
#######################################################
#                                                     #
#                        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   49 (  196),  selected   49 , name T0309AL243_5
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309AL243_5.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Q       8      A       2           -
LGA    I       9      S       3           -
LGA    N      10      K       4           -
LGA    V      11      K       5           -
LGA    K      12      V       6           -
LGA    G      13      H       7           -
LGA    M      17      Q       8           -
LGA    D      18      I       9           -
LGA    V      19      N      10           -
LGA    M      20      V      11           -
LGA    E      21      K      12           -
LGA    V      22      G      13           -
LGA    T      23      F      14           -
LGA    E      24      F      15           -
LGA    Q      25      D      16           #
LGA    T      26      -       -           -
LGA    K      27      M      17           #
LGA    A      29      D      18          2.748
LGA    E      30      V      19          3.542
LGA    Y      31      M      20          1.407
LGA    T      32      E      21          2.998
LGA    Y      33      V      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      A      29           -
LGA    -       -      E      30           -
LGA    -       -      Y      31           -
LGA    -       -      T      32           -
LGA    -       -      Y      33           -
LGA    D      34      D      34          2.071
LGA    F      35      F      35          1.128
LGA    K      36      K      36          1.046
LGA    E      37      E      37          1.068
LGA    I      38      I      38          1.087
LGA    L      39      L      39          0.881
LGA    S      40      S      40          0.601
LGA    E      41      E      41          1.722
LGA    F      42      F      42          3.074
LGA    N      43      N      43          2.934
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    G      44      N      46          3.385
LGA    K      45      V      47          1.850
LGA    N      46      S      48          2.515
LGA    V      47      I      49          1.123
LGA    S      48      T      50          2.093
LGA    I      49      V      51          1.276
LGA    T      50      K      52          1.593
LGA    V      51      E      53          0.480
LGA    K      52      E      54          2.072
LGA    E      53      N      55          1.675
LGA    L      57      E      56          4.864
LGA    P      58      -       -           -
LGA    V      59      L      57          4.759
LGA    K      60      P      58           -
LGA    G      61      V      59           -
LGA    V      62      K      60           -
LGA    E      63      G      61           -
LGA    -       -      V      62           -
LGA    -       -      E      63           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49   62    5.0     26    2.38    38.46     35.147     1.050

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.859227 * X  +   0.343278 * Y  +  -0.379327 * Z  +  30.545532
  Y_new =   0.171852 * X  +   0.504708 * Y  +   0.846012 * Z  + -58.558174
  Z_new =   0.481866 * X  +  -0.792105 * Y  +   0.374666 * Z  + -21.641708 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.128981    2.012612  [ DEG:   -64.6859    115.3141 ]
  Theta =  -0.502784   -2.638809  [ DEG:   -28.8074   -151.1926 ]
  Phi   =   0.197403   -2.944189  [ DEG:    11.3104   -168.6896 ]
 
# 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: T0309AL243_5                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309AL243_5.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   49   62   5.0   26   2.38   38.46  35.147
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL243_5
REMARK Aligment from pdb entry: 1gz5A
ATOM      1  N   GLN     8      45.210 -14.047  -3.600  1.00  0.00              
ATOM      2  CA  GLN     8      44.575 -13.729  -2.320  1.00  0.00              
ATOM      3  C   GLN     8      43.166 -14.321  -2.290  1.00  0.00              
ATOM      4  O   GLN     8      42.508 -14.431  -3.330  1.00  0.00              
ATOM      5  N   ILE     9      42.706 -14.732  -1.116  1.00  0.00              
ATOM      6  CA  ILE     9      41.334 -15.177  -0.964  1.00  0.00              
ATOM      7  C   ILE     9      40.645 -14.338   0.082  1.00  0.00              
ATOM      8  O   ILE     9      41.320 -13.783   0.941  1.00  0.00              
ATOM      9  N   ASN    10      39.311 -14.220  -0.019  1.00  0.00              
ATOM     10  CA  ASN    10      38.517 -13.367   0.876  1.00  0.00              
ATOM     11  C   ASN    10      37.027 -13.645   0.763  1.00  0.00              
ATOM     12  O   ASN    10      36.563 -14.281  -0.195  1.00  0.00              
ATOM     13  N   VAL    11      36.269 -13.208   1.752  1.00  0.00              
ATOM     14  CA  VAL    11      34.840 -13.504   1.814  1.00  0.00              
ATOM     15  C   VAL    11      34.067 -12.220   1.638  1.00  0.00              
ATOM     16  O   VAL    11      34.328 -11.254   2.318  1.00  0.00              
ATOM     17  N   LYS    12      27.363 -11.317  -0.856  1.00  0.00              
ATOM     18  CA  LYS    12      26.661 -10.412  -1.768  1.00  0.00              
ATOM     19  C   LYS    12      25.328  -9.950  -1.160  1.00  0.00              
ATOM     20  O   LYS    12      24.676 -10.703  -0.422  1.00  0.00              
ATOM     21  N   GLY    13      24.975  -8.676  -1.421  1.00  0.00              
ATOM     22  CA  GLY    13      23.835  -8.050  -0.786  1.00  0.00              
ATOM     23  C   GLY    13      22.926  -7.428  -1.805  1.00  0.00              
ATOM     24  O   GLY    13      23.018  -7.713  -3.000  1.00  0.00              
ATOM     25  N   MET    17      22.120  -6.505  -1.312  1.00  0.00              
ATOM     26  CA  MET    17      20.942  -6.000  -1.943  1.00  0.00              
ATOM     27  C   MET    17      20.965  -4.441  -1.717  1.00  0.00              
ATOM     28  O   MET    17      21.784  -3.943  -0.945  1.00  0.00              
ATOM     29  N   ASP    18      20.121  -3.687  -2.422  1.00  0.00              
ATOM     30  CA  ASP    18      19.980  -2.221  -2.208  1.00  0.00              
ATOM     31  C   ASP    18      18.761  -1.936  -1.339  1.00  0.00              
ATOM     32  O   ASP    18      17.677  -1.814  -1.879  1.00  0.00              
ATOM     33  N   VAL    19      18.920  -1.827  -0.017  1.00  0.00              
ATOM     34  CA  VAL    19      17.763  -1.875   0.905  1.00  0.00              
ATOM     35  C   VAL    19      16.879  -0.676   0.708  1.00  0.00              
ATOM     36  O   VAL    19      15.654  -0.801   0.851  1.00  0.00              
ATOM     37  N   MET    20      17.488   0.452   0.377  1.00  0.00              
ATOM     38  CA  MET    20      16.760   1.690   0.179  1.00  0.00              
ATOM     39  C   MET    20      15.890   1.585  -1.069  1.00  0.00              
ATOM     40  O   MET    20      14.730   1.992  -1.032  1.00  0.00              
ATOM     41  N   GLU    21      16.446   1.074  -2.171  1.00  0.00              
ATOM     42  CA  GLU    21      15.664   0.953  -3.394  1.00  0.00              
ATOM     43  C   GLU    21      14.502  -0.054  -3.264  1.00  0.00              
ATOM     44  O   GLU    21      13.383   0.230  -3.756  1.00  0.00              
ATOM     45  N   VAL    22      14.720  -1.198  -2.596  1.00  0.00              
ATOM     46  CA  VAL    22      13.598  -2.103  -2.435  1.00  0.00              
ATOM     47  C   VAL    22      12.515  -1.558  -1.531  1.00  0.00              
ATOM     48  O   VAL    22      11.331  -1.767  -1.823  1.00  0.00              
ATOM     49  N   THR    23      12.912  -0.802  -0.497  1.00  0.00              
ATOM     50  CA  THR    23      11.948  -0.076   0.327  1.00  0.00              
ATOM     51  C   THR    23      11.037   0.693  -0.608  1.00  0.00              
ATOM     52  O   THR    23       9.829   0.482  -0.582  1.00  0.00              
ATOM     53  N   GLU    24      11.632   1.522  -1.472  1.00  0.00              
ATOM     54  CA  GLU    24      10.890   2.385  -2.418  1.00  0.00              
ATOM     55  C   GLU    24       9.989   1.537  -3.287  1.00  0.00              
ATOM     56  O   GLU    24       8.788   1.824  -3.390  1.00  0.00              
ATOM     57  N   GLN    25      10.524   0.467  -3.882  1.00  0.00              
ATOM     58  CA  GLN    25       9.670  -0.251  -4.821  1.00  0.00              
ATOM     59  C   GLN    25       8.560  -1.014  -4.097  1.00  0.00              
ATOM     60  O   GLN    25       7.437  -1.063  -4.611  1.00  0.00              
ATOM     61  N   THR    26       8.861  -1.537  -2.900  1.00  0.00              
ATOM     62  CA  THR    26       7.896  -2.297  -2.092  1.00  0.00              
ATOM     63  C   THR    26       6.696  -1.426  -1.627  1.00  0.00              
ATOM     64  O   THR    26       5.618  -1.949  -1.378  1.00  0.00              
ATOM     65  N   LYS    27       6.887  -0.113  -1.546  1.00  0.00              
ATOM     66  CA  LYS    27       5.851   0.784  -1.030  1.00  0.00              
ATOM     67  C   LYS    27       5.014   1.424  -2.158  1.00  0.00              
ATOM     68  O   LYS    27       4.052   2.141  -1.898  1.00  0.00              
ATOM     69  N   ALA    29       5.384   1.164  -3.408  1.00  0.00              
ATOM     70  CA  ALA    29       4.648   1.670  -4.555  1.00  0.00              
ATOM     71  C   ALA    29       3.299   0.986  -4.665  1.00  0.00              
ATOM     72  O   ALA    29       3.096  -0.096  -4.102  1.00  0.00              
ATOM     73  N   GLU    30       2.358   1.583  -5.388  1.00  0.00              
ATOM     74  CA  GLU    30       0.990   1.041  -5.421  1.00  0.00              
ATOM     75  C   GLU    30       0.952  -0.365  -6.044  1.00  0.00              
ATOM     76  O   GLU    30       1.804  -0.688  -6.895  1.00  0.00              
ATOM     77  N   TYR    31       0.005  -1.209  -5.608  1.00  0.00              
ATOM     78  CA  TYR    31      -0.119  -2.532  -6.228  1.00  0.00              
ATOM     79  C   TYR    31      -0.872  -2.426  -7.551  1.00  0.00              
ATOM     80  O   TYR    31      -1.765  -1.584  -7.678  1.00  0.00              
ATOM     81  N   THR    32      -0.553  -3.280  -8.521  1.00  0.00              
ATOM     82  CA  THR    32      -1.390  -3.417  -9.730  1.00  0.00              
ATOM     83  C   THR    32      -2.851  -3.693  -9.312  1.00  0.00              
ATOM     84  O   THR    32      -3.053  -4.436  -8.314  1.00  0.00              
ATOM     85  N   TYR    33      -3.831  -3.198 -10.075  1.00  0.00              
ATOM     86  CA  TYR    33      -5.228  -3.177  -9.629  1.00  0.00              
ATOM     87  C   TYR    33      -5.738  -4.540  -9.165  1.00  0.00              
ATOM     88  O   TYR    33      -6.350  -4.666  -8.111  1.00  0.00              
ATOM     89  N   ASP    34      -5.421  -5.574  -9.936  1.00  0.00              
ATOM     90  CA  ASP    34      -5.852  -6.922  -9.710  1.00  0.00              
ATOM     91  C   ASP    34      -5.285  -7.473  -8.373  1.00  0.00              
ATOM     92  O   ASP    34      -5.913  -8.324  -7.678  1.00  0.00              
ATOM     93  N   PHE    35      -4.075  -7.047  -8.009  1.00  0.00              
ATOM     94  CA  PHE    35      -3.503  -7.465  -6.722  1.00  0.00              
ATOM     95  C   PHE    35      -4.008  -6.585  -5.558  1.00  0.00              
ATOM     96  O   PHE    35      -4.064  -7.038  -4.418  1.00  0.00              
ATOM     97  N   LYS    36      -4.373  -5.335  -5.859  1.00  0.00              
ATOM     98  CA  LYS    36      -5.040  -4.428  -4.881  1.00  0.00              
ATOM     99  C   LYS    36      -6.358  -5.017  -4.405  1.00  0.00              
ATOM    100  O   LYS    36      -6.673  -4.921  -3.237  1.00  0.00              
ATOM    101  N   GLU    37      -7.061  -5.682  -5.323  1.00  0.00              
ATOM    102  CA  GLU    37      -8.239  -6.516  -5.050  1.00  0.00              
ATOM    103  C   GLU    37      -7.883  -7.662  -4.129  1.00  0.00              
ATOM    104  O   GLU    37      -8.429  -7.776  -3.033  1.00  0.00              
ATOM    105  N   ILE    38      -6.983  -8.535  -4.594  1.00  0.00              
ATOM    106  CA  ILE    38      -6.681  -9.782  -3.873  1.00  0.00              
ATOM    107  C   ILE    38      -6.245  -9.520  -2.434  1.00  0.00              
ATOM    108  O   ILE    38      -6.629 -10.267  -1.541  1.00  0.00              
ATOM    109  N   LEU    39      -5.450  -8.471  -2.212  1.00  0.00              
ATOM    110  CA  LEU    39      -5.086  -8.035  -0.854  1.00  0.00              
ATOM    111  C   LEU    39      -6.332  -7.751   0.012  1.00  0.00              
ATOM    112  O   LEU    39      -6.433  -8.254   1.131  1.00  0.00              
ATOM    113  N   SER    40      -7.290  -7.028  -0.535  1.00  0.00              
ATOM    114  CA  SER    40      -8.548  -6.776   0.174  1.00  0.00              
ATOM    115  C   SER    40      -9.310  -8.076   0.507  1.00  0.00              
ATOM    116  O   SER    40      -9.893  -8.202   1.610  1.00  0.00              
ATOM    117  N   GLU    41      -9.300  -9.035  -0.430  1.00  0.00              
ATOM    118  CA  GLU    41     -10.099 -10.268  -0.325  1.00  0.00              
ATOM    119  C   GLU    41      -9.483 -11.223   0.671  1.00  0.00              
ATOM    120  O   GLU    41     -10.196 -12.061   1.272  1.00  0.00              
ATOM    121  N   PHE    42      -8.155 -11.122   0.827  1.00  0.00              
ATOM    122  CA  PHE    42      -7.369 -12.076   1.612  1.00  0.00              
ATOM    123  C   PHE    42      -7.038 -11.475   2.992  1.00  0.00              
ATOM    124  O   PHE    42      -6.050 -11.846   3.659  1.00  0.00              
ATOM    125  N   ASN    43      -7.866 -10.529   3.386  1.00  0.00              
ATOM    126  CA  ASN    43      -7.757  -9.812   4.654  1.00  0.00              
ATOM    127  C   ASN    43      -7.711 -10.710   5.893  1.00  0.00              
ATOM    128  O   ASN    43      -7.154 -10.298   6.914  1.00  0.00              
ATOM    129  N   GLY    44      -8.335 -11.895   5.838  1.00  0.00              
ATOM    130  CA  GLY    44      -8.281 -12.804   6.981  1.00  0.00              
ATOM    131  C   GLY    44      -7.611 -14.085   6.660  1.00  0.00              
ATOM    132  O   GLY    44      -7.791 -15.103   7.385  1.00  0.00              
ATOM    133  N   LYS    45      -6.845 -14.055   5.562  1.00  0.00              
ATOM    134  CA  LYS    45      -5.995 -15.174   5.193  1.00  0.00              
ATOM    135  C   LYS    45      -4.544 -14.748   5.346  1.00  0.00              
ATOM    136  O   LYS    45      -4.166 -13.688   4.900  1.00  0.00              
ATOM    137  N   ASN    46      -3.738 -15.552   6.025  1.00  0.00              
ATOM    138  CA  ASN    46      -2.303 -15.263   6.077  1.00  0.00              
ATOM    139  C   ASN    46      -1.584 -15.868   4.901  1.00  0.00              
ATOM    140  O   ASN    46      -1.939 -16.957   4.463  1.00  0.00              
ATOM    141  N   VAL    47      -0.589 -15.137   4.383  1.00  0.00              
ATOM    142  CA  VAL    47       0.152 -15.555   3.211  1.00  0.00              
ATOM    143  C   VAL    47       1.570 -16.000   3.534  1.00  0.00              
ATOM    144  O   VAL    47       2.343 -15.194   4.088  1.00  0.00              
ATOM    145  N   SER    48       1.899 -17.251   3.168  1.00  0.00              
ATOM    146  CA  SER    48       3.257 -17.739   3.109  1.00  0.00              
ATOM    147  C   SER    48       3.696 -17.620   1.656  1.00  0.00              
ATOM    148  O   SER    48       3.002 -18.047   0.751  1.00  0.00              
ATOM    149  N   ILE    49       4.847 -17.044   1.418  1.00  0.00              
ATOM    150  CA  ILE    49       5.229 -16.754   0.067  1.00  0.00              
ATOM    151  C   ILE    49       6.674 -17.172  -0.190  1.00  0.00              
ATOM    152  O   ILE    49       7.542 -16.982   0.643  1.00  0.00              
ATOM    153  N   THR    50       6.903 -17.777  -1.323  1.00  0.00              
ATOM    154  CA  THR    50       8.225 -18.195  -1.762  1.00  0.00              
ATOM    155  C   THR    50       8.445 -17.839  -3.210  1.00  0.00              
ATOM    156  O   THR    50       7.530 -17.971  -4.043  1.00  0.00              
ATOM    157  N   VAL    51       9.668 -17.472  -3.558  1.00  0.00              
ATOM    158  CA  VAL    51       9.953 -17.231  -4.976  1.00  0.00              
ATOM    159  C   VAL    51      11.382 -17.664  -5.287  1.00  0.00              
ATOM    160  O   VAL    51      12.294 -17.395  -4.495  1.00  0.00              
ATOM    161  N   LYS    52      11.570 -18.398  -6.378  1.00  0.00              
ATOM    162  CA  LYS    52      12.915 -18.755  -6.852  1.00  0.00              
ATOM    163  C   LYS    52      12.825 -19.389  -8.203  1.00  0.00              
ATOM    164  O   LYS    52      11.752 -19.846  -8.578  1.00  0.00              
ATOM    165  N   GLU    53      13.927 -19.405  -8.936  1.00  0.00              
ATOM    166  CA  GLU    53      14.064 -20.282 -10.102  1.00  0.00              
ATOM    167  C   GLU    53      13.704 -21.718  -9.732  1.00  0.00              
ATOM    168  O   GLU    53      14.014 -22.213  -8.645  1.00  0.00              
ATOM    169  N   LEU    57      13.084 -22.422 -10.644  1.00  0.00              
ATOM    170  CA  LEU    57      12.756 -23.785 -10.433  1.00  0.00              
ATOM    171  C   LEU    57      13.986 -24.632 -10.595  1.00  0.00              
ATOM    172  O   LEU    57      14.235 -25.194 -11.681  1.00  0.00              
ATOM    173  N   PRO    58      16.678 -27.594  -8.615  1.00  0.00              
ATOM    174  CA  PRO    58      16.750 -28.636  -7.545  1.00  0.00              
ATOM    175  C   PRO    58      17.589 -28.217  -6.350  1.00  0.00              
ATOM    176  O   PRO    58      17.529 -28.841  -5.274  1.00  0.00              
ATOM    177  N   VAL    59      18.361 -27.139  -6.492  1.00  0.00              
ATOM    178  CA  VAL    59      19.147 -26.663  -5.335  1.00  0.00              
ATOM    179  C   VAL    59      18.184 -26.087  -4.266  1.00  0.00              
ATOM    180  O   VAL    59      18.494 -26.124  -3.082  1.00  0.00              
ATOM    181  N   LYS    60      17.020 -25.612  -4.717  1.00  0.00              
ATOM    182  CA  LYS    60      16.074 -24.857  -3.896  1.00  0.00              
ATOM    183  C   LYS    60      15.135 -25.717  -3.038  1.00  0.00              
ATOM    184  O   LYS    60      14.395 -25.168  -2.183  1.00  0.00              
ATOM    185  N   GLY    61      15.151 -27.048  -3.206  1.00  0.00              
ATOM    186  CA  GLY    61      14.368 -27.904  -2.314  1.00  0.00              
ATOM    187  C   GLY    61      12.862 -27.654  -2.339  1.00  0.00              
ATOM    188  O   GLY    61      12.171 -27.790  -1.312  1.00  0.00              
ATOM    189  N   VAL    62      12.319 -27.294  -3.494  1.00  0.00              
ATOM    190  CA  VAL    62      10.887 -27.082  -3.604  1.00  0.00              
ATOM    191  C   VAL    62       9.986 -28.308  -3.262  1.00  0.00              
ATOM    192  O   VAL    62       9.009 -28.171  -2.533  1.00  0.00              
ATOM    193  N   GLU    63      10.287 -29.508  -3.722  1.00  0.00              
ATOM    194  CA  GLU    63       9.495 -30.681  -3.264  1.00  0.00              
ATOM    195  C   GLU    63       9.534 -30.841  -1.744  1.00  0.00              
ATOM    196  O   GLU    63       8.488 -31.068  -1.162  1.00  0.00              
END
