
#######################################################
#                                                     #
#                        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 T0358AL381_4
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358AL381_4.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D      31      G      10           -
LGA    D      32      P      11           -
LGA    Q      33      F      12           -
LGA    G      34      -       -           -
LGA    S      35      -       -           -
LGA    H      36      -       -           -
LGA    F      37      -       -           -
LGA    R      38      -       -           -
LGA    L      39      -       -           -
LGA    V      40      -       -           -
LGA    V      41      T      13           #
LGA    R      42      R      14           #
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    -       -      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    D      43      Q      33           #
LGA    T      44      G      34          3.614
LGA    E      45      S      35          1.623
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      H      36          4.974
LGA    V      49      F      37          1.362
LGA    W      50      R      38          2.705
LGA    R      51      L      39           #
LGA    A      52      V      40          4.580
LGA    -       -      V      41           -
LGA    -       -      R      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      V      49           -
LGA    -       -      W      50           -
LGA    W      53      R      51          2.814
LGA    F      55      A      52          1.202
LGA    E      56      W      53           #
LGA    P      57      N      54           -
LGA    D      58      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    A      59      G      60          3.675
LGA    G      60      E      61          2.680
LGA    -       -      G      62           -
LGA    E      61      L      63          2.328
LGA    G      62      N      64          1.665
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    L      63      I      67          2.210
LGA    -       -      R      68           -
LGA    N      64      T      69          2.641
LGA    R      65      S      70          0.948
LGA    Y      66      G      71          0.721
LGA    I      67      I      72          2.208
LGA    -       -      R      73           -
LGA    R      68      T      74          3.018
LGA    T      69      D      75          1.925
LGA    S      70      -       -           -
LGA    G      71      -       -           -
LGA    I      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   66    5.0     19    2.71     5.26     20.020     0.676

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.462777 * X  +   0.100530 * Y  +   0.880756 * Z  + -115.116592
  Y_new =  -0.695810 * X  +  -0.656796 * Y  +  -0.290633 * Z  +  61.463242
  Z_new =   0.549259 * X  +  -0.747338 * Y  +   0.373899 * Z  + -62.193825 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.106902    2.034691  [ DEG:   -63.4208    116.5792 ]
  Theta =  -0.581478   -2.560115  [ DEG:   -33.3162   -146.6838 ]
  Phi   =  -2.157707    0.983886  [ DEG:  -123.6275     56.3725 ]
 
# 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: T0358AL381_4                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_4.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   66   5.0   19   2.71    5.26  20.020
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_4
REMARK Aligment from pdb entry: 2cwiA
ATOM      1  N   ASP    31     -11.455  -4.720 -14.345  1.00  0.00              
ATOM      2  CA  ASP    31     -10.429  -4.411 -15.346  1.00  0.00              
ATOM      3  C   ASP    31     -10.243  -2.912 -15.563  1.00  0.00              
ATOM      4  O   ASP    31      -9.053  -2.395 -15.725  1.00  0.00              
ATOM      5  N   ASP    32     -11.340  -2.163 -15.566  1.00  0.00              
ATOM      6  CA  ASP    32     -11.184  -0.697 -15.877  1.00  0.00              
ATOM      7  C   ASP    32     -10.460  -0.044 -14.711  1.00  0.00              
ATOM      8  O   ASP    32      -9.547   0.804 -14.889  1.00  0.00              
ATOM      9  N   GLN    33     -10.920  -0.398 -13.524  1.00  0.00              
ATOM     10  CA  GLN    33     -10.300   0.116 -12.288  1.00  0.00              
ATOM     11  C   GLN    33      -8.763  -0.156 -12.278  1.00  0.00              
ATOM     12  O   GLN    33      -7.950   0.691 -11.904  1.00  0.00              
ATOM     13  N   GLY    34      -8.367  -1.384 -12.592  1.00  0.00              
ATOM     14  CA  GLY    34      -6.934  -1.740 -12.660  1.00  0.00              
ATOM     15  C   GLY    34      -6.138  -0.907 -13.694  1.00  0.00              
ATOM     16  O   GLY    34      -5.087  -0.344 -13.394  1.00  0.00              
ATOM     17  N   SER    35      -6.696  -0.784 -14.884  1.00  0.00              
ATOM     18  CA  SER    35      -6.117   0.073 -15.932  1.00  0.00              
ATOM     19  C   SER    35      -5.976   1.481 -15.432  1.00  0.00              
ATOM     20  O   SER    35      -4.948   2.070 -15.655  1.00  0.00              
ATOM     21  N   HIS    36      -6.970   1.986 -14.678  1.00  0.00              
ATOM     22  CA  HIS    36      -6.854   3.336 -14.149  1.00  0.00              
ATOM     23  C   HIS    36      -5.834   3.432 -12.996  1.00  0.00              
ATOM     24  O   HIS    36      -5.021   4.344 -12.968  1.00  0.00              
ATOM     25  N   PHE    37      -5.860   2.474 -12.058  1.00  0.00              
ATOM     26  CA  PHE    37      -4.846   2.459 -10.954  1.00  0.00              
ATOM     27  C   PHE    37      -3.394   2.386 -11.471  1.00  0.00              
ATOM     28  O   PHE    37      -2.512   3.046 -10.964  1.00  0.00              
ATOM     29  N   ARG    38      -3.217   1.621 -12.524  1.00  0.00              
ATOM     30  CA  ARG    38      -1.926   1.558 -13.230  1.00  0.00              
ATOM     31  C   ARG    38      -1.487   2.958 -13.687  1.00  0.00              
ATOM     32  O   ARG    38      -0.294   3.338 -13.657  1.00  0.00              
ATOM     33  N   LEU    39      -2.457   3.751 -14.077  1.00  0.00              
ATOM     34  CA  LEU    39      -2.136   5.090 -14.537  1.00  0.00              
ATOM     35  C   LEU    39      -1.908   6.044 -13.357  1.00  0.00              
ATOM     36  O   LEU    39      -0.995   6.874 -13.343  1.00  0.00              
ATOM     37  N   VAL    40      -2.711   5.916 -12.316  1.00  0.00              
ATOM     38  CA  VAL    40      -2.564   6.763 -11.137  1.00  0.00              
ATOM     39  C   VAL    40      -1.206   6.668 -10.544  1.00  0.00              
ATOM     40  O   VAL    40      -0.616   7.678 -10.213  1.00  0.00              
ATOM     41  N   VAL    41      -0.693   5.439 -10.372  1.00  0.00              
ATOM     42  CA  VAL    41       0.559   5.211  -9.709  1.00  0.00              
ATOM     43  C   VAL    41       1.737   5.787 -10.459  1.00  0.00              
ATOM     44  O   VAL    41       2.818   6.006  -9.857  1.00  0.00              
ATOM     45  N   ARG    42       1.521   6.038 -11.767  1.00  0.00              
ATOM     46  CA  ARG    42       2.507   6.699 -12.627  1.00  0.00              
ATOM     47  C   ARG    42       2.762   8.155 -12.358  1.00  0.00              
ATOM     48  O   ARG    42       3.772   8.749 -12.856  1.00  0.00              
ATOM     49  N   ASP    43       1.887   8.791 -11.607  1.00  0.00              
ATOM     50  CA  ASP    43       2.142  10.122 -11.097  1.00  0.00              
ATOM     51  C   ASP    43       3.224  10.196 -10.053  1.00  0.00              
ATOM     52  O   ASP    43       3.526   9.174  -9.400  1.00  0.00              
ATOM     53  N   THR    44       3.753  11.415  -9.779  1.00  0.00              
ATOM     54  CA  THR    44       4.947  11.575  -8.957  1.00  0.00              
ATOM     55  C   THR    44       4.845  11.072  -7.491  1.00  0.00              
ATOM     56  O   THR    44       5.824  10.616  -6.888  1.00  0.00              
ATOM     57  N   GLU    45       3.650  11.136  -6.949  1.00  0.00              
ATOM     58  CA  GLU    45       3.306  10.632  -5.590  1.00  0.00              
ATOM     59  C   GLU    45       3.135   9.105  -5.453  1.00  0.00              
ATOM     60  O   GLU    45       2.964   8.625  -4.365  1.00  0.00              
ATOM     61  N   GLY    46       3.166   8.357  -6.551  1.00  0.00              
ATOM     62  CA  GLY    46       3.174   6.898  -6.524  1.00  0.00              
ATOM     63  C   GLY    46       1.881   6.458  -5.852  1.00  0.00              
ATOM     64  O   GLY    46       0.770   7.114  -5.969  1.00  0.00              
ATOM     65  N   ARG    47       2.002   5.372  -5.072  1.00  0.00              
ATOM     66  CA  ARG    47       0.861   4.918  -4.299  1.00  0.00              
ATOM     67  C   ARG    47       0.381   5.889  -3.202  1.00  0.00              
ATOM     68  O   ARG    47      -0.686   5.646  -2.646  1.00  0.00              
ATOM     69  N   MET    48       1.112   6.952  -2.894  1.00  0.00              
ATOM     70  CA  MET    48       0.709   7.920  -1.874  1.00  0.00              
ATOM     71  C   MET    48      -0.498   8.718  -2.293  1.00  0.00              
ATOM     72  O   MET    48      -1.124   9.423  -1.460  1.00  0.00              
ATOM     73  N   VAL    49      -0.919   8.528  -3.543  1.00  0.00              
ATOM     74  CA  VAL    49      -2.196   9.043  -4.023  1.00  0.00              
ATOM     75  C   VAL    49      -3.316   8.447  -3.310  1.00  0.00              
ATOM     76  O   VAL    49      -4.394   9.046  -3.281  1.00  0.00              
ATOM     77  N   TRP    50      -3.125   7.220  -2.780  1.00  0.00              
ATOM     78  CA  TRP    50      -4.121   6.624  -2.002  1.00  0.00              
ATOM     79  C   TRP    50      -3.826   6.895  -0.542  1.00  0.00              
ATOM     80  O   TRP    50      -2.975   6.215   0.036  1.00  0.00              
ATOM     81  N   ARG    51      -4.600   7.788   0.098  1.00  0.00              
ATOM     82  CA  ARG    51      -4.414   8.049   1.495  1.00  0.00              
ATOM     83  C   ARG    51      -4.547   6.866   2.423  1.00  0.00              
ATOM     84  O   ARG    51      -3.788   6.747   3.419  1.00  0.00              
ATOM     85  N   ALA    52      -5.442   5.939   2.115  1.00  0.00              
ATOM     86  CA  ALA    52      -5.573   4.841   3.085  1.00  0.00              
ATOM     87  C   ALA    52      -4.398   3.864   3.044  1.00  0.00              
ATOM     88  O   ALA    52      -4.085   3.234   4.043  1.00  0.00              
ATOM     89  N   TRP    53      -3.709   3.800   1.907  1.00  0.00              
ATOM     90  CA  TRP    53      -2.468   3.034   1.728  1.00  0.00              
ATOM     91  C   TRP    53      -1.311   3.692   2.573  1.00  0.00              
ATOM     92  O   TRP    53      -0.553   3.023   3.307  1.00  0.00              
ATOM     93  N   PHE    55      -1.175   5.006   2.430  1.00  0.00              
ATOM     94  CA  PHE    55      -0.244   5.803   3.258  1.00  0.00              
ATOM     95  C   PHE    55      -0.514   5.541   4.758  1.00  0.00              
ATOM     96  O   PHE    55       0.392   5.321   5.563  1.00  0.00              
ATOM     97  N   GLU    56      -1.782   5.530   5.144  1.00  0.00              
ATOM     98  CA  GLU    56      -2.106   5.379   6.569  1.00  0.00              
ATOM     99  C   GLU    56      -1.939   3.913   7.085  1.00  0.00              
ATOM    100  O   GLU    56      -1.543   3.665   8.247  1.00  0.00              
ATOM    101  N   PRO    57      -2.277   2.950   6.239  1.00  0.00              
ATOM    102  CA  PRO    57      -2.578   1.541   6.680  1.00  0.00              
ATOM    103  C   PRO    57      -1.683   0.466   6.074  1.00  0.00              
ATOM    104  O   PRO    57      -1.651  -0.646   6.552  1.00  0.00              
ATOM    105  N   ASP    58      -0.805   0.849   5.168  1.00  0.00              
ATOM    106  CA  ASP    58      -0.003  -0.053   4.392  1.00  0.00              
ATOM    107  C   ASP    58       1.429   0.333   4.282  1.00  0.00              
ATOM    108  O   ASP    58       2.296  -0.543   4.412  1.00  0.00              
ATOM    109  N   ALA    59       1.697   1.607   4.008  1.00  0.00              
ATOM    110  CA  ALA    59       3.035   2.070   3.666  1.00  0.00              
ATOM    111  C   ALA    59       3.991   1.796   4.808  1.00  0.00              
ATOM    112  O   ALA    59       5.135   1.350   4.555  1.00  0.00              
ATOM    113  N   GLY    60       3.503   1.975   6.011  1.00  0.00              
ATOM    114  CA  GLY    60       4.292   1.819   7.261  1.00  0.00              
ATOM    115  C   GLY    60       4.448   0.398   7.807  1.00  0.00              
ATOM    116  O   GLY    60       5.207   0.171   8.758  1.00  0.00              
ATOM    117  N   GLU    61       3.861  -0.561   7.088  1.00  0.00              
ATOM    118  CA  GLU    61       3.683  -1.897   7.592  1.00  0.00              
ATOM    119  C   GLU    61       4.651  -2.881   6.941  1.00  0.00              
ATOM    120  O   GLU    61       5.053  -2.759   5.747  1.00  0.00              
ATOM    121  N   GLY    62       4.980  -3.881   7.727  1.00  0.00              
ATOM    122  CA  GLY    62       5.624  -5.091   7.252  1.00  0.00              
ATOM    123  C   GLY    62       4.547  -5.976   6.604  1.00  0.00              
ATOM    124  O   GLY    62       3.696  -6.648   7.298  1.00  0.00              
ATOM    125  N   LEU    63       4.564  -6.022   5.282  1.00  0.00              
ATOM    126  CA  LEU    63       3.538  -6.817   4.535  1.00  0.00              
ATOM    127  C   LEU    63       4.018  -8.156   4.051  1.00  0.00              
ATOM    128  O   LEU    63       3.362  -8.808   3.217  1.00  0.00              
ATOM    129  N   ASN    64       5.148  -8.610   4.601  1.00  0.00              
ATOM    130  CA  ASN    64       5.740  -9.826   4.123  1.00  0.00              
ATOM    131  C   ASN    64       4.814 -11.048   4.296  1.00  0.00              
ATOM    132  O   ASN    64       4.965 -12.031   3.543  1.00  0.00              
ATOM    133  N   ARG    65       3.885 -10.994   5.211  1.00  0.00              
ATOM    134  CA  ARG    65       3.001 -12.132   5.530  1.00  0.00              
ATOM    135  C   ARG    65       1.580 -11.887   5.172  1.00  0.00              
ATOM    136  O   ARG    65       0.722 -12.752   5.332  1.00  0.00              
ATOM    137  N   TYR    66       1.335 -10.721   4.582  1.00  0.00              
ATOM    138  CA  TYR    66      -0.029 -10.277   4.339  1.00  0.00              
ATOM    139  C   TYR    66      -0.781 -11.226   3.396  1.00  0.00              
ATOM    140  O   TYR    66      -1.953 -11.480   3.649  1.00  0.00              
ATOM    141  N   ILE    67      -0.127 -11.720   2.326  1.00  0.00              
ATOM    142  CA  ILE    67      -0.676 -12.681   1.411  1.00  0.00              
ATOM    143  C   ILE    67      -0.259 -14.181   1.638  1.00  0.00              
ATOM    144  O   ILE    67      -0.460 -15.021   0.734  1.00  0.00              
ATOM    145  N   ARG    68       0.283 -14.490   2.806  1.00  0.00              
ATOM    146  CA  ARG    68       0.759 -15.822   3.115  1.00  0.00              
ATOM    147  C   ARG    68      -0.415 -16.857   3.151  1.00  0.00              
ATOM    148  O   ARG    68      -0.185 -17.966   2.801  1.00  0.00              
ATOM    149  N   THR    69      -1.630 -16.517   3.585  1.00  0.00              
ATOM    150  CA  THR    69      -2.708 -17.468   3.538  1.00  0.00              
ATOM    151  C   THR    69      -3.153 -17.755   2.095  1.00  0.00              
ATOM    152  O   THR    69      -3.774 -18.819   1.815  1.00  0.00              
ATOM    153  N   SER    70      -2.747 -16.917   1.156  1.00  0.00              
ATOM    154  CA  SER    70      -3.225 -17.057  -0.214  1.00  0.00              
ATOM    155  C   SER    70      -2.523 -18.183  -0.983  1.00  0.00              
ATOM    156  O   SER    70      -1.261 -18.287  -0.994  1.00  0.00              
ATOM    157  N   GLY    71      -3.365 -18.961  -1.689  1.00  0.00              
ATOM    158  CA  GLY    71      -2.937 -19.858  -2.780  1.00  0.00              
ATOM    159  C   GLY    71      -2.917 -19.100  -4.080  1.00  0.00              
ATOM    160  O   GLY    71      -3.933 -18.705  -4.613  1.00  0.00              
ATOM    161  N   ILE    72      -1.734 -18.834  -4.584  1.00  0.00              
ATOM    162  CA  ILE    72      -1.615 -17.899  -5.678  1.00  0.00              
ATOM    163  C   ILE    72      -0.878 -18.620  -6.816  1.00  0.00              
ATOM    164  O   ILE    72      -0.753 -18.084  -7.902  1.00  0.00              
END
