
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   90 (  669),  selected   90 , name T0359_D1.pdb
# PARAMETERS: T0359TS393_5-D1.T0359_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S       1           -
LGA    S       1      M       2           #
LGA    M       2      S       3           -
LGA    S       3      -       -           -
LGA    E       4      E       4          2.699
LGA    T       5      T       5          1.115
LGA    F       6      F       6          2.467
LGA    D       7      D       7          1.484
LGA    V       8      V       8          1.436
LGA    E       9      E       9          1.878
LGA    L      10      L      10          2.792
LGA    T      11      T      11          2.847
LGA    K      12      K      12          1.984
LGA    N      13      N      13          1.985
LGA    V      14      V      14          2.088
LGA    Q      15      Q      15          1.870
LGA    G      16      G      16          1.800
LGA    L      17      L      17          1.734
LGA    G      18      G      18          1.870
LGA    I      19      I      19          3.772
LGA    T      20      T      20          2.273
LGA    I      21      I      21          1.808
LGA    A      22      A      22          1.060
LGA    G      23      G      23          1.609
LGA    Y      24      -       -           -
LGA    I      25      Y      24          4.146
LGA    G      26      I      25          3.681
LGA    D      27      G      26          6.592
LGA    K      28      D      27           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      -       -           -
LGA    P      32      P      32          1.822
LGA    S      33      S      33          3.535
LGA    G      34      G      34          2.444
LGA    I      35      I      35          1.347
LGA    F      36      F      36          0.664
LGA    V      37      V      37          0.938
LGA    K      38      K      38          0.771
LGA    S      39      S      39          0.698
LGA    I      40      I      40          1.359
LGA    T      41      T      41          1.464
LGA    K      42      K      42          2.071
LGA    S      43      S      43          2.841
LGA    S      44      S      44          0.468
LGA    A      45      A      45          2.529
LGA    V      46      V      46          1.847
LGA    E      47      E      47          1.737
LGA    H      48      H      48          2.723
LGA    D      49      D      49          0.971
LGA    G      50      G      50          1.411
LGA    R      51      R      51          1.638
LGA    I      52      I      52          1.245
LGA    Q      53      Q      53          0.563
LGA    I      54      I      54          0.361
LGA    G      55      G      55          0.733
LGA    D      56      D      56          0.597
LGA    Q      57      Q      57          1.047
LGA    I      58      I      58          0.921
LGA    I      59      I      59          1.438
LGA    A      60      A      60          2.075
LGA    V      61      V      61          2.794
LGA    D      62      D      62          1.117
LGA    G      63      G      63          0.738
LGA    T      64      T      64          0.777
LGA    N      65      N      65          2.148
LGA    L      66      L      66          1.680
LGA    Q      67      Q      67          1.012
LGA    G      68      G      68          3.753
LGA    F      69      F      69          3.038
LGA    T      70      T      70          3.615
LGA    N      71      N      71          2.760
LGA    Q      72      Q      72          2.596
LGA    Q      73      Q      73          2.403
LGA    A      74      A      74          2.368
LGA    V      75      V      75          2.574
LGA    E      76      E      76          2.306
LGA    V      77      V      77          1.817
LGA    L      78      L      78          1.632
LGA    R      79      R      79          2.258
LGA    H      80      H      80          1.741
LGA    T      81      T      81          0.991
LGA    G      82      G      82          0.944
LGA    Q      83      Q      83          2.984
LGA    T      84      T      84          1.707
LGA    V      85      V      85          1.714
LGA    L      86      L      86          1.672
LGA    L      87      L      87          1.190
LGA    T      88      T      88          1.141
LGA    L      89      L      89          1.811
LGA    M      90      M      90          2.033
LGA    R      91      R      91          1.566
LGA    R      92      R      92          2.600
LGA    G      93      G      93          3.278
LGA    E      94      E      94          4.176

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94   90    5.0     86    2.20    96.51     76.014     3.733

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.635647 * X  +   0.728911 * Y  +   0.254245 * Z  +  -4.354580
  Y_new =  -0.199702 * X  +   0.473392 * Y  +  -0.857916 * Z  +  13.830328
  Z_new =  -0.745702 * X  +   0.494559 * Y  +   0.446475 * Z  +  -7.159652 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.836450   -2.305143  [ DEG:    47.9251   -132.0749 ]
  Theta =   0.841588    2.300004  [ DEG:    48.2194    131.7806 ]
  Phi   =  -0.304406    2.837187  [ DEG:   -17.4412    162.5588 ]
 
# 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_5-D1                               
REMARK     2: T0359_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS393_5-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   86   2.20   96.51  76.014
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS393_5-D1
PFRMAT TS
TARGET T0359
MODEL 5
PARENT N/A
ATOM      1  CA  SER     1      10.749   1.496   1.716  1.00 25.00           C
ATOM      2  CA  MET     2       7.302   1.301   3.282  1.00 25.00           C
ATOM      3  CA  SER     3       4.468   2.749   1.145  1.00 25.00           C
ATOM      4  CA  GLU     4       5.156   5.768  -1.002  1.00 25.00           C
ATOM      5  CA  THR     5       3.316   9.009  -0.191  1.00 25.00           C
ATOM      6  CA  PHE     6       2.225  12.644  -0.110  1.00 25.00           C
ATOM      7  CA  ASP     7      -0.749  12.290   2.272  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.258  15.671   1.737  1.00 25.00           C
ATOM      9  CA  GLU     9      -4.647  18.282   2.986  1.00 25.00           C
ATOM     10  CA  LEU    10      -4.778  21.317   0.724  1.00 25.00           C
ATOM     11  CA  THR    11      -7.215  23.946   1.989  1.00 25.00           C
ATOM     12  CA  LYS    12     -10.732  24.508   0.622  1.00 25.00           C
ATOM     13  CA  ASN    13     -11.144  28.225   0.025  1.00 25.00           C
ATOM     14  CA  VAL    14     -12.829  29.868  -2.963  1.00 25.00           C
ATOM     15  CA  GLN    15     -12.284  29.048  -6.601  1.00 25.00           C
ATOM     16  CA  GLY    16     -13.189  25.479  -5.716  1.00 25.00           C
ATOM     17  CA  LEU    17     -10.114  23.490  -4.798  1.00 25.00           C
ATOM     18  CA  GLY    18      -8.157  24.462  -7.953  1.00 25.00           C
ATOM     19  CA  ILE    19      -8.819  20.754  -8.796  1.00 25.00           C
ATOM     20  CA  THR    20      -7.150  19.002 -11.781  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.123  15.403 -13.100  1.00 25.00           C
ATOM     22  CA  ALA    22      -4.968  14.762 -16.143  1.00 25.00           C
ATOM     23  CA  GLY    23      -6.340  11.654 -17.865  1.00 25.00           C
ATOM     24  CA  TYR    24      -2.803  10.302 -17.298  1.00 25.00           C
ATOM     25  CA  ILE    25      -4.106   6.755 -16.910  1.00 25.00           C
ATOM     26  CA  GLY    26      -6.233   6.506 -20.098  1.00 25.00           C
ATOM     27  CA  ASP    27      -7.174   2.836 -19.634  1.00 25.00           C
ATOM     28  CA  LYS    28      -3.600   1.969 -20.591  1.00 25.00           C
ATOM     29  CA  LYS    29      -2.651   4.496 -23.205  1.00 25.00           C
ATOM     30  CA  LEU    30      -0.115   5.626 -20.658  1.00 25.00           C
ATOM     31  CA  GLU    31       0.894   3.713 -17.526  1.00 25.00           C
ATOM     32  CA  PRO    32      -2.058   2.303 -15.583  1.00 25.00           C
ATOM     33  CA  SER    33      -1.105   4.787 -12.932  1.00 25.00           C
ATOM     34  CA  GLY    34      -4.175   5.584 -10.757  1.00 25.00           C
ATOM     35  CA  ILE    35      -4.749   9.111 -12.136  1.00 25.00           C
ATOM     36  CA  PHE    36      -2.524  12.246 -12.297  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.344  15.821 -11.097  1.00 25.00           C
ATOM     38  CA  LYS    38      -1.682  18.059 -14.172  1.00 25.00           C
ATOM     39  CA  SER    39      -1.452  21.739 -13.113  1.00 25.00           C
ATOM     40  CA  ILE    40      -0.737  22.794  -9.588  1.00 25.00           C
ATOM     41  CA  THR    41      -2.413  26.123 -10.544  1.00 25.00           C
ATOM     42  CA  LYS    42      -2.089  29.908 -10.363  1.00 25.00           C
ATOM     43  CA  SER    43      -3.923  31.259  -7.315  1.00 25.00           C
ATOM     44  CA  SER    44      -4.631  28.314  -5.110  1.00 25.00           C
ATOM     45  CA  ALA    45      -5.085  24.853  -3.644  1.00 25.00           C
ATOM     46  CA  VAL    46      -1.362  24.130  -4.181  1.00 25.00           C
ATOM     47  CA  GLU    47       0.389  27.437  -4.997  1.00 25.00           C
ATOM     48  CA  HIS    48       2.268  27.293  -1.662  1.00 25.00           C
ATOM     49  CA  ASP    49       0.334  25.111   0.808  1.00 25.00           C
ATOM     50  CA  GLY    50       2.388  22.270  -0.811  1.00 25.00           C
ATOM     51  CA  ARG    51       3.352  18.806  -2.079  1.00 25.00           C
ATOM     52  CA  ILE    52       0.602  19.055  -4.697  1.00 25.00           C
ATOM     53  CA  GLN    53       3.169  18.189  -7.337  1.00 25.00           C
ATOM     54  CA  ILE    54       2.779  18.038 -11.132  1.00 25.00           C
ATOM     55  CA  GLY    55       2.832  14.414 -12.236  1.00 25.00           C
ATOM     56  CA  ASP    56       1.518  13.340  -8.813  1.00 25.00           C
ATOM     57  CA  GLN    57      -0.177   9.913  -8.342  1.00 25.00           C
ATOM     58  CA  ILE    58      -3.790  10.923  -7.532  1.00 25.00           C
ATOM     59  CA  ILE    59      -6.035   8.274  -5.953  1.00 25.00           C
ATOM     60  CA  ALA    60      -8.835   9.803  -3.812  1.00 25.00           C
ATOM     61  CA  VAL    61     -12.528  10.678  -3.551  1.00 25.00           C
ATOM     62  CA  ASP    62     -12.205  11.244   0.204  1.00 25.00           C
ATOM     63  CA  GLY    63     -11.528   7.807   1.615  1.00 25.00           C
ATOM     64  CA  THR    64     -13.084   6.096  -1.354  1.00 25.00           C
ATOM     65  CA  ASN    65     -11.222   4.278  -4.109  1.00 25.00           C
ATOM     66  CA  LEU    66     -10.622   5.363  -7.670  1.00 25.00           C
ATOM     67  CA  GLN    67      -7.718   2.907  -8.221  1.00 25.00           C
ATOM     68  CA  GLY    68      -7.451   1.763 -11.875  1.00 25.00           C
ATOM     69  CA  PHE    69     -10.042   4.282 -13.066  1.00 25.00           C
ATOM     70  CA  THR    70      -9.596   6.462 -16.185  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.736   9.925 -15.075  1.00 25.00           C
ATOM     72  CA  GLN    72     -14.183  11.482 -15.673  1.00 25.00           C
ATOM     73  CA  GLN    73     -15.501   9.860 -12.464  1.00 25.00           C
ATOM     74  CA  ALA    74     -12.494  11.216 -10.516  1.00 25.00           C
ATOM     75  CA  VAL    75     -13.120  14.716 -11.938  1.00 25.00           C
ATOM     76  CA  GLU    76     -16.808  14.495 -10.929  1.00 25.00           C
ATOM     77  CA  VAL    77     -15.800  13.421  -7.393  1.00 25.00           C
ATOM     78  CA  LEU    78     -13.361  16.365  -7.168  1.00 25.00           C
ATOM     79  CA  ARG    79     -16.114  18.767  -8.318  1.00 25.00           C
ATOM     80  CA  HIS    80     -18.496  17.338  -5.681  1.00 25.00           C
ATOM     81  CA  THR    81     -16.038  17.318  -2.815  1.00 25.00           C
ATOM     82  CA  GLY    82     -17.108  20.129  -0.407  1.00 25.00           C
ATOM     83  CA  GLN    83     -15.112  20.801   2.752  1.00 25.00           C
ATOM     84  CA  THR    84     -11.617  19.317   2.468  1.00 25.00           C
ATOM     85  CA  VAL    85     -10.956  17.411  -0.818  1.00 25.00           C
ATOM     86  CA  LEU    86      -8.481  14.811   0.462  1.00 25.00           C
ATOM     87  CA  LEU    87      -5.517  13.265  -1.317  1.00 25.00           C
ATOM     88  CA  THR    88      -4.166   9.815  -0.518  1.00 25.00           C
ATOM     89  CA  LEU    89      -1.207   9.327  -2.837  1.00 25.00           C
ATOM     90  CA  MET    90       1.126   6.801  -4.411  1.00 25.00           C
ATOM     91  CA  ARG    91       4.133   8.645  -5.861  1.00 25.00           C
ATOM     92  CA  ARG    92       7.905   8.583  -5.702  1.00 25.00           C
ATOM     93  CA  GLY    93      11.579   9.439  -4.921  1.00 25.00           C
ATOM     94  CA  GLU    94      13.779   6.484  -5.813  1.00 25.00           C
TER
END
