
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0358AL243_2
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358AL243_2.T0358.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    V       5      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    L       6      V      20          1.984
LGA    L       7      T      21          4.533
LGA    P       8      T      22           -
LGA    P       9      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    G      10      L      29          3.341
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    P      11      V      40          2.395
LGA    F      12      V      41          4.675
LGA    T      13      R      42          3.220
LGA    R      14      D      43          2.215
LGA    R      15      T      44          1.205
LGA    Q      16      -       -           -
LGA    A      17      E      45           #
LGA    Q      18      G      46           -
LGA    A      19      R      47           -
LGA    V      20      M      48           -
LGA    T      21      V      49           -
LGA    T      22      W      50           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      -       -           -
LGA    N      26      -       -           -
LGA    I      27      -       -           -
LGA    T      28      -       -           -
LGA    L      29      -       -           -
LGA    E      30      R      51           #
LGA    -       -      A      52           -
LGA    D      31      W      53          2.967
LGA    D      32      N      54           -
LGA    Q      33      F      55           -
LGA    G      34      -       -           -
LGA    S      35      E      56          5.777
LGA    H      36      P      57          2.775
LGA    F      37      D      58          3.672
LGA    R      38      A      59          0.990
LGA    L      39      G      60          0.994
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    V      40      L      63          0.662
LGA    V      41      N      64          2.135
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    R      42      I      67          1.528
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    D      43      S      70          2.092
LGA    T      44      G      71          3.211
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    E      45      D      75          2.743
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      -       -           -
LGA    V      49      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   66    5.0     20    2.96     0.00     20.168     0.654

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.105567 * X  +  -0.380196 * Y  +   0.918862 * Z  +   8.191628
  Y_new =   0.824810 * X  +   0.482672 * Y  +   0.294476 * Z  + -39.531590
  Z_new =  -0.555467 * X  +   0.788973 * Y  +   0.262635 * Z  +   7.753576 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.249452   -1.892141  [ DEG:    71.5883   -108.4117 ]
  Theta =   0.588925    2.552668  [ DEG:    33.7429    146.2571 ]
  Phi   =   1.698094   -1.443499  [ DEG:    97.2936    -82.7064 ]
 
# 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_2                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL243_2.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   66   5.0   20   2.96    0.00  20.168
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL243_2
REMARK Aligment from pdb entry: 2gkeA
ATOM      1  N   VAL     5       5.681  -8.551  -2.512  1.00  0.00              
ATOM      2  CA  VAL     5       5.069  -7.570  -3.401  1.00  0.00              
ATOM      3  C   VAL     5       5.199  -6.218  -2.706  1.00  0.00              
ATOM      4  O   VAL     5       4.878  -6.078  -1.528  1.00  0.00              
ATOM      5  N   LEU     6       5.725  -5.251  -3.441  1.00  0.00              
ATOM      6  CA  LEU     6       5.915  -3.890  -2.936  1.00  0.00              
ATOM      7  C   LEU     6       5.089  -2.930  -3.795  1.00  0.00              
ATOM      8  O   LEU     6       5.154  -2.955  -5.014  1.00  0.00              
ATOM      9  N   LEU     7       4.319  -2.080  -3.130  1.00  0.00              
ATOM     10  CA  LEU     7       3.377  -1.202  -3.830  1.00  0.00              
ATOM     11  C   LEU     7       3.634   0.253  -3.475  1.00  0.00              
ATOM     12  O   LEU     7       3.667   0.602  -2.299  1.00  0.00              
ATOM     13  N   PRO     8       3.739   1.095  -4.503  1.00  0.00              
ATOM     14  CA  PRO     8       3.753   2.543  -4.339  1.00  0.00              
ATOM     15  C   PRO     8       2.331   3.020  -4.025  1.00  0.00              
ATOM     16  O   PRO     8       1.488   3.096  -4.917  1.00  0.00              
ATOM     17  N   PRO     9      -3.757   5.037  -4.983  1.00  0.00              
ATOM     18  CA  PRO     9      -4.623   4.881  -3.826  1.00  0.00              
ATOM     19  C   PRO     9      -4.840   3.391  -3.621  1.00  0.00              
ATOM     20  O   PRO     9      -5.627   2.774  -4.337  1.00  0.00              
ATOM     21  N   GLY    10      -4.137   2.837  -2.629  1.00  0.00              
ATOM     22  CA  GLY    10      -4.012   1.392  -2.427  1.00  0.00              
ATOM     23  C   GLY    10      -4.744   0.938  -1.177  1.00  0.00              
ATOM     24  O   GLY    10      -4.430   1.374  -0.069  1.00  0.00              
ATOM     25  N   PRO    11      -5.724   0.064  -1.383  1.00  0.00              
ATOM     26  CA  PRO    11      -6.434  -0.569  -0.290  1.00  0.00              
ATOM     27  C   PRO    11      -7.029  -1.880  -0.747  1.00  0.00              
ATOM     28  O   PRO    11      -7.280  -2.090  -1.922  1.00  0.00              
ATOM     29  N   PHE    12      -7.288  -2.767   0.203  1.00  0.00              
ATOM     30  CA  PHE    12      -7.789  -4.094  -0.146  1.00  0.00              
ATOM     31  C   PHE    12      -8.225  -4.827   1.115  1.00  0.00              
ATOM     32  O   PHE    12      -7.879  -4.447   2.237  1.00  0.00              
ATOM     33  N   THR    13      -8.966  -5.896   0.910  1.00  0.00              
ATOM     34  CA  THR    13      -9.384  -6.756   2.012  1.00  0.00              
ATOM     35  C   THR    13      -8.332  -7.838   2.298  1.00  0.00              
ATOM     36  O   THR    13      -7.496  -8.174   1.435  1.00  0.00              
ATOM     37  N   ARG    14      -8.378  -8.426   3.484  1.00  0.00              
ATOM     38  CA  ARG    14      -7.557  -9.592   3.762  1.00  0.00              
ATOM     39  C   ARG    14      -7.800 -10.756   2.793  1.00  0.00              
ATOM     40  O   ARG    14      -6.878 -11.470   2.449  1.00  0.00              
ATOM     41  N   ARG    15      -9.015 -10.929   2.309  1.00  0.00              
ATOM     42  CA  ARG    15      -9.298 -11.961   1.320  1.00  0.00              
ATOM     43  C   ARG    15      -8.501 -11.720   0.034  1.00  0.00              
ATOM     44  O   ARG    15      -7.949 -12.643  -0.579  1.00  0.00              
ATOM     45  N   GLN    16      -8.447 -10.466  -0.407  1.00  0.00              
ATOM     46  CA  GLN    16      -7.638 -10.121  -1.568  1.00  0.00              
ATOM     47  C   GLN    16      -6.154 -10.427  -1.303  1.00  0.00              
ATOM     48  O   GLN    16      -5.463 -10.987  -2.161  1.00  0.00              
ATOM     49  N   ALA    17      -5.642 -10.057  -0.135  1.00  0.00              
ATOM     50  CA  ALA    17      -4.245 -10.366   0.185  1.00  0.00              
ATOM     51  C   ALA    17      -3.970 -11.863   0.077  1.00  0.00              
ATOM     52  O   ALA    17      -3.003 -12.279  -0.557  1.00  0.00              
ATOM     53  N   GLN    18      -4.861 -12.678   0.621  1.00  0.00              
ATOM     54  CA  GLN    18      -4.687 -14.127   0.632  1.00  0.00              
ATOM     55  C   GLN    18      -4.737 -14.683  -0.775  1.00  0.00              
ATOM     56  O   GLN    18      -3.938 -15.556  -1.130  1.00  0.00              
ATOM     57  N   ALA    19      -5.640 -14.162  -1.599  1.00  0.00              
ATOM     58  CA  ALA    19      -5.715 -14.587  -3.008  1.00  0.00              
ATOM     59  C   ALA    19      -4.409 -14.269  -3.720  1.00  0.00              
ATOM     60  O   ALA    19      -3.880 -15.103  -4.458  1.00  0.00              
ATOM     61  N   VAL    20      -3.916 -13.050  -3.548  1.00  0.00              
ATOM     62  CA  VAL    20      -2.716 -12.630  -4.226  1.00  0.00              
ATOM     63  C   VAL    20      -1.449 -13.342  -3.720  1.00  0.00              
ATOM     64  O   VAL    20      -0.493 -13.512  -4.470  1.00  0.00              
ATOM     65  N   THR    21      -1.440 -13.773  -2.467  1.00  0.00              
ATOM     66  CA  THR    21      -0.296 -14.441  -1.891  1.00  0.00              
ATOM     67  C   THR    21      -0.093 -15.842  -2.449  1.00  0.00              
ATOM     68  O   THR    21       1.002 -16.396  -2.389  1.00  0.00              
ATOM     69  N   THR    22      -1.173 -16.431  -2.934  1.00  0.00              
ATOM     70  CA  THR    22      -1.125 -17.791  -3.448  1.00  0.00              
ATOM     71  C   THR    22      -0.139 -17.906  -4.616  1.00  0.00              
ATOM     72  O   THR    22      -0.181 -17.122  -5.564  1.00  0.00              
ATOM     73  N   THR    23       0.781 -18.868  -4.552  1.00  0.00              
ATOM     74  CA  THR    23       1.889 -18.903  -5.527  1.00  0.00              
ATOM     75  C   THR    23       1.471 -19.484  -6.855  1.00  0.00              
ATOM     76  O   THR    23       2.113 -19.213  -7.848  1.00  0.00              
ATOM     77  N   TYR    24       0.375 -20.222  -6.887  1.00  0.00              
ATOM     78  CA  TYR    24      -0.075 -20.846  -8.133  1.00  0.00              
ATOM     79  C   TYR    24      -1.232 -20.119  -8.787  1.00  0.00              
ATOM     80  O   TYR    24      -1.364 -20.149  -9.987  1.00  0.00              
ATOM     81  N   SER    25      -2.085 -19.466  -8.011  1.00  0.00              
ATOM     82  CA  SER    25      -3.217 -18.777  -8.590  1.00  0.00              
ATOM     83  C   SER    25      -3.200 -17.274  -8.356  1.00  0.00              
ATOM     84  O   SER    25      -4.074 -16.555  -8.854  1.00  0.00              
ATOM     85  N   ASN    26      -2.183 -16.792  -7.648  1.00  0.00              
ATOM     86  CA  ASN    26      -2.007 -15.373  -7.399  1.00  0.00              
ATOM     87  C   ASN    26      -0.664 -14.889  -7.894  1.00  0.00              
ATOM     88  O   ASN    26      -0.130 -15.415  -8.873  1.00  0.00              
ATOM     89  N   ILE    27       4.070  -5.230   0.933  1.00  0.00              
ATOM     90  CA  ILE    27       4.483  -3.989   1.575  1.00  0.00              
ATOM     91  C   ILE    27       3.898  -2.815   0.830  1.00  0.00              
ATOM     92  O   ILE    27       3.838  -2.821  -0.391  1.00  0.00              
ATOM     93  N   THR    28       3.470  -1.808   1.568  1.00  0.00              
ATOM     94  CA  THR    28       3.015  -0.550   0.961  1.00  0.00              
ATOM     95  C   THR    28       3.897   0.614   1.418  1.00  0.00              
ATOM     96  O   THR    28       4.169   0.777   2.606  1.00  0.00              
ATOM     97  N   LEU    29       4.290   1.420   0.439  1.00  0.00              
ATOM     98  CA  LEU    29       4.956   2.698   0.659  1.00  0.00              
ATOM     99  C   LEU    29       3.872   3.766   0.629  1.00  0.00              
ATOM    100  O   LEU    29       3.164   3.917  -0.354  1.00  0.00              
ATOM    101  N   GLU    30       3.712   4.493   1.726  1.00  0.00              
ATOM    102  CA  GLU    30       2.716   5.535   1.818  1.00  0.00              
ATOM    103  C   GLU    30       3.376   6.873   2.138  1.00  0.00              
ATOM    104  O   GLU    30       4.520   6.942   2.584  1.00  0.00              
ATOM    105  N   ASP    31       2.650   7.956   1.875  1.00  0.00              
ATOM    106  CA  ASP    31       3.057   9.274   2.349  1.00  0.00              
ATOM    107  C   ASP    31       3.088   9.275   3.869  1.00  0.00              
ATOM    108  O   ASP    31       2.286   8.591   4.513  1.00  0.00              
ATOM    109  N   ASP    32       3.803  12.126   9.632  1.00  0.00              
ATOM    110  CA  ASP    32       4.697  13.164  10.126  1.00  0.00              
ATOM    111  C   ASP    32       5.466  13.664   8.907  1.00  0.00              
ATOM    112  O   ASP    32       6.324  12.945   8.372  1.00  0.00              
ATOM    113  N   GLN    33       5.152  14.889   8.438  1.00  0.00              
ATOM    114  CA  GLN    33       5.733  15.348   7.180  1.00  0.00              
ATOM    115  C   GLN    33       7.239  15.557   7.220  1.00  0.00              
ATOM    116  O   GLN    33       7.853  15.698   6.170  1.00  0.00              
ATOM    117  N   GLY    34       7.850  15.543   8.403  1.00  0.00              
ATOM    118  CA  GLY    34       9.312  15.541   8.512  1.00  0.00              
ATOM    119  C   GLY    34       9.948  14.209   8.109  1.00  0.00              
ATOM    120  O   GLY    34      11.161  14.137   7.899  1.00  0.00              
ATOM    121  N   SER    35       9.159  13.147   8.051  1.00  0.00              
ATOM    122  CA  SER    35       9.702  11.845   7.617  1.00  0.00              
ATOM    123  C   SER    35       9.565  11.710   6.105  1.00  0.00              
ATOM    124  O   SER    35       8.872  12.500   5.437  1.00  0.00              
ATOM    125  N   HIS    36      10.218  10.708   5.537  1.00  0.00              
ATOM    126  CA  HIS    36      10.102  10.483   4.100  1.00  0.00              
ATOM    127  C   HIS    36       8.886   9.657   3.694  1.00  0.00              
ATOM    128  O   HIS    36       8.210  10.002   2.727  1.00  0.00              
ATOM    129  N   PHE    37       8.612   8.555   4.397  1.00  0.00              
ATOM    130  CA  PHE    37       7.505   7.638   4.037  1.00  0.00              
ATOM    131  C   PHE    37       6.930   6.994   5.288  1.00  0.00              
ATOM    132  O   PHE    37       7.571   6.971   6.331  1.00  0.00              
ATOM    133  N   ARG    38       5.740   6.438   5.112  1.00  0.00              
ATOM    134  CA  ARG    38       5.140   5.468   6.032  1.00  0.00              
ATOM    135  C   ARG    38       5.204   4.084   5.394  1.00  0.00              
ATOM    136  O   ARG    38       5.100   3.934   4.167  1.00  0.00              
ATOM    137  N   LEU    39       5.382   3.071   6.232  1.00  0.00              
ATOM    138  CA  LEU    39       5.636   1.693   5.810  1.00  0.00              
ATOM    139  C   LEU    39       4.622   0.753   6.423  1.00  0.00              
ATOM    140  O   LEU    39       4.546   0.687   7.638  1.00  0.00              
ATOM    141  N   VAL    40       3.856   0.049   5.585  1.00  0.00              
ATOM    142  CA  VAL    40       2.901  -0.948   6.044  1.00  0.00              
ATOM    143  C   VAL    40       3.274  -2.325   5.533  1.00  0.00              
ATOM    144  O   VAL    40       3.867  -2.480   4.444  1.00  0.00              
ATOM    145  N   VAL    41       2.949  -3.335   6.332  1.00  0.00              
ATOM    146  CA  VAL    41       3.343  -4.727   6.062  1.00  0.00              
ATOM    147  C   VAL    41       2.155  -5.669   6.237  1.00  0.00              
ATOM    148  O   VAL    41       1.471  -5.594   7.260  1.00  0.00              
ATOM    149  N   ARG    42       1.958  -6.577   5.278  1.00  0.00              
ATOM    150  CA  ARG    42       0.892  -7.561   5.349  1.00  0.00              
ATOM    151  C   ARG    42       1.496  -8.934   5.126  1.00  0.00              
ATOM    152  O   ARG    42       2.279  -9.133   4.195  1.00  0.00              
ATOM    153  N   ASP    43       1.102  -9.899   5.952  1.00  0.00              
ATOM    154  CA  ASP    43       1.487 -11.276   5.761  1.00  0.00              
ATOM    155  C   ASP    43       0.629 -11.962   4.705  1.00  0.00              
ATOM    156  O   ASP    43      -0.488 -11.536   4.384  1.00  0.00              
ATOM    157  N   THR    44       1.119 -13.089   4.222  1.00  0.00              
ATOM    158  CA  THR    44       0.406 -13.914   3.273  1.00  0.00              
ATOM    159  C   THR    44      -0.964 -14.348   3.758  1.00  0.00              
ATOM    160  O   THR    44      -1.836 -14.620   2.940  1.00  0.00              
ATOM    161  N   GLU    45      -1.163 -14.433   5.073  1.00  0.00              
ATOM    162  CA  GLU    45      -2.475 -14.794   5.641  1.00  0.00              
ATOM    163  C   GLU    45      -3.450 -13.642   5.729  1.00  0.00              
ATOM    164  O   GLU    45      -4.552 -13.822   6.246  1.00  0.00              
ATOM    165  N   GLY    46      -3.059 -12.473   5.227  1.00  0.00              
ATOM    166  CA  GLY    46      -3.896 -11.293   5.231  1.00  0.00              
ATOM    167  C   GLY    46      -3.776 -10.382   6.427  1.00  0.00              
ATOM    168  O   GLY    46      -4.446  -9.358   6.461  1.00  0.00              
ATOM    169  N   ARG    47      -2.943 -10.741   7.409  1.00  0.00              
ATOM    170  CA  ARG    47      -2.777  -9.924   8.610  1.00  0.00              
ATOM    171  C   ARG    47      -1.849  -8.744   8.393  1.00  0.00              
ATOM    172  O   ARG    47      -0.852  -8.857   7.731  1.00  0.00              
ATOM    173  N   MET    48      -2.209  -7.604   8.972  1.00  0.00              
ATOM    174  CA  MET    48      -1.370  -6.417   8.928  1.00  0.00              
ATOM    175  C   MET    48      -0.551  -6.334  10.203  1.00  0.00              
ATOM    176  O   MET    48      -1.111  -6.448  11.314  1.00  0.00              
ATOM    177  N   VAL    49       0.750  -6.132  10.041  1.00  0.00              
ATOM    178  CA  VAL    49       1.667  -6.073  11.177  1.00  0.00              
ATOM    179  C   VAL    49       2.577  -4.833  11.065  1.00  0.00              
ATOM    180  O   VAL    49       2.481  -4.084  10.090  1.00  0.00              
END
