
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0303AL242_4-D2
# Molecule2: number of CA atoms   77 (  602),  selected   77 , name T0303_D2.pdb
# PARAMETERS: T0303AL242_4-D2.T0303_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      18      S      18           -
LGA    -       -      L      19           -
LGA    -       -      P      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      A      23           -
LGA    -       -      L      24           -
LGA    -       -      S      25           -
LGA    -       -      I      26           -
LGA    -       -      N      27           -
LGA    -       -      S      28           -
LGA    L      19      A      29           #
LGA    P      20      L      30          4.699
LGA    D      21      K      31          3.486
LGA    E      72      D      32          4.194
LGA    D      73      V      33          0.877
LGA    E      74      N      34          4.359
LGA    F      75      L      35          1.312
LGA    K      76      P      36          1.967
LGA    Y      77      Q      37          1.823
LGA    F      78      A      38          2.799
LGA    -       -      S      39           -
LGA    -       -      E      40           -
LGA    -       -      N      41           -
LGA    K      79      L      42          3.756
LGA    R      80      V      43          2.724
LGA    -       -      M      44           -
LGA    -       -      T      45           -
LGA    Q      81      W      46          1.120
LGA    F      82      I      47          5.119
LGA    G      83      G      48          4.073
LGA    F      84      N      49          4.405
LGA    -       -      G      50           -
LGA    -       -      A      51           -
LGA    -       -      D      52           -
LGA    -       -      V      53           -
LGA    Y      85      L      54          1.642
LGA    Y      86      S      55          4.774
LGA    -       -      Q      56           -
LGA    -       -      R      57           -
LGA    G      87      A      58          1.210
LGA    E      88      V      59          3.860
LGA    -       -      D      60           -
LGA    -       -      W      61           -
LGA    N      89      A      62          0.934
LGA    L      90      C      63          2.187
LGA    C      91      T      64           #
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      E      67           -
LGA    -       -      K      68           -
LGA    -       -      E      69           -
LGA    -       -      L      70           -
LGA    -       -      T      71           -
LGA    -       -      E      72           -
LGA    -       -      D      73           -
LGA    -       -      E      74           -
LGA    N      92      F      75           #
LGA    I      93      K      76           -
LGA    -       -      Y      77           -
LGA    S      94      F      78           #
LGA    -       -      K      79           -
LGA    -       -      R      80           -
LGA    -       -      Q      81           -
LGA    -       -      F      82           -
LGA    -       -      G      83           -
LGA    -       -      F      84           -
LGA    -       -      Y      85           -
LGA    -       -      Y      86           -
LGA    -       -      G      87           -
LGA    -       -      E      88           -
LGA    -       -      N      89           -
LGA    -       -      L      90           -
LGA    -       -      C      91           -
LGA    -       -      N      92           -
LGA    -       -      I      93           -
LGA    -       -      S      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   77    5.0     21    3.24     4.76     17.207     0.628

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.356199 * X  +   0.885820 * Y  +  -0.297397 * Z  +  -5.249714
  Y_new =  -0.406278 * X  +   0.139793 * Y  +   0.902993 * Z  +  83.292747
  Z_new =   0.841464 * X  +   0.442471 * Y  +   0.310095 * Z  +  31.122690 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.959516   -2.182077  [ DEG:    54.9762   -125.0238 ]
  Theta =  -0.999986   -2.141606  [ DEG:   -57.2950   -122.7050 ]
  Phi   =  -2.290609    0.850984  [ DEG:  -131.2422     48.7578 ]
 
# 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: T0303AL242_4-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303AL242_4-D2.T0303_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   77   5.0   21   3.24    4.76  17.207
REMARK  ---------------------------------------------------------- 
MOLECULE T0303AL242_4-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     69  N   SER    18       2.291  92.571  33.112  1.00  0.00              
ATOM     70  CA  SER    18       2.894  93.840  32.721  1.00  0.00              
ATOM     71  C   SER    18       1.898  94.967  32.905  1.00  0.00              
ATOM     72  O   SER    18       0.719  94.717  33.161  1.00  0.00              
ATOM     73  N   LEU    19       2.381  96.203  32.788  1.00  0.00              
ATOM     74  CA  LEU    19       1.518  97.379  32.866  1.00  0.00              
ATOM     75  C   LEU    19       1.196  97.728  31.416  1.00  0.00              
ATOM     76  O   LEU    19       2.106  97.924  30.607  1.00  0.00              
ATOM     77  N   PRO    20      -0.088  97.800  31.085  1.00  0.00              
ATOM     78  CA  PRO    20      -0.489  98.110  29.720  1.00  0.00              
ATOM     79  C   PRO    20      -0.099  99.529  29.282  1.00  0.00              
ATOM     80  O   PRO    20      -0.001  99.805  28.088  1.00  0.00              
ATOM     81  N   ASP    21       0.144 100.423  30.241  1.00  0.00              
ATOM     82  CA  ASP    21       0.518 101.797  29.905  1.00  0.00              
ATOM     83  C   ASP    21       2.034 102.003  29.893  1.00  0.00              
ATOM     84  O   ASP    21       2.507 103.126  29.718  1.00  0.00              
ATOM     85  N   GLU    72       2.790 100.922  30.052  1.00  0.00              
ATOM     86  CA  GLU    72       4.241 101.028  30.103  1.00  0.00              
ATOM     87  C   GLU    72       5.058 100.045  29.267  1.00  0.00              
ATOM     88  O   GLU    72       5.910 100.453  28.477  1.00  0.00              
ATOM     89  N   ASP    73       4.807  98.754  29.450  1.00  0.00              
ATOM     90  CA  ASP    73       5.576  97.720  28.769  1.00  0.00              
ATOM     91  C   ASP    73       5.220  97.380  27.330  1.00  0.00              
ATOM     92  O   ASP    73       5.966  96.671  26.659  1.00  0.00              
ATOM     93  N   GLU    74       4.087  97.873  26.854  1.00  0.00              
ATOM     94  CA  GLU    74       3.659  97.583  25.497  1.00  0.00              
ATOM     95  C   GLU    74       3.352  98.847  24.716  1.00  0.00              
ATOM     96  O   GLU    74       3.272  99.935  25.280  1.00  0.00              
ATOM     97  N   PHE    75       3.174  98.698  23.410  1.00  0.00              
ATOM     98  CA  PHE    75       2.884  99.834  22.548  1.00  0.00              
ATOM     99  C   PHE    75       1.653  99.520  21.691  1.00  0.00              
ATOM    100  O   PHE    75       1.758  98.876  20.646  1.00  0.00              
ATOM    101  N   LYS    76       0.465  99.953  22.152  1.00  0.00              
ATOM    102  CA  LYS    76      -0.831  99.756  21.489  1.00  0.00              
ATOM    103  C   LYS    76      -0.910 100.547  20.181  1.00  0.00              
ATOM    104  O   LYS    76      -0.159 101.494  19.984  1.00  0.00              
ATOM    105  N   TYR    77      -1.832 100.177  19.281  1.00  0.00              
ATOM    106  CA  TYR    77      -2.801  99.080  19.401  1.00  0.00              
ATOM    107  C   TYR    77      -2.166  97.703  19.236  1.00  0.00              
ATOM    108  O   TYR    77      -0.986  97.578  18.890  1.00  0.00              
ATOM    109  N   PHE    78      -2.968  96.670  19.472  1.00  0.00              
ATOM    110  CA  PHE    78      -2.511  95.295  19.349  1.00  0.00              
ATOM    111  C   PHE    78      -3.212  94.624  18.171  1.00  0.00              
ATOM    112  O   PHE    78      -4.130  95.189  17.585  1.00  0.00              
ATOM    113  N   LYS    79      -2.776  93.413  17.837  1.00  0.00              
ATOM    114  CA  LYS    79      -3.371  92.661  16.735  1.00  0.00              
ATOM    115  C   LYS    79      -2.934  91.202  16.800  1.00  0.00              
ATOM    116  O   LYS    79      -1.854  90.895  17.304  1.00  0.00              
ATOM    117  N   ARG    80      -3.773  90.307  16.290  1.00  0.00              
ATOM    118  CA  ARG    80      -3.430  88.891  16.271  1.00  0.00              
ATOM    119  C   ARG    80      -2.517  88.628  15.085  1.00  0.00              
ATOM    120  O   ARG    80      -2.784  89.075  13.972  1.00  0.00              
ATOM    121  N   GLN    81      -1.433  87.906  15.335  1.00  0.00              
ATOM    122  CA  GLN    81      -0.474  87.582  14.291  1.00  0.00              
ATOM    123  C   GLN    81      -0.952  86.345  13.534  1.00  0.00              
ATOM    124  O   GLN    81      -1.931  85.707  13.925  1.00  0.00              
ATOM    125  N   PHE    82      -0.262  86.010  12.449  1.00  0.00              
ATOM    126  CA  PHE    82      -0.628  84.852  11.642  1.00  0.00              
ATOM    127  C   PHE    82      -0.473  83.551  12.424  1.00  0.00              
ATOM    128  O   PHE    82      -1.153  82.566  12.138  1.00  0.00              
ATOM    129  N   GLY    83       0.422  83.551  13.408  1.00  0.00              
ATOM    130  CA  GLY    83       0.661  82.361  14.221  1.00  0.00              
ATOM    131  C   GLY    83      -0.278  82.277  15.423  1.00  0.00              
ATOM    132  O   GLY    83      -0.054  81.490  16.342  1.00  0.00              
ATOM    133  N   PHE    84      -1.325  83.097  15.414  1.00  0.00              
ATOM    134  CA  PHE    84      -2.296  83.083  16.500  1.00  0.00              
ATOM    135  C   PHE    84      -1.973  83.925  17.725  1.00  0.00              
ATOM    136  O   PHE    84      -2.827  84.115  18.588  1.00  0.00              
ATOM    137  N   TYR    85      -0.748  84.431  17.810  1.00  0.00              
ATOM    138  CA  TYR    85      -0.353  85.236  18.957  1.00  0.00              
ATOM    139  C   TYR    85      -0.909  86.659  18.903  1.00  0.00              
ATOM    140  O   TYR    85      -1.360  87.130  17.859  1.00  0.00              
ATOM    141  N   TYR    86      -0.893  87.334  20.046  1.00  0.00              
ATOM    142  CA  TYR    86      -1.333  88.719  20.119  1.00  0.00              
ATOM    143  C   TYR    86      -0.038  89.519  20.114  1.00  0.00              
ATOM    144  O   TYR    86       0.914  89.179  20.819  1.00  0.00              
ATOM    145  N   GLY    87       0.006  90.571  19.311  1.00  0.00              
ATOM    146  CA  GLY    87       1.217  91.373  19.222  1.00  0.00              
ATOM    147  C   GLY    87       0.929  92.861  19.320  1.00  0.00              
ATOM    148  O   GLY    87      -0.186  93.304  19.050  1.00  0.00              
ATOM    149  N   GLU    88       1.944  93.627  19.705  1.00  0.00              
ATOM    150  CA  GLU    88       1.810  95.072  19.803  1.00  0.00              
ATOM    151  C   GLU    88       2.670  95.670  18.689  1.00  0.00              
ATOM    152  O   GLU    88       3.344  94.936  17.963  1.00  0.00              
ATOM    153  N   ASN    89       2.644  96.991  18.554  1.00  0.00              
ATOM    154  CA  ASN    89       3.397  97.681  17.508  1.00  0.00              
ATOM    155  C   ASN    89       4.888  97.347  17.420  1.00  0.00              
ATOM    156  O   ASN    89       5.498  97.506  16.362  1.00  0.00              
ATOM    157  N   LEU    90       5.479  96.896  18.521  1.00  0.00              
ATOM    158  CA  LEU    90       6.902  96.571  18.523  1.00  0.00              
ATOM    159  C   LEU    90       7.182  95.080  18.384  1.00  0.00              
ATOM    160  O   LEU    90       8.271  94.609  18.721  1.00  0.00              
ATOM    161  N   CYS    91       6.194  94.346  17.882  1.00  0.00              
ATOM    162  CA  CYS    91       6.353  92.919  17.677  1.00  0.00              
ATOM    163  C   CYS    91       6.466  92.068  18.929  1.00  0.00              
ATOM    164  O   CYS    91       6.923  90.925  18.864  1.00  0.00              
ATOM    165  N   ASN    92       6.054  92.609  20.071  1.00  0.00              
ATOM    166  CA  ASN    92       6.118  91.855  21.318  1.00  0.00              
ATOM    167  C   ASN    92       5.012  90.813  21.403  1.00  0.00              
ATOM    168  O   ASN    92       3.878  91.053  20.999  1.00  0.00              
ATOM    169  N   ILE    93       5.355  89.653  21.940  1.00  0.00              
ATOM    170  CA  ILE    93       4.379  88.594  22.113  1.00  0.00              
ATOM    171  C   ILE    93       3.642  88.947  23.402  1.00  0.00              
ATOM    172  O   ILE    93       4.251  88.982  24.466  1.00  0.00              
ATOM    173  N   SER    94       2.345  89.222  23.306  1.00  0.00              
ATOM    174  CA  SER    94       1.559  89.582  24.484  1.00  0.00              
ATOM    175  C   SER    94       0.827  88.350  25.004  1.00  0.00              
ATOM    176  O   SER    94       0.067  87.730  24.270  1.00  0.00              
END
