
#######################################################
#                                                     #
#                        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   36 (  144),  selected   36 , name T0335TS035_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS035_5-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.032
LGA    K       6      K       6          0.610
LGA    I       7      I       7          1.913
LGA    A       8      A       8          2.080
LGA    R       9      R       9          1.467
LGA    I      10      I      10          1.265
LGA    N      11      N      11          1.221
LGA    E      12      E      12          1.346
LGA    L      13      L      13          2.844
LGA    A      14      A      14          2.397
LGA    A      15      A      15          0.777
LGA    K      16      K      16          2.125
LGA    A      17      A      17          3.643
LGA    K      18      K      18          2.691
LGA    A      19      A      19          0.900
LGA    G      20      G      20          1.790
LGA    V      21      V      21          1.529
LGA    I      22      I      22          1.379
LGA    T      23      T      23          1.752
LGA    E      24      E      24          1.976
LGA    E      25      E      25          1.623
LGA    E      26      E      26          1.125
LGA    K      27      K      27          1.209
LGA    A      28      A      28          1.130
LGA    E      29      E      29          0.949
LGA    Q      30      Q      30          0.912
LGA    Q      31      Q      31          0.985
LGA    K      32      K      32          1.075
LGA    L      33      L      33          1.004
LGA    R      34      R      34          1.106
LGA    Q      35      Q      35          0.370
LGA    E      36      E      36          0.598
LGA    Y      37      Y      37          1.176
LGA    L      38      L      38          1.035
LGA    K      39      K      39          1.081
LGA    G      40      G      40          1.145

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     36    1.60   100.00     92.922     2.115

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.368346 * X  +   0.202501 * Y  +   0.907367 * Z  +  -1.939045
  Y_new =   0.054344 * X  +  -0.969631 * Y  +   0.238457 * Z  +   1.689847
  Z_new =   0.928099 * X  +   0.137144 * Y  +   0.346156 * Z  + -11.496814 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.377220   -2.764372  [ DEG:    21.6131   -158.3869 ]
  Theta =  -1.189274   -1.952318  [ DEG:   -68.1404   -111.8596 ]
  Phi   =   2.995116   -0.146477  [ DEG:   171.6075     -8.3925 ]
 
# 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: T0335TS035_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS035_5-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   36   1.60  100.00  92.922
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS035_5-D1
PFRMAT TS
TARGET T0335
MODEL  5  REFINED
PARENT N/A
ATOM     17  N   ALA     5       0.563 -11.729  -5.808  1.00  0.00
ATOM     18  CA  ALA     5       0.856 -11.271  -4.463  1.00  0.00
ATOM     19  C   ALA     5       0.845  -9.754  -4.374  1.00  0.00
ATOM     20  O   ALA     5       0.295  -9.176  -3.438  1.00  0.00
ATOM     21  N   LYS     6       1.452  -9.078  -5.345  1.00  0.00
ATOM     22  CA  LYS     6       1.516  -7.630  -5.290  1.00  0.00
ATOM     23  C   LYS     6       0.141  -7.002  -5.454  1.00  0.00
ATOM     24  O   LYS     6      -0.201  -6.036  -4.773  1.00  0.00
ATOM     25  N   ILE     7      -0.675  -7.537  -6.357  1.00  0.00
ATOM     26  CA  ILE     7      -2.010  -7.001  -6.537  1.00  0.00
ATOM     27  C   ILE     7      -2.828  -7.095  -5.259  1.00  0.00
ATOM     28  O   ILE     7      -3.493  -6.142  -4.858  1.00  0.00
ATOM     29  N   ALA     8      -2.795  -8.246  -4.593  1.00  0.00
ATOM     30  CA  ALA     8      -3.566  -8.401  -3.375  1.00  0.00
ATOM     31  C   ALA     8      -3.105  -7.436  -2.295  1.00  0.00
ATOM     32  O   ALA     8      -3.915  -6.809  -1.614  1.00  0.00
ATOM     33  N   ARG     9      -1.795  -7.298  -2.113  1.00  0.00
ATOM     34  CA  ARG     9      -1.296  -6.419  -1.074  1.00  0.00
ATOM     35  C   ARG     9      -1.617  -4.962  -1.371  1.00  0.00
ATOM     36  O   ARG     9      -1.941  -4.187  -0.472  1.00  0.00
ATOM     37  N   ILE    10      -1.535  -4.561  -2.636  1.00  0.00
ATOM     38  CA  ILE    10      -1.852  -3.190  -2.984  1.00  0.00
ATOM     39  C   ILE    10      -3.323  -2.880  -2.755  1.00  0.00
ATOM     40  O   ILE    10      -3.676  -1.820  -2.240  1.00  0.00
ATOM     41  N   ASN    11      -4.209  -3.798  -3.129  1.00  0.00
ATOM     42  CA  ASN    11      -5.626  -3.561  -2.933  1.00  0.00
ATOM     43  C   ASN    11      -5.979  -3.472  -1.456  1.00  0.00
ATOM     44  O   ASN    11      -6.809  -2.661  -1.049  1.00  0.00
ATOM     45  N   GLU    12      -5.357  -4.303  -0.625  1.00  0.00
ATOM     46  CA  GLU    12      -5.634  -4.250   0.797  1.00  0.00
ATOM     47  C   GLU    12      -5.133  -2.956   1.417  1.00  0.00
ATOM     48  O   GLU    12      -5.775  -2.382   2.296  1.00  0.00
ATOM     49  N   LEU    13      -3.978  -2.469   0.973  1.00  0.00
ATOM     50  CA  LEU    13      -3.507  -1.180   1.440  1.00  0.00
ATOM     51  C   LEU    13      -4.532  -0.085   1.190  1.00  0.00
ATOM     52  O   LEU    13      -4.886   0.672   2.091  1.00  0.00
ATOM     53  N   ALA    14      -5.030   0.019  -0.040  1.00  0.00
ATOM     54  CA  ALA    14      -6.049   1.011  -0.326  1.00  0.00
ATOM     55  C   ALA    14      -7.304   0.777   0.498  1.00  0.00
ATOM     56  O   ALA    14      -7.935   1.718   0.976  1.00  0.00
ATOM     57  N   ALA    15      -7.693  -0.482   0.680  1.00  0.00
ATOM     58  CA  ALA    15      -8.894  -0.767   1.441  1.00  0.00
ATOM     59  C   ALA    15      -8.751  -0.341   2.893  1.00  0.00
ATOM     60  O   ALA    15      -9.651   0.269   3.469  1.00  0.00
ATOM     61  N   LYS    16      -7.618  -0.653   3.516  1.00  0.00
ATOM     62  CA  LYS    16      -7.431  -0.290   4.907  1.00  0.00
ATOM     63  C   LYS    16      -7.548   1.212   5.113  1.00  0.00
ATOM     64  O   LYS    16      -8.345   1.682   5.924  1.00  0.00
ATOM     65  N   ALA    17      -6.758   1.995   4.385  1.00  0.00
ATOM     66  CA  ALA    17      -6.803   3.434   4.558  1.00  0.00
ATOM     67  C   ALA    17      -8.182   3.992   4.246  1.00  0.00
ATOM     68  O   ALA    17      -8.664   4.904   4.914  1.00  0.00
ATOM     69  N   LYS    18      -8.845   3.456   3.224  1.00  0.00
ATOM     70  CA  LYS    18     -10.160   3.956   2.871  1.00  0.00
ATOM     71  C   LYS    18     -11.247   3.321   3.721  1.00  0.00
ATOM     72  O   LYS    18     -12.376   3.806   3.777  1.00  0.00
ATOM     73  N   ALA    19     -10.931   2.221   4.401  1.00  0.00
ATOM     74  CA  ALA    19     -11.932   1.559   5.215  1.00  0.00
ATOM     75  C   ALA    19     -11.757   1.882   6.690  1.00  0.00
ATOM     76  O   ALA    19     -12.598   1.538   7.520  1.00  0.00
ATOM     77  N   GLY    20     -10.663   2.548   7.048  1.00  0.00
ATOM     78  CA  GLY    20     -10.440   2.883   8.440  1.00  0.00
ATOM     79  C   GLY    20      -9.110   3.588   8.641  1.00  0.00
ATOM     80  O   GLY    20      -8.218   3.516   7.796  1.00  0.00
ATOM     81  N   VAL    21      -8.946   4.285   9.762  1.00  0.00
ATOM     82  CA  VAL    21      -7.701   4.988  10.005  1.00  0.00
ATOM     83  C   VAL    21      -6.531   4.026  10.131  1.00  0.00
ATOM     84  O   VAL    21      -6.629   2.988  10.785  1.00  0.00
ATOM     85  N   ILE    22      -5.401   4.348   9.508  1.00  0.00
ATOM     86  CA  ILE    22      -4.251   3.469   9.592  1.00  0.00
ATOM     87  C   ILE    22      -3.208   4.002  10.561  1.00  0.00
ATOM     88  O   ILE    22      -3.061   5.211  10.734  1.00  0.00
ATOM     89  N   THR    23      -2.463   3.113  11.213  1.00  0.00
ATOM     90  CA  THR    23      -1.391   3.563  12.078  1.00  0.00
ATOM     91  C   THR    23      -0.175   4.004  11.280  1.00  0.00
ATOM     92  O   THR    23      -0.089   3.774  10.074  1.00  0.00
ATOM     93  N   GLU    24       0.789   4.645  11.933  1.00  0.00
ATOM     94  CA  GLU    24       2.027   4.980  11.255  1.00  0.00
ATOM     95  C   GLU    24       2.664   3.755  10.617  1.00  0.00
ATOM     96  O   GLU    24       3.057   3.778   9.452  1.00  0.00
ATOM     97  N   GLU    25       2.779   2.664  11.367  1.00  0.00
ATOM     98  CA  GLU    25       3.406   1.474  10.824  1.00  0.00
ATOM     99  C   GLU    25       2.623   0.916   9.647  1.00  0.00
ATOM    100  O   GLU    25       3.197   0.468   8.656  1.00  0.00
ATOM    101  N   GLU    26       1.296   0.932   9.730  1.00  0.00
ATOM    102  CA  GLU    26       0.494   0.439   8.626  1.00  0.00
ATOM    103  C   GLU    26       0.570   1.364   7.422  1.00  0.00
ATOM    104  O   GLU    26       0.666   0.915   6.281  1.00  0.00
ATOM    105  N   LYS    27       0.530   2.674   7.651  1.00  0.00
ATOM    106  CA  LYS    27       0.647   3.606   6.546  1.00  0.00
ATOM    107  C   LYS    27       1.993   3.484   5.851  1.00  0.00
ATOM    108  O   LYS    27       2.076   3.462   4.625  1.00  0.00
ATOM    109  N   ALA    28       3.076   3.401   6.620  1.00  0.00
ATOM    110  CA  ALA    28       4.389   3.298   6.014  1.00  0.00
ATOM    111  C   ALA    28       4.454   2.158   5.012  1.00  0.00
ATOM    112  O   ALA    28       5.119   2.255   3.981  1.00  0.00
ATOM    113  N   GLU    29       3.767   1.053   5.292  1.00  0.00
ATOM    114  CA  GLU    29       3.765  -0.055   4.357  1.00  0.00
ATOM    115  C   GLU    29       3.032   0.297   3.073  1.00  0.00
ATOM    116  O   GLU    29       3.451  -0.077   1.979  1.00  0.00
ATOM    117  N   GLN    30       1.924   1.024   3.178  1.00  0.00
ATOM    118  CA  GLN    30       1.198   1.417   1.986  1.00  0.00
ATOM    119  C   GLN    30       1.948   2.478   1.197  1.00  0.00
ATOM    120  O   GLN    30       1.935   2.483  -0.032  1.00  0.00
ATOM    121  N   GLN    31       2.617   3.397   1.887  1.00  0.00
ATOM    122  CA  GLN    31       3.383   4.411   1.190  1.00  0.00
ATOM    123  C   GLN    31       4.513   3.799   0.378  1.00  0.00
ATOM    124  O   GLN    31       4.761   4.190  -0.762  1.00  0.00
ATOM    125  N   LYS    32       5.223   2.828   0.946  1.00  0.00
ATOM    126  CA  LYS    32       6.320   2.213   0.225  1.00  0.00
ATOM    127  C   LYS    32       5.822   1.380  -0.945  1.00  0.00
ATOM    128  O   LYS    32       6.478   1.284  -1.981  1.00  0.00
ATOM    129  N   LEU    33       4.654   0.761  -0.806  1.00  0.00
ATOM    130  CA  LEU    33       4.104  -0.008  -1.906  1.00  0.00
ATOM    131  C   LEU    33       3.742   0.882  -3.085  1.00  0.00
ATOM    132  O   LEU    33       4.044   0.568  -4.235  1.00  0.00
ATOM    133  N   ARG    34       3.086   2.010  -2.824  1.00  0.00
ATOM    134  CA  ARG    34       2.733   2.910  -3.904  1.00  0.00
ATOM    135  C   ARG    34       3.966   3.425  -4.628  1.00  0.00
ATOM    136  O   ARG    34       4.046   3.386  -5.855  1.00  0.00
ATOM    137  N   GLN    35       4.953   3.920  -3.885  1.00  0.00
ATOM    138  CA  GLN    35       6.112   4.513  -4.522  1.00  0.00
ATOM    139  C   GLN    35       6.806   3.529  -5.450  1.00  0.00
ATOM    140  O   GLN    35       7.151   3.859  -6.583  1.00  0.00
ATOM    141  N   GLU    36       7.025   2.300  -4.989  1.00  0.00
ATOM    142  CA  GLU    36       7.731   1.335  -5.807  1.00  0.00
ATOM    143  C   GLU    36       6.901   0.903  -7.006  1.00  0.00
ATOM    144  O   GLU    36       7.416   0.743  -8.111  1.00  0.00
ATOM    145  N   TYR    37       5.600   0.707  -6.813  1.00  0.00
ATOM    146  CA  TYR    37       4.755   0.310  -7.922  1.00  0.00
ATOM    147  C   TYR    37       4.716   1.376  -9.005  1.00  0.00
ATOM    148  O   TYR    37       4.852   1.079 -10.191  1.00  0.00
ATOM    149  N   LEU    38       4.532   2.635  -8.622  1.00  0.00
ATOM    150  CA  LEU    38       4.500   3.696  -9.610  1.00  0.00
ATOM    151  C   LEU    38       5.846   3.864 -10.295  1.00  0.00
ATOM    152  O   LEU    38       5.919   4.142 -11.491  1.00  0.00
ATOM    153  N   LYS    39       6.937   3.697  -9.554  1.00  0.00
ATOM    154  CA  LYS    39       8.250   3.825 -10.157  1.00  0.00
ATOM    155  C   LYS    39       8.462   2.797 -11.258  1.00  0.00
ATOM    156  O   LYS    39       9.005   3.105 -12.317  1.00  0.00
ATOM    157  N   GLY    40       8.037   1.557 -11.030  1.00  0.00
ATOM    158  CA  GLY    40       8.175   0.544 -12.059  1.00  0.00
ATOM    159  C   GLY    40       7.252   0.815 -13.237  1.00  0.00
ATOM    160  O   GLY    40       7.644   0.676 -14.394  1.00  0.00
TER
END
