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Posted on Sep 26, 2024

0.2. Please write your full name. Pick up letters which signifies AMINO ACIDS. Avoid duplication. Develop a tetra peptide (5 amino acids) molecule, a) Write

0.2. Please write your full name. Pick up letters which signifies AMINO ACIDS. Avoid duplication.

Develop a tetra peptide (5 amino acids) molecule, a) Write the structure of the tetrapeptide, explaining the flexibility of the side chains, determine the molecular weight of this peptide b) Identify the amino acids from your peptide which could fit in the given coordinate c) Define the steps of an algorithm to detect the H-bonds present between the peptide backbone d) What modeling method you would use to model the peptide-explain e) Define columns 10 and 11 in the coordinate file.

Explain the trend of the value given in column 10 and 11.

image text in transcribed

NUOOUUUUUUUUUUUU OVOZUOOOOOZUOOUUUUUU N Coordinate File: 1 2 3 4 5 ATOM 329 N XXX A ATOM 330 CA xxx ATOM 331 XXX A ATOM 332 xxx ATOM 333 XXX A ATOM 334 CG XXX A ATOM 335 CD1 XXX A ATOM 336 CD2 XXX A ATOM 337 CE1 XXX A ATOM 338 CE2 xxx ATOM 339 CZ xxx ATOM 340 N XXX A ATOM 341 xxx ATOM 342 xxx ATOM 343 xxx ATOM 344 xxx ATOM 345 SG xxx ATOM 346 N xxx ATOM 347 xxx ATOM 348 xxx ATOM 349 xxx ATOM 350 XXX A ATOM 351 OG XXX A ATOM 352 N xxx ATOM 353 xxx ATOM 354 xxx ATOM 355 xxx ATOM 356 XXX A ATOM 357 OG1 xxx ATOM 358 CG2 XXX A ATOM 359 N XXX A ATOM 360 CA XXX A ATOM 361 xxx ATOM 362 xxx ATOM 363 XXX A ATOM 364 CG xxx ATOL: 365 CD1 XXX A ATOM 366 CD2 XXX A ATOM 367 CE1 xxx 368 CE2 xx ATOM 369 CZ XOOXA 6 82 82 82 82 82 82 82 82 82 82 82 83 83 83 83 83 83 84 84 84 84 84 84 85 85 85 85 85 85 85 S N 7 -20. 421 -19.840 -18.425 -18.037 -19. Ge8 -20. 764 -20. 876 -21.617 -21.841 -22 597 -22.708 -17.647 -16.200 -15.745 -16.332 -15,801 -16.500 -14.719 -14.198 -15.083 -14.716 -12.796 -11.842 -16,207 -16.971 -17.457 -17,794 -18.162 -19.090 -17.692 -17.486 -18.074 -17.206 -17.653 -18.259 -16986 -16.142 -16.648 -14.965 -15.472 -14. 625 9 13.002 -3.366 12.284 - 4.500 11.799 - 4,163 10.664 - 4.498 13. 230 -5.698 13.105 -6,759 11.954 -7.543 1.172 -7.019 11.863 - 8 550 14.094 -8.029 12.943 -8, 792 12.677 -3.529 12 513 -3.486 12.231 4.920 12.764 -5.874 11.398 -2.509 11.659 -0.863 11. 407 -5.103 11.205 -6.432 1.342 -7.374 10*150 -0.537 10.596 -6.306 11.522 -5.809 9, 812 -. 899 8. 930 -7.788 9,635 -9, 067 8. 968 -10.048 8.239 -7.098 9.224 - 6.634 7.386 -5.925 10.969 - 9.068 11.702 -10.199 11.549 -11.448 11.775 -12.568 13. 191 -9. 869 13.992 - 9.921 14.045 8. 330 14. 710 -11.063 14. 176 -8. 860 15. 450 -11.109 15. 481 -10.000 10 11 1.00 4.85 1.00 6.98 1.00 856 1.00 6.20 1.00 6.50 1.00 7.39 1.00 9.72 1.00 5.87 1.00 8.18 1.00 8.21 1.00 11.09 1.00 9.80 1.00 8.30 1.00 11.96 1.00 7.66 1.00 1.38 1.00 10.49 1.00 6.51 1.00 8.77 1.00 9.93 1.00 6.24 1.00 11 .23 0.90 12.18 1.00. 7.29 1.00 8.16 1.00 7. 13 1.00 6.93 1.00 7.26 0.80 7. 85 1.00 7.11 1.00 87.29 1.00 83.45 1.00 89.23 1.00 89.84 1.00 80.19 1.00 89.91 1.00 89.05 1.00 83.51 1.00 82.16 1. 00 89.10 1.00 88.53 86 86 86 86 86 86 86 86 86 86 86 NUOOUUUUUUUUUUUU OVOZUOOOOOZUOOUUUUUU N Coordinate File: 1 2 3 4 5 ATOM 329 N XXX A ATOM 330 CA xxx ATOM 331 XXX A ATOM 332 xxx ATOM 333 XXX A ATOM 334 CG XXX A ATOM 335 CD1 XXX A ATOM 336 CD2 XXX A ATOM 337 CE1 XXX A ATOM 338 CE2 xxx ATOM 339 CZ xxx ATOM 340 N XXX A ATOM 341 xxx ATOM 342 xxx ATOM 343 xxx ATOM 344 xxx ATOM 345 SG xxx ATOM 346 N xxx ATOM 347 xxx ATOM 348 xxx ATOM 349 xxx ATOM 350 XXX A ATOM 351 OG XXX A ATOM 352 N xxx ATOM 353 xxx ATOM 354 xxx ATOM 355 xxx ATOM 356 XXX A ATOM 357 OG1 xxx ATOM 358 CG2 XXX A ATOM 359 N XXX A ATOM 360 CA XXX A ATOM 361 xxx ATOM 362 xxx ATOM 363 XXX A ATOM 364 CG xxx ATOL: 365 CD1 XXX A ATOM 366 CD2 XXX A ATOM 367 CE1 xxx 368 CE2 xx ATOM 369 CZ XOOXA 6 82 82 82 82 82 82 82 82 82 82 82 83 83 83 83 83 83 84 84 84 84 84 84 85 85 85 85 85 85 85 S N 7 -20. 421 -19.840 -18.425 -18.037 -19. Ge8 -20. 764 -20. 876 -21.617 -21.841 -22 597 -22.708 -17.647 -16.200 -15.745 -16.332 -15,801 -16.500 -14.719 -14.198 -15.083 -14.716 -12.796 -11.842 -16,207 -16.971 -17.457 -17,794 -18.162 -19.090 -17.692 -17.486 -18.074 -17.206 -17.653 -18.259 -16986 -16.142 -16.648 -14.965 -15.472 -14. 625 9 13.002 -3.366 12.284 - 4.500 11.799 - 4,163 10.664 - 4.498 13. 230 -5.698 13.105 -6,759 11.954 -7.543 1.172 -7.019 11.863 - 8 550 14.094 -8.029 12.943 -8, 792 12.677 -3.529 12 513 -3.486 12.231 4.920 12.764 -5.874 11.398 -2.509 11.659 -0.863 11. 407 -5.103 11.205 -6.432 1.342 -7.374 10*150 -0.537 10.596 -6.306 11.522 -5.809 9, 812 -. 899 8. 930 -7.788 9,635 -9, 067 8. 968 -10.048 8.239 -7.098 9.224 - 6.634 7.386 -5.925 10.969 - 9.068 11.702 -10.199 11.549 -11.448 11.775 -12.568 13. 191 -9. 869 13.992 - 9.921 14.045 8. 330 14. 710 -11.063 14. 176 -8. 860 15. 450 -11.109 15. 481 -10.000 10 11 1.00 4.85 1.00 6.98 1.00 856 1.00 6.20 1.00 6.50 1.00 7.39 1.00 9.72 1.00 5.87 1.00 8.18 1.00 8.21 1.00 11.09 1.00 9.80 1.00 8.30 1.00 11.96 1.00 7.66 1.00 1.38 1.00 10.49 1.00 6.51 1.00 8.77 1.00 9.93 1.00 6.24 1.00 11 .23 0.90 12.18 1.00. 7.29 1.00 8.16 1.00 7. 13 1.00 6.93 1.00 7.26 0.80 7. 85 1.00 7.11 1.00 87.29 1.00 83.45 1.00 89.23 1.00 89.84 1.00 80.19 1.00 89.91 1.00 89.05 1.00 83.51 1.00 82.16 1. 00 89.10 1.00 88.53 86 86 86 86 86 86 86 86 86 86 86