
#######################################################
#                                                     #
#                        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   40 (  160),  selected   40 , name T0358AL243_2-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358AL243_2-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    P      11      A      17          0.977
LGA    F      12      Q      18           #
LGA    T      13      A      19           -
LGA    R      14      V      20           -
LGA    R      15      T      21           -
LGA    Q      16      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    A      17      L      29           #
LGA    Q      18      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    A      19      G      34           #
LGA    V      20      S      35          1.692
LGA    T      21      H      36          3.867
LGA    T      22      F      37           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      -       -           -
LGA    N      26      -       -           -
LGA    I      27      R      38          2.234
LGA    T      28      L      39          2.127
LGA    L      29      V      40          2.619
LGA    E      30      V      41          3.612
LGA    D      31      R      42          3.402
LGA    D      32      D      43          4.846
LGA    Q      33      T      44          3.407
LGA    G      34      E      45           -
LGA    S      35      -       -           -
LGA    H      36      G      46          3.997
LGA    F      37      R      47          2.440
LGA    -       -      M      48           -
LGA    R      38      V      49          3.308
LGA    L      39      W      50          2.524
LGA    V      40      R      51          2.423
LGA    V      41      A      52          1.107
LGA    R      42      W      53          1.445
LGA    D      43      N      54          5.114
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      F      55          2.140
LGA    R      47      E      56          2.065
LGA    M      48      P      57           #
LGA    -       -      D      58           -
LGA    V      49      A      59          4.041
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   65    5.0     21    3.04     4.76     20.573     0.668

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.363259 * X  +   0.365711 * Y  +  -0.856912 * Z  +   8.042242
  Y_new =  -0.723927 * X  +  -0.689763 * Y  +   0.012509 * Z  +  39.867054
  Z_new =  -0.586491 * X  +   0.624886 * Y  +   0.515311 * Z  +   7.679730 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.881205   -2.260387  [ DEG:    50.4893   -129.5107 ]
  Theta =   0.626720    2.514873  [ DEG:    35.9084    144.0916 ]
  Phi   =  -2.035875    1.105718  [ DEG:  -116.6470     63.3530 ]
 
# 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-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL243_2-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   65   5.0   21   3.04    4.76  20.573
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL243_2-D1
REMARK Aligment from pdb entry: 2gkeA
ATOM     21  N   GLY    10       0.329  -2.257  -7.186  1.00  0.00              
ATOM     22  CA  GLY    10       0.815  -0.902  -6.912  1.00  0.00              
ATOM     23  C   GLY    10       1.967  -0.911  -5.924  1.00  0.00              
ATOM     24  O   GLY    10       1.818  -1.360  -4.786  1.00  0.00              
ATOM     25  N   PRO    11       3.111  -0.417  -6.385  1.00  0.00              
ATOM     26  CA  PRO    11       4.269  -0.231  -5.535  1.00  0.00              
ATOM     27  C   PRO    11       5.169   0.838  -6.108  1.00  0.00              
ATOM     28  O   PRO    11       5.159   1.109  -7.298  1.00  0.00              
ATOM     29  N   PHE    12       5.984   1.438  -5.252  1.00  0.00              
ATOM     30  CA  PHE    12       6.834   2.540  -5.694  1.00  0.00              
ATOM     31  C   PHE    12       7.831   2.892  -4.598  1.00  0.00              
ATOM     32  O   PHE    12       7.679   2.505  -3.436  1.00  0.00              
ATOM     33  N   THR    13       8.836   3.651  -4.982  1.00  0.00              
ATOM     34  CA  THR    13       9.823   4.148  -4.029  1.00  0.00              
ATOM     35  C   THR    13       9.371   5.479  -3.410  1.00  0.00              
ATOM     36  O   THR    13       8.525   6.203  -3.974  1.00  0.00              
ATOM     37  N   ARG    14       9.947   5.843  -2.274  1.00  0.00              
ATOM     38  CA  ARG    14       9.729   7.172  -1.729  1.00  0.00              
ATOM     39  C   ARG    14      10.124   8.300  -2.691  1.00  0.00              
ATOM     40  O   ARG    14       9.482   9.331  -2.722  1.00  0.00              
ATOM     41  N   ARG    15      11.141   8.102  -3.509  1.00  0.00              
ATOM     42  CA  ARG    15      11.516   9.096  -4.506  1.00  0.00              
ATOM     43  C   ARG    15      10.377   9.330  -5.503  1.00  0.00              
ATOM     44  O   ARG    15      10.071  10.464  -5.894  1.00  0.00              
ATOM     45  N   GLN    16       9.742   8.248  -5.945  1.00  0.00              
ATOM     46  CA  GLN    16       8.586   8.374  -6.823  1.00  0.00              
ATOM     47  C   GLN    16       7.453   9.140  -6.118  1.00  0.00              
ATOM     48  O   GLN    16       6.822  10.020  -6.714  1.00  0.00              
ATOM     49  N   ALA    17       7.170   8.814  -4.863  1.00  0.00              
ATOM     50  CA  ALA    17       6.129   9.546  -4.132  1.00  0.00              
ATOM     51  C   ALA    17       6.418  11.044  -4.107  1.00  0.00              
ATOM     52  O   ALA    17       5.548  11.856  -4.412  1.00  0.00              
ATOM     53  N   GLN    18       7.660  11.411  -3.829  1.00  0.00              
ATOM     54  CA  GLN    18       8.053  12.813  -3.722  1.00  0.00              
ATOM     55  C   GLN    18       7.932  13.505  -5.064  1.00  0.00              
ATOM     56  O   GLN    18       7.456  14.643  -5.137  1.00  0.00              
ATOM     57  N   ALA    19       8.320  12.821  -6.134  1.00  0.00              
ATOM     58  CA  ALA    19       8.173  13.384  -7.488  1.00  0.00              
ATOM     59  C   ALA    19       6.704  13.646  -7.788  1.00  0.00              
ATOM     60  O   ALA    19       6.352  14.705  -8.310  1.00  0.00              
ATOM     61  N   VAL    20       5.855  12.665  -7.514  1.00  0.00              
ATOM     62  CA  VAL    20       4.451  12.790  -7.817  1.00  0.00              
ATOM     63  C   VAL    20       3.728  13.823  -6.935  1.00  0.00              
ATOM     64  O   VAL    20       2.744  14.419  -7.360  1.00  0.00              
ATOM     65  N   THR    21       4.214  14.052  -5.723  1.00  0.00              
ATOM     66  CA  THR    21       3.602  14.991  -4.813  1.00  0.00              
ATOM     67  C   THR    21       3.800  16.437  -5.242  1.00  0.00              
ATOM     68  O   THR    21       3.051  17.326  -4.842  1.00  0.00              
ATOM     69  N   THR    22       4.851  16.672  -6.009  1.00  0.00              
ATOM     70  CA  THR    22       5.183  18.020  -6.444  1.00  0.00              
ATOM     71  C   THR    22       4.040  18.634  -7.260  1.00  0.00              
ATOM     72  O   THR    22       3.532  18.025  -8.202  1.00  0.00              
ATOM     73  N   THR    23       3.601  19.839  -6.896  1.00  0.00              
ATOM     74  CA  THR    23       2.372  20.394  -7.496  1.00  0.00              
ATOM     75  C   THR    23       2.610  20.971  -8.869  1.00  0.00              
ATOM     76  O   THR    23       1.674  21.082  -9.634  1.00  0.00              
ATOM     77  N   TYR    24       3.851  21.275  -9.204  1.00  0.00              
ATOM     78  CA  TYR    24       4.155  21.868 -10.508  1.00  0.00              
ATOM     79  C   TYR    24       4.736  20.880 -11.499  1.00  0.00              
ATOM     80  O   TYR    24       4.546  21.028 -12.682  1.00  0.00              
ATOM     81  N   SER    25       5.453  19.869 -11.032  1.00  0.00              
ATOM     82  CA  SER    25       6.047  18.915 -11.942  1.00  0.00              
ATOM     83  C   SER    25       5.529  17.496 -11.760  1.00  0.00              
ATOM     84  O   SER    25       5.903  16.593 -12.518  1.00  0.00              
ATOM     85  N   ASN    26       4.633  17.307 -10.796  1.00  0.00              
ATOM     86  CA  ASN    26       4.010  16.020 -10.550  1.00  0.00              
ATOM     87  C   ASN    26       2.504  16.111 -10.637  1.00  0.00              
ATOM     88  O   ASN    26       1.967  16.921 -11.396  1.00  0.00              
ATOM     89  N   ILE    27      -2.985   7.595  -1.098  1.00  0.00              
ATOM     90  CA  ILE    27      -3.647   6.501  -0.399  1.00  0.00              
ATOM     91  C   ILE    27      -3.766   5.312  -1.320  1.00  0.00              
ATOM     92  O   ILE    27      -4.035   5.467  -2.504  1.00  0.00              
ATOM     93  N   THR    28      -3.569   4.127  -0.774  1.00  0.00              
ATOM     94  CA  THR    28      -3.797   2.887  -1.528  1.00  0.00              
ATOM     95  C   THR    28      -4.897   2.054  -0.864  1.00  0.00              
ATOM     96  O   THR    28      -4.885   1.833   0.346  1.00  0.00              
ATOM     97  N   LEU    29      -5.808   1.581  -1.705  1.00  0.00              
ATOM     98  CA  LEU    29      -6.821   0.599  -1.336  1.00  0.00              
ATOM     99  C   LEU    29      -6.267  -0.766  -1.720  1.00  0.00              
ATOM    100  O   LEU    29      -5.955  -1.016  -2.874  1.00  0.00              
ATOM    101  N   GLU    30      -6.107  -1.647  -0.743  1.00  0.00              
ATOM    102  CA  GLU    30      -5.590  -2.974  -0.984  1.00  0.00              
ATOM    103  C   GLU    30      -6.593  -4.027  -0.523  1.00  0.00              
ATOM    104  O   GLU    30      -7.516  -3.752   0.242  1.00  0.00              
ATOM    105  N   ASP    31      -6.424  -5.247  -1.022  1.00  0.00              
ATOM    106  CA  ASP    31      -7.155  -6.391  -0.489  1.00  0.00              
ATOM    107  C   ASP    31      -6.780  -6.593   0.970  1.00  0.00              
ATOM    108  O   ASP    31      -5.640  -6.330   1.366  1.00  0.00              
ATOM    109  N   ASP    32      -6.957  -9.783   6.595  1.00  0.00              
ATOM    110  CA  ASP    32      -8.009 -10.500   7.302  1.00  0.00              
ATOM    111  C   ASP    32      -9.203 -10.525   6.352  1.00  0.00              
ATOM    112  O   ASP    32      -9.837  -9.484   6.119  1.00  0.00              
ATOM    113  N   GLN    33      -9.508 -11.704   5.774  1.00  0.00              
ATOM    114  CA  GLN    33     -10.531 -11.752   4.732  1.00  0.00              
ATOM    115  C   GLN    33     -11.936 -11.424   5.213  1.00  0.00              
ATOM    116  O   GLN    33     -12.813 -11.193   4.390  1.00  0.00              
ATOM    117  N   GLY    34     -12.160 -11.361   6.524  1.00  0.00              
ATOM    118  CA  GLY    34     -13.428 -10.863   7.064  1.00  0.00              
ATOM    119  C   GLY    34     -13.600  -9.350   6.910  1.00  0.00              
ATOM    120  O   GLY    34     -14.706  -8.829   7.072  1.00  0.00              
ATOM    121  N   SER    35     -12.516  -8.634   6.651  1.00  0.00              
ATOM    122  CA  SER    35     -12.624  -7.178   6.438  1.00  0.00              
ATOM    123  C   SER    35     -12.853  -6.890   4.959  1.00  0.00              
ATOM    124  O   SER    35     -12.711  -7.773   4.092  1.00  0.00              
ATOM    125  N   HIS    36     -13.207  -5.655   4.642  1.00  0.00              
ATOM    126  CA  HIS    36     -13.401  -5.288   3.244  1.00  0.00              
ATOM    127  C   HIS    36     -12.119  -4.892   2.519  1.00  0.00              
ATOM    128  O   HIS    36     -11.904  -5.314   1.384  1.00  0.00              
ATOM    129  N   PHE    37     -11.275  -4.064   3.142  1.00  0.00              
ATOM    130  CA  PHE    37     -10.043  -3.553   2.496  1.00  0.00              
ATOM    131  C   PHE    37      -8.959  -3.331   3.538  1.00  0.00              
ATOM    132  O   PHE    37      -9.243  -3.231   4.724  1.00  0.00              
ATOM    133  N   ARG    38      -7.740  -3.208   3.032  1.00  0.00              
ATOM    134  CA  ARG    38      -6.599  -2.648   3.761  1.00  0.00              
ATOM    135  C   ARG    38      -6.306  -1.255   3.213  1.00  0.00              
ATOM    136  O   ARG    38      -6.482  -0.981   2.016  1.00  0.00              
ATOM    137  N   LEU    39      -5.861  -0.371   4.097  1.00  0.00              
ATOM    138  CA  LEU    39      -5.681   1.054   3.811  1.00  0.00              
ATOM    139  C   LEU    39      -4.265   1.484   4.123  1.00  0.00              
ATOM    140  O   LEU    39      -3.851   1.350   5.261  1.00  0.00              
ATOM    141  N   VAL    40      -3.543   1.984   3.117  1.00  0.00              
ATOM    142  CA  VAL    40      -2.199   2.510   3.301  1.00  0.00              
ATOM    143  C   VAL    40      -2.149   3.987   2.966  1.00  0.00              
ATOM    144  O   VAL    40      -2.906   4.490   2.109  1.00  0.00              
ATOM    145  N   VAL    41      -1.268   4.698   3.662  1.00  0.00              
ATOM    146  CA  VAL    41      -1.168   6.163   3.564  1.00  0.00              
ATOM    147  C   VAL    41       0.287   6.595   3.406  1.00  0.00              
ATOM    148  O   VAL    41       1.138   6.144   4.176  1.00  0.00              
ATOM    149  N   ARG    42       0.549   7.500   2.459  1.00  0.00              
ATOM    150  CA  ARG    42       1.884   8.029   2.240  1.00  0.00              
ATOM    151  C   ARG    42       1.804   9.543   2.249  1.00  0.00              
ATOM    152  O   ARG    42       0.936  10.131   1.600  1.00  0.00              
ATOM    153  N   ASP    43       2.736  10.185   2.949  1.00  0.00              
ATOM    154  CA  ASP    43       2.859  11.622   2.923  1.00  0.00              
ATOM    155  C   ASP    43       3.599  12.103   1.681  1.00  0.00              
ATOM    156  O   ASP    43       4.346  11.362   1.029  1.00  0.00              
ATOM    157  N   THR    44       3.459  13.386   1.400  1.00  0.00              
ATOM    158  CA  THR    44       4.150  14.032   0.308  1.00  0.00              
ATOM    159  C   THR    44       5.658  13.887   0.375  1.00  0.00              
ATOM    160  O   THR    44       6.318  13.947  -0.656  1.00  0.00              
ATOM    161  N   GLU    45       6.216  13.714   1.573  1.00  0.00              
ATOM    162  CA  GLU    45       7.667  13.510   1.736  1.00  0.00              
ATOM    163  C   GLU    45       8.124  12.088   1.494  1.00  0.00              
ATOM    164  O   GLU    45       9.308  11.798   1.665  1.00  0.00              
ATOM    165  N   GLY    46       7.204  11.213   1.096  1.00  0.00              
ATOM    166  CA  GLY    46       7.506   9.825   0.815  1.00  0.00              
ATOM    167  C   GLY    46       7.374   8.858   1.964  1.00  0.00              
ATOM    168  O   GLY    46       7.594   7.670   1.766  1.00  0.00              
ATOM    169  N   ARG    47       7.030   9.345   3.160  1.00  0.00              
ATOM    170  CA  ARG    47       6.895   8.480   4.331  1.00  0.00              
ATOM    171  C   ARG    47       5.570   7.742   4.364  1.00  0.00              
ATOM    172  O   ARG    47       4.551   8.288   4.032  1.00  0.00              
ATOM    173  N   MET    48       5.615   6.480   4.775  1.00  0.00              
ATOM    174  CA  MET    48       4.413   5.681   4.946  1.00  0.00              
ATOM    175  C   MET    48       3.992   5.713   6.404  1.00  0.00              
ATOM    176  O   MET    48       4.828   5.469   7.300  1.00  0.00              
ATOM    177  N   VAL    49       2.718   6.004   6.631  1.00  0.00              
ATOM    178  CA  VAL    49       2.183   6.113   7.987  1.00  0.00              
ATOM    179  C   VAL    49       0.880   5.299   8.112  1.00  0.00              
ATOM    180  O   VAL    49       0.425   4.706   7.131  1.00  0.00              
END
