
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0335TS168_4
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS168_4.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    S       3      S       3          5.769
LGA    N       4      N       4          1.662
LGA    A       5      A       5          2.189
LGA    K       6      K       6          2.200
LGA    I       7      I       7          1.404
LGA    A       8      A       8          1.230
LGA    R       9      R       9          2.415
LGA    I      10      I      10          2.345
LGA    N      11      N      11          1.247
LGA    E      12      E      12          1.912
LGA    L      13      L      13          3.465
LGA    A      14      A      14          2.588
LGA    A      15      A      15          0.849
LGA    K      16      K      16          2.961
LGA    A      17      A      17          4.188
LGA    K      18      K      18          2.145
LGA    A      19      A      19          1.784
LGA    G      20      G      20          3.161
LGA    V      21      V      21          2.130
LGA    I      22      I      22          2.335
LGA    T      23      T      23          1.624
LGA    E      24      E      24          1.769
LGA    E      25      E      25          1.218
LGA    E      26      E      26          1.714
LGA    K      27      K      27          1.605
LGA    A      28      A      28          0.972
LGA    E      29      E      29          1.045
LGA    Q      30      Q      30          1.570
LGA    Q      31      Q      31          1.872
LGA    K      32      K      32          1.863
LGA    L      33      L      33          1.256
LGA    R      34      R      34          1.539
LGA    Q      35      Q      35          1.191
LGA    E      36      E      36          1.300
LGA    Y      37      Y      37          2.001
LGA    L      38      L      38          1.817
LGA    K      39      K      39          1.796
LGA    G      40      G      40          2.518
LGA    F      41      F      41          1.538
LGA    R      42      -       -           -
LGA    S      43      -       -           -
LGA    S      44      R      42          1.770
LGA    M      45      -       -           -
LGA    K      46      -       -           -
LGA    N      47      -       -           -
LGA    T      48      -       -           -
LGA    L      49      -       -           -
LGA    K      50      -       -           -
LGA    S      51      -       -           -
LGA    V      52      -       -           -
LGA    K      53      -       -           -
LGA    I      54      -       -           -
LGA    I      55      -       -           -
LGA    D      56      -       -           -
LGA    P      57      -       -           -
LGA    E      58      -       -           -
LGA    G      59      -       -           -
LGA    N      60      -       -           -
LGA    D      61      -       -           -
LGA    V      62      -       -           -
LGA    T      63      -       -           -
LGA    P      64      -       -           -
LGA    E      65      -       -           -
LGA    K      66      -       -           -
LGA    L      67      -       -           -
LGA    K      68      -       -           -
LGA    R      69      -       -           -
LGA    E      70      -       -           -
LGA    Q      71      -       -           -
LGA    R      72      -       -           -
LGA    N      73      -       -           -
LGA    N      74      -       -           -
LGA    K      75      -       -           -
LGA    L      76      -       -           -
LGA    H      77      -       -           -
LGA    L      78      -       -           -
LGA    E      79      -       -           -
LGA    H      80      -       -           -
LGA    H      81      -       -           -
LGA    H      82      -       -           -
LGA    H      83      -       -           -
LGA    H      84      -       -           -
LGA    H      85      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   42    5.0     40    2.20    97.50     82.617     1.742

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.117395 * X  +   0.591088 * Y  +   0.798018 * Z  +   4.780733
  Y_new =   0.431580 * X  +  -0.754090 * Y  +   0.495062 * Z  +   2.254593
  Z_new =   0.894403 * X  +   0.286291 * Y  +  -0.343629 * Z  +  -6.576224 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.446968   -0.694625  [ DEG:   140.2009    -39.7991 ]
  Theta =  -1.107095   -2.034498  [ DEG:   -63.4319   -116.5681 ]
  Phi   =   1.305210   -1.836383  [ DEG:    74.7830   -105.2170 ]
 
# 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: T0335TS168_4                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_4.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   42   5.0   40   2.20   97.50  82.617
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_4
PFRMAT TS
TARGET T0335
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      -2.985 -17.905  -8.254  1.00 25.00           C
ATOM      2  CA  ILE     2      -4.660 -14.951  -9.889  1.00 25.00           C
ATOM      3  CA  SER     3      -1.846 -12.828 -11.274  1.00 25.00           C
ATOM      4  CA  ASN     4      -0.538  -9.404 -10.370  1.00 25.00           C
ATOM      5  CA  ALA     5       0.684  -9.993  -6.788  1.00 25.00           C
ATOM      6  CA  LYS     6       2.041  -6.415  -6.636  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.312  -5.063  -7.900  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.165  -7.106  -5.242  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.828  -5.742  -2.531  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.446  -2.169  -3.760  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.228  -2.767  -3.673  1.00 25.00           C
ATOM     12  CA  GLU    12      -4.956  -4.128  -0.104  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.929  -1.050   0.940  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.565   1.246  -0.622  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.337  -0.623   1.248  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.397  -0.265   4.530  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.960   3.486   3.892  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.710   3.831   3.201  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.506   1.966   6.450  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.573   4.446   9.380  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.338   2.035  11.400  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.890   1.937   9.704  1.00 25.00           C
ATOM     23  CA  THR    23      -2.048   3.355  11.850  1.00 25.00           C
ATOM     24  CA  GLU    24       0.964   5.636  11.649  1.00 25.00           C
ATOM     25  CA  GLU    25       3.942   3.330  10.958  1.00 25.00           C
ATOM     26  CA  GLU    26       1.638   0.852   9.162  1.00 25.00           C
ATOM     27  CA  LYS    27       0.188   3.697   7.047  1.00 25.00           C
ATOM     28  CA  ALA    28       3.723   4.864   6.148  1.00 25.00           C
ATOM     29  CA  GLU    29       4.673   1.292   5.145  1.00 25.00           C
ATOM     30  CA  GLN    30       1.535   1.042   2.963  1.00 25.00           C
ATOM     31  CA  GLN    31       2.402   4.379   1.293  1.00 25.00           C
ATOM     32  CA  LYS    32       5.966   3.146   0.625  1.00 25.00           C
ATOM     33  CA  LEU    33       4.590  -0.085  -0.903  1.00 25.00           C
ATOM     34  CA  ARG    34       2.231   1.947  -3.134  1.00 25.00           C
ATOM     35  CA  GLN    35       5.154   4.150  -4.261  1.00 25.00           C
ATOM     36  CA  GLU    36       7.225   1.032  -5.068  1.00 25.00           C
ATOM     37  CA  TYR    37       4.310  -0.412  -7.091  1.00 25.00           C
ATOM     38  CA  LEU    38       3.979   2.886  -9.011  1.00 25.00           C
ATOM     39  CA  LYS    39       7.737   2.861  -9.751  1.00 25.00           C
ATOM     40  CA  GLY    40       7.490  -0.750 -11.004  1.00 25.00           C
ATOM     41  CA  PHE    41       4.546   0.207 -13.259  1.00 25.00           C
ATOM     42  CA  ARG    42       6.542   3.163 -14.653  1.00 25.00           C
ATOM     43  CA  SER    43       9.521   0.856 -15.344  1.00 25.00           C
ATOM     44  CA  SER    44       7.217  -1.621 -17.139  1.00 25.00           C
ATOM     45  CA  MET    45       5.766   1.223 -19.254  1.00 25.00           C
ATOM     46  CA  LYS    46       9.301   2.390 -20.154  1.00 25.00           C
ATOM     47  CA  ASN    47      10.252  -1.182 -21.156  1.00 25.00           C
ATOM     48  CA  THR    48       7.114  -1.430 -23.339  1.00 25.00           C
ATOM     49  CA  LEU    49       7.981   1.906 -25.008  1.00 25.00           C
ATOM     50  CA  LYS    50       5.001   4.049 -23.988  1.00 25.00           C
ATOM     51  CA  SER    51       1.706   3.608 -22.089  1.00 25.00           C
ATOM     52  CA  VAL    52       0.681   3.231 -18.451  1.00 25.00           C
ATOM     53  CA  LYS    53       0.953   3.774 -14.659  1.00 25.00           C
ATOM     54  CA  ILE    54      -1.370   6.799 -14.502  1.00 25.00           C
ATOM     55  CA  ILE    55      -3.282   9.570 -12.736  1.00 25.00           C
ATOM     56  CA  ASP    56      -2.878  11.767 -15.757  1.00 25.00           C
ATOM     57  CA  PRO    57      -4.281  14.644 -13.770  1.00 25.00           C
ATOM     58  CA  GLU    58      -4.389  17.660 -16.087  1.00 25.00           C
ATOM     59  CA  GLY    59      -1.284  19.846 -16.343  1.00 25.00           C
ATOM     60  CA  ASN    60       1.029  18.365 -13.782  1.00 25.00           C
ATOM     61  CA  ASP    61       0.850  15.002 -11.924  1.00 25.00           C
ATOM     62  CA  VAL    62       2.247  11.624 -13.067  1.00 25.00           C
ATOM     63  CA  THR    63       3.983  10.758 -16.390  1.00 25.00           C
ATOM     64  CA  PRO    64       7.614  11.751 -16.664  1.00 25.00           C
ATOM     65  CA  GLU    65      10.511  14.113 -15.831  1.00 25.00           C
ATOM     66  CA  LYS    66      10.291  13.120 -12.139  1.00 25.00           C
ATOM     67  CA  LEU    67      10.341   9.415 -13.108  1.00 25.00           C
ATOM     68  CA  LYS    68      13.413  10.009 -15.316  1.00 25.00           C
ATOM     69  CA  ARG    69      15.166  11.821 -12.433  1.00 25.00           C
ATOM     70  CA  GLU    70      14.355   8.911 -10.079  1.00 25.00           C
ATOM     71  CA  GLN    71      15.754   6.423 -12.632  1.00 25.00           C
ATOM     72  CA  ARG    72      18.949   8.510 -12.952  1.00 25.00           C
ATOM     73  CA  ASN    73      19.310   8.586  -9.140  1.00 25.00           C
ATOM     74  CA  ASN    74      18.860   4.786  -8.996  1.00 25.00           C
ATOM     75  CA  LYS    75      21.833   3.012 -10.702  1.00 25.00           C
ATOM     76  CA  LEU    76      23.883   3.544  -7.504  1.00 25.00           C
ATOM     77  CA  HIS    77      24.193   1.167  -4.623  1.00 25.00           C
ATOM     78  CA  LEU    78      22.513  -1.597  -6.705  1.00 25.00           C
ATOM     79  CA  GLU    79      20.391  -4.678  -6.022  1.00 25.00           C
ATOM     80  CA  HIS    80      20.041  -5.037  -2.250  1.00 25.00           C
ATOM     81  CA  HIS    81      16.673  -6.492  -1.491  1.00 25.00           C
ATOM     82  CA  HIS    82      15.376  -7.712   1.850  1.00 25.00           C
ATOM     83  CA  HIS    83      16.877  -5.321   4.441  1.00 25.00           C
ATOM     84  CA  HIS    84      14.513  -3.107   6.468  1.00 25.00           C
ATOM     85  CA  HIS    85      15.266  -3.126  10.187  1.00 25.00           C
TER
END
