
#######################################################
#                                                     #
#                        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   56 (   56),  selected   56 , name T0349TS677_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS677_1-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    R       2      R       2          1.368
LGA    E       3      E       3          1.185
LGA    L       4      L       4          0.964
LGA    L       5      L       5          1.191
LGA    R       6      R       6          2.374
LGA    T       7      -       -           -
LGA    N       8      T       7          0.901
LGA    D       9      N       8          2.579
LGA    A      10      D       9          3.060
LGA    V      11      A      10          2.317
LGA    -       -      V      11           -
LGA    L      12      L      12          0.895
LGA    L      13      L      13          1.882
LGA    S      14      S      14          1.907
LGA    A      15      A      15          0.919
LGA    V      16      V      16          0.459
LGA    G      17      G      17          1.313
LGA    A      18      A      18          1.123
LGA    L      19      L      19          0.687
LGA    L      20      L      20          0.873
LGA    D      21      D      21          0.864
LGA    G      22      G      22          0.287
LGA    A      23      A      23          1.553
LGA    D      24      D      24          2.035
LGA    I      25      I      25          0.761
LGA    G      26      G      26          1.654
LGA    H      27      H      27          1.058
LGA    L      28      L      28          1.037
LGA    V      29      V      29          1.297
LGA    P      45      P      45          1.485
LGA    R      46      R      46          1.339
LGA    R      47      R      47          0.136
LGA    V      48      V      48          0.605
LGA    L      49      L      49          0.723
LGA    V      50      V      50          0.756
LGA    H      51      H      51          0.946
LGA    E      52      E      52          1.360
LGA    D      53      D      53          1.718
LGA    D      54      D      54          1.160
LGA    L      55      L      55          0.522
LGA    A      56      A      56          0.479
LGA    G      57      G      57          0.428
LGA    A      58      A      58          0.404
LGA    R      59      R      59          0.518
LGA    R      60      R      60          0.481
LGA    L      61      L      61          0.301
LGA    L      62      L      62          0.320
LGA    T      63      T      63          0.308
LGA    D      64      D      64          1.096
LGA    A      65      A      65          2.677
LGA    -       -      G      66           -
LGA    G      66      L      67          1.677
LGA    L      67      A      68          2.924
LGA    A      68      H      69          3.075
LGA    H      69      E      70          6.237
LGA    E      70      L      71           -
LGA    L      71      R      72           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   56   57    5.0     52    1.66    84.62     84.888     2.952

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.672454 * X  +  -0.639051 * Y  +   0.373389 * Z  +   7.585927
  Y_new =   0.704946 * X  +   0.706715 * Y  +  -0.060036 * Z  + -63.163845
  Z_new =  -0.225514 * X  +   0.303591 * Y  +   0.925730 * Z  + -45.665806 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.316895   -2.824697  [ DEG:    18.1568   -161.8432 ]
  Theta =   0.227470    2.914123  [ DEG:    13.0331    166.9669 ]
  Phi   =   0.808983   -2.332609  [ DEG:    46.3513   -133.6487 ]
 
# 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: T0349TS677_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS677_1-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   56   57   5.0   52   1.66   84.62  84.888
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS677_1-D1
PFRMAT TS
TARGET T0349
MODEL  1
PARENT 1YJ7_A
ATOM     22  CA  ARG     2       3.951   8.742  -5.716  1.00 54.00
ATOM     23  CA  GLU     3       3.895   5.123  -4.564  1.00 54.00
ATOM     24  CA  LEU     4       4.840   4.579  -0.935  1.00 54.00
ATOM     25  CA  LEU     5       4.699   0.796  -0.540  1.00 57.00
ATOM     26  CA  ARG     6       3.553  -2.293  -2.463  1.00 68.00
ATOM     27  CA  THR     7       3.140  -5.908  -1.352  1.00 79.00
ATOM     28  CA  ASN     8       1.152  -5.035   1.778  1.00 91.00
ATOM     29  CA  ASP     9      -1.455  -7.235   3.469  1.00 99.00
ATOM     30  CA  ALA    10      -4.949  -5.819   3.589  1.00 99.00
ATOM     31  CA  VAL    11      -4.720  -5.421   7.398  1.00 94.00
ATOM     32  CA  LEU    12      -1.420  -3.518   7.383  1.00 92.00
ATOM     33  CA  LEU    13      -2.341  -1.312   4.400  1.00 92.00
ATOM     34  CA  SER    14      -5.500  -0.439   6.340  1.00 56.00
ATOM     35  CA  ALA    15      -3.523   0.449   9.454  1.00 27.00
ATOM     36  CA  VAL    16      -1.145   2.629   7.411  1.00 46.00
ATOM     37  CA  GLY    17      -3.969   4.280   5.422  1.00 59.00
ATOM     38  CA  ALA    18      -5.947   5.091   8.562  1.00 41.00
ATOM     39  CA  LEU    19      -2.813   6.429  10.281  1.00 50.00
ATOM     40  CA  LEU    20      -2.059   8.779   7.367  1.00 50.00
ATOM     41  CA  ASP    21      -5.632   9.984   6.976  1.00 43.00
ATOM     42  CA  GLY    22      -5.930  10.655  10.709  1.00 32.00
ATOM     43  CA  ALA    23      -2.686  12.658  10.544  1.00 37.00
ATOM     44  CA  ASP    24      -4.037  14.815   7.700  1.00 25.00
ATOM     45  CA  ILE    25      -2.320  13.160   4.779  1.00 37.00
ATOM     46  CA  GLY    26      -4.427  12.024   1.825  1.00 60.00
ATOM     47  CA  HIS    27      -3.779   8.515   0.555  1.00 79.00
ATOM     48  CA  LEU    28      -4.920   6.287  -2.288  1.00 99.00
ATOM     49  CA  VAL    29      -4.952   2.499  -2.345  1.00 99.00
ATOM     56  CA  PRO    45      -1.436  -7.353  -2.429  1.00 94.00
ATOM     57  CA  ARG    46      -2.072  -3.700  -1.550  1.00 58.00
ATOM     58  CA  ARG    47      -0.283  -0.575  -2.754  1.00 45.00
ATOM     59  CA  VAL    48      -0.508   2.798  -0.989  1.00 45.00
ATOM     60  CA  LEU    49       0.309   6.082  -2.749  1.00 55.00
ATOM     61  CA  VAL    50       0.190   9.780  -1.880  1.00 64.00
ATOM     62  CA  HIS    51       0.204  13.060  -3.774  1.00 79.00
ATOM     63  CA  GLU    52       3.867  13.708  -4.556  1.00 62.00
ATOM     64  CA  ASP    53       3.994  16.904  -2.491  1.00 70.00
ATOM     65  CA  ASP    54       2.974  14.901   0.576  1.00 71.00
ATOM     66  CA  LEU    55       5.696  12.261   0.269  1.00 55.00
ATOM     67  CA  ALA    56       8.032  13.558   3.010  1.00 49.00
ATOM     68  CA  GLY    57       5.178  14.147   5.505  1.00 55.00
ATOM     69  CA  ALA    58       3.832  10.660   4.770  1.00 69.00
ATOM     70  CA  ARG    59       7.130   8.819   5.193  1.00 85.00
ATOM     71  CA  ARG    60       7.734  10.821   8.402  1.00 86.00
ATOM     72  CA  LEU    61       4.413   9.696   9.885  1.00 94.00
ATOM     73  CA  LEU    62       4.953   6.088   8.807  1.00 89.00
ATOM     74  CA  THR    63       8.564   6.027  10.126  1.00 71.00
ATOM     75  CA  ASP    64       7.381   7.524  13.442  1.00 35.00
ATOM     76  CA  ALA    65       4.892   4.675  13.831  1.00 35.00
ATOM     77  CA  GLY    66       7.207   1.861  12.740  1.00 34.00
ATOM     78  CA  LEU    67       5.525   1.125   9.387  1.00 40.00
ATOM     79  CA  ALA    68       5.909  -0.978   7.448  1.00 49.00
ATOM     80  CA  HIS    69       6.140  -3.320  10.431  1.00 94.00
ATOM     81  CA  GLU    70       9.207  -5.384  11.072  1.00 99.00
ATOM     82  CA  LEU    71       8.836  -9.148  11.029  1.00 99.00
ATOM     83  CA  ARG    72      10.102 -11.537  13.696  1.00 99.00
TER
END
