
#######################################################
#                                                     #
#                        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   13 (   63),  selected   13 , name T0322TS239_5_1-D1
# Molecule2: number of CA atoms  128 (  980),  selected  128 , name T0322_D1.pdb
# PARAMETERS: T0322TS239_5_1-D1.T0322_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    -       -      G      16           -
LGA    -       -      F      17           -
LGA    -       -      S      18           -
LGA    -       -      Q      19           -
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    -       -      W      22           -
LGA    -       -      S      23           -
LGA    -       -      R      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      G      27           -
LGA    -       -      R      28           -
LGA    -       -      Q      29           -
LGA    -       -      I      30           -
LGA    -       -      G      31           -
LGA    -       -      P      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      H      36           -
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      G      41           -
LGA    -       -      Q      42           -
LGA    -       -      A      43           -
LGA    -       -      R      44           -
LGA    -       -      L      45           -
LGA    -       -      A      46           -
LGA    -       -      F      47           -
LGA    -       -      R      48           -
LGA    -       -      V      49           -
LGA    G      16      E      50          2.872
LGA    -       -      E      51           -
LGA    -       -      H      52           -
LGA    -       -      H      53           -
LGA    -       -      T      54           -
LGA    -       -      N      55           -
LGA    -       -      G      56           -
LGA    -       -      L      57           -
LGA    -       -      G      58           -
LGA    -       -      N      59           -
LGA    -       -      C      60           -
LGA    -       -      H      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      M      64           -
LGA    -       -      L      65           -
LGA    -       -      M      66           -
LGA    -       -      S      67           -
LGA    -       -      F      68           -
LGA    -       -      A      69           -
LGA    -       -      D      70           -
LGA    -       -      M      71           -
LGA    -       -      A      72           -
LGA    -       -      W      73           -
LGA    -       -      G      74           -
LGA    -       -      R      75           -
LGA    -       -      I      76           -
LGA    -       -      I      77           -
LGA    -       -      S      78           -
LGA    -       -      L      79           -
LGA    -       -      Q      80           -
LGA    -       -      K      81           -
LGA    -       -      S      82           -
LGA    -       -      Y      83           -
LGA    -       -      S      84           -
LGA    -       -      W      85           -
LGA    -       -      V      86           -
LGA    -       -      T      87           -
LGA    -       -      V      88           -
LGA    -       -      R      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      C      92           -
LGA    -       -      D      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      G      97           -
LGA    F      17      A      98          5.196
LGA    S      18      K      99          1.515
LGA    Q      19      L     100           #
LGA    Q      29      -       -           -
LGA    I      30      G     101          1.952
LGA    G      31      D     102          2.078
LGA    P      32      W     103          0.822
LGA    L      33      V     104          1.715
LGA    F      34      E     105          0.692
LGA    E      35      G     106          0.824
LGA    H      36      E     107          1.172
LGA    R      37      G     108          1.202
LGA    -       -      E     109           -
LGA    -       -      L     110           -
LGA    -       -      I     111           -
LGA    -       -      S     112           -
LGA    -       -      E     113           -
LGA    -       -      E     114           -
LGA    -       -      D     115           -
LGA    -       -      M     116           -
LGA    -       -      L     117           -
LGA    -       -      F     118           -
LGA    -       -      T     119           -
LGA    -       -      V     120           -
LGA    -       -      R     121           -
LGA    -       -      G     122           -
LGA    -       -      R     123           -
LGA    -       -      I     124           -
LGA    -       -      W     125           -
LGA    -       -      A     126           -
LGA    -       -      G     127           -
LGA    -       -      E     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      L     131           -
LGA    -       -      I     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      T     135           -
LGA    -       -      G     136           -
LGA    -       -      V     137           -
LGA    -       -      F     138           -
LGA    -       -      K     139           -
LGA    -       -      A     140           -
LGA    -       -      L     141           -
LGA    -       -      S     142           -
LGA    -       -      A     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   13  128    5.0     11    2.20     0.00      7.099     0.478

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.256030 * X  +   0.060742 * Y  +   0.964758 * Z  +  -4.079635
  Y_new =   0.611739 * X  +   0.782940 * Y  +   0.113051 * Z  + -20.511282
  Z_new =  -0.748481 * X  +   0.619125 * Y  +  -0.237614 * Z  + -36.050201 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.937251   -1.204341  [ DEG:   110.9963    -69.0037 ]
  Theta =   0.845768    2.295824  [ DEG:    48.4590    131.5410 ]
  Phi   =   1.967173   -1.174420  [ DEG:   112.7107    -67.2893 ]
 
# 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: T0322TS239_5_1-D1                             
REMARK     2: T0322_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_5_1-D1.T0322_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13  128   5.0   11   2.20    0.00   7.099
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_5_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM     76  N   GLY    16      -4.467  -9.606  -7.387  1.00  9.99
ATOM     77  CA  GLY    16      -5.811  -9.606  -6.859  1.00  9.99
ATOM     78  C   GLY    16      -6.882  -9.990  -7.875  1.00  9.99
ATOM     79  O   GLY    16      -8.071  -9.817  -7.604  1.00  9.99
ATOM     80  N   PHE    17      -6.463 -10.514  -9.030  1.00  9.99
ATOM     81  CA  PHE    17      -7.425 -11.000 -10.045  1.00  9.99
ATOM     82  C   PHE    17      -6.958 -12.338 -10.584  1.00  9.99
ATOM     83  O   PHE    17      -5.997 -12.908 -10.091  1.00  9.99
ATOM     84  CB  PHE    17      -7.731  -9.935 -11.128  1.00  9.99
ATOM     85  N   SER    18      -7.620 -12.838 -11.624  1.00  9.99
ATOM     86  CA  SER    18      -7.377 -14.214 -12.040  1.00  9.99
ATOM     87  C   SER    18      -5.928 -14.444 -12.491  1.00  9.99
ATOM     88  O   SER    18      -5.364 -15.508 -12.246  1.00  9.99
ATOM     89  CB  SER    18      -8.350 -14.626 -13.151  1.00  9.99
ATOM     90  N   GLN    19      -5.358 -13.471 -13.189  1.00  9.99
ATOM     91  CA  GLN    19      -3.994 -13.618 -13.679  1.00  9.99
ATOM     92  C   GLN    19      -3.044 -13.874 -12.474  1.00  9.99
ATOM     93  O   GLN    19      -2.219 -14.782 -12.515  1.00  9.99
ATOM     94  CB  GLN    19      -3.540 -12.397 -14.526  1.00  9.99
ATOM     95  N   GLN    29      -3.209 -13.086 -11.416  1.00  9.99
ATOM     96  CA  GLN    29      -2.422 -13.245 -10.201  1.00  9.99
ATOM     97  C   GLN    29      -2.710 -14.565  -9.514  1.00  9.99
ATOM     98  O   GLN    29      -1.784 -15.277  -9.110  1.00  9.99
ATOM     99  CB  GLN    29      -2.704 -12.062  -9.259  1.00  9.99
ATOM    100  N   ILE    30      -3.986 -14.896  -9.398  1.00  9.99
ATOM    101  CA  ILE    30      -4.419 -16.150  -8.758  1.00  9.99
ATOM    102  C   ILE    30      -3.778 -17.371  -9.402  1.00  9.99
ATOM    103  O   ILE    30      -3.389 -18.300  -8.708  1.00  9.99
ATOM    104  CB  ILE    30      -5.948 -16.253  -8.797  1.00  9.99
ATOM    105  N   GLY    31      -3.688 -17.376 -10.735  1.00  9.99
ATOM    106  CA  GLY    31      -3.129 -18.521 -11.432  1.00  9.99
ATOM    107  C   GLY    31      -1.612 -18.454 -11.653  1.00  9.99
ATOM    108  O   GLY    31      -1.037 -19.353 -12.293  1.00  9.99
ATOM    109  N   PRO    32      -0.980 -17.373 -11.180  1.00  9.99
ATOM    110  CA  PRO    32       0.469 -17.169 -11.376  1.00  9.99
ATOM    111  C   PRO    32       0.857 -17.107 -12.839  1.00  9.99
ATOM    112  O   PRO    32       1.889 -17.629 -13.232  1.00  9.99
ATOM    113  CB  PRO    32       1.282 -18.271 -10.656  1.00  9.99
ATOM    114  N   LEU    33       0.005 -16.477 -13.636  1.00  9.99
ATOM    115  CA  LEU    33       0.414 -16.145 -14.990  1.00  9.99
ATOM    116  C   LEU    33       1.454 -15.011 -14.916  1.00  9.99
ATOM    117  O   LEU    33       1.205 -13.990 -14.245  1.00  9.99
ATOM    118  CB  LEU    33      -0.837 -15.783 -15.820  1.00  9.99
ATOM    119  N   PHE    34       2.588 -15.196 -15.602  1.00  9.99
ATOM    120  CA  PHE    34       3.698 -14.250 -15.535  1.00  9.99
ATOM    121  C   PHE    34       4.070 -13.866 -16.964  1.00  9.99
ATOM    122  O   PHE    34       4.477 -14.717 -17.761  1.00  9.99
ATOM    123  CB  PHE    34       4.935 -14.906 -14.894  1.00  9.99
ATOM    124  N   GLU    35       3.999 -12.572 -17.269  1.00  9.99
ATOM    125  CA  GLU    35       4.578 -12.086 -18.534  1.00  9.99
ATOM    126  C   GLU    35       6.112 -12.165 -18.489  1.00  9.99
ATOM    127  O   GLU    35       6.724 -11.771 -17.499  1.00  9.99
ATOM    128  CB  GLU    35       4.081 -10.655 -18.836  1.00  9.99
ATOM    129  N   HIS    36       6.698 -12.704 -19.542  1.00  9.99
ATOM    130  CA  HIS    36       8.128 -13.014 -19.593  1.00  9.99
ATOM    131  C   HIS    36       8.878 -12.254 -20.663  1.00  9.99
ATOM    132  O   HIS    36      10.111 -12.121 -20.581  1.00  9.99
ATOM    133  CB  HIS    36       8.324 -14.483 -19.928  1.00  9.99
ATOM    134  N   ARG    37       8.210 -11.850 -21.744  1.00  9.99
ATOM    135  CA  ARG    37       8.924 -11.254 -22.857  1.00  9.99
ATOM    136  C   ARG    37       8.008 -10.356 -23.660  1.00  9.99
ATOM    137  O   ARG    37       6.893 -10.770 -24.018  1.00  9.99
ATOM    138  CB  ARG    37       9.523 -12.361 -23.737  1.00  9.99
TER
END
