
#######################################################
#                                                     #
#                        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 T0321AL333_5-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321AL333_5-D1.T0321_D1.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      M       1           -
LGA    P      13      W       2           -
LGA    E      14      E       3           -
LGA    D      15      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    F      16      T      26           #
LGA    L      17      H      27           #
LGA    V      18      S      28           #
LGA    D      19      V      29           -
LGA    E      20      I      30           -
LGA    L      21      R      31           -
LGA    V      22      S      32           -
LGA    C      23      -       -           -
LGA    G      24      -       -           -
LGA    Q      53      -       -           -
LGA    N      54      -       -           -
LGA    L      55      G      33           #
LGA    V      62      N      34          4.675
LGA    A      63      G      35          4.337
LGA    A      64      V      36          2.238
LGA    G      65      G      37          0.705
LGA    C      66      L      38          1.243
LGA    V      67      G      39          2.424
LGA    K      68      P      40          2.192
LGA    S      69      N      41          1.662
LGA    W      70      R      42          0.587
LGA    -       -      P      43           -
LGA    N      71      F      44          3.301
LGA    Y      72      E      45          3.163
LGA    V      73      T      46          0.788
LGA    E      74      R      47          0.583
LGA    A      75      M      48          2.845
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    S      76      L      51          2.500
LGA    I      77      T      52          4.815
LGA    -       -      Q      53           -
LGA    -       -      N      54           -
LGA    G      78      L      55          3.784
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      L      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    L      79      A      63          3.754
LGA    -       -      A      64           -
LGA    -       -      G      65           -
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    -       -      S      76           -
LGA    -       -      I      77           -
LGA    -       -      G      78           -
LGA    -       -      L      79           -
LGA    -       -      A      80           -
LGA    V      91      A      81          4.012
LGA    -       -      I      82           -
LGA    -       -      N      83           -
LGA    A      92      A      84          3.759
LGA    R      93      Y      85          2.782
LGA    -       -      Y      86           -
LGA    -       -      N      87           -
LGA    -       -      N      88           -
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    E      94      V      91          3.894
LGA    H      95      A      92           #
LGA    -       -      R      93           -
LGA    G      96      E      94          2.927
LGA    -       -      H      95           -
LGA    -       -      G      96           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   96    5.0     23    3.03     8.70     16.312     0.735

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.626069 * X  +   0.154545 * Y  +   0.764299 * Z  + -212.292267
  Y_new =   0.314306 * X  +   0.846998 * Y  +  -0.428727 * Z  +   5.417356
  Z_new =  -0.713617 * X  +   0.508636 * Y  +   0.481705 * Z  + -78.947250 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.812586   -2.329007  [ DEG:    46.5578   -133.4422 ]
  Theta =   0.794648    2.346944  [ DEG:    45.5300    134.4700 ]
  Phi   =   0.465270   -2.676322  [ DEG:    26.6580   -153.3420 ]
 
# 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: T0321AL333_5-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321AL333_5-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   96   5.0   23   3.03    8.70  16.312
REMARK  ---------------------------------------------------------- 
MOLECULE T0321AL333_5-D1
REMARK Aligment from pdb entry: 1kv3_A
ATOM      1  N   MET     1       3.595  44.345  53.158  1.00  0.00              
ATOM      2  CA  MET     1       2.770  45.219  52.318  1.00  0.00              
ATOM      3  C   MET     1       2.942  46.691  52.684  1.00  0.00              
ATOM      4  O   MET     1       3.115  47.547  51.807  1.00  0.00              
ATOM      5  N   PRO    13       2.916  46.951  53.993  1.00  0.00              
ATOM      6  CA  PRO    13       3.072  48.282  54.579  1.00  0.00              
ATOM      7  C   PRO    13       2.426  49.417  53.796  1.00  0.00              
ATOM      8  O   PRO    13       3.046  49.969  52.877  1.00  0.00              
ATOM      9  N   GLU    14       1.199  49.786  54.169  1.00  0.00              
ATOM     10  CA  GLU    14       0.493  50.893  53.497  1.00  0.00              
ATOM     11  C   GLU    14       1.273  52.173  53.857  1.00  0.00              
ATOM     12  O   GLU    14       0.850  53.288  53.524  1.00  0.00              
ATOM     13  N   ASP    15       2.416  51.989  54.527  1.00  0.00              
ATOM     14  CA  ASP    15       3.217  53.107  54.973  1.00  0.00              
ATOM     15  C   ASP    15       2.608  53.531  56.299  1.00  0.00              
ATOM     16  O   ASP    15       3.207  54.292  57.074  1.00  0.00              
ATOM     17  N   PHE    16       1.385  53.049  56.528  1.00  0.00              
ATOM     18  CA  PHE    16       0.646  53.316  57.734  1.00  0.00              
ATOM     19  C   PHE    16       0.898  52.251  58.759  1.00  0.00              
ATOM     20  O   PHE    16       1.137  51.082  58.421  1.00  0.00              
ATOM     21  N   LEU    17       0.813  52.661  60.021  1.00  0.00              
ATOM     22  CA  LEU    17       1.000  51.742  61.135  1.00  0.00              
ATOM     23  C   LEU    17       0.054  52.150  62.226  1.00  0.00              
ATOM     24  O   LEU    17      -0.376  53.315  62.268  1.00  0.00              
ATOM     25  N   VAL    18      -0.233  51.211  63.123  1.00  0.00              
ATOM     26  CA  VAL    18      -1.101  51.512  64.223  1.00  0.00              
ATOM     27  C   VAL    18      -0.931  50.578  65.384  1.00  0.00              
ATOM     28  O   VAL    18      -0.741  49.353  65.213  1.00  0.00              
ATOM     29  N   ASP    19      -0.446  55.572  80.828  1.00  0.00              
ATOM     30  CA  ASP    19      -0.007  55.247  82.194  1.00  0.00              
ATOM     31  C   ASP    19      -0.835  54.117  82.787  1.00  0.00              
ATOM     32  O   ASP    19      -1.895  53.771  82.278  1.00  0.00              
ATOM     33  N   GLU    20      -0.350  53.567  83.893  1.00  0.00              
ATOM     34  CA  GLU    20      -1.028  52.503  84.628  1.00  0.00              
ATOM     35  C   GLU    20      -2.484  52.898  85.009  1.00  0.00              
ATOM     36  O   GLU    20      -2.779  54.076  85.233  1.00  0.00              
ATOM     37  N   LEU    21      -3.403  51.940  84.951  1.00  0.00              
ATOM     38  CA  LEU    21      -4.792  52.190  85.359  1.00  0.00              
ATOM     39  C   LEU    21      -5.069  51.197  86.433  1.00  0.00              
ATOM     40  O   LEU    21      -4.520  50.085  86.419  1.00  0.00              
ATOM     41  N   VAL    22      -5.992  51.542  87.315  1.00  0.00              
ATOM     42  CA  VAL    22      -6.309  50.633  88.413  1.00  0.00              
ATOM     43  C   VAL    22      -7.686  50.018  88.294  1.00  0.00              
ATOM     44  O   VAL    22      -8.588  50.612  87.694  1.00  0.00              
ATOM     45  N   CYS    23      -7.832  48.820  88.838  1.00  0.00              
ATOM     46  CA  CYS    23      -9.106  48.107  88.859  1.00  0.00              
ATOM     47  C   CYS    23     -10.011  49.041  89.622  1.00  0.00              
ATOM     48  O   CYS    23      -9.669  49.457  90.691  1.00  0.00              
ATOM     49  N   GLY    24     -11.105  49.480  89.038  1.00  0.00              
ATOM     50  CA  GLY    24     -11.965  50.354  89.801  1.00  0.00              
ATOM     51  C   GLY    24     -12.036  51.746  89.267  1.00  0.00              
ATOM     52  O   GLY    24     -12.926  52.508  89.641  1.00  0.00              
ATOM     53  N   GLN    53     -11.183  52.063  88.312  1.00  0.00              
ATOM     54  CA  GLN    53     -11.193  53.398  87.793  1.00  0.00              
ATOM     55  C   GLN    53     -11.579  53.446  86.339  1.00  0.00              
ATOM     56  O   GLN    53     -11.692  52.395  85.718  1.00  0.00              
ATOM     57  N   ASN    54     -11.846  54.661  85.840  1.00  0.00              
ATOM     58  CA  ASN    54     -12.173  54.914  84.441  1.00  0.00              
ATOM     59  C   ASN    54     -10.841  55.342  83.875  1.00  0.00              
ATOM     60  O   ASN    54      -9.982  55.844  84.624  1.00  0.00              
ATOM     61  N   LEU    55     -10.631  55.137  82.576  1.00  0.00              
ATOM     62  CA  LEU    55      -9.344  55.514  81.943  1.00  0.00              
ATOM     63  C   LEU    55      -9.424  55.536  80.441  1.00  0.00              
ATOM     64  O   LEU    55     -10.324  54.956  79.882  1.00  0.00              
ATOM     65  N   VAL    62      -8.510  56.246  79.794  1.00  0.00              
ATOM     66  CA  VAL    62      -8.498  56.293  78.346  1.00  0.00              
ATOM     67  C   VAL    62      -7.317  55.476  77.808  1.00  0.00              
ATOM     68  O   VAL    62      -6.346  55.266  78.520  1.00  0.00              
ATOM     69  N   ALA    63      -7.487  54.845  76.653  1.00  0.00              
ATOM     70  CA  ALA    63      -6.387  54.134  76.001  1.00  0.00              
ATOM     71  C   ALA    63      -6.465  54.777  74.653  1.00  0.00              
ATOM     72  O   ALA    63      -7.433  55.462  74.364  1.00  0.00              
ATOM     73  N   ALA    64      -5.492  54.514  73.800  1.00  0.00              
ATOM     74  CA  ALA    64      -5.491  55.170  72.513  1.00  0.00              
ATOM     75  C   ALA    64      -5.119  54.289  71.332  1.00  0.00              
ATOM     76  O   ALA    64      -4.327  53.340  71.456  1.00  0.00              
ATOM     77  N   GLY    65      -5.735  54.585  70.190  1.00  0.00              
ATOM     78  CA  GLY    65      -5.388  53.893  68.965  1.00  0.00              
ATOM     79  C   GLY    65      -4.427  54.944  68.394  1.00  0.00              
ATOM     80  O   GLY    65      -4.780  56.105  68.208  1.00  0.00              
ATOM     81  N   CYS    66      -3.177  54.564  68.228  1.00  0.00              
ATOM     82  CA  CYS    66      -2.176  55.504  67.731  1.00  0.00              
ATOM     83  C   CYS    66      -1.768  55.169  66.315  1.00  0.00              
ATOM     84  O   CYS    66      -1.091  54.167  66.065  1.00  0.00              
ATOM     85  N   VAL    67      -2.147  56.055  65.404  1.00  0.00              
ATOM     86  CA  VAL    67      -1.930  55.879  63.963  1.00  0.00              
ATOM     87  C   VAL    67      -0.786  56.712  63.456  1.00  0.00              
ATOM     88  O   VAL    67      -0.691  57.918  63.762  1.00  0.00              
ATOM     89  N   LYS    68       0.068  56.068  62.663  1.00  0.00              
ATOM     90  CA  LYS    68       1.225  56.738  62.098  1.00  0.00              
ATOM     91  C   LYS    68       1.153  56.717  60.577  1.00  0.00              
ATOM     92  O   LYS    68       1.090  55.655  59.961  1.00  0.00              
ATOM     93  N   SER    69       1.150  57.895  59.981  1.00  0.00              
ATOM     94  CA  SER    69       1.130  58.002  58.540  1.00  0.00              
ATOM     95  C   SER    69       2.479  58.549  58.065  1.00  0.00              
ATOM     96  O   SER    69       2.668  59.750  57.998  1.00  0.00              
ATOM     97  N   TRP    70       3.426  57.672  57.765  1.00  0.00              
ATOM     98  CA  TRP    70       4.723  58.125  57.294  1.00  0.00              
ATOM     99  C   TRP    70       4.678  58.126  55.772  1.00  0.00              
ATOM    100  O   TRP    70       5.478  57.449  55.108  1.00  0.00              
ATOM    101  N   ASN    71       3.775  58.944  55.241  1.00  0.00              
ATOM    102  CA  ASN    71       3.519  59.013  53.813  1.00  0.00              
ATOM    103  C   ASN    71       3.176  60.432  53.410  1.00  0.00              
ATOM    104  O   ASN    71       2.782  61.250  54.242  1.00  0.00              
ATOM    105  N   TYR    72       3.327  60.720  52.121  1.00  0.00              
ATOM    106  CA  TYR    72       3.022  62.044  51.595  1.00  0.00              
ATOM    107  C   TYR    72       1.533  62.244  51.314  1.00  0.00              
ATOM    108  O   TYR    72       1.085  63.375  51.191  1.00  0.00              
ATOM    109  N   VAL    73       0.776  61.145  51.186  1.00  0.00              
ATOM    110  CA  VAL    73      -0.665  61.216  50.907  1.00  0.00              
ATOM    111  C   VAL    73      -1.484  61.412  52.149  1.00  0.00              
ATOM    112  O   VAL    73      -1.050  61.096  53.250  1.00  0.00              
ATOM    113  N   GLU    74      -2.651  62.008  51.985  1.00  0.00              
ATOM    114  CA  GLU    74      -3.554  62.145  53.115  1.00  0.00              
ATOM    115  C   GLU    74      -4.693  61.169  52.890  1.00  0.00              
ATOM    116  O   GLU    74      -5.297  61.143  51.826  1.00  0.00              
ATOM    117  N   ALA    75      -4.893  60.289  53.860  1.00  0.00              
ATOM    118  CA  ALA    75      -5.906  59.288  53.771  1.00  0.00              
ATOM    119  C   ALA    75      -7.154  59.698  54.535  1.00  0.00              
ATOM    120  O   ALA    75      -7.132  60.616  55.349  1.00  0.00              
ATOM    121  N   SER    76      -8.278  59.103  54.161  1.00  0.00              
ATOM    122  CA  SER    76      -9.547  59.323  54.863  1.00  0.00              
ATOM    123  C   SER    76     -10.042  57.920  55.114  1.00  0.00              
ATOM    124  O   SER    76     -10.399  57.196  54.179  1.00  0.00              
ATOM    125  N   ILE    77      -9.997  57.520  56.376  1.00  0.00              
ATOM    126  CA  ILE    77     -10.363  56.165  56.728  1.00  0.00              
ATOM    127  C   ILE    77     -11.453  56.078  57.748  1.00  0.00              
ATOM    128  O   ILE    77     -11.990  57.087  58.223  1.00  0.00              
ATOM    129  N   GLY    78     -11.734  54.836  58.109  1.00  0.00              
ATOM    130  CA  GLY    78     -12.695  54.557  59.134  1.00  0.00              
ATOM    131  C   GLY    78     -11.934  53.713  60.131  1.00  0.00              
ATOM    132  O   GLY    78     -11.105  52.878  59.760  1.00  0.00              
ATOM    133  N   LEU    79     -12.155  54.037  61.399  1.00  0.00              
ATOM    134  CA  LEU    79     -11.496  53.412  62.499  1.00  0.00              
ATOM    135  C   LEU    79     -12.533  52.849  63.450  1.00  0.00              
ATOM    136  O   LEU    79     -13.392  53.563  63.982  1.00  0.00              
ATOM    137  N   VAL    91     -12.485  51.549  63.640  1.00  0.00              
ATOM    138  CA  VAL    91     -13.436  50.931  64.522  1.00  0.00              
ATOM    139  C   VAL    91     -12.712  50.453  65.774  1.00  0.00              
ATOM    140  O   VAL    91     -11.869  49.546  65.705  1.00  0.00              
ATOM    141  N   ALA    92     -13.049  51.069  66.910  1.00  0.00              
ATOM    142  CA  ALA    92     -12.450  50.751  68.204  1.00  0.00              
ATOM    143  C   ALA    92     -13.398  49.991  69.104  1.00  0.00              
ATOM    144  O   ALA    92     -14.499  50.468  69.382  1.00  0.00              
ATOM    145  N   ARG    93     -12.927  48.907  69.703  1.00  0.00              
ATOM    146  CA  ARG    93     -13.802  48.124  70.552  1.00  0.00              
ATOM    147  C   ARG    93     -13.010  47.542  71.707  1.00  0.00              
ATOM    148  O   ARG    93     -11.928  47.000  71.497  1.00  0.00              
ATOM    149  N   GLU    94     -13.527  47.644  72.928  1.00  0.00              
ATOM    150  CA  GLU    94     -12.814  47.110  74.073  1.00  0.00              
ATOM    151  C   GLU    94     -13.720  46.118  74.731  1.00  0.00              
ATOM    152  O   GLU    94     -14.868  46.422  74.973  1.00  0.00              
ATOM    153  N   HIS    95     -13.181  44.975  75.128  1.00  0.00              
ATOM    154  CA  HIS    95     -13.990  43.944  75.730  1.00  0.00              
ATOM    155  C   HIS    95     -13.189  43.252  76.819  1.00  0.00              
ATOM    156  O   HIS    95     -11.978  43.156  76.704  1.00  0.00              
ATOM    157  N   GLY    96     -13.855  42.792  77.879  1.00  0.00              
ATOM    158  CA  GLY    96     -13.200  42.072  78.973  1.00  0.00              
ATOM    159  C   GLY    96     -12.750  40.713  78.388  1.00  0.00              
ATOM    160  O   GLY    96     -13.297  40.291  77.367  1.00  0.00              
END
