
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0350AL381_1-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350AL381_1-D1.T0350_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    -       -      M       1           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    S      36      E       4           #
LGA    Y      37      R       5          1.687
LGA    T      38      L       6          3.891
LGA    N      39      T       7          2.458
LGA    L      40      T       8          3.572
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    A      41      P      53           #
LGA    E      42      S      54          5.021
LGA    M      43      Q      55           #
LGA    V      44      V      56          4.945
LGA    G      45      H      57          4.942
LGA    E      46      L      58          2.622
LGA    M      47      -       -           -
LGA    N      48      K      59           #
LGA    K      49      F      60          2.767
LGA    L      50      E      61           #
LGA    L      51      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    E      52      V      71          2.123
LGA    P      53      K      72          2.019
LGA    -       -      V      73           -
LGA    -       -      I      74           -
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    S      54      I      85          3.997
LGA    Q      55      P      86          2.670
LGA    V      56      P      87          4.053
LGA    -       -      K      88           -
LGA    H      57      R      89          2.842
LGA    L      58      W      90          2.835
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    K      59      Y      94          2.191
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    F      60      M      97          1.543
LGA    E      61      T      98          1.621
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    L      62      L     101          0.960
LGA    H      63      G     102          1.169
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28   91    5.0     21    3.10     9.52     14.543     0.656

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.518392 * X  +   0.807590 * Y  +  -0.281192 * Z  + -16.243242
  Y_new =   0.813384 * X  +   0.364157 * Y  +  -0.453648 * Z  + -12.738289
  Z_new =  -0.263963 * X  +  -0.463884 * Y  +  -0.845656 * Z  +   0.840062 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.639864    0.501729  [ DEG:  -151.2531     28.7469 ]
  Theta =   0.267129    2.874464  [ DEG:    15.3054    164.6946 ]
  Phi   =   2.138212   -1.003381  [ DEG:   122.5105    -57.4895 ]
 
# 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: T0350AL381_1-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_1-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28   91   5.0   21   3.10    9.52  14.543
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_1-D1
REMARK Aligment from pdb entry: 1t6sA
ATOM     57  N   SER    36      13.186   0.544  -1.181  1.00  0.00              
ATOM     58  CA  SER    36      12.650   1.728  -0.520  1.00  0.00              
ATOM     59  C   SER    36      11.528   2.149  -1.490  1.00  0.00              
ATOM     60  O   SER    36      11.573   1.816  -2.677  1.00  0.00              
ATOM     61  N   TYR    37      10.495   2.849  -0.997  1.00  0.00              
ATOM     62  CA  TYR    37       9.408   3.268  -1.892  1.00  0.00              
ATOM     63  C   TYR    37       9.902   4.117  -3.056  1.00  0.00              
ATOM     64  O   TYR    37       9.351   4.072  -4.162  1.00  0.00              
ATOM     65  N   THR    38      10.965   4.870  -2.811  1.00  0.00              
ATOM     66  CA  THR    38      11.531   5.713  -3.834  1.00  0.00              
ATOM     67  C   THR    38      12.362   4.882  -4.814  1.00  0.00              
ATOM     68  O   THR    38      12.313   5.097  -6.031  1.00  0.00              
ATOM     69  N   ASN    39      13.125   3.931  -4.283  1.00  0.00              
ATOM     70  CA  ASN    39      13.949   3.064  -5.123  1.00  0.00              
ATOM     71  C   ASN    39      13.077   2.225  -6.056  1.00  0.00              
ATOM     72  O   ASN    39      13.412   2.049  -7.224  1.00  0.00              
ATOM     73  N   LEU    40      11.941   1.736  -5.555  1.00  0.00              
ATOM     74  CA  LEU    40      11.054   0.907  -6.377  1.00  0.00              
ATOM     75  C   LEU    40      10.460   1.696  -7.534  1.00  0.00              
ATOM     76  O   LEU    40      10.378   1.207  -8.663  1.00  0.00              
ATOM     77  N   ALA    41      10.022   2.913  -7.248  1.00  0.00              
ATOM     78  CA  ALA    41       9.430   3.753  -8.281  1.00  0.00              
ATOM     79  C   ALA    41      10.456   4.094  -9.355  1.00  0.00              
ATOM     80  O   ALA    41      10.116   4.206 -10.534  1.00  0.00              
ATOM     81  N   GLU    42      11.710   4.262  -8.928  1.00  0.00              
ATOM     82  CA  GLU    42      12.829   4.586  -9.823  1.00  0.00              
ATOM     83  C   GLU    42      13.119   3.412 -10.756  1.00  0.00              
ATOM     84  O   GLU    42      13.492   3.605 -11.910  1.00  0.00              
ATOM     85  N   MET    43      12.957   2.190 -10.252  1.00  0.00              
ATOM     86  CA  MET    43      13.197   1.001 -11.068  1.00  0.00              
ATOM     87  C   MET    43      12.062   0.893 -12.077  1.00  0.00              
ATOM     88  O   MET    43      12.277   0.564 -13.241  1.00  0.00              
ATOM     89  N   VAL    44      10.848   1.178 -11.622  1.00  0.00              
ATOM     90  CA  VAL    44       9.689   1.126 -12.491  1.00  0.00              
ATOM     91  C   VAL    44       9.820   2.182 -13.586  1.00  0.00              
ATOM     92  O   VAL    44       9.488   1.914 -14.735  1.00  0.00              
ATOM     93  N   GLY    45      10.306   3.377 -13.230  1.00  0.00              
ATOM     94  CA  GLY    45      10.497   4.448 -14.219  1.00  0.00              
ATOM     95  C   GLY    45      11.454   4.001 -15.321  1.00  0.00              
ATOM     96  O   GLY    45      11.206   4.266 -16.498  1.00  0.00              
ATOM     97  N   GLU    46      12.545   3.332 -14.944  1.00  0.00              
ATOM     98  CA  GLU    46      13.518   2.856 -15.929  1.00  0.00              
ATOM     99  C   GLU    46      12.875   1.883 -16.917  1.00  0.00              
ATOM    100  O   GLU    46      13.085   1.991 -18.128  1.00  0.00              
ATOM    101  N   MET    47      12.084   0.941 -16.401  1.00  0.00              
ATOM    102  CA  MET    47      11.407  -0.019 -17.263  1.00  0.00              
ATOM    103  C   MET    47      10.500   0.757 -18.228  1.00  0.00              
ATOM    104  O   MET    47      10.536   0.530 -19.440  1.00  0.00              
ATOM    105  N   ASN    48       9.682   1.661 -17.694  1.00  0.00              
ATOM    106  CA  ASN    48       8.789   2.454 -18.542  1.00  0.00              
ATOM    107  C   ASN    48       9.594   3.242 -19.582  1.00  0.00              
ATOM    108  O   ASN    48       9.123   3.466 -20.699  1.00  0.00              
ATOM    109  N   LYS    49      10.807   3.659 -19.225  1.00  0.00              
ATOM    110  CA  LYS    49      11.639   4.374 -20.190  1.00  0.00              
ATOM    111  C   LYS    49      12.038   3.421 -21.323  1.00  0.00              
ATOM    112  O   LYS    49      12.037   3.810 -22.498  1.00  0.00              
ATOM    113  N   LEU    50      12.353   2.171 -20.985  1.00  0.00              
ATOM    114  CA  LEU    50      12.711   1.179 -22.005  1.00  0.00              
ATOM    115  C   LEU    50      11.526   0.843 -22.914  1.00  0.00              
ATOM    116  O   LEU    50      11.710   0.570 -24.107  1.00  0.00              
ATOM    117  N   LEU    51      10.318   0.843 -22.343  1.00  0.00              
ATOM    118  CA  LEU    51       9.096   0.554 -23.114  1.00  0.00              
ATOM    119  C   LEU    51       8.896   1.669 -24.135  1.00  0.00              
ATOM    120  O   LEU    51       8.560   1.420 -25.295  1.00  0.00              
ATOM    121  N   GLU    52       9.094   2.902 -23.689  1.00  0.00              
ATOM    122  CA  GLU    52       8.965   4.052 -24.571  1.00  0.00              
ATOM    123  C   GLU    52      10.022   3.976 -25.677  1.00  0.00              
ATOM    124  O   GLU    52       9.726   4.207 -26.842  1.00  0.00              
ATOM    125  N   PRO    53      11.244   3.628 -25.288  1.00  0.00              
ATOM    126  CA  PRO    53      12.384   3.524 -26.197  1.00  0.00              
ATOM    127  C   PRO    53      12.263   2.466 -27.297  1.00  0.00              
ATOM    128  O   PRO    53      12.622   2.724 -28.451  1.00  0.00              
ATOM    129  N   SER    54      11.773   1.283 -26.933  1.00  0.00              
ATOM    130  CA  SER    54      11.629   0.176 -27.870  1.00  0.00              
ATOM    131  C   SER    54      10.270   0.144 -28.586  1.00  0.00              
ATOM    132  O   SER    54      10.035  -0.707 -29.439  1.00  0.00              
ATOM    133  N   GLN    55       9.381   1.069 -28.243  1.00  0.00              
ATOM    134  CA  GLN    55       8.094   1.128 -28.908  1.00  0.00              
ATOM    135  C   GLN    55       7.040   0.137 -28.452  1.00  0.00              
ATOM    136  O   GLN    55       6.239  -0.325 -29.265  1.00  0.00              
ATOM    137  N   VAL    56       7.032  -0.180 -27.160  1.00  0.00              
ATOM    138  CA  VAL    56       6.050  -1.107 -26.595  1.00  0.00              
ATOM    139  C   VAL    56       4.700  -0.398 -26.449  1.00  0.00              
ATOM    140  O   VAL    56       4.636   0.820 -26.290  1.00  0.00              
ATOM    141  N   HIS    57       3.619  -1.169 -26.497  1.00  0.00              
ATOM    142  CA  HIS    57       2.275  -0.603 -26.414  1.00  0.00              
ATOM    143  C   HIS    57       1.662  -0.602 -25.014  1.00  0.00              
ATOM    144  O   HIS    57       0.463  -0.367 -24.853  1.00  0.00              
ATOM    145  N   LEU    58       2.490  -0.860 -24.007  1.00  0.00              
ATOM    146  CA  LEU    58       2.025  -0.892 -22.624  1.00  0.00              
ATOM    147  C   LEU    58       2.980  -0.163 -21.679  1.00  0.00              
ATOM    148  O   LEU    58       4.132   0.123 -22.030  1.00  0.00              
ATOM    149  N   LYS    59       2.489   0.133 -20.480  1.00  0.00              
ATOM    150  CA  LYS    59       3.276   0.836 -19.460  1.00  0.00              
ATOM    151  C   LYS    59       2.871   0.376 -18.081  1.00  0.00              
ATOM    152  O   LYS    59       1.734  -0.050 -17.874  1.00  0.00              
ATOM    153  N   PHE    60       3.803   0.473 -17.138  1.00  0.00              
ATOM    154  CA  PHE    60       3.514   0.128 -15.755  1.00  0.00              
ATOM    155  C   PHE    60       2.993   1.397 -15.050  1.00  0.00              
ATOM    156  O   PHE    60       3.594   2.473 -15.136  1.00  0.00              
ATOM    157  N   GLU    61       1.863   1.248 -14.366  1.00  0.00              
ATOM    158  CA  GLU    61       1.208   2.325 -13.634  1.00  0.00              
ATOM    159  C   GLU    61       1.087   2.031 -12.135  1.00  0.00              
ATOM    160  O   GLU    61       0.746   0.912 -11.714  1.00  0.00              
ATOM    161  N   LEU    62       1.350   3.056 -11.334  1.00  0.00              
ATOM    162  CA  LEU    62       1.251   2.960  -9.887  1.00  0.00              
ATOM    163  C   LEU    62      -0.152   3.415  -9.520  1.00  0.00              
ATOM    164  O   LEU    62      -0.439   4.616  -9.527  1.00  0.00              
ATOM    165  N   HIS    63      -1.034   2.468  -9.220  1.00  0.00              
ATOM    166  CA  HIS    63      -2.404   2.818  -8.844  1.00  0.00              
ATOM    167  C   HIS    63      -2.661   2.398  -7.401  1.00  0.00              
ATOM    168  O   HIS    63      -2.637   1.212  -7.087  1.00  0.00              
END
