
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0335AL243_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL243_3-D1.T0335_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    -       -      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    A       5      A       8          1.646
LGA    K       6      R       9          0.612
LGA    I       7      I      10          1.033
LGA    A       8      N      11          1.439
LGA    R       9      E      12          0.881
LGA    I      10      L      13          0.593
LGA    N      11      A      14          0.930
LGA    E      12      A      15          0.988
LGA    L      13      K      16          1.148
LGA    A      14      A      17          0.685
LGA    A      15      K      18          1.140
LGA    K      16      A      19          1.891
LGA    A      17      G      20          1.474
LGA    K      18      V      21          2.208
LGA    A      19      I      22          2.340
LGA    G      20      T      23          3.664
LGA    V      21      E      24          4.136
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    -       -      K      27           -
LGA    T      23      A      28          2.359
LGA    E      24      E      29          1.508
LGA    E      25      Q      30           -
LGA    E      26      Q      31           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      -       -           -
LGA    Q      31      K      32          3.662
LGA    K      32      -       -           -
LGA    L      33      L      33          3.898
LGA    R      34      R      34          2.359
LGA    Q      35      Q      35          0.455
LGA    -       -      E      36           -
LGA    E      36      Y      37          3.068
LGA    Y      37      L      38           #
LGA    L      38      K      39           -
LGA    K      39      G      40           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   36    5.0     24    2.15    29.17     54.720     1.069

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.518331 * X  +  -0.838978 * Y  +  -0.165679 * Z  +  69.898422
  Y_new =  -0.855158 * X  +   0.507095 * Y  +   0.107516 * Z  +  58.248402
  Z_new =  -0.006189 * X  +   0.197411 * Y  +  -0.980301 * Z  +  -2.644471 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.942873   -0.198720  [ DEG:   168.6142    -11.3858 ]
  Theta =   0.006189    3.135404  [ DEG:     0.3546    179.6454 ]
  Phi   =  -2.115706    1.025887  [ DEG:  -121.2210     58.7790 ]
 
# 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: T0335AL243_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL243_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   36   5.0   24   2.15   29.17  54.720
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL243_3-D1
REMARK Aligment from pdb entry: 1fy7A
ATOM      5  N   ALA     5      -2.362  -5.355  -5.783  1.00  0.00              
ATOM      6  CA  ALA     5      -3.663  -5.677  -5.214  1.00  0.00              
ATOM      7  C   ALA     5      -3.524  -5.864  -3.704  1.00  0.00              
ATOM      8  O   ALA     5      -4.361  -5.390  -2.930  1.00  0.00              
ATOM      9  N   LYS     6      -2.467  -6.560  -3.292  1.00  0.00              
ATOM     10  CA  LYS     6      -2.205  -6.791  -1.871  1.00  0.00              
ATOM     11  C   LYS     6      -2.063  -5.444  -1.157  1.00  0.00              
ATOM     12  O   LYS     6      -2.648  -5.219  -0.092  1.00  0.00              
ATOM     13  N   ILE     7      -1.275  -4.552  -1.744  1.00  0.00              
ATOM     14  CA  ILE     7      -1.070  -3.242  -1.157  1.00  0.00              
ATOM     15  C   ILE     7      -2.375  -2.452  -1.090  1.00  0.00              
ATOM     16  O   ILE     7      -2.715  -1.894  -0.057  1.00  0.00              
ATOM     17  N   ALA     8      -3.101  -2.403  -2.199  1.00  0.00              
ATOM     18  CA  ALA     8      -4.367  -1.677  -2.234  1.00  0.00              
ATOM     19  C   ALA     8      -5.310  -2.189  -1.137  1.00  0.00              
ATOM     20  O   ALA     8      -5.972  -1.402  -0.460  1.00  0.00              
ATOM     21  N   ARG     9      -5.339  -3.505  -0.944  1.00  0.00              
ATOM     22  CA  ARG     9      -6.189  -4.093   0.082  1.00  0.00              
ATOM     23  C   ARG     9      -5.762  -3.632   1.479  1.00  0.00              
ATOM     24  O   ARG     9      -6.598  -3.309   2.315  1.00  0.00              
ATOM     25  N   ILE    10      -4.458  -3.596   1.741  1.00  0.00              
ATOM     26  CA  ILE    10      -3.989  -3.176   3.058  1.00  0.00              
ATOM     27  C   ILE    10      -4.466  -1.761   3.366  1.00  0.00              
ATOM     28  O   ILE    10      -4.764  -1.451   4.515  1.00  0.00              
ATOM     29  N   ASN    11      -4.531  -0.899   2.354  1.00  0.00              
ATOM     30  CA  ASN    11      -5.002   0.455   2.597  1.00  0.00              
ATOM     31  C   ASN    11      -6.522   0.500   2.811  1.00  0.00              
ATOM     32  O   ASN    11      -7.018   1.365   3.514  1.00  0.00              
ATOM     33  N   GLU    12      -7.255  -0.434   2.215  1.00  0.00              
ATOM     34  CA  GLU    12      -8.705  -0.478   2.416  1.00  0.00              
ATOM     35  C   GLU    12      -9.008  -0.843   3.872  1.00  0.00              
ATOM     36  O   GLU    12     -10.003  -0.397   4.445  1.00  0.00              
ATOM     37  N   LEU    13      -8.143  -1.648   4.483  1.00  0.00              
ATOM     38  CA  LEU    13      -8.330  -2.013   5.887  1.00  0.00              
ATOM     39  C   LEU    13      -8.097  -0.753   6.723  1.00  0.00              
ATOM     40  O   LEU    13      -8.882  -0.420   7.614  1.00  0.00              
ATOM     41  N   ALA    14      -7.012  -0.044   6.418  1.00  0.00              
ATOM     42  CA  ALA    14      -6.687   1.184   7.132  1.00  0.00              
ATOM     43  C   ALA    14      -7.844   2.194   7.017  1.00  0.00              
ATOM     44  O   ALA    14      -8.221   2.855   7.992  1.00  0.00              
ATOM     45  N   ALA    15      -8.392   2.317   5.812  1.00  0.00              
ATOM     46  CA  ALA    15      -9.491   3.244   5.580  1.00  0.00              
ATOM     47  C   ALA    15     -10.686   2.846   6.445  1.00  0.00              
ATOM     48  O   ALA    15     -11.293   3.683   7.123  1.00  0.00              
ATOM     49  N   LYS    16     -11.016   1.560   6.433  1.00  0.00              
ATOM     50  CA  LYS    16     -12.137   1.084   7.236  1.00  0.00              
ATOM     51  C   LYS    16     -11.866   1.371   8.716  1.00  0.00              
ATOM     52  O   LYS    16     -12.797   1.617   9.481  1.00  0.00              
ATOM     53  N   ALA    17     -10.591   1.362   9.112  1.00  0.00              
ATOM     54  CA  ALA    17     -10.212   1.625  10.506  1.00  0.00              
ATOM     55  C   ALA    17     -10.139   3.108  10.851  1.00  0.00              
ATOM     56  O   ALA    17      -9.905   3.459  12.005  1.00  0.00              
ATOM     57  N   LYS    18     -10.299   3.974   9.855  1.00  0.00              
ATOM     58  CA  LYS    18     -10.239   5.416  10.086  1.00  0.00              
ATOM     59  C   LYS    18      -8.862   5.849  10.560  1.00  0.00              
ATOM     60  O   LYS    18      -8.739   6.721  11.420  1.00  0.00              
ATOM     61  N   ALA    19      -7.828   5.245   9.979  1.00  0.00              
ATOM     62  CA  ALA    19      -6.452   5.586  10.331  1.00  0.00              
ATOM     63  C   ALA    19      -5.561   5.601   9.097  1.00  0.00              
ATOM     64  O   ALA    19      -5.826   4.907   8.113  1.00  0.00              
ATOM     65  N   GLY    20      -4.515   6.413   9.143  1.00  0.00              
ATOM     66  CA  GLY    20      -3.560   6.437   8.050  1.00  0.00              
ATOM     67  C   GLY    20      -2.600   5.311   8.412  1.00  0.00              
ATOM     68  O   GLY    20      -2.566   4.865   9.562  1.00  0.00              
ATOM     69  N   VAL    21      -1.848   4.829   7.433  1.00  0.00              
ATOM     70  CA  VAL    21      -0.909   3.759   7.692  1.00  0.00              
ATOM     71  C   VAL    21       0.179   3.735   6.642  1.00  0.00              
ATOM     72  O   VAL    21       0.037   4.348   5.578  1.00  0.00              
ATOM     73  N   THR    23       1.275   3.046   6.954  1.00  0.00              
ATOM     74  CA  THR    23       2.410   2.929   6.031  1.00  0.00              
ATOM     75  C   THR    23       3.089   1.585   6.307  1.00  0.00              
ATOM     76  O   THR    23       3.039   1.077   7.418  1.00  0.00              
ATOM     77  N   GLU    24       3.704   0.979   5.286  1.00  0.00              
ATOM     78  CA  GLU    24       4.379  -0.310   5.466  1.00  0.00              
ATOM     79  C   GLU    24       5.559  -0.211   6.426  1.00  0.00              
ATOM     80  O   GLU    24       6.184   0.844   6.556  1.00  0.00              
ATOM     81  N   GLU    25       5.865  -1.316   7.095  1.00  0.00              
ATOM     82  CA  GLU    25       6.968  -1.347   8.045  1.00  0.00              
ATOM     83  C   GLU    25       8.288  -1.040   7.341  1.00  0.00              
ATOM     84  O   GLU    25       8.506  -1.486   6.213  1.00  0.00              
ATOM     85  N   GLU    26       9.153  -0.278   8.011  1.00  0.00              
ATOM     86  CA  GLU    26      10.468   0.065   7.468  1.00  0.00              
ATOM     87  C   GLU    26      11.496  -0.762   8.244  1.00  0.00              
ATOM     88  O   GLU    26      11.296  -1.050   9.433  1.00  0.00              
ATOM     89  N   LYS    27      12.064  -1.355   4.010  1.00  0.00              
ATOM     90  CA  LYS    27      11.460  -2.201   2.988  1.00  0.00              
ATOM     91  C   LYS    27      12.552  -2.693   2.053  1.00  0.00              
ATOM     92  O   LYS    27      13.569  -2.026   1.879  1.00  0.00              
ATOM     93  N   ALA    28      12.353  -3.865   1.462  1.00  0.00              
ATOM     94  CA  ALA    28      13.316  -4.385   0.503  1.00  0.00              
ATOM     95  C   ALA    28      13.173  -3.457  -0.709  1.00  0.00              
ATOM     96  O   ALA    28      12.176  -2.730  -0.822  1.00  0.00              
ATOM     97  N   GLU    29      14.137  -3.484  -1.624  1.00  0.00              
ATOM     98  CA  GLU    29      14.056  -2.634  -2.809  1.00  0.00              
ATOM     99  C   GLU    29      12.799  -2.999  -3.606  1.00  0.00              
ATOM    100  O   GLU    29      12.067  -2.123  -4.092  1.00  0.00              
ATOM    101  N   GLN    30      12.568  -4.300  -3.760  1.00  0.00              
ATOM    102  CA  GLN    30      11.386  -4.780  -4.483  1.00  0.00              
ATOM    103  C   GLN    30      10.125  -4.187  -3.845  1.00  0.00              
ATOM    104  O   GLN    30       9.250  -3.652  -4.530  1.00  0.00              
ATOM    105  N   GLN    31       9.812  -1.492  -1.735  1.00  0.00              
ATOM    106  CA  GLN    31       9.718  -0.040  -1.841  1.00  0.00              
ATOM    107  C   GLN    31       9.337   0.408  -3.248  1.00  0.00              
ATOM    108  O   GLN    31       8.532   1.328  -3.421  1.00  0.00              
ATOM    109  N   LYS    32       9.898  -0.241  -4.263  1.00  0.00              
ATOM    110  CA  LYS    32       9.560   0.139  -5.631  1.00  0.00              
ATOM    111  C   LYS    32       8.089  -0.156  -5.943  1.00  0.00              
ATOM    112  O   LYS    32       7.454   0.587  -6.690  1.00  0.00              
ATOM    113  N   LEU    33       7.552  -1.231  -5.370  1.00  0.00              
ATOM    114  CA  LEU    33       6.149  -1.567  -5.587  1.00  0.00              
ATOM    115  C   LEU    33       5.238  -0.537  -4.913  1.00  0.00              
ATOM    116  O   LEU    33       4.207  -0.150  -5.468  1.00  0.00              
ATOM    117  N   ARG    34       5.610  -0.098  -3.715  1.00  0.00              
ATOM    118  CA  ARG    34       4.815   0.910  -3.016  1.00  0.00              
ATOM    119  C   ARG    34       4.858   2.258  -3.741  1.00  0.00              
ATOM    120  O   ARG    34       3.852   2.969  -3.829  1.00  0.00              
ATOM    121  N   GLN    35       6.029   2.621  -4.252  1.00  0.00              
ATOM    122  CA  GLN    35       6.161   3.878  -4.971  1.00  0.00              
ATOM    123  C   GLN    35       5.252   3.892  -6.196  1.00  0.00              
ATOM    124  O   GLN    35       4.630   4.917  -6.508  1.00  0.00              
ATOM    125  N   GLU    36       5.163   2.756  -6.886  1.00  0.00              
ATOM    126  CA  GLU    36       4.314   2.667  -8.071  1.00  0.00              
ATOM    127  C   GLU    36       2.858   2.770  -7.630  1.00  0.00              
ATOM    128  O   GLU    36       2.055   3.460  -8.257  1.00  0.00              
ATOM    129  N   TYR    37       2.517   2.073  -6.553  1.00  0.00              
ATOM    130  CA  TYR    37       1.147   2.112  -6.050  1.00  0.00              
ATOM    131  C   TYR    37       0.772   3.534  -5.637  1.00  0.00              
ATOM    132  O   TYR    37      -0.291   4.043  -6.019  1.00  0.00              
ATOM    133  N   LEU    38      -3.629  17.747   0.896  1.00  0.00              
ATOM    134  CA  LEU    38      -3.006  16.604   1.536  1.00  0.00              
ATOM    135  C   LEU    38      -4.022  15.899   2.431  1.00  0.00              
ATOM    136  O   LEU    38      -4.136  14.672   2.405  1.00  0.00              
ATOM    137  N   LYS    39      -4.762  16.675   3.223  1.00  0.00              
ATOM    138  CA  LYS    39      -5.781  16.119   4.109  1.00  0.00              
ATOM    139  C   LYS    39      -6.776  15.274   3.336  1.00  0.00              
ATOM    140  O   LYS    39      -7.093  14.151   3.732  1.00  0.00              
ATOM    141  N   GLY    40      -7.283  15.826   2.240  1.00  0.00              
ATOM    142  CA  GLY    40      -8.252  15.118   1.414  1.00  0.00              
ATOM    143  C   GLY    40      -7.667  13.813   0.896  1.00  0.00              
ATOM    144  O   GLY    40      -8.346  12.781   0.876  1.00  0.00              
END
