.060  1.00  0.00              
ATOM    101  N   SER    51      -0.493   2.952   9.124  1.00  0.00              
ATOM    102  CA  SER    51       0.733   2.201   9.283  1.00  0.00              
ATOM    103  C   SER    51       1.187   1.680   7.910  1.00  0.00              
ATOM    104  O   SER    51       2.368   1.724   7.568  1.00  0.00              
ATOM    105  N   VAL    52       0.255   1.190   7.107  1.00  0.00              
ATOM    106  CA  VAL    52       0.631   0.676   5.787  1.00  0.00              
ATOM    107  C   VAL    52       1.075   1.802   4.865  1.00  0.00              
ATOM    108  O   VAL    52       2.038   1.648   4.107  1.00  0.00              
ATOM    109  N   LYS    53       0.392   2.941   4.928  1.00  0.00              
ATOM    110  CA  LYS    53       0.783   4.051   4.065  1.00  0.00              
ATOM    111  C   LYS    53       2.198   4.522   4.400  1.00  0.00              
ATOM    112  O   LYS    53       2.919   5.005   3.529  1.00  0.00              
ATOM    113  N   ILE    54       2.602   4.385   5.664  1.00  0.00              
ATOM    114  CA  ILE    54       3.958   4.766   6.031  1.00  0.00              
ATOM    115  C   ILE    54       4.917   3.743   5.479  1.00  0.00              
ATOM    116  O   ILE    54       6.013   4.085   5.055  1.00  0.00              
ATOM    117  N   ILE    55       4.512   2.479   5.491  1.00  0.00              
ATOM    118  CA  ILE    55       5.358   1.406   4.978  1.00  0.00              
ATOM    119  C   ILE    55       5.573   1.517   3.489  1.00  0.00              
ATOM    120  O   ILE    55       6.693   1.353   2.990  1.00  0.00              
ATOM    121  N   ASP    56       4.489   1.773   2.775  1.00  0.00              
ATOM    122  CA  ASP    56       4.545   1.874   1.322  1.00  0.00              
ATOM    123  C   ASP    56       3.850   3.129   0.800  1.00  0.00              
ATOM    124  O   ASP    56       2.726   3.071   0.319  1.00  0.00              
ATOM    125  N   PRO    57       4.516   4.285   0.897  1.00  0.00              
ATOM    126  CA  PRO    57       3.958   5.557   0.427  1.00  0.00              
ATOM    127  C   PRO    57       3.613   5.539  -1.054  1.00  0.00              
ATOM    128  O   PRO    57       2.762   6.315  -1.499  1.00  0.00              
ATOM    129  N   GLU    58       4.273   4.674  -1.827  1.00  0.00              
ATOM    130  CA  GLU    58       3.972   4.581  -3.258  1.00  0.00              
ATOM    131  C   GLU    58       2.629   3.902  -3.511  1.00  0.00              
ATOM    132  O   GLU    58       2.055   4.045  -4.578  1.00  0.00              
ATOM    133  N   GLY    59       2.151   3.138  -2.530  1.00  0.00              
ATOM    134  CA  GLY    59       0.865   2.479  -2.672  1.00  0.00              
ATOM    135  C   GLY    59       0.846   1.568  -3.886  1.00  0.00              
ATOM    136  O   GLY    59       1.753   0.771  -4.056  1.00  0.00              
ATOM    137  N   ASN    60      -0.176   1.681  -4.731  1.00  0.00              
ATOM    138  CA  ASN    60      -0.264   0.811  -5.898  1.00  0.00              
ATOM    139  C   ASN    60       0.842   1.000  -6.938  1.00  0.00              
ATOM    140  O   ASN    60       1.085   0.084  -7.760  1.00  0.00              
ATOM    141  N   ASP    61       1.484   2.178  -6.918  1.00  0.00              
ATOM    142  CA  ASP    61       2.577   2.486  -7.857  1.00  0.00              
ATOM    143  C   ASP    61       3.875   1.752  -7.469  1.00  0.00              
ATOM    144  O   ASP    61       4.874   1.769  -8.209  1.00  0.00              
ATOM    145  N   VAL    62       3.854   1.065  -6.326  1.00  0.00              
ATOM    146  CA  VAL    62       5.026   0.322  -5.862  1.00  0.00              
ATOM    147  C   VAL    62       5.483  -0.696  -6.896  1.00  0.00              
ATOM    148  O   VAL    62       6.692  -0.888  -7.087  1.00  0.00              
ATOM    149  N   THR    63       4.557  -1.366  -7.575  1.00  0.00              
ATOM    150  CA  THR    63       5.007  -2.364  -8.552  1.00  0.00              
ATOM    151  C   THR    63       5.839  -1.722  -9.658  1.00  0.00              
ATOM    152  O   THR    63       6.989  -2.070  -9.834  1.00  0.00              
ATOM    153  N   PRO    64       5.268  -0.765 -10.408  1.00  0.00              
ATOM    154  CA  PRO    64       6.047  -0.122 -11.479  1.00  0.00              
ATOM    155  C   PRO    64       7.267   0.692 -11.024  1.00  0.00              
ATOM    156  O   PRO    64       8.321   0.661 -11.670  1.00  0.00              
ATOM    157  N   GLU    65       7.124   1.430  -9.918  1.00  0.00              
ATOM    158  CA  GLU    65       8.207   2.269  -9.413  1.00  0.00              
ATOM    159  C   GLU    65       9.370   1.556  -8.722  1.00  0.00              
ATOM    160  O   GLU    65      10.520   1.960  -8.896  1.00  0.00              
ATOM    161  N   LYS    66       9.095   0.494  -7.962  1.00  0.00              
ATOM    162  CA  LYS    66      10.175  -0.194  -7.240  1.00  0.00              
ATOM    163  C   LYS    66      10.493  -1.598  -7.698  1.00  0.00              
ATOM    164  O   LYS    66      11.659  -1.949  -7.856  1.00  0.00              
ATOM    165  N   LEU    67       9.452  -2.395  -7.902  1.00  0.00              
ATOM    166  CA  LEU    67       9.610  -3.792  -8.286  1.00  0.00              
ATOM    167  C   LEU    67      10.119  -4.052  -9.716  1.00  0.00              
ATOM    168  O   LEU    67      11.040  -4.866  -9.920  1.00  0.00              
ATOM    169  N   LYS    68       9.534  -3.379 -10.708  1.00  0.00              
ATOM    170  CA  LYS    68       9.970  -3.590 -12.079  1.00  0.00              
ATOM    171  C   LYS    68      11.453  -3.202 -12.217  1.00  0.00              
ATOM    172  O   LYS    68      12.232  -3.939 -12.803  1.00  0.00              
END
