
#######################################################
#                                                     #
#                        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   15 (  125),  selected   15 , name T0335TS389_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS389_4-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    A      19      K      18          2.192
LGA    -       -      A      19           -
LGA    G      20      G      20          3.866
LGA    V      21      V      21          2.825
LGA    I      22      I      22          2.242
LGA    T      23      T      23          1.214
LGA    E      24      E      24          1.525
LGA    E      25      E      25          1.130
LGA    E      26      E      26          0.555
LGA    K      27      K      27          0.675
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    Q      30      Q      30          0.613
LGA    Q      31      Q      31          1.292
LGA    K      32      K      32          1.176
LGA    L      33      L      33          0.812
LGA    R      34      R      34          0.611
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    Y      37      Y      37          0.701
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   36    5.0     15    1.70    93.33     39.693     0.832

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.923744 * X  +   0.282508 * Y  +  -0.258624 * Z  +   2.050451
  Y_new =  -0.261963 * X  +   0.026588 * Y  +   0.964712 * Z  +  -6.161444
  Z_new =   0.279415 * X  +   0.958896 * Y  +   0.049446 * Z  +  -4.252417 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.519277   -1.622316  [ DEG:    87.0481    -92.9519 ]
  Theta =  -0.283185   -2.858407  [ DEG:   -16.2253   -163.7747 ]
  Phi   =  -2.865260    0.276333  [ DEG:  -164.1673     15.8327 ]
 
# 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: T0335TS389_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS389_4-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   36   5.0   15   1.70   93.33  39.693
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS389_4-D1
PFRMAT TS
TARGET T0335
MODEL  4
PARENT N/A
ATOM      2  N   ALA    19      -8.280   4.037   5.030  1.00  0.00
ATOM      3  CA  ALA    19      -7.473   5.109   5.536  1.00  0.00
ATOM      4  CB  ALA    19      -7.684   6.367   4.707  1.00  0.00
ATOM      5  O   ALA    19      -7.242   6.140   7.716  1.00  0.00
ATOM      6  C   ALA    19      -7.874   5.384   6.979  1.00  0.00
ATOM      7  N   GLY    20      -8.964   4.752   7.384  1.00  0.00
ATOM      8  CA  GLY    20      -9.441   4.891   8.750  1.00  0.00
ATOM      9  O   GLY    20      -8.197   4.088  10.648  1.00  0.00
ATOM     10  C   GLY    20      -8.822   3.807   9.633  1.00  0.00
ATOM     11  N   VAL    21      -9.021   2.574   9.189  1.00  0.00
ATOM     12  CA  VAL    21      -8.542   1.372   9.813  1.00  0.00
ATOM     13  CB  VAL    21      -8.692   0.153   8.882  1.00  0.00
ATOM     14  CG1 VAL    21      -7.988  -1.057   9.475  1.00  0.00
ATOM     15  CG2 VAL    21     -10.160  -0.191   8.690  1.00  0.00
ATOM     16  O   VAL    21      -6.638   1.237  11.226  1.00  0.00
ATOM     17  C   VAL    21      -7.096   1.530  10.152  1.00  0.00
ATOM     18  N   ILE    22      -6.354   1.926   9.166  1.00  0.00
ATOM     19  CA  ILE    22      -4.935   1.929   9.332  1.00  0.00
ATOM     20  CB  ILE    22      -4.208   1.944   7.974  1.00  0.00
ATOM     21  CG1 ILE    22      -4.551   3.220   7.201  1.00  0.00
ATOM     22  CG2 ILE    22      -4.621   0.746   7.135  1.00  0.00
ATOM     23  CD1 ILE    22      -3.719   3.419   5.952  1.00  0.00
ATOM     24  O   ILE    22      -4.478   4.180  10.046  1.00  0.00
ATOM     25  C   ILE    22      -4.195   3.013  10.061  1.00  0.00
ATOM     26  N   THR    23      -3.120   2.585  10.662  1.00  0.00
ATOM     27  CA  THR    23      -2.235   3.522  11.288  1.00  0.00
ATOM     28  CB  THR    23      -1.190   2.810  12.171  1.00  0.00
ATOM     29  CG2 THR    23      -1.877   1.977  13.241  1.00  0.00
ATOM     30  OG1 THR    23      -0.382   1.949  11.358  1.00  0.00
ATOM     31  O   THR    23      -1.287   3.950   9.098  1.00  0.00
ATOM     32  C   THR    23      -1.473   4.346  10.235  1.00  0.00
ATOM     33  N   GLU    24      -1.003   5.510  10.612  1.00  0.00
ATOM     34  CA  GLU    24      -0.223   6.344   9.726  1.00  0.00
ATOM     35  CB  GLU    24       0.139   7.663  10.411  1.00  0.00
ATOM     36  CG  GLU    24      -1.038   8.604  10.603  1.00  0.00
ATOM     37  CD  GLU    24      -0.663   9.860  11.368  1.00  0.00
ATOM     38  OE1 GLU    24       0.503   9.959  11.808  1.00  0.00
ATOM     39  OE2 GLU    24      -1.532  10.741  11.527  1.00  0.00
ATOM     40  O   GLU    24       1.593   5.702   8.231  1.00  0.00
ATOM     41  C   GLU    24       1.082   5.616   9.334  1.00  0.00
ATOM     42  N   GLU    25       1.593   4.805  10.228  1.00  0.00
ATOM     43  CA  GLU    25       2.787   4.018   9.994  1.00  0.00
ATOM     44  CB  GLU    25       3.153   3.215  11.244  1.00  0.00
ATOM     45  CG  GLU    25       4.425   2.391  11.101  1.00  0.00
ATOM     46  CD  GLU    25       4.774   1.638  12.370  1.00  0.00
ATOM     47  OE1 GLU    25       4.030   1.770  13.365  1.00  0.00
ATOM     48  OE2 GLU    25       5.792   0.914  12.369  1.00  0.00
ATOM     49  O   GLU    25       3.428   2.950   7.925  1.00  0.00
ATOM     50  C   GLU    25       2.594   3.028   8.844  1.00  0.00
ATOM     51  N   GLU    26       1.513   2.238   8.951  1.00  0.00
ATOM     52  CA  GLU    26       1.123   1.276   7.936  1.00  0.00
ATOM     53  CB  GLU    26      -0.192   0.595   8.319  1.00  0.00
ATOM     54  CG  GLU    26      -0.655  -0.463   7.332  1.00  0.00
ATOM     55  CD  GLU    26      -1.941  -1.138   7.761  1.00  0.00
ATOM     56  OE1 GLU    26      -2.465  -0.788   8.840  1.00  0.00
ATOM     57  OE2 GLU    26      -2.426  -2.020   7.019  1.00  0.00
ATOM     58  O   GLU    26       1.411   1.516   5.572  1.00  0.00
ATOM     59  C   GLU    26       0.936   1.990   6.587  1.00  0.00
ATOM     60  N   LYS    27       0.206   3.121   6.573  1.00  0.00
ATOM     61  CA  LYS    27      -0.036   3.893   5.359  1.00  0.00
ATOM     62  CB  LYS    27      -0.759   5.200   5.690  1.00  0.00
ATOM     63  CG  LYS    27      -1.112   6.040   4.473  1.00  0.00
ATOM     64  CD  LYS    27      -1.889   7.284   4.867  1.00  0.00
ATOM     65  CE  LYS    27      -2.232   8.131   3.651  1.00  0.00
ATOM     66  NZ  LYS    27      -2.996   9.354   4.024  1.00  0.00
ATOM     67  O   LYS    27       1.473   4.013   3.480  1.00  0.00
ATOM     68  C   LYS    27       1.294   4.231   4.674  1.00  0.00
ATOM     72  N   GLN    30       2.971   1.375   3.111  1.00  0.00
ATOM     73  CA  GLN    30       2.208   1.000   1.935  1.00  0.00
ATOM     74  CB  GLN    30       0.707   1.049   2.230  1.00  0.00
ATOM     75  CG  GLN    30       0.222  -0.050   3.161  1.00  0.00
ATOM     76  CD  GLN    30      -1.243   0.096   3.522  1.00  0.00
ATOM     77  OE1 GLN    30      -1.889   1.074   3.148  1.00  0.00
ATOM     78  NE2 GLN    30      -1.771  -0.880   4.251  1.00  0.00
ATOM     79  O   GLN    30       2.639   1.525  -0.355  1.00  0.00
ATOM     80  C   GLN    30       2.506   1.958   0.778  1.00  0.00
ATOM     81  N   GLN    31       2.640   3.248   1.033  1.00  0.00
ATOM     82  CA  GLN    31       2.960   4.241  -0.007  1.00  0.00
ATOM     83  CB  GLN    31       3.031   5.644   0.597  1.00  0.00
ATOM     84  CG  GLN    31       1.685   6.204   1.025  1.00  0.00
ATOM     85  CD  GLN    31       1.807   7.546   1.720  1.00  0.00
ATOM     86  OE1 GLN    31       2.912   8.030   1.969  1.00  0.00
ATOM     87  NE2 GLN    31       0.668   8.152   2.037  1.00  0.00
ATOM     88  O   GLN    31       4.542   3.913  -1.914  1.00  0.00
ATOM     89  C   GLN    31       4.343   3.921  -0.676  1.00  0.00
ATOM     90  N   LYS    32       5.303   3.581   0.186  1.00  0.00
ATOM     91  CA  LYS    32       6.642   3.211  -0.229  1.00  0.00
ATOM     92  CB  LYS    32       7.460   2.725   0.969  1.00  0.00
ATOM     93  CG  LYS    32       8.897   2.362   0.633  1.00  0.00
ATOM     94  CD  LYS    32       9.662   1.937   1.875  1.00  0.00
ATOM     95  CE  LYS    32      11.091   1.541   1.534  1.00  0.00
ATOM     96  NZ  LYS    32      11.862   1.146   2.745  1.00  0.00
ATOM     97  O   LYS    32       7.015   2.322  -2.378  1.00  0.00
ATOM     98  C   LYS    32       6.564   2.106  -1.248  1.00  0.00
ATOM     99  N   LEU    33       5.936   0.989  -0.855  1.00  0.00
ATOM    100  CA  LEU    33       5.697  -0.155  -1.735  1.00  0.00
ATOM    101  CB  LEU    33       4.773  -1.168  -1.057  1.00  0.00
ATOM    102  CG  LEU    33       5.372  -1.960   0.108  1.00  0.00
ATOM    103  CD1 LEU    33       4.301  -2.785   0.804  1.00  0.00
ATOM    104  CD2 LEU    33       6.456  -2.906  -0.388  1.00  0.00
ATOM    105  O   LEU    33       5.528  -0.056  -4.207  1.00  0.00
ATOM    106  C   LEU    33       5.021   0.249  -3.099  1.00  0.00
ATOM    107  N   ARG    34       3.877   0.978  -2.990  1.00  0.00
ATOM    108  CA  ARG    34       3.119   1.438  -4.109  1.00  0.00
ATOM    109  CB  ARG    34       1.975   2.341  -3.646  1.00  0.00
ATOM    110  CG  ARG    34       0.895   1.620  -2.857  1.00  0.00
ATOM    111  CD  ARG    34      -0.196   2.579  -2.407  1.00  0.00
ATOM    112  NE  ARG    34      -1.231   1.905  -1.628  1.00  0.00
ATOM    113  CZ  ARG    34      -2.260   2.524  -1.056  1.00  0.00
ATOM    114  NH1 ARG    34      -3.151   1.828  -0.366  1.00  0.00
ATOM    115  NH2 ARG    34      -2.392   3.838  -1.179  1.00  0.00
ATOM    116  O   ARG    34       4.244   1.896  -6.160  1.00  0.00
ATOM    117  C   ARG    34       4.102   2.198  -4.960  1.00  0.00
ATOM    121  N   TYR    37       6.117   0.015  -6.971  1.00  0.00
ATOM    122  CA  TYR    37       5.488  -0.581  -8.124  1.00  0.00
ATOM    123  CB  TYR    37       4.127  -1.170  -7.746  1.00  0.00
ATOM    124  CG  TYR    37       4.211  -2.350  -6.805  1.00  0.00
ATOM    125  CD1 TYR    37       4.045  -2.181  -5.436  1.00  0.00
ATOM    126  CD2 TYR    37       4.455  -3.630  -7.288  1.00  0.00
ATOM    127  CE1 TYR    37       4.118  -3.253  -4.567  1.00  0.00
ATOM    128  CE2 TYR    37       4.532  -4.714  -6.435  1.00  0.00
ATOM    129  CZ  TYR    37       4.361  -4.516  -5.063  1.00  0.00
ATOM    130  OH  TYR    37       4.436  -5.585  -4.201  1.00  0.00
ATOM    131  O   TYR    37       5.249   0.040 -10.441  1.00  0.00
ATOM    132  C   TYR    37       5.240   0.404  -9.264  1.00  0.00
TER
END
