
#######################################################
#                                                     #
#                        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   51 (  204),  selected   51 , name T0358AL333_3-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358AL333_3-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T      23      G      10           -
LGA    Y      24      P      11           -
LGA    S      25      F      12           -
LGA    N      26      T      13           -
LGA    I      27      R      14           -
LGA    T      28      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    L      29      Q      18          3.184
LGA    E      30      A      19          3.713
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    D      31      T      22           #
LGA    D      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      T      23          4.240
LGA    S      35      Y      24          4.714
LGA    H      36      S      25           -
LGA    F      37      N      26           #
LGA    R      38      I      27           #
LGA    L      39      T      28           #
LGA    V      40      L      29          4.902
LGA    V      41      E      30          4.544
LGA    R      42      -       -           -
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    V      49      -       -           -
LGA    W      50      -       -           -
LGA    R      51      D      31          4.761
LGA    A      52      D      32           #
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    W      53      H      36          4.216
LGA    N      54      F      37          3.200
LGA    F      55      R      38          1.629
LGA    E      56      L      39          4.240
LGA    P      57      -       -           -
LGA    D      58      -       -           -
LGA    A      59      V      40          1.941
LGA    G      60      V      41          3.917
LGA    E      61      -       -           -
LGA    G      62      R      42          1.666
LGA    L      63      -       -           -
LGA    N      64      -       -           -
LGA    R      65      D      43          2.476
LGA    Y      66      T      44          4.552
LGA    I      67      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      V      49           -
LGA    -       -      W      50           -
LGA    -       -      R      51           -
LGA    -       -      A      52           -
LGA    -       -      W      53           -
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    R      68      Y      66          3.670
LGA    T      69      I      67          4.071
LGA    S      70      R      68          3.361
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    G      71      G      71          2.547
LGA    I      72      I      72          2.934
LGA    R      73      R      73          2.675
LGA    T      74      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   51   65    5.0     22    3.65    13.64     19.828     0.587

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.309509 * X  +  -0.448971 * Y  +   0.838230 * Z  +   2.149330
  Y_new =   0.493972 * X  +   0.677325 * Y  +   0.545182 * Z  + -32.570469
  Z_new =  -0.812525 * X  +   0.582800 * Y  +   0.012141 * Z  +  14.131710 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.549967   -1.591626  [ DEG:    88.8065    -91.1935 ]
  Theta =   0.948470    2.193122  [ DEG:    54.3433    125.6567 ]
  Phi   =   2.130525   -1.011068  [ DEG:   122.0701    -57.9299 ]
 
# 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: T0358AL333_3-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL333_3-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   51   65   5.0   22   3.65   13.64  19.828
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL333_3-D1
REMARK Aligment from pdb entry: 1eg3_A
ATOM     17  N   THR    23      -6.368  -7.153 -16.470  1.00  0.00              
ATOM     18  CA  THR    23      -5.553  -5.956 -16.226  1.00  0.00              
ATOM     19  C   THR    23      -5.116  -5.978 -14.769  1.00  0.00              
ATOM     20  O   THR    23      -3.953  -5.635 -14.463  1.00  0.00              
ATOM     21  N   TYR    24      -6.092  -6.282 -13.859  1.00  0.00              
ATOM     22  CA  TYR    24      -5.698  -6.267 -12.433  1.00  0.00              
ATOM     23  C   TYR    24      -4.567  -7.251 -12.151  1.00  0.00              
ATOM     24  O   TYR    24      -3.675  -6.975 -11.328  1.00  0.00              
ATOM     25  N   SER    25      -4.678  -8.500 -12.647  1.00  0.00              
ATOM     26  CA  SER    25      -3.623  -9.488 -12.401  1.00  0.00              
ATOM     27  C   SER    25      -2.239  -9.050 -12.915  1.00  0.00              
ATOM     28  O   SER    25      -1.186  -9.216 -12.276  1.00  0.00              
ATOM     29  N   ASN    26      -2.286  -8.506 -14.122  1.00  0.00              
ATOM     30  CA  ASN    26      -1.053  -8.001 -14.760  1.00  0.00              
ATOM     31  C   ASN    26      -0.447  -6.860 -13.959  1.00  0.00              
ATOM     32  O   ASN    26       0.771  -6.878 -13.700  1.00  0.00              
ATOM     33  N   ILE    27      -1.221  -5.866 -13.552  1.00  0.00              
ATOM     34  CA  ILE    27      -0.636  -4.750 -12.776  1.00  0.00              
ATOM     35  C   ILE    27      -0.132  -5.190 -11.433  1.00  0.00              
ATOM     36  O   ILE    27       0.946  -4.763 -10.937  1.00  0.00              
ATOM     37  N   THR    28      -0.886  -6.099 -10.770  1.00  0.00              
ATOM     38  CA  THR    28      -0.439  -6.589  -9.455  1.00  0.00              
ATOM     39  C   THR    28       0.909  -7.307  -9.628  1.00  0.00              
ATOM     40  O   THR    28       1.898  -7.175  -8.855  1.00  0.00              
ATOM     41  N   LEU    29       4.100  -5.162  -9.566  1.00  0.00              
ATOM     42  CA  LEU    29       4.716  -4.655  -8.341  1.00  0.00              
ATOM     43  C   LEU    29       4.987  -5.780  -7.334  1.00  0.00              
ATOM     44  O   LEU    29       5.818  -5.549  -6.440  1.00  0.00              
ATOM     45  N   GLU    30       4.336  -6.929  -7.378  1.00  0.00              
ATOM     46  CA  GLU    30       4.555  -7.999  -6.418  1.00  0.00              
ATOM     47  C   GLU    30       5.975  -8.592  -6.591  1.00  0.00              
ATOM     48  O   GLU    30       6.654  -8.441  -7.608  1.00  0.00              
ATOM     49  N   ASP    31       6.432  -9.275  -5.550  1.00  0.00              
ATOM     50  CA  ASP    31       7.732  -9.929  -5.603  1.00  0.00              
ATOM     51  C   ASP    31       7.714 -11.042  -6.631  1.00  0.00              
ATOM     52  O   ASP    31       6.666 -11.505  -7.092  1.00  0.00              
ATOM     53  N   ASP    32       8.906 -11.610  -6.865  1.00  0.00              
ATOM     54  CA  ASP    32       9.042 -12.743  -7.768  1.00  0.00              
ATOM     55  C   ASP    32       8.208 -13.925  -7.318  1.00  0.00              
ATOM     56  O   ASP    32       7.804 -14.755  -8.145  1.00  0.00              
ATOM     57  N   GLN    33       7.881 -14.068  -6.044  1.00  0.00              
ATOM     58  CA  GLN    33       7.012 -15.169  -5.608  1.00  0.00              
ATOM     59  C   GLN    33       5.553 -14.770  -5.438  1.00  0.00              
ATOM     60  O   GLN    33       4.772 -15.510  -4.834  1.00  0.00              
ATOM     61  N   GLY    34       5.165 -13.588  -5.902  1.00  0.00              
ATOM     62  CA  GLY    34       3.775 -13.199  -5.973  1.00  0.00              
ATOM     63  C   GLY    34       3.152 -12.507  -4.769  1.00  0.00              
ATOM     64  O   GLY    34       1.921 -12.473  -4.650  1.00  0.00              
ATOM     65  N   SER    35       3.978 -11.936  -3.930  1.00  0.00              
ATOM     66  CA  SER    35       3.539 -11.271  -2.728  1.00  0.00              
ATOM     67  C   SER    35       3.773  -9.766  -2.807  1.00  0.00              
ATOM     68  O   SER    35       4.767  -9.267  -3.306  1.00  0.00              
ATOM     69  N   HIS    36       4.953  -1.973  -1.925  1.00  0.00              
ATOM     70  CA  HIS    36       4.744  -2.384  -3.316  1.00  0.00              
ATOM     71  C   HIS    36       3.324  -2.028  -3.809  1.00  0.00              
ATOM     72  O   HIS    36       3.129  -1.598  -4.932  1.00  0.00              
ATOM     73  N   PHE    37       2.321  -2.256  -2.959  1.00  0.00              
ATOM     74  CA  PHE    37       0.934  -1.875  -3.367  1.00  0.00              
ATOM     75  C   PHE    37       0.892  -0.370  -3.619  1.00  0.00              
ATOM     76  O   PHE    37       0.200   0.149  -4.514  1.00  0.00              
ATOM     77  N   ARG    38       1.538   0.406  -2.736  1.00  0.00              
ATOM     78  CA  ARG    38       1.552   1.884  -2.880  1.00  0.00              
ATOM     79  C   ARG    38       2.104   2.288  -4.249  1.00  0.00              
ATOM     80  O   ARG    38       1.580   3.242  -4.852  1.00  0.00              
ATOM     81  N   LEU    39       3.129   1.576  -4.788  1.00  0.00              
ATOM     82  CA  LEU    39       3.725   1.892  -6.069  1.00  0.00              
ATOM     83  C   LEU    39       2.676   1.809  -7.179  1.00  0.00              
ATOM     84  O   LEU    39       2.587   2.666  -8.057  1.00  0.00              
ATOM     85  N   VAL    40       1.896   0.754  -7.118  1.00  0.00              
ATOM     86  CA  VAL    40       0.813   0.554  -8.090  1.00  0.00              
ATOM     87  C   VAL    40      -0.316   1.572  -7.968  1.00  0.00              
ATOM     88  O   VAL    40      -0.764   2.184  -8.948  1.00  0.00              
ATOM     89  N   VAL    41      -0.778   1.827  -6.755  1.00  0.00              
ATOM     90  CA  VAL    41      -1.859   2.788  -6.585  1.00  0.00              
ATOM     91  C   VAL    41      -1.389   4.196  -6.940  1.00  0.00              
ATOM     92  O   VAL    41      -2.196   4.952  -7.429  1.00  0.00              
ATOM     93  N   ARG    42      -0.132   4.550  -6.636  1.00  0.00              
ATOM     94  CA  ARG    42       0.392   5.865  -6.992  1.00  0.00              
ATOM     95  C   ARG    42       0.442   5.995  -8.523  1.00  0.00              
ATOM     96  O   ARG    42      -0.068   7.024  -8.998  1.00  0.00              
ATOM     97  N   ASP    43       0.959   5.068  -9.276  1.00  0.00              
ATOM     98  CA  ASP    43       0.942   5.288 -10.724  1.00  0.00              
ATOM     99  C   ASP    43      -0.490   5.355 -11.241  1.00  0.00              
ATOM    100  O   ASP    43      -0.754   6.003 -12.259  1.00  0.00              
ATOM    101  N   THR    44      -1.379   4.521 -10.726  1.00  0.00              
ATOM    102  CA  THR    44      -2.737   4.477 -11.229  1.00  0.00              
ATOM    103  C   THR    44      -3.482   5.794 -11.020  1.00  0.00              
ATOM    104  O   THR    44      -4.089   6.292 -11.970  1.00  0.00              
ATOM    105  N   GLU    45      -9.637  15.311 -11.950  1.00  0.00              
ATOM    106  CA  GLU    45     -10.640  14.674 -11.108  1.00  0.00              
ATOM    107  C   GLU    45     -10.076  13.948  -9.884  1.00  0.00              
ATOM    108  O   GLU    45     -10.846  13.159  -9.317  1.00  0.00              
ATOM    109  N   GLY    46      -8.883  14.194  -9.378  1.00  0.00              
ATOM    110  CA  GLY    46      -8.348  13.352  -8.283  1.00  0.00              
ATOM    111  C   GLY    46      -9.089  13.518  -6.994  1.00  0.00              
ATOM    112  O   GLY    46      -9.157  12.599  -6.180  1.00  0.00              
ATOM    113  N   ARG    47      -9.776  14.680  -6.776  1.00  0.00              
ATOM    114  CA  ARG    47     -10.524  14.869  -5.540  1.00  0.00              
ATOM    115  C   ARG    47     -11.645  13.862  -5.354  1.00  0.00              
ATOM    116  O   ARG    47     -11.994  13.571  -4.209  1.00  0.00              
ATOM    117  N   VAL    49     -12.278  13.332  -6.387  1.00  0.00              
ATOM    118  CA  VAL    49     -13.316  12.341  -6.210  1.00  0.00              
ATOM    119  C   VAL    49     -12.822  10.929  -6.033  1.00  0.00              
ATOM    120  O   VAL    49     -13.689  10.053  -5.931  1.00  0.00              
ATOM    121  N   TRP    50     -11.539  10.670  -6.131  1.00  0.00              
ATOM    122  CA  TRP    50     -10.921   9.371  -5.946  1.00  0.00              
ATOM    123  C   TRP    50     -10.011   9.305  -4.706  1.00  0.00              
ATOM    124  O   TRP    50      -9.095   8.480  -4.692  1.00  0.00              
ATOM    125  N   ARG    51     -10.262  10.177  -3.748  1.00  0.00              
ATOM    126  CA  ARG    51      -9.595  10.174  -2.445  1.00  0.00              
ATOM    127  C   ARG    51      -8.394  11.119  -2.337  1.00  0.00              
ATOM    128  O   ARG    51      -7.725  11.150  -1.256  1.00  0.00              
ATOM    129  N   ALA    52      -8.064  11.760  -3.434  1.00  0.00              
ATOM    130  CA  ALA    52      -6.957  12.726  -3.510  1.00  0.00              
ATOM    131  C   ALA    52      -5.638  12.077  -3.914  1.00  0.00              
ATOM    132  O   ALA    52      -5.588  10.841  -4.072  1.00  0.00              
ATOM    133  N   TRP    53      -4.592  12.837  -4.116  1.00  0.00              
ATOM    134  CA  TRP    53      -3.262  12.390  -4.561  1.00  0.00              
ATOM    135  C   TRP    53      -2.477  11.573  -3.577  1.00  0.00              
ATOM    136  O   TRP    53      -1.525  10.918  -4.094  1.00  0.00              
ATOM    137  N   ASN    54      -2.757  11.483  -2.296  1.00  0.00              
ATOM    138  CA  ASN    54      -1.985  10.591  -1.410  1.00  0.00              
ATOM    139  C   ASN    54      -2.724   9.264  -1.353  1.00  0.00              
ATOM    140  O   ASN    54      -3.850   9.293  -0.802  1.00  0.00              
ATOM    141  N   PHE    55      -2.157   8.174  -1.858  1.00  0.00              
ATOM    142  CA  PHE    55      -2.943   6.925  -1.824  1.00  0.00              
ATOM    143  C   PHE    55      -2.662   6.102  -0.590  1.00  0.00              
ATOM    144  O   PHE    55      -3.111   4.963  -0.393  1.00  0.00              
ATOM    145  N   GLU    56      -1.890   6.669   0.381  1.00  0.00              
ATOM    146  CA  GLU    56      -1.588   5.947   1.606  1.00  0.00              
ATOM    147  C   GLU    56      -2.811   5.531   2.375  1.00  0.00              
ATOM    148  O   GLU    56      -2.817   4.373   2.823  1.00  0.00              
ATOM    149  N   PRO    57      -3.885   6.292   2.495  1.00  0.00              
ATOM    150  CA  PRO    57      -5.109   5.825   3.126  1.00  0.00              
ATOM    151  C   PRO    57      -5.702   4.599   2.376  1.00  0.00              
ATOM    152  O   PRO    57      -6.285   3.692   3.026  1.00  0.00              
ATOM    153  N   ASP    58      -5.626   4.546   1.059  1.00  0.00              
ATOM    154  CA  ASP    58      -6.104   3.367   0.311  1.00  0.00              
ATOM    155  C   ASP    58      -5.268   2.124   0.524  1.00  0.00              
ATOM    156  O   ASP    58      -5.834   1.020   0.684  1.00  0.00              
ATOM    157  N   ALA    59      -3.924   2.265   0.624  1.00  0.00              
ATOM    158  CA  ALA    59      -3.098   1.090   0.970  1.00  0.00              
ATOM    159  C   ALA    59      -3.487   0.534   2.337  1.00  0.00              
ATOM    160  O   ALA    59      -3.706  -0.671   2.554  1.00  0.00              
ATOM    161  N   GLY    60      -3.533   1.448   3.352  1.00  0.00              
ATOM    162  CA  GLY    60      -3.937   1.017   4.685  1.00  0.00              
ATOM    163  C   GLY    60      -5.309   0.325   4.641  1.00  0.00              
ATOM    164  O   GLY    60      -5.457  -0.672   5.352  1.00  0.00              
ATOM    165  N   GLU    61      -6.329   0.848   3.969  1.00  0.00              
ATOM    166  CA  GLU    61      -7.619   0.193   3.874  1.00  0.00              
ATOM    167  C   GLU    61      -7.532  -1.201   3.268  1.00  0.00              
ATOM    168  O   GLU    61      -8.123  -2.150   3.795  1.00  0.00              
ATOM    169  N   GLY    62      -6.779  -1.434   2.165  1.00  0.00              
ATOM    170  CA  GLY    62      -6.632  -2.787   1.626  1.00  0.00              
ATOM    171  C   GLY    62      -5.964  -3.702   2.673  1.00  0.00              
ATOM    172  O   GLY    62      -6.362  -4.867   2.859  1.00  0.00              
ATOM    173  N   LEU    63      -4.898  -3.250   3.356  1.00  0.00              
ATOM    174  CA  LEU    63      -4.238  -4.148   4.345  1.00  0.00              
ATOM    175  C   LEU    63      -5.129  -4.431   5.559  1.00  0.00              
ATOM    176  O   LEU    63      -5.095  -5.564   6.111  1.00  0.00              
ATOM    177  N   ASN    64      -5.954  -3.499   6.002  1.00  0.00              
ATOM    178  CA  ASN    64      -6.968  -3.719   7.026  1.00  0.00              
ATOM    179  C   ASN    64      -7.984  -4.776   6.579  1.00  0.00              
ATOM    180  O   ASN    64      -8.377  -5.675   7.354  1.00  0.00              
ATOM    181  N   ARG    65      -8.426  -4.696   5.332  1.00  0.00              
ATOM    182  CA  ARG    65      -9.343  -5.663   4.742  1.00  0.00              
ATOM    183  C   ARG    65      -8.701  -7.056   4.743  1.00  0.00              
ATOM    184  O   ARG    65      -9.373  -8.084   4.911  1.00  0.00              
ATOM    185  N   TYR    66      -7.396  -7.105   4.528  1.00  0.00              
ATOM    186  CA  TYR    66      -6.652  -8.364   4.586  1.00  0.00              
ATOM    187  C   TYR    66      -6.285  -8.795   5.999  1.00  0.00              
ATOM    188  O   TYR    66      -5.345  -9.598   6.198  1.00  0.00              
ATOM    189  N   ILE    67      -6.874  -8.202   7.021  1.00  0.00              
ATOM    190  CA  ILE    67      -6.650  -8.573   8.415  1.00  0.00              
ATOM    191  C   ILE    67      -5.245  -8.223   8.875  1.00  0.00              
ATOM    192  O   ILE    67      -4.670  -8.885   9.780  1.00  0.00              
ATOM    193  N   ARG    68      -4.685  -7.111   8.375  1.00  0.00              
ATOM    194  CA  ARG    68      -3.373  -6.659   8.817  1.00  0.00              
ATOM    195  C   ARG    68      -2.249  -7.663   8.597  1.00  0.00              
ATOM    196  O   ARG    68      -1.306  -7.661   9.401  1.00  0.00              
ATOM    197  N   THR    69      -2.280  -8.474   7.555  1.00  0.00              
ATOM    198  CA  THR    69      -1.177  -9.385   7.267  1.00  0.00              
ATOM    199  C   THR    69      -0.056  -8.553   6.617  1.00  0.00              
ATOM    200  O   THR    69      -0.317  -7.525   5.981  1.00  0.00              
ATOM    201  N   SER    70       1.198  -9.002   6.746  1.00  0.00              
ATOM    202  CA  SER    70       2.344  -8.298   6.232  1.00  0.00              
ATOM    203  C   SER    70       2.366  -8.231   4.711  1.00  0.00              
ATOM    204  O   SER    70       2.932  -7.309   4.142  1.00  0.00              
ATOM    205  N   GLY    71       1.841  -9.243   4.042  1.00  0.00              
ATOM    206  CA  GLY    71       1.767  -9.193   2.581  1.00  0.00              
ATOM    207  C   GLY    71       0.575  -9.964   2.042  1.00  0.00              
ATOM    208  O   GLY    71      -0.071 -10.737   2.744  1.00  0.00              
ATOM    209  N   ILE    72       0.151  -9.587   0.835  1.00  0.00              
ATOM    210  CA  ILE    72      -1.030 -10.209   0.220  1.00  0.00              
ATOM    211  C   ILE    72      -0.670 -10.828  -1.123  1.00  0.00              
ATOM    212  O   ILE    72       0.310 -10.365  -1.721  1.00  0.00              
ATOM    213  N   ARG    73      -1.496 -11.706  -1.644  1.00  0.00              
ATOM    214  CA  ARG    73      -1.308 -12.297  -2.971  1.00  0.00              
ATOM    215  C   ARG    73      -2.388 -11.786  -3.931  1.00  0.00              
ATOM    216  O   ARG    73      -3.317 -11.047  -3.563  1.00  0.00              
ATOM    217  N   THR    74      -2.303 -12.171  -5.177  1.00  0.00              
ATOM    218  CA  THR    74      -3.217 -11.604  -6.187  1.00  0.00              
ATOM    219  C   THR    74      -4.690 -11.853  -5.920  1.00  0.00              
ATOM    220  O   THR    74      -5.588 -11.022  -6.162  1.00  0.00              
END
