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Complex

1. Distance calculation

We calculate the distance between residues from every two chains within a protein complex. The pp.dist.all_vs_all makes a all-against-all comparison between residues.

Python 

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import pypropel as pp

df = pp.dist.all_vs_all(
    pdb_fp=to('data/pdb/complex/pdbtm/'),
    pdb_name='1aij',
)
print(df)

Output 

D:\Programming\anaconda3\envs\prot\Lib\site-packages\Bio\PDB\Atom.py:232: PDBConstructionWarning: Could not assign element 'M' for Atom (name=MG) with given element 'M'
  warnings.warn(msg, PDBConstructionWarning)
28/07/2024 18:41:22 logger: ============>chain 1 L and chain2 M
D:\Programming\anaconda3\envs\prot\Lib\site-packages\Bio\PDB\Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
  warnings.warn(
D:\Programming\anaconda3\envs\prot\Lib\site-packages\Bio\PDB\Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
  warnings.warn(
28/07/2024 18:41:36 logger: ============>chain 1 L and chain2 H
D:\Programming\anaconda3\envs\prot\Lib\site-packages\Bio\PDB\Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
  warnings.warn(
28/07/2024 18:41:46 logger: ============>chain 1 M and chain2 H
       res_fas_id1 res1  res_pdb_id1  ...       dist chain1  chain2
0                1    A            1  ...  33.363850      L       M
1                1    A            1  ...  27.019474      L       M
2                1    A            1  ...  29.652020      L       M
3                1    A            1  ...  28.374273      L       M
4                1    A            1  ...  29.460558      L       M
...            ...  ...          ...  ...        ...    ...     ...
74041          301    H          301  ...  61.372215      M       H
74042          301    H          301  ...  64.072952      M       H
74043          301    H          301  ...  62.540863      M       H
74044          301    H          301  ...  60.712658      M       H
74045          301    H          301  ...  65.942444      M       H

[227753 rows x 9 columns]

Tip

All chains of a protein can be seen by pp.str.chains.

Python 

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import pypropel as pp

chains = pp.str.chains(
    pdb_fp=to('data/pdb/complex/pdbtm/'),
    pdb_name='1aij',
)
print(chains)

Output 

['L', 'M', 'H']

2. Check interaction

It checks if a residue in the chain 1 has a minimum distance against all of residues in the chain 2. It stops the calculations of the minimum distance of each residue to each residue in the chain 2 when it detects a minimum distance of less than thres, 6 by default. pp.dist.check_chain_complex checks every two chains within a complex.

Python 

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import pypropel as pp

pp.dist.check_chain_complex(
    pdb_fp=to('data/pdb/complex/pdbtm/'),
    prot_name='1aij',
    sv_fp=to('data/pdb/complex/pdbtm/'),
    thres=5.5,
)

Output 

28/07/2024 19:57:40 logger: =========>Protein PDB code: 1aij
D:\Programming\anaconda3\envs\prot\Lib\site-packages\Bio\PDB\Atom.py:232: PDBConstructionWarning: Could not assign element 'M' for Atom (name=MG) with given element 'M'
  warnings.warn(msg, PDBConstructionWarning)
28/07/2024 19:57:40 logger: =========>Protein chain 1: L
28/07/2024 19:57:40 logger: ============>Protein chain 2: M
28/07/2024 19:57:40 logger: ==================>residue 1 ID: 0
28/07/2024 19:57:40 logger: ==================>residue 0 and residue 252 in interaction
28/07/2024 19:57:40 logger: ============>Protein chain 2: H
28/07/2024 19:57:40 logger: ==================>residue 1 ID: 0
28/07/2024 19:57:40 logger: ==================>residue 0 and residue 31 in interaction
28/07/2024 19:57:40 logger: =========>Protein chain 1: M
28/07/2024 19:57:40 logger: ============>Protein chain 2: H
28/07/2024 19:57:40 logger: ==================>residue 1 ID: 0
28/07/2024 19:57:40 logger: ==================>residue 0 and residue 186 in interaction
28/07/2024 19:57:40 logger: =========>Protein chain 1: H

The results are saved to the 1aij.ccheck file. It has the following content. 

1aij    L
1aij    M
1aij    L
1aij    H
1aij    M
1aij    H

3. dist file

We can calculate the distance of a residue from a target protein away from residues from the rest of chains in the protein complex.

Python 

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import pypropel as pp

pp.dist.complex_calc_all(
    pdb_fp=to('data/pdb/complex/pdbtm/'),
    prot_name='1aij',
    prot_chain='L',
    method='heavy',
    sv_fp=to('data/pdb/complex/pdbtm/'),
)

It returns a file 1aijL.dist, having the following content.

Output 

       0  1    2         M          H
0      1  A    1  3.359507   3.820152
1      2  L    2  4.832898   2.840868
2      3  L    3  3.621853   3.450767
3      4  S    4  6.046180   2.841488
4      5  F    5  3.438960   3.688982
..   ... ..  ...       ...        ...
276  277  G  277  2.910155  43.177975
277  278  G  278  3.036153  40.448544
278  279  I  279  2.979592  36.381111
279  280  N  280  2.980944  38.922234
280  281  G  281  3.484761  42.785561

[281 rows x 5 columns]

The above columns correspond to different items in the following table.

Column Description
0 fasta id 1
1 residue 1
2 pdb id 1
M chain 1 distance
H chain 2 distance

4. pdbinter file

We can calculate the distance of a residue from a target protein away from residues from the rest of chains in the protein complex.

Python 

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import pypropel as pp

pp.dist.complex_calc_all(
    pdb_fp=to('data/pdb/complex/pdbtm/'),
    prot_name='1aij',
    prot_chain='L',
    method='heavy',
    sv_fp=to('data/pdb/complex/pdbtm/'),
)

It returns a file 1aijL.pdbinter, having the following content.

Output 

L   1   A   M   253 R   3.3595068
L   2   L   M   253 R   4.832898
L   3   L   M   246 E   5.9632444
L   3   L   M   249 A   4.6895933
L   3   L   M   250 L   3.7801166
...
L   227 L   H   173 E   3.6427267
L   227 L   H   175 M   3.9549832
L   227 L   H   177 R   5.680695
L   228 G   H   173 E   5.4361606

[643 rows x 7 columns]

The above columns correspond to different items in the following table.

Column Description
chain1 chain 1
pos1 pdb id 1
aa1 residue 1
chain2 chain 2
pos2 pdb id 2
aa2 residue 2
dist distance

5. Submission to the server

Python 

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import pypropel as pp

from pypropel.util.Reader import Reader as pfreader

df = pfreader().generic(df_fpn=to('data/ex/final.txt'), header=0)
prots = df.prot.unique()[2000:]

param_config = {
    'pdb_fp': '-fp',
    'pdb_fn': '-fn',
    'sv_fp': '-op',
}
value_config = {
    'tool_fp': '/path/to/python',
    'script_fpn': './Complex.py',
    'pdb_fp': '/path/to/protein complex files/',
    'sv_fp': '/path/to/save/results/',
}

for key, prot in enumerate(prots):
    order_list = [
        value_config['tool_fp'],
        value_config['script_fpn'],

        param_config['pdb_fp'], value_config['pdb_fp'],
        param_config['pdb_fn'], prot,
        param_config['sv_fp'], value_config['sv_fp'],
    ]
    pp.dist.cloud_check(
        order_list=order_list,
        job_fp='/path/to/save/job files/',
        job_fn=str(key),
        cpu=2,
        memory=10,
        method='script',
        submission_method='sbatch',
    )

Tip

the final.txt file is obtained from running TMKit's tmkit.collate for a set of proteins.

Unnamed: 0  prot    chain   prot_mark   rez met bio_name    head    desc    mthm    seq_aa  seq_len nchain  met1
0   2a06    C   2a06C   2.1 x-ray diffraction   bovine cytochrome bc1 complex with stigmatellin bound   oxidoreductase  OXIDOREDUCTASE  8   NNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTTAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILLLTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALMLLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILILALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFLLILVLMPTAGTIENKLLKW   365.0   20.0    x-ray diffraction
4   2a06    P   2a06P   2.1     bovine cytochrome bc1 complex with stigmatellin bound   oxidoreductase  OXIDOREDUCTASE  8   LMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTTAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILLLTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALMLLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILILALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFLLILVLMPTAGTIENKLLKW  370.0   20.0    x-ray diffraction
77  4a01    A   4a01A   2.35    x-ray diffraction   crystal structure of the h-translocating pyrophosphatase    hydrolase   HYDROLASE   16  GAAILPDLGTEILIPVCAVIGIAFALFQWLLVSKVKLSAVDHNVVVKCAEIQNAISEGATSFLFTEYKYVGIFMVAFAILIFLFLGSVEGFSTSPQACSYDKTKTCKPALATAIFSTVSFLLGGVTSLVSGFLGMKIATYANARTTLEARKGVGKAFITAFRSGAVMGFLLAANGLLVLYIAINLFKIYYGDDWGGLFEAITGYGLGGSSMALFGRVGGGIYTKAADVGADLVGKVERNIPEDDPRNPAVIADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGLNHELTAMLYPLIVSSVGILVCLLTTLFATDFFEIKAVKEIEPALKKQLVISTVLMTIGVAVVSFVALPTSFTIFNFGVQKDVKSWQLFLCVAVGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAISIFVSFTFAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTTAAIGKGFAIGSAALVSLALFGAFVSRASITTVDVLTPKVFIGLIVGAMLPYWFSAMTMKSVGSAALKMVEEVRRQFNTIPGLMEGTAKPDYATCVKISTDASIKEMIPPGALVMLTPLVVGILFGVETLSGVLAGSLVSGVQIAISASNTGGAWDNAKKYIEAGASEHARSLGPKGSDCHKAAVIGDTIGDPLKDTSGPSLNILIKLMAVESLVFAPFFATHGGLLFKIF    740.0   2.0 x-ray diffraction
78  4a01    B   4a01B   2.35        crystal structure of the h-translocating pyrophosphatase    hydrolase   HYDROLASE   16  GAAILPDLGTEILIPVCAVIGIAFALFQWLLVSKVKLSAVDHNVVVKCAEIQNAISEGATSFLFTEYKYVGIFMVAFAILIFLFLGSVEGFSTSPQACSYDKTKTCKPALATAIFSTVSFLLGGVTSLVSGFLGMKIATYANARTTLEARKGVGKAFITAFRSGAVMGFLLAANGLLVLYIAINLFKIYYGDDWGGLFEAITGYGLGGSSMALFGRVGGGIYTKAADVGADLVGKVERNIPEDDPRNPAVIADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGLNHELTAMLYPLIVSSVGILVCLLTTLFATDFFEIKAVKEIEPALKKQLVISTVLMTIGVAVVSFVALPTSFTIFNFGVQKDVKSWQLFLCVAVGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAISIFVSFTFAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTTAAIGKGFAIGSAALVSLALFGAFVSRASITTVDVLTPKVFIGLIVGAMLPYWFSAMTMKSVGSAALKMVEEVRRQFNTIPGLMEGTAKPDYATCVKISTDASIKEMIPPGALVMLTPLVVGILFGVETLSGVLAGSLVSGVQIAISASNTGGAWDNAKKYIEAGASEHARSLGPKGSDCHKAAVIGDTIGDPLKDTSGPSLNILIKLMAVESLVFAPFFATHGGLLFKIF    740.0   2.0 x-ray diffraction
79  7a0w    A   7a0wA   2.04    x-ray diffraction   structure of dimeric sodium proton antiporter nhaa, at ph 8.5, crystallized with chimeric fab antibodies    membrane protein    MEMBRANE PROTEIN    12  ASGGIILIIAAALAMLMANMGATSGWYHDFLETPVQLRVGALEINKNMLLWINDALMAVFFLLIGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPALLYLAFNYSDPVTREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALAIIDDLGAIVIIALFYTSDLSIVSLGVAAFAIAVLALLNLCGVRRTGVYILVGAVLWTAVLKSGVHATLAGVIVGFFIPLKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVTIDGLTSMLPLGIIAGLLIGKPLGISLFCWLALRFKLAHLPQGTTYQQIMAVGILCGIGFTMSIFIASLAFGNVDPELINWAKLGILIGSLLSAVVGYSW    368.0   2.0 x-ray diffraction