
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms  106 ( 1704),  selected  106 , name T0314.pdb
# PARAMETERS: T0314AL381_1.T0314.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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          4.521
LGA    Y      28      D      43          1.836
LGA    I      29      D      44          4.157
LGA    V      30      S      45          2.627
LGA    -       -      I      46           -
LGA    R      31      T      47          1.475
LGA    F      32      P      48          4.742
LGA    -       -      T      49           -
LGA    -       -      S      50           -
LGA    -       -      E      51           -
LGA    S      33      F      52          1.584
LGA    E      34      V      53          1.036
LGA    D      35      W      54          0.289
LGA    S      36      S      55          1.421
LGA    F      37      S      56          2.258
LGA    G      38      V      57          1.197
LGA    M      39      R      58          1.818
LGA    D      40      D      59          2.130
LGA    V      41      D      60          4.385
LGA    A      42      V      61           -
LGA    D      43      M      62           #
LGA    D      44      -       -           -
LGA    S      45      -       -           -
LGA    I      46      -       -           -
LGA    T      47      R      63           #
LGA    P      48      L      64           #
LGA    T      49      G      65          0.987
LGA    -       -      R      66           -
LGA    S      50      E      67          3.140
LGA    E      51      Q      68           -
LGA    F      52      L      69           -
LGA    -       -      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    V      53      Y      90          4.848
LGA    W      54      -       -           -
LGA    S      55      L      91           #
LGA    S      56      R      92          1.980
LGA    V      57      R      93          3.162
LGA    R      58      Q      94          4.933
LGA    D      59      D      95          3.948
LGA    D      60      -       -           -
LGA    V      61      -       -           -
LGA    M      62      L      96           #
LGA    R      63      P      97           #
LGA    -       -      E      98           -
LGA    -       -      I      99           -
LGA    L      64      T     100           #
LGA    G      65      A     101           -
LGA    R      66      Q     102           -
LGA    E      67      R     103           -
LGA    -       -      Q     104           -
LGA    -       -      L     105           -
LGA    -       -      R     106           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41  106    5.0     22    3.02    13.64     13.866     0.706

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.041374 * X  +  -0.944253 * Y  +   0.326612 * Z  +  52.488575
  Y_new =  -0.713915 * X  +   0.200758 * Y  +   0.670837 * Z  +  32.945225
  Z_new =  -0.699009 * X  +  -0.260928 * Y  +  -0.665810 * Z  +  28.472155 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.768092    0.373500  [ DEG:  -158.6000     21.4000 ]
  Theta =   0.774011    2.367581  [ DEG:    44.3476    135.6524 ]
  Phi   =  -1.512908    1.628685  [ DEG:   -86.6832     93.3168 ]
 
# 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_1                                  
REMARK     2: T0314.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314AL381_1.T0314.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41  106   5.0   22   3.02   13.64  13.866
REMARK  ---------------------------------------------------------- 
MOLECULE T0314AL381_1
REMARK Aligment from pdb entry: 1vepA
ATOM      1  N   ARG    27      32.756   5.656 -30.045  1.00  0.00              
ATOM      2  CA  ARG    27      32.312   5.247 -28.726  1.00  0.00              
ATOM      3  C   ARG    27      31.034   6.021 -28.465  1.00  0.00              
ATOM      4  O   ARG    27      30.757   7.017 -29.133  1.00  0.00              
ATOM      5  N   TYR    28      30.253   5.561 -27.499  1.00  0.00              
ATOM      6  CA  TYR    28      29.025   6.253 -27.166  1.00  0.00              
ATOM      7  C   TYR    28      28.824   6.316 -25.659  1.00  0.00              
ATOM      8  O   TYR    28      29.371   5.507 -24.901  1.00  0.00              
ATOM      9  N   ILE    29      28.040   7.301 -25.243  1.00  0.00              
ATOM     10  CA  ILE    29      27.708   7.495 -23.851  1.00  0.00              
ATOM     11  C   ILE    29      26.198   7.583 -23.801  1.00  0.00              
ATOM     12  O   ILE    29      25.608   8.615 -24.141  1.00  0.00              
ATOM     13  N   VAL    30      25.545   6.493 -23.407  1.00  0.00              
ATOM     14  CA  VAL    30      24.090   6.550 -23.347  1.00  0.00              
ATOM     15  C   VAL    30      23.601   7.297 -22.119  1.00  0.00              
ATOM     16  O   VAL    30      24.189   7.204 -21.045  1.00  0.00              
ATOM     17  N   ARG    31      22.540   8.068 -22.297  1.00  0.00              
ATOM     18  CA  ARG    31      21.924   8.763 -21.188  1.00  0.00              
ATOM     19  C   ARG    31      20.623   7.990 -21.032  1.00  0.00              
ATOM     20  O   ARG    31      19.845   7.896 -21.977  1.00  0.00              
ATOM     21  N   PHE    32      20.401   7.391 -19.869  1.00  0.00              
ATOM     22  CA  PHE    32      19.155   6.668 -19.660  1.00  0.00              
ATOM     23  C   PHE    32      18.175   7.750 -19.256  1.00  0.00              
ATOM     24  O   PHE    32      18.045   8.093 -18.084  1.00  0.00              
ATOM     25  N   SER    33      17.496   8.297 -20.257  1.00  0.00              
ATOM     26  CA  SER    33      16.581   9.403 -20.041  1.00  0.00              
ATOM     27  C   SER    33      15.198   9.043 -19.533  1.00  0.00              
ATOM     28  O   SER    33      14.277   8.797 -20.307  1.00  0.00              
ATOM     29  N   GLU    34      15.067   9.041 -18.212  1.00  0.00              
ATOM     30  CA  GLU    34      13.805   8.732 -17.561  1.00  0.00              
ATOM     31  C   GLU    34      12.967   9.991 -17.382  1.00  0.00              
ATOM     32  O   GLU    34      12.145  10.070 -16.475  1.00  0.00              
ATOM     33  N   ASP    35      13.188  10.982 -18.237  1.00  0.00              
ATOM     34  CA  ASP    35      12.406  12.210 -18.180  1.00  0.00              
ATOM     35  C   ASP    35      11.716  12.413 -19.528  1.00  0.00              
ATOM     36  O   ASP    35      11.950  11.668 -20.473  1.00  0.00              
ATOM     37  N   SER    36      10.869  13.424 -19.615  1.00  0.00              
ATOM     38  CA  SER    36      10.148  13.691 -20.849  1.00  0.00              
ATOM     39  C   SER    36      10.951  14.528 -21.834  1.00  0.00              
ATOM     40  O   SER    36      11.738  15.389 -21.438  1.00  0.00              
ATOM     41  N   PHE    37      10.756  14.254 -23.121  1.00  0.00              
ATOM     42  CA  PHE    37      11.419  15.002 -24.186  1.00  0.00              
ATOM     43  C   PHE    37      10.359  15.907 -24.783  1.00  0.00              
ATOM     44  O   PHE    37       9.343  15.423 -25.272  1.00  0.00              
ATOM     45  N   GLY    38      10.590  17.212 -24.750  1.00  0.00              
ATOM     46  CA  GLY    38       9.616  18.131 -25.307  1.00  0.00              
ATOM     47  C   GLY    38       9.021  18.986 -24.212  1.00  0.00              
ATOM     48  O   GLY    38       8.635  18.474 -23.164  1.00  0.00              
ATOM     49  N   MET    39       8.946  20.292 -24.448  1.00  0.00              
ATOM     50  CA  MET    39       8.409  21.190 -23.440  1.00  0.00              
ATOM     51  C   MET    39       9.499  22.088 -22.877  1.00  0.00              
ATOM     52  O   MET    39       9.243  23.237 -22.509  1.00  0.00              
ATOM     53  N   ASP    40      10.718  21.559 -22.805  1.00  0.00              
ATOM     54  CA  ASP    40      11.859  22.320 -22.305  1.00  0.00              
ATOM     55  C   ASP    40      12.357  23.258 -23.399  1.00  0.00              
ATOM     56  O   ASP    40      11.977  23.120 -24.564  1.00  0.00              
ATOM     57  N   VAL    41      13.206  24.211 -23.025  1.00  0.00              
ATOM     58  CA  VAL    41      13.745  25.165 -23.987  1.00  0.00              
ATOM     59  C   VAL    41      14.565  24.459 -25.070  1.00  0.00              
ATOM     60  O   VAL    41      15.501  23.715 -24.771  1.00  0.00              
ATOM     61  N   ALA    42      14.194  24.688 -26.327  1.00  0.00              
ATOM     62  CA  ALA    42      14.910  24.084 -27.439  1.00  0.00              
ATOM     63  C   ALA    42      14.611  22.617 -27.705  1.00  0.00              
ATOM     64  O   ALA    42      15.369  21.944 -28.408  1.00  0.00              
ATOM     65  N   ASP    43      13.511  22.116 -27.150  1.00  0.00              
ATOM     66  CA  ASP    43      13.126  20.720 -27.348  1.00  0.00              
ATOM     67  C   ASP    43      12.316  20.539 -28.632  1.00  0.00              
ATOM     68  O   ASP    43      11.256  21.145 -28.816  1.00  0.00              
ATOM     69  N   ASP    44      12.841  19.695 -29.514  1.00  0.00              
ATOM     70  CA  ASP    44      12.226  19.395 -30.802  1.00  0.00              
ATOM     71  C   ASP    44      11.852  17.913 -30.791  1.00  0.00              
ATOM     72  O   ASP    44      12.336  17.120 -31.602  1.00  0.00              
ATOM     73  N   SER    45      10.978  17.553 -29.854  1.00  0.00              
ATOM     74  CA  SER    45      10.548  16.170 -29.680  1.00  0.00              
ATOM     75  C   SER    45       9.311  16.099 -28.794  1.00  0.00              
ATOM     76  O   SER    45       8.845  17.108 -28.257  1.00  0.00              
ATOM     77  N   ILE    46       8.799  14.885 -28.634  1.00  0.00              
ATOM     78  CA  ILE    46       7.637  14.643 -27.800  1.00  0.00              
ATOM     79  C   ILE    46       7.663  13.198 -27.321  1.00  0.00              
ATOM     80  O   ILE    46       7.051  12.314 -27.926  1.00  0.00              
ATOM     81  N   THR    47       8.383  12.960 -26.233  1.00  0.00              
ATOM     82  CA  THR    47       8.489  11.622 -25.677  1.00  0.00              
ATOM     83  C   THR    47       8.266  11.647 -24.169  1.00  0.00              
ATOM     84  O   THR    47       9.215  11.727 -23.393  1.00  0.00              
ATOM     85  N   PRO    48       7.000  11.605 -23.736  1.00  0.00              
ATOM     86  CA  PRO    48       6.705  11.618 -22.303  1.00  0.00              
ATOM     87  C   PRO    48       7.071  10.252 -21.753  1.00  0.00              
ATOM     88  O   PRO    48       7.233   9.305 -22.518  1.00  0.00              
ATOM     89  N   THR    49       7.215  10.140 -20.440  1.00  0.00              
ATOM     90  CA  THR    49       7.550   8.848 -19.863  1.00  0.00              
ATOM     91  C   THR    49       6.308   7.963 -19.995  1.00  0.00              
ATOM     92  O   THR    49       5.203   8.467 -20.171  1.00  0.00              
ATOM     93  N   SER    50       6.479   6.635 -19.931  1.00  0.00              
ATOM     94  CA  SER    50       5.365   5.686 -20.051  1.00  0.00              
ATOM     95  C   SER    50       4.120   6.126 -19.279  1.00  0.00              
ATOM     96  O   SER    50       4.182   6.417 -18.082  1.00  0.00              
ATOM     97  N   GLU    51       2.990   6.170 -19.976  1.00  0.00              
ATOM     98  CA  GLU    51       1.730   6.597 -19.381  1.00  0.00              
ATOM     99  C   GLU    51       1.245   5.716 -18.240  1.00  0.00              
ATOM    100  O   GLU    51       0.628   6.208 -17.300  1.00  0.00              
ATOM    101  N   PHE    52       1.517   4.418 -18.320  1.00  0.00              
ATOM    102  CA  PHE    52       1.075   3.487 -17.289  1.00  0.00              
ATOM    103  C   PHE    52       1.702   3.701 -15.912  1.00  0.00              
ATOM    104  O   PHE    52       1.100   3.371 -14.891  1.00  0.00              
ATOM    105  N   VAL    53       2.910   4.251 -15.878  1.00  0.00              
ATOM    106  CA  VAL    53       3.584   4.476 -14.609  1.00  0.00              
ATOM    107  C   VAL    53       2.746   5.343 -13.661  1.00  0.00              
ATOM    108  O   VAL    53       2.823   5.201 -12.444  1.00  0.00              
ATOM    109  N   TRP    54       1.937   6.234 -14.221  1.00  0.00              
ATOM    110  CA  TRP    54       1.111   7.124 -13.410  1.00  0.00              
ATOM    111  C   TRP    54      -0.015   6.424 -12.648  1.00  0.00              
ATOM    112  O   TRP    54      -0.508   6.945 -11.644  1.00  0.00              
ATOM    113  N   SER    55      -0.419   5.249 -13.119  1.00  0.00              
ATOM    114  CA  SER    55      -1.501   4.511 -12.476  1.00  0.00              
ATOM    115  C   SER    55      -1.055   3.683 -11.289  1.00  0.00              
ATOM    116  O   SER    55      -1.877   3.050 -10.631  1.00  0.00              
ATOM    117  N   SER    56       0.241   3.683 -11.009  1.00  0.00              
ATOM    118  CA  SER    56       0.750   2.908  -9.891  1.00  0.00              
ATOM    119  C   SER    56       0.398   3.493  -8.524  1.00  0.00              
ATOM    120  O   SER    56       0.615   2.848  -7.498  1.00  0.00              
ATOM    121  N   VAL    57      -0.144   4.709  -8.516  1.00  0.00              
ATOM    122  CA  VAL    57      -0.524   5.380  -7.274  1.00  0.00              
ATOM    123  C   VAL    57      -1.861   6.102  -7.424  1.00  0.00              
ATOM    124  O   VAL    57      -2.215   6.572  -8.506  1.00  0.00              
ATOM    125  N   ARG    58      -2.595   6.192  -6.322  1.00  0.00              
ATOM    126  CA  ARG    58      -3.886   6.861  -6.314  1.00  0.00              
ATOM    127  C   ARG    58      -3.723   8.249  -5.707  1.00  0.00              
ATOM    128  O   ARG    58      -4.553   9.133  -5.918  1.00  0.00              
ATOM    129  N   ASP    59      -2.649   8.435  -4.946  1.00  0.00              
ATOM    130  CA  ASP    59      -2.381   9.725  -4.324  1.00  0.00              
ATOM    131  C   ASP    59      -1.672  10.629  -5.326  1.00  0.00              
ATOM    132  O   ASP    59      -1.678  10.362  -6.525  1.00  0.00              
ATOM    133  N   ASP    60      -1.065  11.702  -4.830  1.00  0.00              
ATOM    134  CA  ASP    60      -0.350  12.627  -5.698  1.00  0.00              
ATOM    135  C   ASP    60       1.143  12.570  -5.394  1.00  0.00              
ATOM    136  O   ASP    60       1.838  13.584  -5.451  1.00  0.00              
ATOM    137  N   VAL    61       1.630  11.366  -5.095  1.00  0.00              
ATOM    138  CA  VAL    61       3.031  11.154  -4.759  1.00  0.00              
ATOM    139  C   VAL    61       3.994  11.081  -5.944  1.00  0.00              
ATOM    140  O   VAL    61       5.199  11.316  -5.792  1.00  0.00              
ATOM    141  N   MET    62       3.466  10.764  -7.120  1.00  0.00              
ATOM    142  CA  MET    62       4.285  10.616  -8.316  1.00  0.00              
ATOM    143  C   MET    62       4.695  11.881  -9.062  1.00  0.00              
ATOM    144  O   MET    62       5.702  11.877  -9.770  1.00  0.00              
ATOM    145  N   ARG    63       3.934  12.958  -8.916  1.00  0.00              
ATOM    146  CA  ARG    63       4.256  14.175  -9.643  1.00  0.00              
ATOM    147  C   ARG    63       4.557  15.392  -8.774  1.00  0.00              
ATOM    148  O   ARG    63       4.672  15.282  -7.556  1.00  0.00              
ATOM    149  N   LEU    64       4.715  16.547  -9.418  1.00  0.00              
ATOM    150  CA  LEU    64       5.026  17.789  -8.720  1.00  0.00              
ATOM    151  C   LEU    64       3.866  18.760  -8.780  1.00  0.00              
ATOM    152  O   LEU    64       2.997  18.653  -9.642  1.00  0.00              
ATOM    153  N   GLY    65       3.881  19.723  -7.867  1.00  0.00              
ATOM    154  CA  GLY    65       2.854  20.750  -7.792  1.00  0.00              
ATOM    155  C   GLY    65       3.533  21.989  -7.232  1.00  0.00              
ATOM    156  O   GLY    65       4.169  21.932  -6.182  1.00  0.00              
ATOM    157  N   ARG    66       3.398  23.107  -7.935  1.00  0.00              
ATOM    158  CA  ARG    66       4.038  24.354  -7.526  1.00  0.00              
ATOM    159  C   ARG    66       3.276  25.184  -6.511  1.00  0.00              
ATOM    160  O   ARG    66       2.147  24.875  -6.140  1.00  0.00              
ATOM    161  N   GLU    67       3.928  26.262  -6.085  1.00  0.00              
ATOM    162  CA  GLU    67       3.367  27.205  -5.136  1.00  0.00              
ATOM    163  C   GLU    67       1.956  27.605  -5.537  1.00  0.00              
ATOM    164  O   GLU    67       1.081  27.753  -4.694  1.00  0.00              
END
