Hi everyone,
I would like to find the helix ID and the length of each helix in the following PDB file:
https://files.rcsb.org/view/5O5Z.pdb
I can't seem to find it all.
Many Thanks,
Ish
Your PDB file has HELIX and SHEET records describing where secondary structure exists.
I found 23 HELICES in subunitA (their corresponding lengths are the last number in the strings - 26,3,13,11,etc) and 24 HELICES in subunit B (their lengths are 24,3,13,11,16, etc).
HELIX 1 AA1 LYS A 2 ILE A 27 1 26
HELIX 2 AA2 PRO A 28 VAL A 30 5 3
HELIX 3 AA3 ASP A 48 GLY A 60 1 13
HELIX 4 AA4 GLY A 60 ASN A 70 1 11
HELIX 5 AA5 SER A 77 GLY A 92 1 16
HELIX 6 AA6 SER A 101 GLY A 112 1 12
HELIX 7 AA7 GLY A 120 GLY A 130 1 11
HELIX 8 AA8 PRO A 145 GLU A 150 1 6
HELIX 9 AA9 HIS A 171 ALA A 175 5 5
HELIX 10 AB1 TYR A 213 VAL A 217 5 5
HELIX 11 AB2 ARG A 220 GLY A 226 1 7
HELIX 12 AB3 GLY A 226 ARG A 232 1 7
HELIX 13 AB4 GLY A 241 LEU A 245 5 5
HELIX 14 AB5 THR A 254 TYR A 272 1 19
HELIX 15 AB6 ASN A 285 LEU A 296 1 12
HELIX 16 AB7 PRO A 297 PHE A 299 5 3
HELIX 17 AB8 GLU A 306 GLY A 317 1 12
HELIX 18 AB9 ASP A 318 GLU A 327 1 10
HELIX 19 AC1 HIS A 329 GLY A 345 1 17
HELIX 20 AC2 GLY A 384 GLY A 399 1 16
HELIX 21 AC3 GLY A 403 GLY A 422 1 20
HELIX 22 AC4 ARG A 426 VAL A 436 5 11
HELIX 23 AC5 ASN A 439 PHE A 453 1 15
HELIX 24 AC6 SER B 4 ILE B 27 1 24
HELIX 25 AC7 PRO B 28 VAL B 30 5 3
HELIX 26 AC8 ASP B 48 GLY B 60 1 13
HELIX 27 AC9 GLY B 60 ASN B 70 1 11
HELIX 28 AD1 SER B 77 GLY B 92 1 16
HELIX 29 AD2 SER B 101 GLY B 112 1 12
HELIX 30 AD3 GLY B 120 GLY B 130 1 11
HELIX 31 AD4 PRO B 145 GLU B 150 1 6
HELIX 32 AD5 HIS B 171 ALA B 175 5 5
HELIX 33 AD6 TYR B 213 VAL B 217 5 5
HELIX 34 AD7 ARG B 220 GLY B 226 1 7
HELIX 35 AD8 GLY B 226 ARG B 232 1 7
HELIX 36 AD9 GLY B 241 LEU B 245 5 5
HELIX 37 AE1 THR B 254 TYR B 272 1 19
HELIX 38 AE2 ASN B 285 LEU B 296 1 12
HELIX 39 AE3 PRO B 297 PHE B 299 5 3
HELIX 40 AE4 ASN B 305 GLY B 317 1 13
HELIX 41 AE5 ASP B 318 GLU B 327 1 10
HELIX 42 AE6 HIS B 329 GLY B 345 1 17
HELIX 43 AE7 GLY B 384 GLY B 399 1 16
HELIX 44 AE8 GLY B 403 GLY B 422 1 20
HELIX 45 AE9 ILE B 427 ALA B 433 1 7
HELIX 46 AF1 LEU B 434 VAL B 436 5 3
HELIX 47 AF2 ASN B 439 LYS B 451 1 13
I hope I didn't forget how to treat pdb-files.
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version 2.3.6
Hi Natasha,
Can you post a screenshot of it, please?
I am very new to this
thanks,
Ish
I did.
Let's consider this line:
This is helix 47 of subunit B starting from asparagine 439 going to lysine 451. Its length is 13 amino acids.
Thank you very much, the documentation is very confusing to me. Thank you also for the explanation for the different lines.
See also this link.
https://proteinstructures.com/Structure/Structure/proteinstructure-databases2.html
There is some useful information inside.
f=open('5ogb.pdb') lines=f.readlines()
print lines[337] print lines[338]
print "helixID= AA2"
How can I modify the code so it can print the following please? :
the helix id of each helix and the length, in a list
sheetID, number of strands and the total number of residues, also a list.