123 lines
4.3 KiB
R
123 lines
4.3 KiB
R
gene = "embB"
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drug = "ethambutol"
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# interacting chain B
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#==========
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# LIGPLUS
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#===========
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aa_ligplus_emb = c(299, 302, 303, 306, 334, 594, 988, 1028)
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aa_ligplus_emb_hbond = c(299, 594)
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aa_ligplus_ca = c(952, 954, 959)
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aa_ligplus_ca_hbond = c(952, 954, 959)
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aa_ligplus_cdl = c(460, 665, 568, 601, 572, 579, 580, 583)
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aa_ligplus_cdl_hbond = c(601, 568, 665)
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aa_ligplus_dsl = c(435, 442, 489, 452, 330, 589, 509, 446, 445, 506, 592, 590, 514, 403, 515)
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aa_ligplus_dsl_hbond = c(445, 590, 592, 403)
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#==========
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# PLIP
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#===========
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aa_plip_emb = c(299, 302, 303, 327, 594, 988, 1028)
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aa_plip_emb_hbond = c(299, 327, 594)
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aa_plip_ca = c(952, 954, 959)
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aa_plip_cdl = c(456, 572, 579, 583, 568)
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#aa_plip_cdl_sb = c(537, 568, 601, 665)
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aa_plip_dsl = c(330, 435, 446, 452, 489, 506, 589, 590, 445, 403, 595)
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aa_plip_dsl_hbond = c(445, 590)
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#aa_plip_dsl_sb = c(403, 595)
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#==========
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# Arpeggio
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#===========
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# emb:1402, 1403
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aa_arpeg_emb = c(298, 299, 302, 303, 306, 318, 327, 334, 403, 445, 592, 594, 988, 1028)
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aa_arpeg_ca = c(847, 853, 854, 952, 954, 955, 956, 959, 960)
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aa_arpeg_cdl = c(456, 457, 460, 461, 521, 525, 533, 537, 554, 558, 568
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, 569, 572, 573, 575, 576, 579, 580, 582, 583, 586, 601, 605, 616, 658
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, 661, 662, 665)
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aa_arpeg_dsl = c(299, 322, 329, 330, 403, 435, 438, 439, 442, 445, 446
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, 449, 452, 455, 486, 489, 490, 493, 506, 509, 510, 513, 514
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, 515, 587, 589, 590, 592, 595)
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##############################################################
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active_aa_pos = sort(unique(c(aa_ligplus_emb
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, aa_plip_emb
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, aa_arpeg_emb
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, aa_ligplus_ca
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, aa_plip_ca
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, aa_arpeg_ca
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, aa_ligplus_cdl
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, aa_plip_cdl
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, aa_arpeg_cdl
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, aa_ligplus_dsl
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, aa_plip_dsl
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, aa_arpeg_dsl)))
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##############################################################
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cat("\nNo. of active site residues for gene"
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, gene, ":"
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, length(active_aa_pos)
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, "\nThese are:\n"
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, active_aa_pos)
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##############################################################
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aa_pos_emb = sort(unique(c( aa_ligplus_emb
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, aa_plip_emb
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, aa_arpeg_emb)))
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aa_pos_drug = aa_pos_emb
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aa_pos_emb_hbond = sort(unique(c( aa_ligplus_emb_hbond
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, aa_plip_emb_hbond)))
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aa_pos_ca = sort(unique(c( aa_ligplus_ca
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, aa_plip_ca
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, aa_arpeg_ca)))
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aa_pos_cdl = sort(unique(c( aa_ligplus_cdl
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, aa_plip_cdl
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, aa_arpeg_cdl )))
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aa_pos_cdl_hbond = sort(unique(c( aa_ligplus_cdl_hbond )))
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aa_pos_dsl = sort(unique(c( aa_ligplus_dsl
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, aa_plip_dsl
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, aa_arpeg_dsl)))
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aa_pos_dsl_hbond = sort(unique(c( aa_ligplus_dsl_hbond
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, aa_plip_dsl_hbond)))
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cat("\n==================================================="
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, "\nActive site residues for", gene, "comprise of..."
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, "\n==================================================="
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, "\nNo. of", drug, "binding residues:" , length(aa_pos_emb), "\n"
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, aa_pos_emb
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, "\nNo. of co-factor 'Ca' binding residues:", length(aa_pos_ca) , "\n"
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, aa_pos_ca
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, "\nNo. of ligand 'CDL' binding residues:" , length(aa_pos_cdl), "\n"
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, aa_pos_cdl
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, "\nNo. of ligand 'DPA' binding residues:" , length(aa_pos_dsl), "\n"
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, aa_pos_dsl, "\n"
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)
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##############################################################
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# var for position customisation for plots
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# aa_pos_lig1 = aa_pos_ca
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# aa_pos_lig2 = aa_pos_cdl
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# aa_pos_lig3 = aa_pos_dsl
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aa_pos_lig1 = aa_pos_dsl #slategray
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aa_pos_lig2 = aa_pos_cdl #navy blue
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aa_pos_lig3 = aa_pos_ca #purple
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tile_map=data.frame(tile=c("EMB","DPA","CDL","Ca"),
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tile_colour=c("green","darkslategrey","navyblue","purple"))
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drug_main_res = c(299 , 302, 303 , 306 , 327 , 592 , 594, 988, 1028)
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