
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0350TS383_2-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350TS383_2-D1.T0350_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
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           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
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           -
LGA    E      61      E      61          2.389
LGA    L      62      L      62          1.576
LGA    -       -      H      63           -
LGA    H      63      D      64          2.295
LGA    D      64      K      65           #
LGA    -       -      L      66           -
LGA    K      65      N      67          3.495
LGA    L      66      E      68          1.063
LGA    N      67      Y      69          3.733
LGA    E      68      Y      70          1.407
LGA    Y      69      V      71          1.691
LGA    Y      70      K      72          1.161
LGA    V      71      V      73          0.842
LGA    K      72      I      74          1.149
LGA    V      73      E      75          1.948
LGA    I      74      D      76          4.008
LGA    E      75      S      77          2.902
LGA    D      76      T      78          2.067
LGA    -       -      N      79           -
LGA    S      77      E      80          2.545
LGA    T      78      V      81          0.659
LGA    -       -      I      82           -
LGA    N      79      R      83          3.428
LGA    E      80      E      84          2.146
LGA    V      81      I      85          1.748
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    I      82      F      93          3.074
LGA    R      83      Y      94          3.179
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    E      84      T      98          3.426
LGA    -       -      E      99           -
LGA    I      85      F     100           #
LGA    P      86      L     101          2.417
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26   91    5.0     24    2.46    16.67     19.614     0.938

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.284876 * X  +  -0.721738 * Y  +   0.630824 * Z  +   9.814423
  Y_new =  -0.924520 * X  +   0.380704 * Y  +   0.018063 * Z  +   2.795909
  Z_new =  -0.253194 * X  +  -0.578064 * Y  +  -0.775716 * Z  + -22.229437 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.501170    0.640423  [ DEG:  -143.3065     36.6935 ]
  Theta =   0.255981    2.885612  [ DEG:    14.6666    165.3334 ]
  Phi   =  -1.869699    1.271894  [ DEG:  -107.1259     72.8741 ]
 
# 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: T0350TS383_2-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS383_2-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26   91   5.0   24   2.46   16.67  19.614
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS383_2-D1
PFRMAT TS
TARGET T0350
MODEL 2
PARENT 1g5vA
ATOM      1  N   GLU    61      13.777   7.869 -25.749  1.00  0.00
ATOM      2  CA  GLU    61      13.562   8.083 -27.178  1.00  0.00
ATOM      3  C   GLU    61      12.432   7.204 -27.696  1.00  0.00
ATOM      4  O   GLU    61      12.122   6.167 -27.113  1.00  0.00
ATOM      5  N   LEU    62      11.811   7.629 -28.791  1.00  0.00
ATOM      6  CA  LEU    62      10.708   6.882 -29.386  1.00  0.00
ATOM      7  C   LEU    62      10.776   6.909 -30.908  1.00  0.00
ATOM      8  O   LEU    62      11.197   7.900 -31.503  1.00  0.00
ATOM      9  N   HIS    63      10.351   5.813 -31.532  1.00  0.00
ATOM     10  CA  HIS    63      10.354   5.712 -32.985  1.00  0.00
ATOM     11  C   HIS    63       8.980   5.287 -33.497  1.00  0.00
ATOM     12  O   HIS    63       8.688   4.097 -33.609  1.00  0.00
ATOM     13  N   ASP    64       8.139   6.273 -33.796  1.00  0.00
ATOM     14  CA  ASP    64       6.787   6.015 -34.285  1.00  0.00
ATOM     15  C   ASP    64       6.795   5.116 -35.520  1.00  0.00
ATOM     16  O   ASP    64       5.793   4.473 -35.833  1.00  0.00
ATOM     17  N   LYS    65       7.926   5.077 -36.221  1.00  0.00
ATOM     18  CA  LYS    65       8.052   4.256 -37.422  1.00  0.00
ATOM     19  C   LYS    65       7.675   2.804 -37.138  1.00  0.00
ATOM     20  O   LYS    65       6.674   2.302 -37.645  1.00  0.00
ATOM     21  N   LEU    66       8.486   2.134 -36.322  1.00  0.00
ATOM     22  CA  LEU    66       8.239   0.741 -35.970  1.00  0.00
ATOM     23  C   LEU    66       7.499   0.633 -34.639  1.00  0.00
ATOM     24  O   LEU    66       7.564  -0.396 -33.965  1.00  0.00
ATOM     25  N   ASN    67       6.792   1.702 -34.275  1.00  0.00
ATOM     26  CA  ASN    67       6.028   1.742 -33.030  1.00  0.00
ATOM     27  C   ASN    67       6.826   1.153 -31.868  1.00  0.00
ATOM     28  O   ASN    67       6.415   0.164 -31.256  1.00  0.00
ATOM     29  N   GLU    68       7.968   1.764 -31.568  1.00  0.00
ATOM     30  CA  GLU    68       8.821   1.297 -30.482  1.00  0.00
ATOM     31  C   GLU    68       9.363   2.470 -29.670  1.00  0.00
ATOM     32  O   GLU    68       9.047   3.626 -29.947  1.00  0.00
ATOM     33  N   TYR    69      10.181   2.162 -28.669  1.00  0.00
ATOM     34  CA  TYR    69      10.769   3.189 -27.817  1.00  0.00
ATOM     35  C   TYR    69      11.915   2.624 -26.986  1.00  0.00
ATOM     36  O   TYR    69      12.131   1.412 -26.951  1.00  0.00
ATOM     37  N   TYR    70      12.644   3.509 -26.316  1.00  0.00
ATOM     38  CA  TYR    70      13.768   3.110 -25.480  1.00  0.00
ATOM     39  C   TYR    70      13.560   3.580 -24.044  1.00  0.00
ATOM     40  O   TYR    70      13.296   4.757 -23.802  1.00  0.00
ATOM     41  N   VAL    71      13.673   2.655 -23.095  1.00  0.00
ATOM     42  CA  VAL    71      13.487   2.987 -21.689  1.00  0.00
ATOM     43  C   VAL    71      14.797   2.905 -20.914  1.00  0.00
ATOM     44  O   VAL    71      15.623   2.024 -21.159  1.00  0.00
ATOM     45  N   LYS    72      14.969   3.824 -19.970  1.00  0.00
ATOM     46  CA  LYS    72      16.167   3.863 -19.141  1.00  0.00
ATOM     47  C   LYS    72      15.861   3.349 -17.739  1.00  0.00
ATOM     48  O   LYS    72      14.905   3.793 -17.102  1.00  0.00
ATOM     49  N   VAL    73      16.672   2.411 -17.263  1.00  0.00
ATOM     50  CA  VAL    73      16.477   1.837 -15.936  1.00  0.00
ATOM     51  C   VAL    73      17.019   2.763 -14.853  1.00  0.00
ATOM     52  O   VAL    73      18.229   2.875 -14.664  1.00  0.00
ATOM     53  N   ILE    74      16.107   3.429 -14.152  1.00  0.00
ATOM     54  CA  ILE    74      16.479   4.355 -13.088  1.00  0.00
ATOM     55  C   ILE    74      17.317   3.665 -12.015  1.00  0.00
ATOM     56  O   ILE    74      16.799   2.886 -11.216  1.00  0.00
ATOM     57  N   GLU    75      18.615   3.959 -12.005  1.00  0.00
ATOM     58  CA  GLU    75      19.502   3.364 -11.023  1.00  0.00
ATOM     59  C   GLU    75      20.452   2.348 -11.626  1.00  0.00
ATOM     60  O   GLU    75      21.527   2.096 -11.081  1.00  0.00
ATOM     61  N   ASP    76      21.029   2.410 -15.206  1.00  0.00
ATOM     62  CA  ASP    76      21.648   3.077 -16.338  1.00  0.00
ATOM     63  C   ASP    76      21.385   2.370 -17.655  1.00  0.00
ATOM     64  O   ASP    76      21.273   3.016 -18.698  1.00  0.00
ATOM     65  N   SER    77      21.294   1.043 -17.612  1.00  0.00
ATOM     66  CA  SER    77      21.052   0.248 -18.812  1.00  0.00
ATOM     67  C   SER    77      19.817   0.735 -19.565  1.00  0.00
ATOM     68  O   SER    77      18.828   1.144 -18.957  1.00  0.00
ATOM     69  N   THR    78      19.883   0.681 -20.892  1.00  0.00
ATOM     70  CA  THR    78      18.774   1.106 -21.738  1.00  0.00
ATOM     71  C   THR    78      18.373  -0.015 -22.690  1.00  0.00
ATOM     72  O   THR    78      19.209  -0.542 -23.424  1.00  0.00
ATOM     73  N   ASN    79      17.096  -0.382 -22.671  1.00  0.00
ATOM     74  CA  ASN    79      16.599  -1.452 -23.532  1.00  0.00
ATOM     75  C   ASN    79      15.389  -0.995 -24.341  1.00  0.00
ATOM     76  O   ASN    79      14.556  -0.228 -23.853  1.00  0.00
ATOM     77  N   GLU    80      15.297  -1.472 -25.579  1.00  0.00
ATOM     78  CA  GLU    80      14.189  -1.119 -26.460  1.00  0.00
ATOM     79  C   GLU    80      12.959  -1.966 -26.148  1.00  0.00
ATOM     80  O   GLU    80      13.043  -3.191 -26.053  1.00  0.00
ATOM     81  N   VAL    81      11.815  -1.305 -25.991  1.00  0.00
ATOM     82  CA  VAL    81      10.566  -1.992 -25.686  1.00  0.00
ATOM     83  C   VAL    81       9.426  -1.456 -26.547  1.00  0.00
ATOM     84  O   VAL    81       9.602  -0.498 -27.301  1.00  0.00
ATOM     85  N   ILE    82       4.282  -0.569 -22.363  1.00  0.00
ATOM     86  CA  ILE    82       4.738   0.381 -21.355  1.00  0.00
ATOM     87  C   ILE    82       3.762   0.444 -20.183  1.00  0.00
ATOM     88  O   ILE    82       2.569   0.680 -20.372  1.00  0.00
ATOM     89  N   ARG    83       4.276   0.230 -18.977  1.00  0.00
ATOM     90  CA  ARG    83       3.448   0.263 -17.776  1.00  0.00
ATOM     91  C   ARG    83       3.434   1.659 -17.161  1.00  0.00
ATOM     92  O   ARG    83       4.386   2.425 -17.313  1.00  0.00
ATOM     93  N   GLU    84       2.347   1.984 -16.467  1.00  0.00
ATOM     94  CA  GLU    84       2.205   3.287 -15.828  1.00  0.00
ATOM     95  C   GLU    84       3.101   3.390 -14.593  1.00  0.00
ATOM     96  O   GLU    84       3.484   2.376 -14.011  1.00  0.00
ATOM     97  N   ILE    85       3.450   4.623 -14.175  1.00  0.00
ATOM     98  CA  ILE    85       4.306   4.846 -13.003  1.00  0.00
ATOM     99  C   ILE    85       3.653   4.375 -11.708  1.00  0.00
ATOM    100  O   ILE    85       2.532   3.864 -11.716  1.00  0.00
ATOM    101  N   PRO    86       4.362   4.550 -10.596  1.00  0.00
ATOM    102  CA  PRO    86       3.852   4.140  -9.292  1.00  0.00
ATOM    103  C   PRO    86       3.747   5.331  -8.344  1.00  0.00
ATOM    104  O   PRO    86       4.455   6.327  -8.500  1.00  0.00
TER
END
