
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0350TS393_1-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350TS393_1-D1.T0350_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    N       2      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    I       3      Q      10           #
LGA    E       4      P      11           -
LGA    R       5      V      12           -
LGA    L       6      W      13           #
LGA    T       7      D      14          2.989
LGA    -       -      R      15           -
LGA    T       8      Y      16          4.625
LGA    L       9      D      17          4.245
LGA    Q      10      T      18          4.295
LGA    P      11      Q      19          5.254
LGA    V      12      -       -           -
LGA    W      13      -       -           -
LGA    D      14      I      20           #
LGA    R      15      H      21           -
LGA    Y      16      -       -           -
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    Q      19      -       -           -
LGA    I      20      -       -           -
LGA    H      21      -       -           -
LGA    S      36      -       -           -
LGA    Y      37      -       -           -
LGA    T      38      -       -           -
LGA    N      39      -       -           -
LGA    L      40      -       -           -
LGA    A      41      -       -           -
LGA    E      42      -       -           -
LGA    M      43      -       -           -
LGA    V      44      S      36           #
LGA    G      45      Y      37          4.854
LGA    E      46      T      38          2.389
LGA    M      47      N      39          1.985
LGA    N      48      L      40          1.573
LGA    K      49      A      41          4.868
LGA    L      50      E      42           #
LGA    -       -      M      43           -
LGA    L      51      V      44          4.595
LGA    E      52      -       -           -
LGA    P      53      -       -           -
LGA    S      54      -       -           -
LGA    Q      55      -       -           -
LGA    V      56      -       -           -
LGA    H      57      -       -           -
LGA    L      58      -       -           -
LGA    K      59      -       -           -
LGA    F      60      G      45          4.217
LGA    E      61      E      46          3.260
LGA    L      62      M      47          1.501
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    H      63      L      50           #
LGA    D      64      L      51           -
LGA    K      65      E      52           -
LGA    L      66      P      53           -
LGA    N      67      S      54           -
LGA    E      68      Q      55           -
LGA    Y      69      V      56           -
LGA    Y      70      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    -       -      F      60           -
LGA    V      71      E      61          4.930
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    K      72      V      71          3.015
LGA    V      73      K      72          3.605
LGA    -       -      V      73           -
LGA    I      74      I      74          1.458
LGA    E      75      E      75          2.532
LGA    D      76      D      76          2.507
LGA    S      77      S      77           #
LGA    T      78      T      78           -
LGA    N      79      N      79           #
LGA    E      80      E      80           -
LGA    V      81      -       -           -
LGA    I      82      -       -           -
LGA    R      83      V      81           #
LGA    E      84      I      82           #
LGA    -       -      R      83           -
LGA    I      85      E      84          3.014
LGA    P      86      I      85          3.197
LGA    -       -      P      86           -
LGA    P      87      P      87          1.022
LGA    K      88      K      88          2.465
LGA    R      89      R      89          2.734
LGA    W      90      W      90          2.512
LGA    L      91      L      91          2.396
LGA    D      92      D      92          1.879
LGA    F      93      F      93          1.795
LGA    Y      94      Y      94          1.673
LGA    A      95      A      95          1.344
LGA    A      96      A      96          1.600
LGA    M      97      M      97          1.936
LGA    T      98      T      98          1.280
LGA    E      99      E      99          0.838
LGA    F     100      F     100          1.403
LGA    L     101      L     101          2.410
LGA    G     102      G     102          2.171
LGA    L     103      L     103          1.447
LGA    F     104      F     104          1.687
LGA    V     105      V     105          4.364

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     41    3.00    56.10     29.935     1.322

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.521483 * X  +   0.053070 * Y  +   0.851610 * Z  +   0.000824
  Y_new =  -0.232092 * X  +  -0.969255 * Y  +  -0.081721 * Z  +  -0.055556
  Z_new =   0.821090 * X  +  -0.240268 * Y  +   0.517767 * Z  + -18.333717 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.434474    2.707119  [ DEG:   -24.8935    155.1065 ]
  Theta =  -0.963318   -2.178274  [ DEG:   -55.1941   -124.8059 ]
  Phi   =  -2.722852    0.418740  [ DEG:  -156.0079     23.9920 ]
 
# 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: T0350TS393_1-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS393_1-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91   91   5.0   41   3.00   56.10  29.935
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS393_1-D1
PFRMAT TS
TARGET T0350
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      18.919 -11.822  -8.959  1.00 25.00           C
ATOM      2  CA  ASN     2      16.092 -11.782 -11.432  1.00 25.00           C
ATOM      3  CA  ILE     3      12.713 -12.781 -10.095  1.00 25.00           C
ATOM      4  CA  GLU     4      12.576 -16.038 -12.075  1.00 25.00           C
ATOM      5  CA  ARG     5      11.431 -16.887 -15.593  1.00 25.00           C
ATOM      6  CA  LEU     6      10.800 -13.158 -16.172  1.00 25.00           C
ATOM      7  CA  THR     7       7.453 -11.511 -15.894  1.00 25.00           C
ATOM      8  CA  THR     8       5.465 -12.302 -18.978  1.00 25.00           C
ATOM      9  CA  LEU     9       2.013 -11.339 -20.203  1.00 25.00           C
ATOM     10  CA  GLN    10       0.575 -14.719 -21.182  1.00 25.00           C
ATOM     11  CA  PRO    11      -2.230 -14.749 -18.596  1.00 25.00           C
ATOM     12  CA  VAL    12      -5.361 -13.192 -17.141  1.00 25.00           C
ATOM     13  CA  TRP    13      -4.055 -10.039 -18.821  1.00 25.00           C
ATOM     14  CA  ASP    14      -4.385 -10.677 -22.582  1.00 25.00           C
ATOM     15  CA  ARG    15      -7.301 -13.077 -21.943  1.00 25.00           C
ATOM     16  CA  TYR    16      -9.008 -10.455 -19.734  1.00 25.00           C
ATOM     17  CA  ASP    17      -8.550  -7.816 -22.471  1.00 25.00           C
ATOM     18  CA  THR    18     -10.053 -10.204 -25.060  1.00 25.00           C
ATOM     19  CA  GLN    19     -13.038 -10.864 -22.755  1.00 25.00           C
ATOM     20  CA  ILE    20     -13.549  -7.096 -22.297  1.00 25.00           C
ATOM     21  CA  HIS    21     -13.435  -6.595 -26.092  1.00 25.00           C
ATOM     36  CA  SER    36     -15.555   3.391 -29.219  1.00 25.00           C
ATOM     37  CA  TYR    37     -12.373   2.508 -31.012  1.00 25.00           C
ATOM     38  CA  THR    38     -11.014   4.906 -33.670  1.00 25.00           C
ATOM     39  CA  ASN    39     -10.750   7.693 -31.057  1.00 25.00           C
ATOM     40  CA  LEU    40      -8.882   5.331 -28.691  1.00 25.00           C
ATOM     41  CA  ALA    41      -6.477   4.369 -31.511  1.00 25.00           C
ATOM     42  CA  GLU    42      -5.862   8.069 -32.283  1.00 25.00           C
ATOM     43  CA  MET    43      -5.163   8.750 -28.580  1.00 25.00           C
ATOM     44  CA  VAL    44      -2.702   5.817 -28.480  1.00 25.00           C
ATOM     45  CA  GLY    45      -0.938   7.159 -31.603  1.00 25.00           C
ATOM     46  CA  GLU    46      -0.693  10.630 -30.003  1.00 25.00           C
ATOM     47  CA  MET    47       0.776   9.087 -26.821  1.00 25.00           C
ATOM     48  CA  ASN    48       3.339   7.156 -28.911  1.00 25.00           C
ATOM     49  CA  LYS    49       4.298  10.373 -30.753  1.00 25.00           C
ATOM     50  CA  LEU    50       4.721  12.191 -27.409  1.00 25.00           C
ATOM     51  CA  LEU    51       6.933   9.346 -26.114  1.00 25.00           C
ATOM     52  CA  GLU    52       9.061   9.521 -29.293  1.00 25.00           C
ATOM     53  CA  PRO    53       9.428  13.309 -28.869  1.00 25.00           C
ATOM     54  CA  SER    54      10.459  13.311 -25.246  1.00 25.00           C
ATOM     55  CA  GLN    55      14.249  13.469 -24.944  1.00 25.00           C
ATOM     56  CA  VAL    56      14.116   9.978 -26.453  1.00 25.00           C
ATOM     57  CA  HIS    57      16.139   8.895 -23.478  1.00 25.00           C
ATOM     58  CA  LEU    58      14.929   8.876 -19.827  1.00 25.00           C
ATOM     59  CA  LYS    59      11.973  11.138 -20.729  1.00 25.00           C
ATOM     60  CA  PHE    60       8.423  11.063 -19.249  1.00 25.00           C
ATOM     61  CA  GLU    61       5.216  12.394 -17.765  1.00 25.00           C
ATOM     62  CA  LEU    62       3.769   8.983 -16.684  1.00 25.00           C
ATOM     63  CA  HIS    63       0.289  10.121 -15.543  1.00 25.00           C
ATOM     64  CA  ASP    64      -1.808  12.910 -16.910  1.00 25.00           C
ATOM     65  CA  LYS    65      -5.104  11.189 -15.924  1.00 25.00           C
ATOM     66  CA  LEU    66      -3.911   7.734 -16.971  1.00 25.00           C
ATOM     67  CA  ASN    67      -1.977   8.976 -20.004  1.00 25.00           C
ATOM     68  CA  GLU    68       1.356   7.906 -21.338  1.00 25.00           C
ATOM     69  CA  TYR    69       1.839   5.674 -24.357  1.00 25.00           C
ATOM     70  CA  TYR    70       5.359   5.035 -22.984  1.00 25.00           C
ATOM     71  CA  VAL    71       9.087   5.180 -23.808  1.00 25.00           C
ATOM     72  CA  LYS    72      12.614   4.676 -25.296  1.00 25.00           C
ATOM     73  CA  VAL    73      14.902   4.172 -22.288  1.00 25.00           C
ATOM     74  CA  ILE    74      18.123   4.577 -20.303  1.00 25.00           C
ATOM     75  CA  GLU    75      16.172   4.826 -17.072  1.00 25.00           C
ATOM     76  CA  ASP    76      17.431   7.809 -15.050  1.00 25.00           C
ATOM     77  CA  SER    77      16.442   7.835 -11.393  1.00 25.00           C
ATOM     78  CA  THR    78      14.800  11.061 -10.168  1.00 25.00           C
ATOM     79  CA  ASN    79      16.133  12.906 -13.274  1.00 25.00           C
ATOM     80  CA  GLU    80      13.342  11.053 -15.147  1.00 25.00           C
ATOM     81  CA  VAL    81      10.479   8.537 -15.293  1.00 25.00           C
ATOM     82  CA  ILE    82      10.136   6.026 -18.181  1.00 25.00           C
ATOM     83  CA  ARG    83       8.485   2.809 -19.361  1.00 25.00           C
ATOM     84  CA  GLU    84      11.112   0.845 -21.302  1.00 25.00           C
ATOM     85  CA  ILE    85      10.501   0.277 -24.984  1.00 25.00           C
ATOM     86  CA  PRO    86       8.436   0.336 -28.129  1.00 25.00           C
ATOM     87  CA  PRO    87       4.855   0.118 -29.350  1.00 25.00           C
ATOM     88  CA  LYS    88       2.479  -2.539 -27.949  1.00 25.00           C
ATOM     89  CA  ARG    89       5.087  -3.520 -25.321  1.00 25.00           C
ATOM     90  CA  TRP    90       5.518   0.157 -24.340  1.00 25.00           C
ATOM     91  CA  LEU    91       1.721   0.540 -24.014  1.00 25.00           C
ATOM     92  CA  ASP    92       1.569  -2.590 -21.813  1.00 25.00           C
ATOM     93  CA  PHE    93       4.379  -1.207 -19.609  1.00 25.00           C
ATOM     94  CA  TYR    94       2.516   2.122 -19.280  1.00 25.00           C
ATOM     95  CA  ALA    95      -0.687   0.262 -18.304  1.00 25.00           C
ATOM     96  CA  ALA    96       1.250  -1.743 -15.677  1.00 25.00           C
ATOM     97  CA  MET    97       2.740   1.493 -14.271  1.00 25.00           C
ATOM     98  CA  THR    98      -0.753   3.053 -14.092  1.00 25.00           C
ATOM     99  CA  GLU    99      -2.070  -0.045 -12.265  1.00 25.00           C
ATOM    100  CA  PHE   100       0.842   0.150  -9.784  1.00 25.00           C
ATOM    101  CA  LEU   101       0.108   3.859  -9.177  1.00 25.00           C
ATOM    102  CA  GLY   102      -3.588   3.056  -8.574  1.00 25.00           C
ATOM    103  CA  LEU   103      -2.610   0.304  -6.095  1.00 25.00           C
ATOM    104  CA  PHE   104      -0.294   2.743  -4.265  1.00 25.00           C
ATOM    105  CA  VAL   105       3.175   3.965  -5.100  1.00 25.00           C
TER
END
