
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms  106 ( 1704),  selected  106 , name T0314.pdb
# PARAMETERS: T0314AL381_3.T0314.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    R      27      M      39          3.130
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    Y      28      A      42          2.873
LGA    I      29      D      43          2.435
LGA    -       -      D      44           -
LGA    -       -      S      45           -
LGA    V      30      I      46          0.693
LGA    R      31      T      47          0.899
LGA    F      32      P      48          4.408
LGA    -       -      T      49           -
LGA    -       -      S      50           -
LGA    -       -      E      51           -
LGA    S      33      F      52          1.518
LGA    E      34      V      53          1.419
LGA    D      35      W      54          0.706
LGA    S      36      S      55          0.833
LGA    F      37      S      56          2.714
LGA    G      38      V      57          2.114
LGA    M      39      R      58          1.012
LGA    D      40      D      59          1.530
LGA    V      41      D      60          5.192
LGA    A      42      V      61           -
LGA    D      43      M      62           #
LGA    D      44      -       -           -
LGA    S      45      -       -           -
LGA    I      46      -       -           -
LGA    T      47      -       -           -
LGA    P      48      R      63          5.041
LGA    -       -      L      64           -
LGA    T      49      G      65          1.331
LGA    -       -      R      66           -
LGA    S      50      E      67          3.086
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          5.155
LGA    W      54      -       -           -
LGA    S      55      L      91           #
LGA    S      56      R      92          1.976
LGA    V      57      R      93          2.818
LGA    R      58      Q      94          4.519
LGA    D      59      D      95          3.293
LGA    D      60      L      96          4.261
LGA    V      61      -       -           -
LGA    M      62      P      97           #
LGA    -       -      E      98           -
LGA    R      63      I      99          3.363
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     25    3.02    12.00     15.470     0.801

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.054915 * X  +  -0.928146 * Y  +   0.368144 * Z  +  51.770927
  Y_new =  -0.732108 * X  +   0.213287 * Y  +   0.646936 * Z  +  33.320232
  Z_new =  -0.678972 * X  +  -0.305048 * Y  +  -0.667790 * Z  +  29.737448 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.713097    0.428496  [ DEG:  -155.4490     24.5510 ]
  Theta =   0.746361    2.395232  [ DEG:    42.7633    137.2367 ]
  Phi   =  -1.495927    1.645666  [ DEG:   -85.7103     94.2897 ]
 
# 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_3                                  
REMARK     2: T0314.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314AL381_3.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   25   3.02   12.00  15.470
REMARK  ---------------------------------------------------------- 
MOLECULE T0314AL381_3
REMARK Aligment from pdb entry: 1venA
ATOM      1  N   ARG    27      33.676   4.797 -29.101  1.00  0.00              
ATOM      2  CA  ARG    27      33.142   4.427 -27.801  1.00  0.00              
ATOM      3  C   ARG    27      31.877   5.260 -27.620  1.00  0.00              
ATOM      4  O   ARG    27      31.698   6.291 -28.280  1.00  0.00              
ATOM      5  N   TYR    28      30.995   4.806 -26.742  1.00  0.00              
ATOM      6  CA  TYR    28      29.768   5.532 -26.492  1.00  0.00              
ATOM      7  C   TYR    28      29.512   5.663 -25.001  1.00  0.00              
ATOM      8  O   TYR    28      30.013   4.874 -24.193  1.00  0.00              
ATOM      9  N   ILE    29      28.735   6.680 -24.656  1.00  0.00              
ATOM     10  CA  ILE    29      28.370   6.953 -23.286  1.00  0.00              
ATOM     11  C   ILE    29      26.863   7.081 -23.278  1.00  0.00              
ATOM     12  O   ILE    29      26.318   8.128 -23.626  1.00  0.00              
ATOM     13  N   VAL    30      26.162   6.006 -22.903  1.00  0.00              
ATOM     14  CA  VAL    30      24.706   6.095 -22.882  1.00  0.00              
ATOM     15  C   VAL    30      24.179   6.875 -21.689  1.00  0.00              
ATOM     16  O   VAL    30      24.736   6.798 -20.597  1.00  0.00              
ATOM     17  N   ARG    31      23.120   7.641 -21.917  1.00  0.00              
ATOM     18  CA  ARG    31      22.460   8.380 -20.854  1.00  0.00              
ATOM     19  C   ARG    31      21.127   7.656 -20.724  1.00  0.00              
ATOM     20  O   ARG    31      20.363   7.588 -21.684  1.00  0.00              
ATOM     21  N   PHE    32      20.858   7.078 -19.561  1.00  0.00              
ATOM     22  CA  PHE    32      19.591   6.388 -19.369  1.00  0.00              
ATOM     23  C   PHE    32      18.618   7.485 -18.990  1.00  0.00              
ATOM     24  O   PHE    32      18.404   7.779 -17.822  1.00  0.00              
ATOM     25  N   SER    33      18.046   8.106 -20.015  1.00  0.00              
ATOM     26  CA  SER    33      17.130   9.225 -19.836  1.00  0.00              
ATOM     27  C   SER    33      15.714   8.872 -19.417  1.00  0.00              
ATOM     28  O   SER    33      14.843   8.619 -20.250  1.00  0.00              
ATOM     29  N   GLU    34      15.496   8.882 -18.109  1.00  0.00              
ATOM     30  CA  GLU    34      14.194   8.580 -17.549  1.00  0.00              
ATOM     31  C   GLU    34      13.380   9.862 -17.399  1.00  0.00              
ATOM     32  O   GLU    34      12.587   9.996 -16.473  1.00  0.00              
ATOM     33  N   ASP    35      13.607  10.811 -18.302  1.00  0.00              
ATOM     34  CA  ASP    35      12.875  12.070 -18.296  1.00  0.00              
ATOM     35  C   ASP    35      12.293  12.295 -19.692  1.00  0.00              
ATOM     36  O   ASP    35      12.652  11.598 -20.642  1.00  0.00              
ATOM     37  N   SER    36      11.400  13.268 -19.814  1.00  0.00              
ATOM     38  CA  SER    36      10.770  13.562 -21.094  1.00  0.00              
ATOM     39  C   SER    36      11.633  14.368 -22.064  1.00  0.00              
ATOM     40  O   SER    36      12.360  15.279 -21.666  1.00  0.00              
ATOM     41  N   PHE    37      11.557  14.011 -23.344  1.00  0.00              
ATOM     42  CA  PHE    37      12.280  14.739 -24.382  1.00  0.00              
ATOM     43  C   PHE    37      11.228  15.629 -25.032  1.00  0.00              
ATOM     44  O   PHE    37      10.192  15.141 -25.495  1.00  0.00              
ATOM     45  N   GLY    38      11.486  16.930 -25.061  1.00  0.00              
ATOM     46  CA  GLY    38      10.540  17.846 -25.670  1.00  0.00              
ATOM     47  C   GLY    38       9.934  18.760 -24.630  1.00  0.00              
ATOM     48  O   GLY    38       9.538  18.306 -23.558  1.00  0.00              
ATOM     49  N   MET    39       9.863  20.050 -24.937  1.00  0.00              
ATOM     50  CA  MET    39       9.301  20.995 -23.988  1.00  0.00              
ATOM     51  C   MET    39      10.371  21.859 -23.344  1.00  0.00              
ATOM     52  O   MET    39      10.069  22.905 -22.765  1.00  0.00              
ATOM     53  N   ASP    40      11.623  21.418 -23.437  1.00  0.00              
ATOM     54  CA  ASP    40      12.750  22.160 -22.880  1.00  0.00              
ATOM     55  C   ASP    40      13.451  22.965 -23.978  1.00  0.00              
ATOM     56  O   ASP    40      13.218  22.745 -25.171  1.00  0.00              
ATOM     57  N   VAL    41      14.306  23.899 -23.566  1.00  0.00              
ATOM     58  CA  VAL    41      15.035  24.742 -24.507  1.00  0.00              
ATOM     59  C   VAL    41      15.930  23.912 -25.426  1.00  0.00              
ATOM     60  O   VAL    41      16.805  23.171 -24.964  1.00  0.00              
ATOM     61  N   ALA    42      15.689  24.032 -26.730  1.00  0.00              
ATOM     62  CA  ALA    42      16.482  23.304 -27.707  1.00  0.00              
ATOM     63  C   ALA    42      15.945  21.931 -28.065  1.00  0.00              
ATOM     64  O   ALA    42      16.474  21.264 -28.957  1.00  0.00              
ATOM     65  N   ASP    43      14.892  21.506 -27.374  1.00  0.00              
ATOM     66  CA  ASP    43      14.293  20.201 -27.625  1.00  0.00              
ATOM     67  C   ASP    43      13.559  20.131 -28.961  1.00  0.00              
ATOM     68  O   ASP    43      12.678  20.943 -29.260  1.00  0.00              
ATOM     69  N   ASP    44      13.946  19.141 -29.756  1.00  0.00              
ATOM     70  CA  ASP    44      13.374  18.891 -31.069  1.00  0.00              
ATOM     71  C   ASP    44      13.037  17.404 -31.076  1.00  0.00              
ATOM     72  O   ASP    44      13.620  16.610 -31.812  1.00  0.00              
ATOM     73  N   SER    45      12.085  17.047 -30.225  1.00  0.00              
ATOM     74  CA  SER    45      11.650  15.665 -30.049  1.00  0.00              
ATOM     75  C   SER    45      10.368  15.700 -29.237  1.00  0.00              
ATOM     76  O   SER    45       9.931  16.757 -28.780  1.00  0.00              
ATOM     77  N   ILE    46       9.786  14.526 -29.045  1.00  0.00              
ATOM     78  CA  ILE    46       8.579  14.389 -28.256  1.00  0.00              
ATOM     79  C   ILE    46       8.551  12.964 -27.734  1.00  0.00              
ATOM     80  O   ILE    46       7.937  12.083 -28.339  1.00  0.00              
ATOM     81  N   THR    47       9.235  12.732 -26.618  1.00  0.00              
ATOM     82  CA  THR    47       9.277  11.405 -26.036  1.00  0.00              
ATOM     83  C   THR    47       9.000  11.454 -24.541  1.00  0.00              
ATOM     84  O   THR    47       9.919  11.515 -23.730  1.00  0.00              
ATOM     85  N   PRO    48       7.716  11.455 -24.163  1.00  0.00              
ATOM     86  CA  PRO    48       7.367  11.491 -22.744  1.00  0.00              
ATOM     87  C   PRO    48       7.694  10.142 -22.124  1.00  0.00              
ATOM     88  O   PRO    48       7.943   9.172 -22.838  1.00  0.00              
ATOM     89  N   THR    49       7.718  10.076 -20.800  1.00  0.00              
ATOM     90  CA  THR    49       8.005   8.810 -20.149  1.00  0.00              
ATOM     91  C   THR    49       6.735   7.967 -20.297  1.00  0.00              
ATOM     92  O   THR    49       5.646   8.516 -20.482  1.00  0.00              
ATOM     93  N   SER    50       6.857   6.631 -20.228  1.00  0.00              
ATOM     94  CA  SER    50       5.702   5.737 -20.368  1.00  0.00              
ATOM     95  C   SER    50       4.455   6.266 -19.656  1.00  0.00              
ATOM     96  O   SER    50       4.497   6.598 -18.473  1.00  0.00              
ATOM     97  N   GLU    51       3.347   6.342 -20.383  1.00  0.00              
ATOM     98  CA  GLU    51       2.106   6.857 -19.818  1.00  0.00              
ATOM     99  C   GLU    51       1.496   5.969 -18.736  1.00  0.00              
ATOM    100  O   GLU    51       0.726   6.445 -17.899  1.00  0.00              
ATOM    101  N   PHE    52       1.847   4.687 -18.739  1.00  0.00              
ATOM    102  CA  PHE    52       1.308   3.764 -17.745  1.00  0.00              
ATOM    103  C   PHE    52       1.890   3.955 -16.344  1.00  0.00              
ATOM    104  O   PHE    52       1.275   3.561 -15.352  1.00  0.00              
ATOM    105  N   VAL    53       3.074   4.548 -16.257  1.00  0.00              
ATOM    106  CA  VAL    53       3.692   4.754 -14.957  1.00  0.00              
ATOM    107  C   VAL    53       2.816   5.649 -14.073  1.00  0.00              
ATOM    108  O   VAL    53       2.796   5.501 -12.855  1.00  0.00              
ATOM    109  N   TRP    54       2.079   6.564 -14.692  1.00  0.00              
ATOM    110  CA  TRP    54       1.227   7.481 -13.940  1.00  0.00              
ATOM    111  C   TRP    54       0.029   6.824 -13.260  1.00  0.00              
ATOM    112  O   TRP    54      -0.558   7.397 -12.338  1.00  0.00              
ATOM    113  N   SER    55      -0.335   5.624 -13.703  1.00  0.00              
ATOM    114  CA  SER    55      -1.476   4.931 -13.114  1.00  0.00              
ATOM    115  C   SER    55      -1.098   4.020 -11.956  1.00  0.00              
ATOM    116  O   SER    55      -1.946   3.304 -11.429  1.00  0.00              
ATOM    117  N   SER    56       0.164   4.047 -11.547  1.00  0.00              
ATOM    118  CA  SER    56       0.587   3.195 -10.446  1.00  0.00              
ATOM    119  C   SER    56       0.349   3.800  -9.065  1.00  0.00              
ATOM    120  O   SER    56       0.669   3.180  -8.052  1.00  0.00              
ATOM    121  N   VAL    57      -0.225   5.001  -9.031  1.00  0.00              
ATOM    122  CA  VAL    57      -0.527   5.698  -7.779  1.00  0.00              
ATOM    123  C   VAL    57      -1.838   6.474  -7.912  1.00  0.00              
ATOM    124  O   VAL    57      -2.131   7.035  -8.966  1.00  0.00              
ATOM    125  N   ARG    58      -2.619   6.511  -6.835  1.00  0.00              
ATOM    126  CA  ARG    58      -3.893   7.219  -6.839  1.00  0.00              
ATOM    127  C   ARG    58      -3.746   8.623  -6.263  1.00  0.00              
ATOM    128  O   ARG    58      -4.595   9.486  -6.486  1.00  0.00              
ATOM    129  N   ASP    59      -2.677   8.844  -5.506  1.00  0.00              
ATOM    130  CA  ASP    59      -2.434  10.151  -4.914  1.00  0.00              
ATOM    131  C   ASP    59      -1.720  11.030  -5.931  1.00  0.00              
ATOM    132  O   ASP    59      -1.738  10.742  -7.124  1.00  0.00              
ATOM    133  N   ASP    60      -1.098  12.105  -5.459  1.00  0.00              
ATOM    134  CA  ASP    60      -0.379  13.006  -6.351  1.00  0.00              
ATOM    135  C   ASP    60       1.097  12.979  -5.978  1.00  0.00              
ATOM    136  O   ASP    60       1.781  14.004  -5.992  1.00  0.00              
ATOM    137  N   VAL    61       1.576  11.782  -5.651  1.00  0.00              
ATOM    138  CA  VAL    61       2.958  11.580  -5.244  1.00  0.00              
ATOM    139  C   VAL    61       3.957  11.495  -6.400  1.00  0.00              
ATOM    140  O   VAL    61       5.150  11.723  -6.212  1.00  0.00              
ATOM    141  N   MET    62       3.462  11.177  -7.589  1.00  0.00              
ATOM    142  CA  MET    62       4.304  11.008  -8.772  1.00  0.00              
ATOM    143  C   MET    62       4.737  12.251  -9.551  1.00  0.00              
ATOM    144  O   MET    62       5.735  12.211 -10.263  1.00  0.00              
ATOM    145  N   ARG    63       4.005  13.351  -9.434  1.00  0.00              
ATOM    146  CA  ARG    63       4.366  14.542 -10.190  1.00  0.00              
ATOM    147  C   ARG    63       4.629  15.783  -9.337  1.00  0.00              
ATOM    148  O   ARG    63       4.683  15.706  -8.107  1.00  0.00              
ATOM    149  N   LEU    64       4.805  16.921 -10.002  1.00  0.00              
ATOM    150  CA  LEU    64       5.081  18.180  -9.323  1.00  0.00              
ATOM    151  C   LEU    64       3.932  19.176  -9.466  1.00  0.00              
ATOM    152  O   LEU    64       3.158  19.118 -10.421  1.00  0.00              
ATOM    153  N   GLY    65       3.853  20.105  -8.521  1.00  0.00              
ATOM    154  CA  GLY    65       2.832  21.146  -8.521  1.00  0.00              
ATOM    155  C   GLY    65       3.528  22.391  -7.973  1.00  0.00              
ATOM    156  O   GLY    65       4.084  22.363  -6.875  1.00  0.00              
ATOM    157  N   ARG    66       3.508  23.475  -8.744  1.00  0.00              
ATOM    158  CA  ARG    66       4.179  24.712  -8.350  1.00  0.00              
ATOM    159  C   ARG    66       3.395  25.593  -7.388  1.00  0.00              
ATOM    160  O   ARG    66       2.240  25.318  -7.060  1.00  0.00              
ATOM    161  N   GLU    67       4.045  26.672  -6.962  1.00  0.00              
ATOM    162  CA  GLU    67       3.447  27.635  -6.048  1.00  0.00              
ATOM    163  C   GLU    67       2.068  28.066  -6.527  1.00  0.00              
ATOM    164  O   GLU    67       1.207  28.406  -5.726  1.00  0.00              
END
