Task 1

Explored tRNA: 1ffy

I used the "einverted" program from the EMBOSS package — search for inverted regions in nucleotide sequences.

Einverted parameters: Gap penalty 8, Minimum score threshold 0, Match score 3, Mismatch score -4

Results

Compare with description obtained earlier using find_pair.

Area of the structure	Positions in the structure (find_pair)	Prediction results with einverted	Prediction results with Zuker algorithm
Acceptor stem	1-7 66-72	1-7 57-63	1-7 67-73
D-stem	10-13 22-25	—	—
T-stem	49-53 61-65	—	—
Anticodon stem	26-32 38-44	23-32 40-49	—
Total number of canonical nucleotides pairs	20	14	27

I'm not sure why, but einverted and Zuker algorithm performed poorly with the task.

Task 2. Search for DNA-protein contacts in a given structure

Ex.1

Links to scripts:

script1 script2

Ex.2

script3

Contacts of protein atoms with	Polar	Non-polar	Total
2'-deoxyribose residues	1	20	21
phosphoric acid residues	13	60	73
residues of nitrogenous bases from the side of the major groove	4	9	13
residues of nitrogenous bases from the side of the minor groove	0	1	1

Contacts between DNA and non-polar atoms (C, P, S) of the protein are the most often countered

Ex.3

Ex.4

Lys461 has the largest number of contacts with DNA — 3, but I don't know where they are

Besides Lys461, Val462 should be important for DNA sequence recognition, because they both recognise nitrogenous bases

But how valine can interact with thymine remains a mystery. Troubles with the nucplot or with me?