
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0358AL243_4-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358AL243_4-D1.T0358_D1.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    G      10      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    F      12      T      22          2.779
LGA    T      13      T      23           -
LGA    R      14      Y      24           -
LGA    R      15      -       -           -
LGA    Q      16      S      25          3.592
LGA    A      17      N      26          2.874
LGA    Q      18      -       -           -
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    T      22      -       -           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      -       -           -
LGA    N      26      -       -           -
LGA    I      27      -       -           -
LGA    T      28      I      27          3.185
LGA    L      29      T      28           #
LGA    E      30      L      29          4.074
LGA    -       -      E      30           -
LGA    D      31      D      31           #
LGA    D      32      D      32          3.407
LGA    Q      33      Q      33          2.104
LGA    G      34      G      34          3.090
LGA    S      35      S      35          4.005
LGA    H      36      H      36          2.772
LGA    F      37      F      37          3.123
LGA    R      38      R      38          3.565
LGA    L      39      L      39          1.258
LGA    V      40      V      40          2.345
LGA    V      41      V      41          2.400
LGA    R      42      R      42          0.387
LGA    D      43      D      43          1.962
LGA    T      44      T      44          2.831
LGA    E      45      E      45          2.100
LGA    G      46      G      46          2.013
LGA    E      56      R      47          3.329
LGA    P      57      M      48          2.292
LGA    D      58      V      49           #
LGA    A      59      W      50          2.500
LGA    G      60      R      51          3.189
LGA    E      61      A      52          5.264
LGA    G      62      -       -           -
LGA    L      63      W      53           #
LGA    N      64      N      54          5.928
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    R      65      D      58          2.641
LGA    Y      66      A      59          3.017
LGA    I      67      G      60          4.045
LGA    R      68      E      61           -
LGA    T      69      G      62           -
LGA    S      70      L      63           -
LGA    G      71      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   65    5.0     29    3.16    55.17     27.502     0.891

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.220415 * X  +  -0.959128 * Y  +  -0.177455 * Z  +  16.480986
  Y_new =  -0.163288 * X  +  -0.215645 * Y  +   0.962722 * Z  + -50.713333
  Z_new =  -0.961641 * X  +  -0.183223 * Y  +  -0.204145 * Z  +  67.063469 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.410154    0.731438  [ DEG:  -138.0917     41.9083 ]
  Theta =   1.292925    1.848668  [ DEG:    74.0791    105.9209 ]
  Phi   =  -0.637599    2.503994  [ DEG:   -36.5317    143.4683 ]
 
# 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: T0358AL243_4-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL243_4-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   65   5.0   29   3.16   55.17  27.502
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL243_4-D1
REMARK Aligment from pdb entry: 1t6kA
ATOM     21  N   GLY    10       2.145  -4.400 -10.435  1.00  0.00              
ATOM     22  CA  GLY    10       2.044  -5.639 -11.226  1.00  0.00              
ATOM     23  C   GLY    10       1.054  -6.630 -10.616  1.00  0.00              
ATOM     24  O   GLY    10       0.860  -7.739 -11.162  1.00  0.00              
ATOM     25  N   PHE    12       0.459  -6.267  -9.476  1.00  0.00              
ATOM     26  CA  PHE    12      -0.567  -7.072  -8.836  1.00  0.00              
ATOM     27  C   PHE    12      -1.971  -6.576  -9.163  1.00  0.00              
ATOM     28  O   PHE    12      -2.343  -5.459  -8.787  1.00  0.00              
ATOM     29  N   THR    13      -2.768  -7.395  -9.848  1.00  0.00              
ATOM     30  CA  THR    13      -4.183  -7.085 -10.025  1.00  0.00              
ATOM     31  C   THR    13      -4.899  -7.077  -8.670  1.00  0.00              
ATOM     32  O   THR    13      -4.452  -7.686  -7.706  1.00  0.00              
ATOM     33  N   ARG    14      -5.981  -6.349  -8.570  1.00  0.00              
ATOM     34  CA  ARG    14      -6.677  -6.232  -7.296  1.00  0.00              
ATOM     35  C   ARG    14      -7.238  -7.545  -6.787  1.00  0.00              
ATOM     36  O   ARG    14      -7.329  -7.687  -5.565  1.00  0.00              
ATOM     37  N   ARG    15      -7.579  -8.490  -7.680  1.00  0.00              
ATOM     38  CA  ARG    15      -8.008  -9.797  -7.206  1.00  0.00              
ATOM     39  C   ARG    15      -6.857 -10.497  -6.434  1.00  0.00              
ATOM     40  O   ARG    15      -7.130 -11.198  -5.466  1.00  0.00              
ATOM     41  N   GLN    16      -5.607 -10.311  -6.892  1.00  0.00              
ATOM     42  CA  GLN    16      -4.410 -10.847  -6.255  1.00  0.00              
ATOM     43  C   GLN    16      -4.120 -10.074  -4.972  1.00  0.00              
ATOM     44  O   GLN    16      -3.715 -10.654  -3.998  1.00  0.00              
ATOM     45  N   ALA    17      -4.291  -8.752  -4.996  1.00  0.00              
ATOM     46  CA  ALA    17      -4.123  -7.992  -3.755  1.00  0.00              
ATOM     47  C   ALA    17      -5.079  -8.524  -2.693  1.00  0.00              
ATOM     48  O   ALA    17      -4.683  -8.699  -1.517  1.00  0.00              
ATOM     49  N   GLN    18      -6.341  -8.793  -3.076  1.00  0.00              
ATOM     50  CA  GLN    18      -7.291  -9.316  -2.095  1.00  0.00              
ATOM     51  C   GLN    18      -6.818 -10.698  -1.547  1.00  0.00              
ATOM     52  O   GLN    18      -6.926 -11.005  -0.348  1.00  0.00              
ATOM     53  N   ALA    19      -6.354 -11.565  -2.445  1.00  0.00              
ATOM     54  CA  ALA    19      -5.874 -12.886  -2.027  1.00  0.00              
ATOM     55  C   ALA    19      -4.667 -12.785  -1.072  1.00  0.00              
ATOM     56  O   ALA    19      -4.530 -13.559  -0.140  1.00  0.00              
ATOM     57  N   VAL    20      -3.779 -11.826  -1.314  1.00  0.00              
ATOM     58  CA  VAL    20      -2.631 -11.620  -0.435  1.00  0.00              
ATOM     59  C   VAL    20      -3.115 -11.087   0.882  1.00  0.00              
ATOM     60  O   VAL    20      -2.623 -11.525   1.944  1.00  0.00              
ATOM     61  N   THR    21      -4.094 -10.161   0.849  1.00  0.00              
ATOM     62  CA  THR    21      -4.598  -9.657   2.147  1.00  0.00              
ATOM     63  C   THR    21      -5.220 -10.808   2.956  1.00  0.00              
ATOM     64  O   THR    21      -5.049 -10.863   4.156  1.00  0.00              
ATOM     65  N   THR    22      -5.930 -11.719   2.278  1.00  0.00              
ATOM     66  CA  THR    22      -6.514 -12.879   2.938  1.00  0.00              
ATOM     67  C   THR    22      -5.421 -13.772   3.545  1.00  0.00              
ATOM     68  O   THR    22      -5.510 -14.173   4.739  1.00  0.00              
ATOM     69  N   THR    23      -4.369 -13.991   2.765  1.00  0.00              
ATOM     70  CA  THR    23      -3.216 -14.787   3.152  1.00  0.00              
ATOM     71  C   THR    23      -2.564 -14.210   4.392  1.00  0.00              
ATOM     72  O   THR    23      -2.288 -14.954   5.343  1.00  0.00              
ATOM     73  N   TYR    24      -2.327 -12.884   4.416  1.00  0.00              
ATOM     74  CA  TYR    24      -1.685 -12.283   5.583  1.00  0.00              
ATOM     75  C   TYR    24      -2.610 -12.284   6.804  1.00  0.00              
ATOM     76  O   TYR    24      -2.119 -12.416   7.987  1.00  0.00              
ATOM     77  N   SER    25      -5.648  -5.189   8.128  1.00  0.00              
ATOM     78  CA  SER    25      -5.535  -4.708   6.752  1.00  0.00              
ATOM     79  C   SER    25      -4.148  -4.993   6.216  1.00  0.00              
ATOM     80  O   SER    25      -3.159  -5.063   6.986  1.00  0.00              
ATOM     81  N   ASN    26      -4.077  -5.143   4.899  1.00  0.00              
ATOM     82  CA  ASN    26      -2.819  -5.093   4.149  1.00  0.00              
ATOM     83  C   ASN    26      -2.966  -3.933   3.138  1.00  0.00              
ATOM     84  O   ASN    26      -4.061  -3.728   2.585  1.00  0.00              
ATOM     85  N   ILE    27      -1.895  -3.175   2.872  1.00  0.00              
ATOM     86  CA  ILE    27      -2.004  -2.104   1.875  1.00  0.00              
ATOM     87  C   ILE    27      -0.960  -2.311   0.806  1.00  0.00              
ATOM     88  O   ILE    27       0.037  -3.055   1.000  1.00  0.00              
ATOM     89  N   THR    28      -1.214  -1.685  -0.330  1.00  0.00              
ATOM     90  CA  THR    28      -0.435  -1.888  -1.555  1.00  0.00              
ATOM     91  C   THR    28      -0.080  -0.521  -2.116  1.00  0.00              
ATOM     92  O   THR    28      -0.962   0.345  -2.299  1.00  0.00              
ATOM     93  N   LEU    29       1.212  -0.326  -2.366  1.00  0.00              
ATOM     94  CA  LEU    29       1.741   0.964  -2.767  1.00  0.00              
ATOM     95  C   LEU    29       1.872   0.952  -4.300  1.00  0.00              
ATOM     96  O   LEU    29       2.623   0.129  -4.862  1.00  0.00              
ATOM     97  N   GLU    30       1.141   1.858  -4.949  1.00  0.00              
ATOM     98  CA  GLU    30       1.023   1.908  -6.407  1.00  0.00              
ATOM     99  C   GLU    30       1.498   3.289  -6.914  1.00  0.00              
ATOM    100  O   GLU    30       1.534   4.257  -6.149  1.00  0.00              
ATOM    101  N   ASP    31       1.217   6.899  -8.534  1.00  0.00              
ATOM    102  CA  ASP    31       0.095   7.845  -8.362  1.00  0.00              
ATOM    103  C   ASP    31      -0.629   8.092  -9.699  1.00  0.00              
ATOM    104  O   ASP    31      -0.034   7.959 -10.785  1.00  0.00              
ATOM    105  N   ASP    32      -1.916   8.401  -9.623  1.00  0.00              
ATOM    106  CA  ASP    32      -2.650   8.718 -10.870  1.00  0.00              
ATOM    107  C   ASP    32      -3.175  10.146 -10.926  1.00  0.00              
ATOM    108  O   ASP    32      -3.709  10.544 -11.991  1.00  0.00              
ATOM    109  N   GLN    33      -3.053  10.900  -9.818  1.00  0.00              
ATOM    110  CA  GLN    33      -3.554  12.287  -9.726  1.00  0.00              
ATOM    111  C   GLN    33      -2.650  13.304  -9.050  1.00  0.00              
ATOM    112  O   GLN    33      -3.137  14.190  -8.316  1.00  0.00              
ATOM    113  N   GLY    34      -1.359  13.184  -9.306  1.00  0.00              
ATOM    114  CA  GLY    34      -0.397  14.125  -8.755  1.00  0.00              
ATOM    115  C   GLY    34       0.074  13.920  -7.341  1.00  0.00              
ATOM    116  O   GLY    34       0.808  14.778  -6.811  1.00  0.00              
ATOM    117  N   SER    35      -0.314  12.811  -6.720  1.00  0.00              
ATOM    118  CA  SER    35       0.169  12.516  -5.376  1.00  0.00              
ATOM    119  C   SER    35       1.509  11.840  -5.451  1.00  0.00              
ATOM    120  O   SER    35       2.110  11.679  -6.535  1.00  0.00              
ATOM    121  N   HIS    36       2.010  11.436  -4.292  1.00  0.00              
ATOM    122  CA  HIS    36       3.249  10.676  -4.238  1.00  0.00              
ATOM    123  C   HIS    36       3.112   9.182  -4.558  1.00  0.00              
ATOM    124  O   HIS    36       4.039   8.554  -5.085  1.00  0.00              
ATOM    125  N   PHE    37       1.966   8.613  -4.206  1.00  0.00              
ATOM    126  CA  PHE    37       1.700   7.177  -4.392  1.00  0.00              
ATOM    127  C   PHE    37       0.207   7.017  -4.212  1.00  0.00              
ATOM    128  O   PHE    37      -0.433   7.898  -3.614  1.00  0.00              
ATOM    129  N   ARG    38      -0.344   5.941  -4.798  1.00  0.00              
ATOM    130  CA  ARG    38      -1.740   5.550  -4.645  1.00  0.00              
ATOM    131  C   ARG    38      -1.711   4.337  -3.737  1.00  0.00              
ATOM    132  O   ARG    38      -0.902   3.404  -3.951  1.00  0.00              
ATOM    133  N   LEU    39      -2.513   4.385  -2.679  1.00  0.00              
ATOM    134  CA  LEU    39      -2.547   3.277  -1.696  1.00  0.00              
ATOM    135  C   LEU    39      -3.895   2.586  -1.783  1.00  0.00              
ATOM    136  O   LEU    39      -4.924   3.246  -1.673  1.00  0.00              
ATOM    137  N   VAL    40      -3.919   1.259  -2.010  1.00  0.00              
ATOM    138  CA  VAL    40      -5.133   0.479  -1.825  1.00  0.00              
ATOM    139  C   VAL    40      -5.092  -0.335  -0.541  1.00  0.00              
ATOM    140  O   VAL    40      -4.060  -0.936  -0.220  1.00  0.00              
ATOM    141  N   VAL    41      -6.225  -0.358   0.172  1.00  0.00              
ATOM    142  CA  VAL    41      -6.319  -0.908   1.499  1.00  0.00              
ATOM    143  C   VAL    41      -7.287  -2.085   1.441  1.00  0.00              
ATOM    144  O   VAL    41      -8.447  -1.906   1.063  1.00  0.00              
ATOM    145  N   ARG    42      -6.853  -3.245   1.917  1.00  0.00              
ATOM    146  CA  ARG    42      -7.714  -4.441   1.917  1.00  0.00              
ATOM    147  C   ARG    42      -7.780  -5.063   3.284  1.00  0.00              
ATOM    148  O   ARG    42      -6.740  -5.236   3.927  1.00  0.00              
ATOM    149  N   ASP    43      -8.996  -5.415   3.745  1.00  0.00              
ATOM    150  CA  ASP    43      -9.102  -6.361   4.849  1.00  0.00              
ATOM    151  C   ASP    43      -8.912  -7.734   4.232  1.00  0.00              
ATOM    152  O   ASP    43      -8.756  -7.812   3.016  1.00  0.00              
ATOM    153  N   THR    44      -8.893  -8.807   5.034  1.00  0.00              
ATOM    154  CA  THR    44      -8.884 -10.162   4.466  1.00  0.00              
ATOM    155  C   THR    44     -10.081 -10.459   3.553  1.00  0.00              
ATOM    156  O   THR    44     -10.002 -11.427   2.819  1.00  0.00              
ATOM    157  N   GLU    45     -11.134  -9.640   3.582  1.00  0.00              
ATOM    158  CA  GLU    45     -12.370  -9.941   2.853  1.00  0.00              
ATOM    159  C   GLU    45     -12.731  -8.919   1.795  1.00  0.00              
ATOM    160  O   GLU    45     -13.275  -9.287   0.732  1.00  0.00              
ATOM    161  N   GLY    46     -12.464  -7.625   2.039  1.00  0.00              
ATOM    162  CA  GLY    46     -12.840  -6.613   1.035  1.00  0.00              
ATOM    163  C   GLY    46     -11.877  -5.433   0.995  1.00  0.00              
ATOM    164  O   GLY    46     -11.129  -5.246   1.921  1.00  0.00              
ATOM    165  N   GLU    56     -11.948  -4.658  -0.066  1.00  0.00              
ATOM    166  CA  GLU    56     -11.290  -3.344  -0.137  1.00  0.00              
ATOM    167  C   GLU    56     -12.010  -2.260   0.694  1.00  0.00              
ATOM    168  O   GLU    56     -13.277  -2.243   0.803  1.00  0.00              
ATOM    169  N   PRO    57     -11.229  -1.374   1.294  1.00  0.00              
ATOM    170  CA  PRO    57     -11.750  -0.260   2.079  1.00  0.00              
ATOM    171  C   PRO    57     -11.392   1.057   1.387  1.00  0.00              
ATOM    172  O   PRO    57     -10.327   1.184   0.810  1.00  0.00              
ATOM    173  N   ASP    58      -5.485   3.582  10.847  1.00  0.00              
ATOM    174  CA  ASP    58      -4.245   2.924  11.239  1.00  0.00              
ATOM    175  C   ASP    58      -3.505   2.351  10.038  1.00  0.00              
ATOM    176  O   ASP    58      -2.256   2.433  10.007  1.00  0.00              
ATOM    177  N   ALA    59      -4.192   1.762   9.042  1.00  0.00              
ATOM    178  CA  ALA    59      -3.461   1.265   7.849  1.00  0.00              
ATOM    179  C   ALA    59      -2.764   2.350   7.054  1.00  0.00              
ATOM    180  O   ALA    59      -1.630   2.190   6.588  1.00  0.00              
ATOM    181  N   GLY    60      -3.409   3.500   6.961  1.00  0.00              
ATOM    182  CA  GLY    60      -2.792   4.598   6.258  1.00  0.00              
ATOM    183  C   GLY    60      -1.622   5.186   7.013  1.00  0.00              
ATOM    184  O   GLY    60      -0.591   5.497   6.414  1.00  0.00              
ATOM    185  N   GLU    61      -1.780   5.361   8.314  1.00  0.00              
ATOM    186  CA  GLU    61      -0.671   5.840   9.142  1.00  0.00              
ATOM    187  C   GLU    61       0.539   4.891   8.980  1.00  0.00              
ATOM    188  O   GLU    61       1.704   5.345   8.763  1.00  0.00              
ATOM    189  N   GLY    62       0.289   3.580   9.091  1.00  0.00              
ATOM    190  CA  GLY    62       1.389   2.598   8.937  1.00  0.00              
ATOM    191  C   GLY    62       2.048   2.632   7.577  1.00  0.00              
ATOM    192  O   GLY    62       3.280   2.510   7.445  1.00  0.00              
ATOM    193  N   LEU    63       1.224   2.756   6.537  1.00  0.00              
ATOM    194  CA  LEU    63       1.744   2.899   5.194  1.00  0.00              
ATOM    195  C   LEU    63       2.675   4.136   5.054  1.00  0.00              
ATOM    196  O   LEU    63       3.729   4.061   4.406  1.00  0.00              
ATOM    197  N   ASN    64       2.223   5.284   5.567  1.00  0.00              
ATOM    198  CA  ASN    64       3.005   6.544   5.492  1.00  0.00              
ATOM    199  C   ASN    64       4.318   6.339   6.230  1.00  0.00              
ATOM    200  O   ASN    64       5.369   6.801   5.750  1.00  0.00              
ATOM    201  N   ARG    65       4.294   5.646   7.380  1.00  0.00              
ATOM    202  CA  ARG    65       5.527   5.451   8.126  1.00  0.00              
ATOM    203  C   ARG    65       6.465   4.505   7.372  1.00  0.00              
ATOM    204  O   ARG    65       7.681   4.726   7.336  1.00  0.00              
ATOM    205  N   TYR    66       5.889   3.469   6.763  1.00  0.00              
ATOM    206  CA  TYR    66       6.669   2.506   5.952  1.00  0.00              
ATOM    207  C   TYR    66       7.295   3.175   4.744  1.00  0.00              
ATOM    208  O   TYR    66       8.489   2.981   4.463  1.00  0.00              
ATOM    209  N   ILE    67       6.498   3.984   4.034  1.00  0.00              
ATOM    210  CA  ILE    67       6.951   4.554   2.772  1.00  0.00              
ATOM    211  C   ILE    67       7.945   5.677   3.013  1.00  0.00              
ATOM    212  O   ILE    67       8.820   5.961   2.181  1.00  0.00              
ATOM    213  N   ARG    68       7.808   6.291   4.190  1.00  0.00              
ATOM    214  CA  ARG    68       8.661   7.383   4.630  1.00  0.00              
ATOM    215  C   ARG    68      10.103   6.935   4.701  1.00  0.00              
ATOM    216  O   ARG    68      11.011   7.761   4.598  1.00  0.00              
ATOM    217  N   THR    69      10.325   5.630   4.834  1.00  0.00              
ATOM    218  CA  THR    69      11.669   5.061   4.786  1.00  0.00              
ATOM    219  C   THR    69      12.383   5.162   3.433  1.00  0.00              
ATOM    220  O   THR    69      13.623   5.018   3.390  1.00  0.00              
ATOM    221  N   SER    70      11.625   5.369   2.349  1.00  0.00              
ATOM    222  CA  SER    70      12.154   5.391   0.971  1.00  0.00              
ATOM    223  C   SER    70      12.078   6.758   0.305  1.00  0.00              
ATOM    224  O   SER    70      12.220   6.890  -0.915  1.00  0.00              
ATOM    225  N   GLY    71      11.818   7.773   1.113  1.00  0.00              
ATOM    226  CA  GLY    71      11.828   9.144   0.653  1.00  0.00              
ATOM    227  C   GLY    71      12.450  10.036   1.715  1.00  0.00              
ATOM    228  O   GLY    71      12.601   9.627   2.875  1.00  0.00              
END
