
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0314AL381_2-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314AL381_2-D1.T0314_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    -       -      S       2           -
LGA    -       -      I       3           -
LGA    -       -      T       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      I       8           -
LGA    -       -      C       9           -
LGA    -       -      Q      10           -
LGA    -       -      A      11           -
LGA    -       -      A      12           -
LGA    -       -      D      13           -
LGA    -       -      A      14           -
LGA    -       -      L      15           -
LGA    -       -      K      16           -
LGA    -       -      G      17           -
LGA    -       -      F      18           -
LGA    -       -      V      19           -
LGA    -       -      G      20           -
LGA    -       -      F      21           -
LGA    -       -      N      22           -
LGA    -       -      R      23           -
LGA    -       -      K      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    -       -      R      27           -
LGA    -       -      Y      28           -
LGA    -       -      I      29           -
LGA    -       -      V      30           -
LGA    -       -      R      31           -
LGA    -       -      F      32           -
LGA    -       -      S      33           -
LGA    -       -      E      34           -
LGA    -       -      D      35           -
LGA    -       -      S      36           -
LGA    -       -      F      37           -
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    R      27      A      42           #
LGA    Y      28      D      43          1.950
LGA    I      29      D      44          4.694
LGA    V      30      S      45          3.330
LGA    -       -      I      46           -
LGA    R      31      T      47          1.705
LGA    F      32      P      48          4.272
LGA    -       -      T      49           -
LGA    -       -      S      50           -
LGA    -       -      E      51           -
LGA    S      33      F      52          1.980
LGA    E      34      V      53          1.606
LGA    D      35      W      54          0.749
LGA    S      36      S      55          0.729
LGA    F      37      S      56          2.895
LGA    G      38      V      57          1.944
LGA    M      39      R      58          1.070
LGA    D      40      D      59          1.349
LGA    V      41      D      60          5.225
LGA    A      42      V      61           -
LGA    D      43      -       -           -
LGA    D      44      -       -           -
LGA    S      45      -       -           -
LGA    I      46      -       -           -
LGA    T      47      -       -           -
LGA    P      48      M      62           #
LGA    -       -      R      63           -
LGA    -       -      L      64           -
LGA    T      49      G      65          1.776
LGA    -       -      R      66           -
LGA    S      50      E      67          2.693
LGA    E      51      Q      68           -
LGA    F      52      -       -           -
LGA    V      53      L      69           #
LGA    W      54      Q      70           -
LGA    -       -      I      71           -
LGA    -       -      L      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    -       -      Q      75           -
LGA    -       -      N      76           -
LGA    -       -      I      77           -
LGA    -       -      N      78           -
LGA    -       -      E      79           -
LGA    -       -      R      80           -
LGA    -       -      L      81           -
LGA    -       -      N      82           -
LGA    -       -      I      83           -
LGA    -       -      G      84           -
LGA    -       -      E      85           -
LGA    -       -      P      86           -
LGA    -       -      L      87           -
LGA    -       -      L      88           -
LGA    -       -      V      89           -
LGA    -       -      Y      90           -
LGA    S      55      L      91          5.527
LGA    S      56      R      92          1.360
LGA    V      57      R      93          2.266
LGA    R      58      Q      94          4.402
LGA    D      59      D      95          3.415
LGA    D      60      L      96          4.023
LGA    V      61      -       -           -
LGA    M      62      P      97           #
LGA    -       -      E      98           -
LGA    R      63      I      99          2.963
LGA    L      64      T     100           #
LGA    G      65      A     101           -
LGA    R      66      Q     102           -
LGA    E      67      R     103           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41  103    5.0     23    3.04    13.04     14.441     0.733

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.117176 * X  +  -0.941986 * Y  +   0.314535 * Z  +  49.572948
  Y_new =  -0.731139 * X  +   0.132514 * Y  +   0.669235 * Z  +  37.010166
  Z_new =  -0.672090 * X  +  -0.308387 * Y  +  -0.673195 * Z  +  29.092169 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.712028    0.429565  [ DEG:  -155.3877     24.6123 ]
  Theta =   0.737028    2.404564  [ DEG:    42.2286    137.7714 ]
  Phi   =  -1.411883    1.729710  [ DEG:   -80.8949     99.1051 ]
 
# 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: T0314AL381_2-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314AL381_2-D1.T0314_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41  103   5.0   23   3.04   13.04  14.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0314AL381_2-D1
REMARK Aligment from pdb entry: 1veoA
ATOM      1  N   ARG    27      33.970   6.595 -29.352  1.00  0.00              
ATOM      2  CA  ARG    27      33.459   6.219 -28.045  1.00  0.00              
ATOM      3  C   ARG    27      32.124   6.948 -27.881  1.00  0.00              
ATOM      4  O   ARG    27      31.876   7.982 -28.511  1.00  0.00              
ATOM      5  N   TYR    28      31.255   6.404 -27.046  1.00  0.00              
ATOM      6  CA  TYR    28      29.970   7.030 -26.820  1.00  0.00              
ATOM      7  C   TYR    28      29.711   7.158 -25.334  1.00  0.00              
ATOM      8  O   TYR    28      30.269   6.417 -24.520  1.00  0.00              
ATOM      9  N   ILE    29      28.877   8.126 -24.986  1.00  0.00              
ATOM     10  CA  ILE    29      28.502   8.353 -23.607  1.00  0.00              
ATOM     11  C   ILE    29      26.996   8.356 -23.621  1.00  0.00              
ATOM     12  O   ILE    29      26.372   9.338 -24.026  1.00  0.00              
ATOM     13  N   VAL    30      26.384   7.240 -23.218  1.00  0.00              
ATOM     14  CA  VAL    30      24.928   7.168 -23.199  1.00  0.00              
ATOM     15  C   VAL    30      24.330   7.927 -22.021  1.00  0.00              
ATOM     16  O   VAL    30      24.905   7.969 -20.933  1.00  0.00              
ATOM     17  N   ARG    31      23.188   8.551 -22.261  1.00  0.00              
ATOM     18  CA  ARG    31      22.476   9.248 -21.208  1.00  0.00              
ATOM     19  C   ARG    31      21.202   8.433 -21.068  1.00  0.00              
ATOM     20  O   ARG    31      20.444   8.294 -22.027  1.00  0.00              
ATOM     21  N   PHE    32      20.979   7.862 -19.892  1.00  0.00              
ATOM     22  CA  PHE    32      19.778   7.078 -19.682  1.00  0.00              
ATOM     23  C   PHE    32      18.713   8.078 -19.304  1.00  0.00              
ATOM     24  O   PHE    32      18.419   8.301 -18.135  1.00  0.00              
ATOM     25  N   SER    33      18.155   8.691 -20.335  1.00  0.00              
ATOM     26  CA  SER    33      17.155   9.730 -20.197  1.00  0.00              
ATOM     27  C   SER    33      15.791   9.235 -19.766  1.00  0.00              
ATOM     28  O   SER    33      14.972   8.825 -20.589  1.00  0.00              
ATOM     29  N   GLU    34      15.562   9.290 -18.458  1.00  0.00              
ATOM     30  CA  GLU    34      14.298   8.871 -17.873  1.00  0.00              
ATOM     31  C   GLU    34      13.357  10.066 -17.820  1.00  0.00              
ATOM     32  O   GLU    34      12.423  10.094 -17.030  1.00  0.00              
ATOM     33  N   ASP    35      13.622  11.064 -18.655  1.00  0.00              
ATOM     34  CA  ASP    35      12.782  12.257 -18.708  1.00  0.00              
ATOM     35  C   ASP    35      12.189  12.397 -20.104  1.00  0.00              
ATOM     36  O   ASP    35      12.613  11.720 -21.039  1.00  0.00              
ATOM     37  N   SER    36      11.210  13.282 -20.239  1.00  0.00              
ATOM     38  CA  SER    36      10.546  13.513 -21.513  1.00  0.00              
ATOM     39  C   SER    36      11.346  14.375 -22.487  1.00  0.00              
ATOM     40  O   SER    36      11.984  15.349 -22.084  1.00  0.00              
ATOM     41  N   PHE    37      11.314  14.005 -23.764  1.00  0.00              
ATOM     42  CA  PHE    37      11.994  14.778 -24.807  1.00  0.00              
ATOM     43  C   PHE    37      10.928  15.652 -25.449  1.00  0.00              
ATOM     44  O   PHE    37       9.922  15.142 -25.939  1.00  0.00              
ATOM     45  N   GLY    38      11.146  16.959 -25.456  1.00  0.00              
ATOM     46  CA  GLY    38      10.169  17.852 -26.052  1.00  0.00              
ATOM     47  C   GLY    38       9.519  18.701 -24.979  1.00  0.00              
ATOM     48  O   GLY    38       9.159  18.196 -23.916  1.00  0.00              
ATOM     49  N   MET    39       9.378  19.995 -25.247  1.00  0.00              
ATOM     50  CA  MET    39       8.773  20.877 -24.265  1.00  0.00              
ATOM     51  C   MET    39       9.790  21.797 -23.615  1.00  0.00              
ATOM     52  O   MET    39       9.427  22.785 -22.976  1.00  0.00              
ATOM     53  N   ASP    40      11.071  21.475 -23.766  1.00  0.00              
ATOM     54  CA  ASP    40      12.121  22.305 -23.194  1.00  0.00              
ATOM     55  C   ASP    40      12.851  23.070 -24.296  1.00  0.00              
ATOM     56  O   ASP    40      12.721  22.746 -25.478  1.00  0.00              
ATOM     57  N   VAL    41      13.607  24.094 -23.896  1.00  0.00              
ATOM     58  CA  VAL    41      14.359  24.925 -24.829  1.00  0.00              
ATOM     59  C   VAL    41      15.244  24.081 -25.748  1.00  0.00              
ATOM     60  O   VAL    41      16.065  23.282 -25.283  1.00  0.00              
ATOM     61  N   ALA    42      15.060  24.255 -27.054  1.00  0.00              
ATOM     62  CA  ALA    42      15.862  23.520 -28.016  1.00  0.00              
ATOM     63  C   ALA    42      15.334  22.152 -28.402  1.00  0.00              
ATOM     64  O   ALA    42      15.851  21.526 -29.328  1.00  0.00              
ATOM     65  N   ASP    43      14.308  21.676 -27.706  1.00  0.00              
ATOM     66  CA  ASP    43      13.750  20.368 -28.019  1.00  0.00              
ATOM     67  C   ASP    43      13.070  20.338 -29.383  1.00  0.00              
ATOM     68  O   ASP    43      12.365  21.263 -29.779  1.00  0.00              
ATOM     69  N   ASP    44      13.320  19.254 -30.099  1.00  0.00              
ATOM     70  CA  ASP    44      12.778  19.023 -31.427  1.00  0.00              
ATOM     71  C   ASP    44      12.633  17.504 -31.476  1.00  0.00              
ATOM     72  O   ASP    44      13.377  16.792 -32.151  1.00  0.00              
ATOM     73  N   SER    45      11.660  17.028 -30.706  1.00  0.00              
ATOM     74  CA  SER    45      11.377  15.606 -30.551  1.00  0.00              
ATOM     75  C   SER    45      10.107  15.534 -29.729  1.00  0.00              
ATOM     76  O   SER    45       9.626  16.543 -29.219  1.00  0.00              
ATOM     77  N   ILE    46       9.577  14.329 -29.582  1.00  0.00              
ATOM     78  CA  ILE    46       8.381  14.127 -28.787  1.00  0.00              
ATOM     79  C   ILE    46       8.468  12.722 -28.219  1.00  0.00              
ATOM     80  O   ILE    46       7.926  11.774 -28.790  1.00  0.00              
ATOM     81  N   THR    47       9.170  12.590 -27.101  1.00  0.00              
ATOM     82  CA  THR    47       9.340  11.288 -26.470  1.00  0.00              
ATOM     83  C   THR    47       9.015  11.320 -24.980  1.00  0.00              
ATOM     84  O   THR    47       9.898  11.501 -24.140  1.00  0.00              
ATOM     85  N   PRO    48       7.729  11.159 -24.635  1.00  0.00              
ATOM     86  CA  PRO    48       7.345  11.169 -23.219  1.00  0.00              
ATOM     87  C   PRO    48       7.821   9.884 -22.560  1.00  0.00              
ATOM     88  O   PRO    48       8.215   8.942 -23.246  1.00  0.00              
ATOM     89  N   THR    49       7.805   9.838 -21.237  1.00  0.00              
ATOM     90  CA  THR    49       8.219   8.620 -20.561  1.00  0.00              
ATOM     91  C   THR    49       7.058   7.630 -20.727  1.00  0.00              
ATOM     92  O   THR    49       5.929   8.043 -20.965  1.00  0.00              
ATOM     93  N   SER    50       7.321   6.320 -20.617  1.00  0.00              
ATOM     94  CA  SER    50       6.258   5.313 -20.772  1.00  0.00              
ATOM     95  C   SER    50       4.937   5.725 -20.110  1.00  0.00              
ATOM     96  O   SER    50       4.892   6.031 -18.922  1.00  0.00              
ATOM     97  N   GLU    51       3.863   5.729 -20.891  1.00  0.00              
ATOM     98  CA  GLU    51       2.560   6.128 -20.373  1.00  0.00              
ATOM     99  C   GLU    51       2.036   5.256 -19.236  1.00  0.00              
ATOM    100  O   GLU    51       1.234   5.713 -18.419  1.00  0.00              
ATOM    101  N   PHE    52       2.490   4.010 -19.174  1.00  0.00              
ATOM    102  CA  PHE    52       2.025   3.092 -18.142  1.00  0.00              
ATOM    103  C   PHE    52       2.553   3.380 -16.741  1.00  0.00              
ATOM    104  O   PHE    52       1.923   3.007 -15.751  1.00  0.00              
ATOM    105  N   VAL    53       3.701   4.037 -16.650  1.00  0.00              
ATOM    106  CA  VAL    53       4.279   4.323 -15.346  1.00  0.00              
ATOM    107  C   VAL    53       3.318   5.106 -14.448  1.00  0.00              
ATOM    108  O   VAL    53       3.291   4.909 -13.235  1.00  0.00              
ATOM    109  N   TRP    54       2.511   5.974 -15.043  1.00  0.00              
ATOM    110  CA  TRP    54       1.580   6.790 -14.267  1.00  0.00              
ATOM    111  C   TRP    54       0.472   5.999 -13.583  1.00  0.00              
ATOM    112  O   TRP    54      -0.147   6.487 -12.640  1.00  0.00              
ATOM    113  N   SER    55       0.226   4.779 -14.049  1.00  0.00              
ATOM    114  CA  SER    55      -0.834   3.954 -13.476  1.00  0.00              
ATOM    115  C   SER    55      -0.430   3.175 -12.241  1.00  0.00              
ATOM    116  O   SER    55      -1.275   2.585 -11.572  1.00  0.00              
ATOM    117  N   SER    56       0.862   3.171 -11.930  1.00  0.00              
ATOM    118  CA  SER    56       1.334   2.438 -10.769  1.00  0.00              
ATOM    119  C   SER    56       0.995   3.112  -9.444  1.00  0.00              
ATOM    120  O   SER    56       1.407   2.640  -8.386  1.00  0.00              
ATOM    121  N   VAL    57       0.237   4.203  -9.503  1.00  0.00              
ATOM    122  CA  VAL    57      -0.156   4.935  -8.301  1.00  0.00              
ATOM    123  C   VAL    57      -1.531   5.572  -8.430  1.00  0.00              
ATOM    124  O   VAL    57      -1.909   6.067  -9.494  1.00  0.00              
ATOM    125  N   ARG    58      -2.275   5.566  -7.330  1.00  0.00              
ATOM    126  CA  ARG    58      -3.614   6.141  -7.306  1.00  0.00              
ATOM    127  C   ARG    58      -3.558   7.563  -6.764  1.00  0.00              
ATOM    128  O   ARG    58      -4.421   8.391  -7.071  1.00  0.00              
ATOM    129  N   ASP    59      -2.545   7.843  -5.950  1.00  0.00              
ATOM    130  CA  ASP    59      -2.386   9.171  -5.376  1.00  0.00              
ATOM    131  C   ASP    59      -1.747  10.101  -6.405  1.00  0.00              
ATOM    132  O   ASP    59      -1.809   9.836  -7.609  1.00  0.00              
ATOM    133  N   ASP    60      -1.150  11.193  -5.928  1.00  0.00              
ATOM    134  CA  ASP    60      -0.495  12.152  -6.812  1.00  0.00              
ATOM    135  C   ASP    60       0.993  12.228  -6.481  1.00  0.00              
ATOM    136  O   ASP    60       1.637  13.257  -6.679  1.00  0.00              
ATOM    137  N   VAL    61       1.525  11.111  -5.993  1.00  0.00              
ATOM    138  CA  VAL    61       2.926  11.008  -5.608  1.00  0.00              
ATOM    139  C   VAL    61       3.916  10.994  -6.777  1.00  0.00              
ATOM    140  O   VAL    61       5.095  11.296  -6.598  1.00  0.00              
ATOM    141  N   MET    62       3.434  10.655  -7.966  1.00  0.00              
ATOM    142  CA  MET    62       4.286  10.560  -9.148  1.00  0.00              
ATOM    143  C   MET    62       4.650  11.833  -9.915  1.00  0.00              
ATOM    144  O   MET    62       5.701  11.889 -10.543  1.00  0.00              
ATOM    145  N   ARG    63       3.803  12.850  -9.877  1.00  0.00              
ATOM    146  CA  ARG    63       4.098  14.059 -10.639  1.00  0.00              
ATOM    147  C   ARG    63       4.274  15.330  -9.819  1.00  0.00              
ATOM    148  O   ARG    63       4.371  15.281  -8.591  1.00  0.00              
ATOM    149  N   LEU    64       4.335  16.466 -10.514  1.00  0.00              
ATOM    150  CA  LEU    64       4.517  17.757  -9.868  1.00  0.00              
ATOM    151  C   LEU    64       3.303  18.645 -10.040  1.00  0.00              
ATOM    152  O   LEU    64       2.576  18.536 -11.027  1.00  0.00              
ATOM    153  N   GLY    65       3.111  19.542  -9.081  1.00  0.00              
ATOM    154  CA  GLY    65       2.010  20.500  -9.090  1.00  0.00              
ATOM    155  C   GLY    65       2.600  21.795  -8.551  1.00  0.00              
ATOM    156  O   GLY    65       3.155  21.816  -7.455  1.00  0.00              
ATOM    157  N   ARG    66       2.491  22.870  -9.322  1.00  0.00              
ATOM    158  CA  ARG    66       3.061  24.150  -8.926  1.00  0.00              
ATOM    159  C   ARG    66       2.199  24.972  -7.988  1.00  0.00              
ATOM    160  O   ARG    66       1.054  24.633  -7.704  1.00  0.00              
ATOM    161  N   GLU    67       2.773  26.074  -7.525  1.00  0.00              
ATOM    162  CA  GLU    67       2.100  26.994  -6.628  1.00  0.00              
ATOM    163  C   GLU    67       0.695  27.299  -7.117  1.00  0.00              
ATOM    164  O   GLU    67      -0.203  27.545  -6.320  1.00  0.00              
END
