
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0326AL044_1
# Molecule2: number of CA atoms  289 ( 2373),  selected  289 , name T0326.pdb
# PARAMETERS: T0326AL044_1.T0326.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    I       3      P       2           -
LGA    V       5      I       3           -
LGA    -       -      N       4           -
LGA    -       -      V       5           -
LGA    -       -      P       6           -
LGA    -       -      S       7           -
LGA    -       -      G       8           -
LGA    -       -      L       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      V      12           -
LGA    -       -      K      13           -
LGA    -       -      V      14           -
LGA    -       -      L      15           -
LGA    -       -      A      16           -
LGA    -       -      K      17           -
LGA    -       -      E      18           -
LGA    -       -      G      19           -
LGA    -       -      I      20           -
LGA    -       -      F      21           -
LGA    -       -      V      22           -
LGA    -       -      M      23           -
LGA    -       -      T      24           -
LGA    -       -      E      25           -
LGA    -       -      K      26           -
LGA    P       6      I      33          0.576
LGA    S       7      R      34          1.000
LGA    G       8      P      35          0.786
LGA    L       9      L      36          1.460
LGA    E      18      E      37          0.850
LGA    G      19      I      38          1.198
LGA    I      20      L      39          2.192
LGA    F      21      I      40          3.291
LGA    -       -      L      41           -
LGA    -       -      N      42           -
LGA    -       -      L      43           -
LGA    -       -      M      44           -
LGA    -       -      P      45           -
LGA    -       -      D      46           -
LGA    -       -      K      47           -
LGA    -       -      I      48           -
LGA    -       -      K      49           -
LGA    -       -      T      50           -
LGA    -       -      E      51           -
LGA    -       -      I      52           -
LGA    -       -      Q      53           -
LGA    -       -      L      54           -
LGA    -       -      L      55           -
LGA    -       -      R      56           -
LGA    -       -      L      57           -
LGA    -       -      L      58           -
LGA    -       -      G      59           -
LGA    -       -      N      60           -
LGA    -       -      T      61           -
LGA    -       -      P      62           -
LGA    -       -      L      63           -
LGA    -       -      Q      64           -
LGA    -       -      V      65           -
LGA    -       -      N      66           -
LGA    -       -      V      67           -
LGA    -       -      T      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      Y      71           -
LGA    -       -      T      72           -
LGA    -       -      E      73           -
LGA    -       -      T      74           -
LGA    -       -      H      75           -
LGA    -       -      K      76           -
LGA    -       -      P      77           -
LGA    -       -      K      78           -
LGA    -       -      H      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      I      82           -
LGA    -       -      E      83           -
LGA    -       -      H      84           -
LGA    -       -      I      85           -
LGA    -       -      L      86           -
LGA    -       -      K      87           -
LGA    -       -      F      88           -
LGA    -       -      Y      89           -
LGA    -       -      T      90           -
LGA    -       -      T      91           -
LGA    -       -      F      92           -
LGA    -       -      S      93           -
LGA    -       -      A      94           -
LGA    -       -      V      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      R      98           -
LGA    -       -      K      99           -
LGA    -       -      F     100           -
LGA    -       -      D     101           -
LGA    V      22      G     102          4.626
LGA    T      24      F     103          4.424
LGA    K      26      I     104          3.690
LGA    R      27      I     105          0.813
LGA    A      28      T     106          4.156
LGA    H      30      -       -           -
LGA    Q      31      G     107          2.823
LGA    D      32      A     108          1.890
LGA    I      33      P     109          2.422
LGA    R      34      V     110          2.309
LGA    P      35      E     111          1.993
LGA    L      36      L     112          3.194
LGA    L      39      L     113          3.427
LGA    I      40      P     114          2.459
LGA    -       -      F     115           -
LGA    -       -      E     116           -
LGA    -       -      E     117           -
LGA    -       -      V     118           -
LGA    -       -      D     119           -
LGA    -       -      Y     120           -
LGA    -       -      W     121           -
LGA    -       -      E     122           -
LGA    -       -      E     123           -
LGA    -       -      L     124           -
LGA    -       -      T     125           -
LGA    -       -      E     126           -
LGA    -       -      I     127           -
LGA    -       -      M     128           -
LGA    -       -      E     129           -
LGA    -       -      W     130           -
LGA    -       -      S     131           -
LGA    -       -      R     132           -
LGA    -       -      H     133           -
LGA    -       -      N     134           -
LGA    -       -      V     135           -
LGA    -       -      Y     136           -
LGA    -       -      S     137           -
LGA    -       -      T     138           -
LGA    -       -      M     139           -
LGA    -       -      F     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      W     143           -
LGA    -       -      A     144           -
LGA    -       -      A     145           -
LGA    -       -      Q     146           -
LGA    -       -      A     147           -
LGA    -       -      G     148           -
LGA    -       -      L     149           -
LGA    -       -      Y     150           -
LGA    -       -      Y     151           -
LGA    -       -      F     152           -
LGA    -       -      Y     153           -
LGA    -       -      G     154           -
LGA    -       -      I     155           -
LGA    -       -      P     156           -
LGA    -       -      K     157           -
LGA    -       -      Y     158           -
LGA    -       -      E     159           -
LGA    -       -      L     160           -
LGA    -       -      P     161           -
LGA    -       -      Q     162           -
LGA    -       -      K     163           -
LGA    -       -      L     164           -
LGA    -       -      S     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      Y     168           -
LGA    -       -      K     169           -
LGA    -       -      H     170           -
LGA    -       -      R     171           -
LGA    -       -      V     172           -
LGA    -       -      A     173           -
LGA    -       -      K     174           -
LGA    -       -      D     175           -
LGA    -       -      S     176           -
LGA    -       -      V     177           -
LGA    -       -      L     178           -
LGA    -       -      F     179           -
LGA    -       -      R     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    -       -      D     183           -
LGA    -       -      D     184           -
LGA    -       -      F     185           -
LGA    -       -      F     186           -
LGA    -       -      W     187           -
LGA    -       -      A     188           -
LGA    -       -      P     189           -
LGA    -       -      H     190           -
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      Y     193           -
LGA    -       -      T     194           -
LGA    -       -      E     195           -
LGA    -       -      V     196           -
LGA    -       -      K     197           -
LGA    -       -      K     198           -
LGA    -       -      E     199           -
LGA    -       -      D     200           -
LGA    -       -      I     201           -
LGA    -       -      D     202           -
LGA    -       -      K     203           -
LGA    -       -      V     204           -
LGA    -       -      P     205           -
LGA    -       -      E     206           -
LGA    -       -      L     207           -
LGA    -       -      E     208           -
LGA    -       -      I     209           -
LGA    -       -      L     210           -
LGA    -       -      A     211           -
LGA    -       -      E     212           -
LGA    -       -      S     213           -
LGA    -       -      D     214           -
LGA    -       -      E     215           -
LGA    -       -      A     216           -
LGA    -       -      G     217           -
LGA    -       -      V     218           -
LGA    -       -      Y     219           -
LGA    -       -      V     220           -
LGA    -       -      V     221           -
LGA    -       -      A     222           -
LGA    -       -      N     223           -
LGA    -       -      K     224           -
LGA    -       -      S     225           -
LGA    -       -      E     226           -
LGA    -       -      R     227           -
LGA    -       -      Q     228           -
LGA    -       -      I     229           -
LGA    -       -      F     230           -
LGA    -       -      V     231           -
LGA    -       -      T     232           -
LGA    -       -      G     233           -
LGA    -       -      H     234           -
LGA    -       -      P     235           -
LGA    -       -      E     236           -
LGA    -       -      Y     237           -
LGA    -       -      D     238           -
LGA    -       -      R     239           -
LGA    -       -      Y     240           -
LGA    -       -      T     241           -
LGA    -       -      L     242           -
LGA    -       -      R     243           -
LGA    -       -      D     244           -
LGA    -       -      E     245           -
LGA    -       -      Y     246           -
LGA    -       -      Y     247           -
LGA    -       -      R     248           -
LGA    -       -      D     249           -
LGA    -       -      I     250           -
LGA    -       -      G     251           -
LGA    -       -      R     252           -
LGA    -       -      N     253           -
LGA    -       -      L     254           -
LGA    -       -      K     255           -
LGA    -       -      V     256           -
LGA    -       -      P     257           -
LGA    -       -      I     258           -
LGA    -       -      P     259           -
LGA    -       -      A     260           -
LGA    -       -      N     261           -
LGA    -       -      Y     262           -
LGA    -       -      F     263           -
LGA    -       -      P     264           -
LGA    -       -      N     265           -
LGA    -       -      D     266           -
LGA    -       -      D     267           -
LGA    -       -      P     268           -
LGA    -       -      T     269           -
LGA    -       -      K     270           -
LGA    -       -      T     271           -
LGA    -       -      P     272           -
LGA    -       -      I     273           -
LGA    -       -      L     274           -
LGA    -       -      T     275           -
LGA    -       -      W     276           -
LGA    -       -      W     277           -
LGA    -       -      S     278           -
LGA    -       -      H     279           -
LGA    -       -      A     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      F     283           -
LGA    -       -      F     284           -
LGA    -       -      S     285           -
LGA    -       -      N     286           -
LGA    -       -      W     287           -
LGA    -       -      L     288           -
LGA    -       -      N     289           -
LGA    -       -      Y     290           -
LGA    -       -      C     291           -
LGA    -       -      I     292           -
LGA    -       -      Y     293           -
LGA    -       -      Q     294           -
LGA    -       -      K     295           -
LGA    -       -      T     296           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24  289    5.0     21    2.66    19.05      4.781     0.760

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.726246 * X  +   0.407983 * Y  +  -0.553278 * Z  +  62.246468
  Y_new =   0.256176 * X  +  -0.586251 * Y  +  -0.768560 * Z  +  46.692268
  Z_new =  -0.637919 * X  +  -0.699900 * Y  +   0.321247 * Z  +  33.777088 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.140491    2.001101  [ DEG:   -65.3453    114.6547 ]
  Theta =   0.691793    2.449800  [ DEG:    39.6368    140.3632 ]
  Phi   =   2.802480   -0.339113  [ DEG:   160.5703    -19.4297 ]
 
# 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: T0326AL044_1                                  
REMARK     2: T0326.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0326AL044_1.T0326.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  289   5.0   21   2.66   19.05   4.781
REMARK  ---------------------------------------------------------- 
MOLECULE T0326AL044_1
REMARK Aligment from pdb entry: 1vcm_A
ATOM      1  N   ILE     3       7.564   1.074  26.819  1.00  0.00              
ATOM      2  CA  ILE     3       7.805   1.500  25.449  1.00  0.00              
ATOM      3  C   ILE     3       7.141   0.466  24.553  1.00  0.00              
ATOM      4  O   ILE     3       7.244  -0.730  24.816  1.00  0.00              
ATOM      5  N   VAL     5       6.445   0.927  23.513  1.00  0.00              
ATOM      6  CA  VAL     5       5.766   0.026  22.576  1.00  0.00              
ATOM      7  C   VAL     5       6.785  -0.813  21.807  1.00  0.00              
ATOM      8  O   VAL     5       7.778  -0.293  21.295  1.00  0.00              
ATOM      9  N   PRO     6       6.523  -2.113  21.724  1.00  0.00              
ATOM     10  CA  PRO     6       7.405  -3.050  21.047  1.00  0.00              
ATOM     11  C   PRO     6       7.915  -2.622  19.668  1.00  0.00              
ATOM     12  O   PRO     6       7.136  -2.254  18.780  1.00  0.00              
ATOM     13  N   SER     7       9.234  -2.681  19.505  1.00  0.00              
ATOM     14  CA  SER     7       9.886  -2.352  18.246  1.00  0.00              
ATOM     15  C   SER     7      10.690  -3.584  17.844  1.00  0.00              
ATOM     16  O   SER     7      11.453  -4.118  18.650  1.00  0.00              
ATOM     17  N   GLY     8      10.511  -4.055  16.614  1.00  0.00              
ATOM     18  CA  GLY     8      11.251  -5.226  16.162  1.00  0.00              
ATOM     19  C   GLY     8      12.661  -4.788  15.792  1.00  0.00              
ATOM     20  O   GLY     8      12.860  -4.017  14.858  1.00  0.00              
ATOM     21  N   LEU     9      13.663  -5.270  16.537  1.00  0.00              
ATOM     22  CA  LEU     9      15.065  -4.927  16.293  1.00  0.00              
ATOM     23  C   LEU     9      15.632  -5.521  15.008  1.00  0.00              
ATOM     24  O   LEU     9      15.245  -6.605  14.580  1.00  0.00              
ATOM     25  N   GLU    18      16.553  -4.791  14.394  1.00  0.00              
ATOM     26  CA  GLU    18      17.205  -5.255  13.181  1.00  0.00              
ATOM     27  C   GLU    18      18.587  -5.659  13.645  1.00  0.00              
ATOM     28  O   GLU    18      19.439  -4.808  13.907  1.00  0.00              
ATOM     29  N   GLY    19      18.804  -6.959  13.768  1.00  0.00              
ATOM     30  CA  GLY    19      20.085  -7.461  14.225  1.00  0.00              
ATOM     31  C   GLY    19      20.870  -8.128  13.089  1.00  0.00              
ATOM     32  O   GLY    19      21.811  -8.890  13.337  1.00  0.00              
ATOM     33  N   ILE    20      20.482  -7.827  11.849  1.00  0.00              
ATOM     34  CA  ILE    20      21.120  -8.400  10.661  1.00  0.00              
ATOM     35  C   ILE    20      22.643  -8.314  10.701  1.00  0.00              
ATOM     36  O   ILE    20      23.338  -9.268  10.335  1.00  0.00              
ATOM     37  N   PHE    21      23.169  -7.176  11.141  1.00  0.00              
ATOM     38  CA  PHE    21      24.614  -7.030  11.212  1.00  0.00              
ATOM     39  C   PHE    21      25.259  -8.065  12.133  1.00  0.00              
ATOM     40  O   PHE    21      26.177  -8.778  11.728  1.00  0.00              
ATOM     41  N   VAL    22      24.790  -8.129  13.379  1.00  0.00              
ATOM     42  CA  VAL    22      25.333  -9.075  14.339  1.00  0.00              
ATOM     43  C   VAL    22      25.199 -10.501  13.824  1.00  0.00              
ATOM     44  O   VAL    22      26.121 -11.304  13.960  1.00  0.00              
ATOM     45  N   THR    24      24.055 -10.811  13.219  1.00  0.00              
ATOM     46  CA  THR    24      23.832 -12.154  12.687  1.00  0.00              
ATOM     47  C   THR    24      24.864 -12.526  11.623  1.00  0.00              
ATOM     48  O   THR    24      25.389 -13.637  11.625  1.00  0.00              
ATOM     49  N   LYS    26      25.147 -11.593  10.716  1.00  0.00              
ATOM     50  CA  LYS    26      26.106 -11.832   9.646  1.00  0.00              
ATOM     51  C   LYS    26      27.524 -11.923  10.193  1.00  0.00              
ATOM     52  O   LYS    26      28.305 -12.784   9.781  1.00  0.00              
ATOM     53  N   ARG    27      27.854 -11.042  11.127  1.00  0.00              
ATOM     54  CA  ARG    27      29.185 -11.036  11.720  1.00  0.00              
ATOM     55  C   ARG    27      29.487 -12.360  12.420  1.00  0.00              
ATOM     56  O   ARG    27      30.618 -12.854  12.374  1.00  0.00              
ATOM     57  N   ALA    28      28.482 -12.932  13.077  1.00  0.00              
ATOM     58  CA  ALA    28      28.675 -14.193  13.779  1.00  0.00              
ATOM     59  C   ALA    28      28.738 -15.331  12.775  1.00  0.00              
ATOM     60  O   ALA    28      29.397 -16.343  13.017  1.00  0.00              
ATOM     61  N   HIS    30      28.059 -15.166  11.644  1.00  0.00              
ATOM     62  CA  HIS    30      28.073 -16.193  10.613  1.00  0.00              
ATOM     63  C   HIS    30      29.488 -16.248  10.033  1.00  0.00              
ATOM     64  O   HIS    30      30.085 -17.324   9.903  1.00  0.00              
ATOM     65  N   GLN    31      32.028 -19.381  10.371  1.00  0.00              
ATOM     66  CA  GLN    31      32.363 -20.010   9.097  1.00  0.00              
ATOM     67  C   GLN    31      33.247 -19.117   8.236  1.00  0.00              
ATOM     68  O   GLN    31      32.799 -18.563   7.232  1.00  0.00              
ATOM     69  N   ASP    32      34.519 -18.960   8.623  1.00  0.00              
ATOM     70  CA  ASP    32      35.427 -18.120   7.845  1.00  0.00              
ATOM     71  C   ASP    32      35.617 -18.678   6.440  1.00  0.00              
ATOM     72  O   ASP    32      35.570 -19.892   6.226  1.00  0.00              
ATOM     73  N   ILE    33      35.820 -17.777   5.489  1.00  0.00              
ATOM     74  CA  ILE    33      36.022 -18.143   4.099  1.00  0.00              
ATOM     75  C   ILE    33      37.467 -18.609   3.938  1.00  0.00              
ATOM     76  O   ILE    33      37.748 -19.583   3.240  1.00  0.00              
ATOM     77  N   ARG    34      38.378 -17.903   4.603  1.00  0.00              
ATOM     78  CA  ARG    34      39.805 -18.205   4.549  1.00  0.00              
ATOM     79  C   ARG    34      40.411 -18.079   5.947  1.00  0.00              
ATOM     80  O   ARG    34      39.691 -17.914   6.926  1.00  0.00              
ATOM     81  N   PRO    35      41.735 -18.153   6.038  1.00  0.00              
ATOM     82  CA  PRO    35      42.415 -18.041   7.325  1.00  0.00              
ATOM     83  C   PRO    35      43.876 -17.648   7.123  1.00  0.00              
ATOM     84  O   PRO    35      44.593 -18.278   6.346  1.00  0.00              
ATOM     85  N   LEU    36      44.307 -16.599   7.819  1.00  0.00              
ATOM     86  CA  LEU    36      45.685 -16.124   7.731  1.00  0.00              
ATOM     87  C   LEU    36      46.180 -15.775   9.115  1.00  0.00              
ATOM     88  O   LEU    36      45.427 -15.248   9.930  1.00  0.00              
ATOM     89  N   LEU    39      47.448 -16.066   9.381  1.00  0.00              
ATOM     90  CA  LEU    39      48.027 -15.759  10.679  1.00  0.00              
ATOM     91  C   LEU    39      48.976 -14.585  10.535  1.00  0.00              
ATOM     92  O   LEU    39      49.693 -14.473   9.537  1.00  0.00              
ATOM     93  N   ILE    40      48.954 -13.689  11.513  1.00  0.00              
ATOM     94  CA  ILE    40      49.855 -12.554  11.495  1.00  0.00              
ATOM     95  C   ILE    40      50.518 -12.519  12.856  1.00  0.00              
ATOM     96  O   ILE    40      49.988 -13.066  13.824  1.00  0.00              
END
