
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0359TS393_4-D1
# Molecule2: number of CA atoms   90 (  669),  selected   90 , name T0359_D1.pdb
# PARAMETERS: T0359TS393_4-D1.T0359_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    S       3      S       3          4.640
LGA    E       4      E       4          3.413
LGA    T       5      T       5          2.061
LGA    F       6      F       6          1.188
LGA    D       7      D       7          2.645
LGA    V       8      V       8          1.236
LGA    E       9      E       9          0.842
LGA    L      10      L      10          2.947
LGA    T      11      -       -           -
LGA    K      12      T      11          1.342
LGA    N      13      K      12          3.582
LGA    V      14      N      13          1.902
LGA    Q      15      V      14          3.114
LGA    G      16      Q      15          4.114
LGA    L      17      G      16          2.766
LGA    G      18      L      17          2.297
LGA    -       -      G      18           -
LGA    I      19      I      19          0.965
LGA    T      20      T      20          1.274
LGA    I      21      I      21          2.475
LGA    A      22      A      22          0.873
LGA    G      23      G      23          1.073
LGA    Y      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      Y      24          4.624
LGA    D      27      I      25          4.485
LGA    K      28      G      26           -
LGA    K      29      D      27           -
LGA    L      30      -       -           -
LGA    E      31      P      32          1.620
LGA    P      32      S      33          3.546
LGA    S      33      -       -           -
LGA    G      34      G      34          2.220
LGA    I      35      I      35          1.578
LGA    F      36      F      36          1.697
LGA    V      37      V      37          0.916
LGA    K      38      K      38          0.886
LGA    S      39      S      39          1.079
LGA    I      40      I      40          0.805
LGA    T      41      T      41          1.914
LGA    K      42      K      42          1.846
LGA    S      43      S      43          3.299
LGA    S      44      S      44          2.037
LGA    A      45      A      45          1.672
LGA    V      46      V      46          1.427
LGA    E      47      E      47          1.302
LGA    H      48      H      48          1.523
LGA    D      49      D      49          0.488
LGA    G      50      G      50          1.372
LGA    R      51      R      51          1.780
LGA    I      52      I      52          1.836
LGA    Q      53      Q      53          1.286
LGA    I      54      I      54          0.824
LGA    G      55      G      55          1.260
LGA    D      56      D      56          1.429
LGA    Q      57      Q      57          1.333
LGA    I      58      I      58          0.640
LGA    I      59      I      59          0.706
LGA    A      60      A      60          1.073
LGA    V      61      V      61          1.056
LGA    D      62      D      62          1.802
LGA    G      63      G      63          1.061
LGA    T      64      T      64          0.550
LGA    N      65      N      65          2.572
LGA    L      66      L      66          2.328
LGA    Q      67      Q      67          2.108
LGA    G      68      G      68          2.933
LGA    F      69      F      69          2.968
LGA    T      70      T      70          3.367
LGA    N      71      N      71          3.107
LGA    Q      72      Q      72          2.157
LGA    Q      73      Q      73          1.820
LGA    A      74      A      74          2.322
LGA    V      75      V      75          2.170
LGA    E      76      E      76          1.435
LGA    V      77      V      77          1.320
LGA    L      78      L      78          1.271
LGA    R      79      R      79          2.054
LGA    H      80      H      80          2.504
LGA    T      81      T      81          2.052
LGA    G      82      G      82          1.683
LGA    Q      83      Q      83          2.463
LGA    T      84      T      84          2.016
LGA    V      85      V      85          1.293
LGA    L      86      L      86          1.426
LGA    L      87      L      87          1.074
LGA    T      88      T      88          1.162
LGA    L      89      L      89          1.199
LGA    M      90      M      90          0.718
LGA    R      91      R      91          1.462
LGA    R      92      R      92          2.499
LGA    G      93      G      93          1.784
LGA    E      94      E      94          3.221

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94   90    5.0     85    2.13    87.06     77.144     3.806

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.334356 * X  +   0.580411 * Y  +  -0.742516 * Z  +  -4.450647
  Y_new =  -0.715537 * X  +  -0.669091 * Y  +  -0.200809 * Z  +  13.619457
  Z_new =  -0.613362 * X  +   0.464156 * Y  +   0.639020 * Z  +  -6.864940 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.628197   -2.513396  [ DEG:    35.9930   -144.0070 ]
  Theta =   0.660310    2.481282  [ DEG:    37.8330    142.1670 ]
  Phi   =  -2.007926    1.133666  [ DEG:  -115.0457     64.9543 ]
 
# 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: T0359TS393_4-D1                               
REMARK     2: T0359_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS393_4-D1.T0359_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94   90   5.0   85   2.13   87.06  77.144
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS393_4-D1
PFRMAT TS
TARGET T0359
MODEL 4
PARENT N/A
ATOM      1  CA  SER     1       8.537  -1.718   0.713  1.00 25.00           C
ATOM      2  CA  MET     2       5.718   0.582   1.887  1.00 25.00           C
ATOM      3  CA  SER     3       5.295   2.921  -1.124  1.00 25.00           C
ATOM      4  CA  GLU     4       5.005   6.063   0.899  1.00 25.00           C
ATOM      5  CA  THR     5       1.259   6.796   0.423  1.00 25.00           C
ATOM      6  CA  PHE     6       1.941  10.474   1.100  1.00 25.00           C
ATOM      7  CA  ASP     7       0.474  13.692   2.506  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.647  15.682   3.084  1.00 25.00           C
ATOM      9  CA  GLU     9      -5.417  17.969   4.277  1.00 25.00           C
ATOM     10  CA  LEU    10      -5.175  19.447   0.751  1.00 25.00           C
ATOM     11  CA  THR    11      -7.733  22.186   1.501  1.00 25.00           C
ATOM     12  CA  LYS    12     -10.994  24.246   1.323  1.00 25.00           C
ATOM     13  CA  ASN    13     -11.435  28.025   1.095  1.00 25.00           C
ATOM     14  CA  VAL    14     -11.885  30.805  -1.467  1.00 25.00           C
ATOM     15  CA  GLN    15     -13.947  28.268  -3.371  1.00 25.00           C
ATOM     16  CA  GLY    16     -13.013  25.937  -6.248  1.00 25.00           C
ATOM     17  CA  LEU    17     -11.043  23.020  -4.847  1.00 25.00           C
ATOM     18  CA  GLY    18      -8.020  23.974  -6.981  1.00 25.00           C
ATOM     19  CA  ILE    19      -6.185  21.571  -9.367  1.00 25.00           C
ATOM     20  CA  THR    20      -7.057  20.290 -12.880  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.991  16.799 -14.100  1.00 25.00           C
ATOM     22  CA  ALA    22      -5.508  14.884 -16.320  1.00 25.00           C
ATOM     23  CA  GLY    23      -4.848  11.232 -17.154  1.00 25.00           C
ATOM     24  CA  TYR    24      -2.365   8.472 -16.289  1.00 25.00           C
ATOM     25  CA  ILE    25      -4.653   5.477 -16.495  1.00 25.00           C
ATOM     26  CA  GLY    26      -3.721   4.575 -20.029  1.00 25.00           C
ATOM     27  CA  ASP    27      -7.449   4.071 -20.495  1.00 25.00           C
ATOM     28  CA  LYS    28      -8.007   0.910 -18.517  1.00 25.00           C
ATOM     29  CA  LYS    29      -5.750  -1.964 -17.324  1.00 25.00           C
ATOM     30  CA  LEU    30      -3.104  -1.807 -14.548  1.00 25.00           C
ATOM     31  CA  GLU    31      -1.865   1.140 -16.611  1.00 25.00           C
ATOM     32  CA  PRO    32       0.174   4.066 -15.210  1.00 25.00           C
ATOM     33  CA  SER    33      -0.919   3.137 -11.679  1.00 25.00           C
ATOM     34  CA  GLY    34      -3.875   5.425 -11.150  1.00 25.00           C
ATOM     35  CA  ILE    35      -4.936   9.100 -11.625  1.00 25.00           C
ATOM     36  CA  PHE    36      -3.924  12.732 -12.086  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.374  15.989 -10.868  1.00 25.00           C
ATOM     38  CA  LYS    38      -1.422  17.592 -14.242  1.00 25.00           C
ATOM     39  CA  SER    39      -1.608  21.311 -13.434  1.00 25.00           C
ATOM     40  CA  ILE    40      -1.740  23.766 -10.554  1.00 25.00           C
ATOM     41  CA  THR    41      -4.306  26.531 -10.912  1.00 25.00           C
ATOM     42  CA  LYS    42      -2.297  29.326  -9.323  1.00 25.00           C
ATOM     43  CA  SER    43      -4.775  30.892  -6.935  1.00 25.00           C
ATOM     44  CA  SER    44      -6.331  28.229  -4.694  1.00 25.00           C
ATOM     45  CA  ALA    45      -4.814  25.287  -2.876  1.00 25.00           C
ATOM     46  CA  VAL    46      -2.329  22.472  -3.738  1.00 25.00           C
ATOM     47  CA  GLU    47      -0.253  25.403  -5.067  1.00 25.00           C
ATOM     48  CA  HIS    48       0.362  26.623  -1.489  1.00 25.00           C
ATOM     49  CA  ASP    49       0.388  24.070   1.312  1.00 25.00           C
ATOM     50  CA  GLY    50       3.803  22.900  -0.005  1.00 25.00           C
ATOM     51  CA  ARG    51       3.286  19.996  -2.470  1.00 25.00           C
ATOM     52  CA  ILE    52       1.480  19.170  -5.676  1.00 25.00           C
ATOM     53  CA  GLN    53       4.323  18.487  -8.152  1.00 25.00           C
ATOM     54  CA  ILE    54       2.961  17.686 -11.576  1.00 25.00           C
ATOM     55  CA  GLY    55       2.486  14.079 -12.627  1.00 25.00           C
ATOM     56  CA  ASP    56       2.969  13.412  -8.897  1.00 25.00           C
ATOM     57  CA  GLN    57      -0.467  11.731  -8.614  1.00 25.00           C
ATOM     58  CA  ILE    58      -3.743  10.708  -6.916  1.00 25.00           C
ATOM     59  CA  ILE    59      -5.639   7.932  -5.127  1.00 25.00           C
ATOM     60  CA  ALA    60      -8.127   9.485  -2.679  1.00 25.00           C
ATOM     61  CA  VAL    61     -11.027  11.972  -2.123  1.00 25.00           C
ATOM     62  CA  ASP    62     -10.692  10.750   1.480  1.00 25.00           C
ATOM     63  CA  GLY    63     -11.383   7.020   1.960  1.00 25.00           C
ATOM     64  CA  THR    64     -12.927   6.328  -1.447  1.00 25.00           C
ATOM     65  CA  ASN    65     -11.203   5.232  -4.656  1.00 25.00           C
ATOM     66  CA  LEU    66      -9.990   7.339  -7.541  1.00 25.00           C
ATOM     67  CA  GLN    67      -8.370   4.081  -8.488  1.00 25.00           C
ATOM     68  CA  GLY    68      -9.815   2.004 -11.393  1.00 25.00           C
ATOM     69  CA  PHE    69     -11.619   4.853 -13.058  1.00 25.00           C
ATOM     70  CA  THR    70     -10.209   6.558 -16.147  1.00 25.00           C
ATOM     71  CA  ASN    71      -9.899  10.336 -15.682  1.00 25.00           C
ATOM     72  CA  GLN    72     -13.623  11.226 -15.601  1.00 25.00           C
ATOM     73  CA  GLN    73     -14.040   9.281 -12.327  1.00 25.00           C
ATOM     74  CA  ALA    74     -11.038  11.122 -10.822  1.00 25.00           C
ATOM     75  CA  VAL    75     -12.531  14.482 -11.894  1.00 25.00           C
ATOM     76  CA  GLU    76     -15.881  13.529 -10.302  1.00 25.00           C
ATOM     77  CA  VAL    77     -14.092  12.555  -7.060  1.00 25.00           C
ATOM     78  CA  LEU    78     -12.230  15.902  -7.052  1.00 25.00           C
ATOM     79  CA  ARG    79     -15.533  17.768  -7.573  1.00 25.00           C
ATOM     80  CA  HIS    80     -17.115  15.828  -4.675  1.00 25.00           C
ATOM     81  CA  THR    81     -15.617  17.971  -2.007  1.00 25.00           C
ATOM     82  CA  GLY    82     -17.162  21.179  -0.742  1.00 25.00           C
ATOM     83  CA  GLN    83     -14.736  20.941   2.150  1.00 25.00           C
ATOM     84  CA  THR    84     -11.497  19.303   3.388  1.00 25.00           C
ATOM     85  CA  VAL    85     -10.954  18.208  -0.201  1.00 25.00           C
ATOM     86  CA  LEU    86      -8.529  15.459   0.813  1.00 25.00           C
ATOM     87  CA  LEU    87      -6.223  14.104  -1.815  1.00 25.00           C
ATOM     88  CA  THR    88      -3.635  11.908  -0.207  1.00 25.00           C
ATOM     89  CA  LEU    89      -0.833  12.053  -2.771  1.00 25.00           C
ATOM     90  CA  MET    90       0.927   8.971  -4.134  1.00 25.00           C
ATOM     91  CA  ARG    91       4.567   8.854  -5.266  1.00 25.00           C
ATOM     92  CA  ARG    92       8.209   8.806  -6.148  1.00 25.00           C
ATOM     93  CA  GLY    93      11.847   9.221  -7.140  1.00 25.00           C
ATOM     94  CA  GLU    94      12.828   5.643  -6.145  1.00 25.00           C
TER
END
