
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0300AL242_5
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300AL242_5.T0300  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       7           -
LGA    -       -      K       8           -
LGA    -       -      T       9           -
LGA    -       -      Y      10           -
LGA    -       -      E      11           -
LGA    -       -      E      12           -
LGA    -       -      M      13           -
LGA    -       -      V      14           -
LGA    -       -      K      15           -
LGA    -       -      E      16           -
LGA    -       -      V      17           -
LGA    -       -      E      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      K      21           -
LGA    -       -      L      22           -
LGA    -       -      E      23           -
LGA    -       -      N      24           -
LGA    -       -      K      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      Q      29           -
LGA    -       -      K      30           -
LGA    -       -      V      31           -
LGA    -       -      S      39           -
LGA    -       -      D      40           -
LGA    -       -      D      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      L      44           -
LGA    E      12      T      45          1.162
LGA    M      13      A      46          1.284
LGA    V      14      A      47          0.672
LGA    K      15      K      48          0.542
LGA    E      16      R      49          0.300
LGA    V      17      E      50          0.362
LGA    E      18      S      51          0.354
LGA    R      19      I      52          0.241
LGA    L      20      I      53          0.103
LGA    K      21      V      54          0.371
LGA    L      22      S      55          0.108
LGA    E      23      S      56          0.774
LGA    N      24      S      57          1.064
LGA    K      25      R      58          0.786
LGA    T      26      A      59          0.954
LGA    L      27      L      60          1.615
LGA    K      28      G      61          1.489
LGA    Q      29      A      62          1.169
LGA    K      30      V      63          1.195
LGA    V      31      A      64          1.080
LGA    K      32      M      65          0.743
LGA    S      33      R      66          0.591
LGA    S      34      K      67          0.617
LGA    G      35      I      68          0.446
LGA    A      36      E      69          1.108
LGA    V      37      A      70          1.479
LGA    S      38      K      71          0.685
LGA    S      39      V      72          2.240
LGA    -       -      R      73           -
LGA    D      40      S      74          1.938
LGA    -       -      R      75           -
LGA    -       -      A      76           -
LGA    -       -      A      77           -
LGA    -       -      K      78           -
LGA    -       -      A      79           -
LGA    -       -      V      80           -
LGA    -       -      T      81           -
LGA    -       -      E      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      S      87           -
LGA    -       -      L      88           -
LGA    -       -      L      89           -
LGA    -       -      Q      90           -
LGA    -       -      S      91           -
LGA    -       -      L      92           -
LGA    -       -      T      93           -
LGA    -       -      L      94           -
LGA    -       -      R      95           -
LGA    -       -      V      96           -
LGA    -       -      D      97           -
LGA    -       -      V      98           -
LGA    -       -      S      99           -
LGA    -       -      M     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29   89    5.0     29    1.03     6.90     31.796     2.577

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.428486 * X  +   0.831191 * Y  +  -0.354290 * Z  +  12.182452
  Y_new =   0.675658 * X  +   0.034416 * Y  +  -0.736412 * Z  + -19.886976
  Z_new =  -0.599905 * X  +  -0.554920 * Y  +  -0.576348 * Z  +  30.710028 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.375133    0.766459  [ DEG:  -136.0851     43.9149 ]
  Theta =   0.643383    2.498210  [ DEG:    36.8631    143.1369 ]
  Phi   =   2.135967   -1.005626  [ DEG:   122.3819    -57.6181 ]
 
# 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: T0300AL242_5                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300AL242_5.T0300 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29   89   5.0   29   1.03    6.90  31.796
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL242_5
REMARK Aligment from pdb entry: 1p9i_A
ATOM      1  N   GLU    12      55.102 -13.506 -19.196  1.00  0.00              
ATOM      2  CA  GLU    12      53.787 -13.934 -18.713  1.00  0.00              
ATOM      3  C   GLU    12      53.806 -14.383 -17.272  1.00  0.00              
ATOM      4  O   GLU    12      52.764 -14.564 -16.630  1.00  0.00              
ATOM      5  N   MET    13      54.968 -14.620 -16.698  1.00  0.00              
ATOM      6  CA  MET    13      54.992 -15.008 -15.279  1.00  0.00              
ATOM      7  C   MET    13      54.508 -13.854 -14.409  1.00  0.00              
ATOM      8  O   MET    13      53.740 -14.081 -13.480  1.00  0.00              
ATOM      9  N   VAL    14      54.901 -12.604 -14.705  1.00  0.00              
ATOM     10  CA  VAL    14      54.399 -11.502 -13.892  1.00  0.00              
ATOM     11  C   VAL    14      52.901 -11.370 -14.048  1.00  0.00              
ATOM     12  O   VAL    14      52.229 -10.952 -13.102  1.00  0.00              
ATOM     13  N   LYS    15      52.338 -11.651 -15.206  1.00  0.00              
ATOM     14  CA  LYS    15      50.887 -11.572 -15.333  1.00  0.00              
ATOM     15  C   LYS    15      50.195 -12.625 -14.512  1.00  0.00              
ATOM     16  O   LYS    15      49.149 -12.357 -13.923  1.00  0.00              
ATOM     17  N   GLU    16      50.780 -13.831 -14.443  1.00  0.00              
ATOM     18  CA  GLU    16      50.190 -14.852 -13.558  1.00  0.00              
ATOM     19  C   GLU    16      50.284 -14.418 -12.100  1.00  0.00              
ATOM     20  O   GLU    16      49.315 -14.542 -11.341  1.00  0.00              
ATOM     21  N   VAL    17      51.436 -13.902 -11.676  1.00  0.00              
ATOM     22  CA  VAL    17      51.587 -13.399 -10.322  1.00  0.00              
ATOM     23  C   VAL    17      50.510 -12.331 -10.067  1.00  0.00              
ATOM     24  O   VAL    17      49.867 -12.330  -9.032  1.00  0.00              
ATOM     25  N   GLU    18      50.330 -11.384 -10.988  1.00  0.00              
ATOM     26  CA  GLU    18      49.391 -10.323 -10.804  1.00  0.00              
ATOM     27  C   GLU    18      47.975 -10.845 -10.659  1.00  0.00              
ATOM     28  O   GLU    18      47.172 -10.385  -9.838  1.00  0.00              
ATOM     29  N   ARG    19      47.615 -11.813 -11.456  1.00  0.00              
ATOM     30  CA  ARG    19      46.275 -12.361 -11.388  1.00  0.00              
ATOM     31  C   ARG    19      46.031 -13.082 -10.054  1.00  0.00              
ATOM     32  O   ARG    19      45.014 -12.915  -9.434  1.00  0.00              
ATOM     33  N   LEU    20      47.019 -13.873  -9.637  1.00  0.00              
ATOM     34  CA  LEU    20      46.936 -14.559  -8.367  1.00  0.00              
ATOM     35  C   LEU    20      46.844 -13.580  -7.208  1.00  0.00              
ATOM     36  O   LEU    20      46.086 -13.802  -6.241  1.00  0.00              
ATOM     37  N   LYS    21      47.616 -12.484  -7.288  1.00  0.00              
ATOM     38  CA  LYS    21      47.563 -11.475  -6.240  1.00  0.00              
ATOM     39  C   LYS    21      46.183 -10.823  -6.184  1.00  0.00              
ATOM     40  O   LYS    21      45.628 -10.574  -5.120  1.00  0.00              
ATOM     41  N   LEU    22      45.668 -10.513  -7.354  1.00  0.00              
ATOM     42  CA  LEU    22      44.352  -9.893  -7.367  1.00  0.00              
ATOM     43  C   LEU    22      43.310 -10.844  -6.776  1.00  0.00              
ATOM     44  O   LEU    22      42.444 -10.443  -6.021  1.00  0.00              
ATOM     45  N   GLU    23      43.343 -12.111  -7.178  1.00  0.00              
ATOM     46  CA  GLU    23      42.407 -13.110  -6.679  1.00  0.00              
ATOM     47  C   GLU    23      42.554 -13.258  -5.173  1.00  0.00              
ATOM     48  O   GLU    23      41.539 -13.301  -4.480  1.00  0.00              
ATOM     49  N   ASN    24      43.810 -13.313  -4.716  1.00  0.00              
ATOM     50  CA  ASN    24      44.007 -13.468  -3.273  1.00  0.00              
ATOM     51  C   ASN    24      43.414 -12.304  -2.512  1.00  0.00              
ATOM     52  O   ASN    24      42.828 -12.467  -1.440  1.00  0.00              
ATOM     53  N   LYS    25      43.611 -11.088  -3.027  1.00  0.00              
ATOM     54  CA  LYS    25      43.049  -9.926  -2.317  1.00  0.00              
ATOM     55  C   LYS    25      41.539 -10.011  -2.281  1.00  0.00              
ATOM     56  O   LYS    25      40.915  -9.732  -1.241  1.00  0.00              
ATOM     57  N   THR    26      40.934 -10.386  -3.400  1.00  0.00              
ATOM     58  CA  THR    26      39.483 -10.507  -3.465  1.00  0.00              
ATOM     59  C   THR    26      38.960 -11.557  -2.523  1.00  0.00              
ATOM     60  O   THR    26      37.953 -11.392  -1.802  1.00  0.00              
ATOM     61  N   LEU    27      39.647 -12.692  -2.497  1.00  0.00              
ATOM     62  CA  LEU    27      39.187 -13.780  -1.626  1.00  0.00              
ATOM     63  C   LEU    27      39.313 -13.381  -0.177  1.00  0.00              
ATOM     64  O   LEU    27      38.465 -13.723   0.634  1.00  0.00              
ATOM     65  N   LYS    28      40.387 -12.700   0.209  1.00  0.00              
ATOM     66  CA  LYS    28      40.538 -12.263   1.602  1.00  0.00              
ATOM     67  C   LYS    28      39.384 -11.330   1.962  1.00  0.00              
ATOM     68  O   LYS    28      38.869 -11.401   3.071  1.00  0.00              
ATOM     69  N   GLN    29      38.958 -10.470   1.033  1.00  0.00              
ATOM     70  CA  GLN    29      37.892  -9.547   1.363  1.00  0.00              
ATOM     71  C   GLN    29      36.570 -10.305   1.466  1.00  0.00              
ATOM     72  O   GLN    29      35.705  -9.995   2.303  1.00  0.00              
ATOM     73  N   LYS    30      36.416 -11.310   0.602  1.00  0.00              
ATOM     74  CA  LYS    30      35.200 -12.118   0.670  1.00  0.00              
ATOM     75  C   LYS    30      35.141 -12.901   1.984  1.00  0.00              
ATOM     76  O   LYS    30      34.069 -13.018   2.591  1.00  0.00              
ATOM     77  N   VAL    31      36.280 -13.413   2.409  1.00  0.00              
ATOM     78  CA  VAL    31      36.312 -14.055   3.730  1.00  0.00              
ATOM     79  C   VAL    31      35.894 -13.061   4.805  1.00  0.00              
ATOM     80  O   VAL    31      35.111 -13.421   5.680  1.00  0.00              
ATOM     81  N   LYS    32      36.361 -11.822   4.760  1.00  0.00              
ATOM     82  CA  LYS    32      36.036 -10.823   5.770  1.00  0.00              
ATOM     83  C   LYS    32      34.542 -10.562   5.766  1.00  0.00              
ATOM     84  O   LYS    32      33.902 -10.452   6.810  1.00  0.00              
ATOM     85  N   SER    33      33.965 -10.474   4.573  1.00  0.00              
ATOM     86  CA  SER    33      32.533 -10.244   4.435  1.00  0.00              
ATOM     87  C   SER    33      31.778 -11.400   5.048  1.00  0.00              
ATOM     88  O   SER    33      30.841 -11.241   5.839  1.00  0.00              
ATOM     89  N   SER    34      32.155 -12.632   4.674  1.00  0.00              
ATOM     90  CA  SER    34      31.391 -13.793   5.139  1.00  0.00              
ATOM     91  C   SER    34      31.561 -14.054   6.611  1.00  0.00              
ATOM     92  O   SER    34      30.625 -14.436   7.281  1.00  0.00              
ATOM     93  N   GLY    35      32.737 -13.798   7.163  1.00  0.00              
ATOM     94  CA  GLY    35      32.933 -13.812   8.610  1.00  0.00              
ATOM     95  C   GLY    35      31.967 -12.905   9.349  1.00  0.00              
ATOM     96  O   GLY    35      31.321 -13.246  10.329  1.00  0.00              
ATOM     97  N   ALA    36      31.917 -11.688   8.804  1.00  0.00              
ATOM     98  CA  ALA    36      30.999 -10.693   9.429  1.00  0.00              
ATOM     99  C   ALA    36      29.578 -11.151   9.313  1.00  0.00              
ATOM    100  O   ALA    36      28.731 -10.966  10.221  1.00  0.00              
ATOM    101  N   VAL    37      29.190 -11.805   8.220  1.00  0.00              
ATOM    102  CA  VAL    37      27.849 -12.303   8.072  1.00  0.00              
ATOM    103  C   VAL    37      27.578 -13.453   9.044  1.00  0.00              
ATOM    104  O   VAL    37      26.488 -13.549   9.600  1.00  0.00              
ATOM    105  N   SER    38      28.562 -14.318   9.273  1.00  0.00              
ATOM    106  CA  SER    38      28.414 -15.409  10.219  1.00  0.00              
ATOM    107  C   SER    38      28.152 -14.826  11.599  1.00  0.00              
ATOM    108  O   SER    38      27.379 -15.357  12.387  1.00  0.00              
ATOM    109  N   SER    39      28.787 -13.673  11.906  1.00  0.00              
ATOM    110  CA  SER    39      28.571 -13.062  13.219  1.00  0.00              
ATOM    111  C   SER    39      27.162 -12.533  13.365  1.00  0.00              
ATOM    112  O   SER    39      26.802 -12.190  14.513  1.00  0.00              
ATOM    113  N   ASP    40      26.362 -12.478  12.311  1.00  0.00              
ATOM    114  CA  ASP    40      24.934 -12.093  12.497  1.00  0.00              
ATOM    115  C   ASP    40      24.147 -13.285  12.966  1.00  0.00              
ATOM    116  O   ASP    40      24.578 -14.444  12.828  1.00  0.00              
END
