Contacts of the helix formed by residues 432 - 464 (chain A) in PDB entry 5I4E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 432 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ASP* 3.2 44.6 - - + +
389A ALA* 3.6 1.3 - - - -
431A GLN* 1.3 75.6 - - - +
433A LYS* 1.3 59.3 + - - +
434A GLU* 3.7 7.9 + - - +
435A GLN* 2.8 41.6 + - - +
436A ALA* 2.9 28.2 + - - +
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Residues in contact with LYS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.3 30.4 + - + +
381A LYS* 4.1 26.7 - - + +
382A ARG* 4.7 17.0 - - + +
387A ASP 3.6 5.7 + - - -
389A ALA* 3.6 12.5 - - - +
432A THR* 1.3 72.2 - - - +
434A GLU* 1.4 55.6 + - - +
436A ALA* 3.8 1.0 - - - +
437A ASP* 2.8 63.4 + - - +
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A THR* 3.2 7.4 + - - +
433A LYS* 1.4 76.9 - - - +
435A GLN* 1.4 55.3 + - + +
437A ASP* 3.2 6.3 + - - +
438A PHE* 2.9 70.2 + - + -
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Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA 4.1 3.5 + - - +
431A GLN* 3.4 34.2 + - - +
432A THR* 2.8 44.6 + - - +
434A GLU* 1.4 75.1 - - + +
436A ALA* 1.4 61.2 + - - +
438A PHE* 3.2 10.7 + - - +
439A ALA* 3.1 21.5 + - - +
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Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.6 20.6 - - + -
389A ALA* 3.8 12.8 - - + -
415A LEU* 4.0 15.5 - - + +
416A LEU* 4.5 3.1 - - + -
431A GLN* 4.2 12.9 - - + +
432A THR 2.9 17.9 + - - +
433A LYS 3.9 0.2 - - - +
435A GLN* 1.4 73.8 - - - +
437A ASP* 1.4 62.9 + - - +
439A ALA* 3.3 10.2 + - - +
440A LEU* 3.1 25.3 + - - +
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Residues in contact with ASP 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 4.5 15.3 + - - +
378A ILE 4.6 4.3 - - - +
380A LEU* 3.8 20.7 + - - +
433A LYS* 2.8 60.6 + - - +
434A GLU* 3.7 6.4 - - + +
436A ALA* 1.4 68.9 - - - +
438A PHE* 1.3 64.1 + - - +
440A LEU* 3.4 12.6 + - - +
441A GLU* 3.3 30.7 + - - +
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Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLU* 2.9 54.9 + - + -
435A GLN* 3.4 11.4 - - - +
437A ASP* 1.3 73.9 - - - +
439A ALA* 1.4 51.8 + - - +
441A GLU* 3.1 21.1 + - + +
442A ALA* 2.8 35.7 + - - +
609A GLU* 3.7 35.4 - - + -
612A MET* 5.8 12.8 - - + -
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 4.1 15.0 - - + +
431A GLN* 5.2 6.1 - - - +
435A GLN 3.1 12.2 + - - +
436A ALA* 3.4 13.2 - - - +
438A PHE* 1.4 71.9 - - - +
440A LEU* 1.3 59.2 + - - +
442A ALA* 3.2 7.3 + - - +
443A LEU* 2.8 41.1 + - + +
619A ASN* 4.7 17.4 + - + +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 5.3 5.2 - - - +
329A PHE* 5.1 1.3 - - + -
375A PHE* 3.8 42.8 - - + +
378A ILE* 3.9 33.0 - - + +
380A LEU* 3.6 29.2 - - + -
411A PHE* 4.1 3.4 - - + -
415A LEU* 3.8 25.8 - - + -
436A ALA 3.1 12.2 + - - +
437A ASP* 3.5 16.8 - - - +
438A PHE 3.3 0.2 - - - -
439A ALA* 1.3 75.6 - - - +
441A GLU* 1.3 58.3 + - + +
443A LEU* 3.2 6.5 + - - +
444A ALA* 2.9 30.3 + - - +
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 3.7 30.1 - - + +
293A ARG* 3.4 30.0 + - - -
328A ARG* 3.4 32.4 + - - +
329A PHE* 4.1 11.5 - - + -
437A ASP* 3.3 17.0 + - - +
438A PHE* 3.1 25.4 + - + +
440A LEU* 1.3 71.9 - - - +
442A ALA* 1.4 65.9 + - - +
444A ALA 3.5 0.4 + - - +
445A LYS* 3.1 33.0 + - - +
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 5.5 0.7 + - - -
438A PHE 2.8 19.6 + - - +
439A ALA* 3.2 9.4 + - - +
441A GLU* 1.4 71.9 - - - +
443A LEU* 1.4 57.0 + - + +
445A LYS* 3.5 16.3 + - - +
446A ALA* 2.9 30.7 + - - +
617A PRO* 3.5 25.1 - - + +
618A LEU* 3.6 11.2 - - + +
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PHE* 3.8 20.4 - - + -
411A PHE* 5.0 0.4 - - + -
415A LEU* 4.4 11.0 - - + -
439A ALA 2.8 25.9 + - - +
440A LEU* 3.6 4.0 - - - +
442A ALA* 1.4 75.2 - - - +
444A ALA* 1.3 57.0 + - - +
446A ALA* 3.5 4.5 + - - +
447A THR* 2.7 37.9 + - - -
618A LEU* 5.0 4.7 - - + -
619A ASN* 4.6 20.4 - - + +
622A VAL* 3.6 47.8 - - + -
623A ALA* 4.5 6.5 - - + +
626A LEU* 4.1 15.0 - - + -
638A TRP* 4.2 11.5 - - + -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 4.3 2.7 - - + -
329A PHE* 3.5 31.6 - - + -
372A VAL* 3.4 24.3 - - + +
375A PHE* 3.6 24.9 - - + -
440A LEU 2.9 14.7 + - - +
441A GLU 4.0 3.1 - - - +
443A LEU* 1.3 77.1 - - - +
445A LYS* 1.4 55.6 + - - +
447A THR* 3.6 0.4 + - - -
448A TYR* 3.1 21.1 + - - +
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Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 3.3 47.2 - - + +
289A SER* 3.6 27.7 - - - +
291A ALA* 4.9 0.9 - - - -
292A ILE* 3.8 26.2 - - + +
441A GLU* 3.1 26.2 + - - +
442A ALA* 3.8 15.6 - - - +
444A ALA* 1.4 72.8 - - - +
446A ALA* 1.4 60.6 + - - +
447A THR 3.3 0.4 - - - -
448A TYR* 3.4 2.9 + - - +
449A GLU* 3.1 30.1 + - - +
613A LYS* 5.3 13.5 - - - +
616A ASP* 5.2 4.4 + - - -
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 4.5 5.6 - - - +
442A ALA 2.9 19.7 + - - +
443A LEU 3.8 2.7 - - - +
445A LYS* 1.4 75.2 - - - +
447A THR* 1.3 56.3 + - - +
449A GLU* 3.8 14.3 - - - +
450A ARG* 3.2 36.0 + - - +
618A LEU* 3.6 23.8 - - + -
638A TRP* 3.7 20.6 - - + -
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Residues in contact with THR 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A MET* 3.9 31.6 - - + +
372A VAL* 4.1 10.3 - - + +
375A PHE* 4.2 10.8 - - + -
404A LEU* 4.6 10.3 - - + +
443A LEU 2.7 22.0 + - - -
444A ALA* 3.8 6.7 - - - -
445A LYS 3.3 0.2 - - - -
446A ALA* 1.3 74.7 - - - +
448A TYR* 1.4 59.4 + - - +
450A ARG* 3.6 2.2 + - - +
451A LEU* 3.0 28.1 + - - +
626A LEU* 4.5 2.6 - - - +
637A ILE* 4.3 2.9 - - + +
638A TRP* 3.2 29.6 + - - +
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Residues in contact with TYR 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 2.7 54.7 + + + -
286A LEU* 4.1 11.4 - - + -
288A LYS* 5.3 2.7 - - + +
291A ALA* 4.2 9.6 - - + -
301A PHE* 3.5 34.3 - + - -
303A ILE* 3.3 17.8 - - + +
304A PHE* 3.5 28.7 - + - -
369A VAL* 4.6 6.5 - - + -
372A VAL* 3.8 19.7 - - + +
444A ALA 3.1 17.3 + - - +
445A LYS 3.4 4.2 + - - +
447A THR* 1.4 77.7 - - - +
449A GLU* 1.3 57.4 + - - +
451A LEU* 3.2 11.8 + - + +
452A PHE* 2.9 26.9 + - + +
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 4.0 22.2 - - + +
288A LYS* 3.1 43.0 + - + +
445A LYS 3.1 17.8 + - - +
446A ALA* 3.8 11.0 - - - +
448A TYR* 1.3 75.5 - - - +
450A ARG* 1.3 57.3 + - - +
452A PHE* 3.2 6.5 + - + +
453A ARG* 2.9 52.9 + - - +
616A ASP* 4.7 2.1 - - - +
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Residues in contact with ARG 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA* 3.2 22.1 + - - +
447A THR* 4.0 4.9 - - - +
449A GLU* 1.3 73.0 + - - +
451A LEU* 1.3 65.2 + - - +
453A ARG* 3.6 31.7 - - - +
454A TRP* 3.0 25.3 + - - +
618A LEU* 5.1 7.3 - - - +
637A ILE* 2.9 43.0 + - + +
638A TRP* 3.4 47.6 - - - +
640A ASP* 2.9 35.3 + - - +
641A VAL* 4.7 4.0 - - - +
642A GLU 5.4 1.4 - - - +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 4.0 18.8 - - + -
365A MET* 3.6 48.2 - - + +
368A MET* 3.9 22.2 - - + -
369A VAL* 4.0 16.6 - - + +
372A VAL* 5.7 0.2 - - + -
447A THR 3.0 16.1 + - - +
448A TYR* 3.2 18.6 + - + +
450A ARG* 1.3 74.1 - - - +
452A PHE* 1.3 58.1 + - - +
454A TRP* 3.3 13.5 + - + +
455A LEU* 2.9 29.0 + - + +
633A LEU* 4.3 11.0 - - + -
637A ILE* 4.5 6.2 - - + +
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Residues in contact with PHE 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.0 20.9 - - + -
248A PHE* 4.5 22.6 - - + -
249A GLY* 4.6 4.9 - - - -
262A PHE* 3.9 31.6 - + + -
283A THR* 3.2 44.9 - - + -
286A LEU* 3.7 35.4 - - + -
448A TYR* 2.9 13.5 + - + +
449A GLU* 3.2 8.9 + - + +
451A LEU* 1.3 76.9 - - - +
453A ARG* 1.3 65.4 + - + +
455A LEU* 3.2 11.6 + - + +
456A VAL* 3.0 29.0 + - + +
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Residues in contact with ARG 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR* 6.0 0.7 - - - -
449A GLU* 2.9 43.3 + - - +
450A ARG* 3.6 36.8 - - - +
452A PHE* 1.3 81.0 - - + +
454A TRP* 1.3 60.4 + - - +
456A VAL* 3.5 6.5 + - + +
457A LEU* 3.2 21.9 + - - +
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Residues in contact with TRP 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A PHE* 3.7 29.2 - + - -
361A GLU* 3.7 24.9 - - + -
365A MET* 3.6 28.0 - - + -
450A ARG 3.0 16.7 + - - +
451A LEU* 3.5 17.5 - - + +
453A ARG* 1.3 74.3 - - - +
455A LEU* 1.4 64.5 + - + +
457A LEU* 3.3 20.1 + - + +
458A ARG* 3.0 46.3 + - + +
461A ARG* 5.8 0.4 - - - +
632A ARG* 5.0 7.0 - - - +
633A LEU* 3.7 25.5 - - + +
636A GLU* 4.0 26.6 + - + +
637A ILE* 4.1 14.8 - - + -
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 3.6 32.5 - - + +
245A LEU* 4.5 11.7 - - + -
248A PHE* 3.7 41.7 - - + -
357A PHE* 3.8 20.9 - - + -
365A MET* 4.4 15.7 - - + -
451A LEU* 2.9 16.9 + - + +
452A PHE* 3.2 13.2 + - + +
454A TRP* 1.4 82.5 - - + +
456A VAL* 1.3 57.2 + - - +
458A ARG* 3.5 3.1 + - - +
459A LEU* 3.1 37.0 + - + +
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.7 25.1 - - + -
281A ILE* 3.6 34.5 - - + +
283A THR* 3.8 29.2 - - + +
452A PHE* 3.0 22.6 + - + +
453A ARG* 3.8 6.5 - - + +
454A TRP 3.3 0.2 - - - -
455A LEU* 1.3 73.3 - - - +
457A LEU* 1.3 60.0 + - - +
459A LEU* 3.4 8.7 + - - +
460A ASN* 2.9 33.9 + - - +
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Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG 3.2 13.5 + - - +
454A TRP* 3.5 25.4 - - + +
456A VAL* 1.3 74.8 - - - +
458A ARG* 1.3 59.3 + - + +
460A ASN* 3.4 11.8 + - + +
461A ARG* 2.9 39.1 + - + +
636A GLU* 5.4 7.2 - - - +
639A LYS* 6.2 2.7 - - - -
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Residues in contact with ARG 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLY* 3.1 29.7 + - - +
357A PHE* 3.1 28.0 - - + +
361A GLU* 2.8 40.7 + - - -
454A TRP* 3.0 44.2 + - + +
455A LEU 3.8 0.9 - - - +
457A LEU* 1.3 75.9 - - + +
459A LEU* 1.4 59.1 + - - +
461A ARG* 2.7 51.5 + - - +
462A ALA* 3.0 29.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA* 4.1 11.7 - - + +
244A ILE* 3.9 25.4 - - + -
245A LEU* 3.6 41.7 - - + -
281A ILE* 4.5 8.3 - - + -
355A LEU* 3.6 30.5 - - + -
357A PHE* 4.2 8.1 - - + -
455A LEU* 3.1 24.1 + - + +
456A VAL* 3.4 5.6 + - - +
458A ARG* 1.4 71.7 - - - +
460A ASN* 1.4 54.0 + - - +
462A ALA* 3.1 5.4 + - - -
463A LEU* 2.6 50.3 + - + +
----------------------------------------------------------
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Residues in contact with ASN 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA 4.2 0.7 - - - +
280A ASN* 3.1 23.1 + - - +
281A ILE* 2.6 52.1 + - - +
282A GLU* 5.5 0.2 + - - -
456A VAL* 2.9 22.1 + - - +
457A LEU* 3.4 12.5 - - - +
459A LEU* 1.4 76.4 - - - +
461A ARG* 1.3 54.7 + - - +
463A LEU* 4.5 1.3 - - - +
464A ASP* 2.6 42.8 + - + +
----------------------------------------------------------
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Residues in contact with ARG 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLU* 5.0 1.8 + - - -
454A TRP* 5.8 0.8 - - - +
457A LEU* 2.9 27.9 + - + +
458A ARG* 2.7 58.0 + - - +
460A ASN* 1.3 78.5 - - - +
462A ALA* 1.3 60.5 + - - +
464A ASP 3.6 10.3 - - - +
465A ARG* 5.5 0.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN* 3.6 10.3 - - - +
355A LEU* 3.8 23.6 - - + -
356A GLY* 4.1 16.8 - - - +
357A PHE* 6.5 0.2 - - + -
458A ARG* 3.0 17.3 + - - +
459A LEU 3.6 5.2 - - - +
461A ARG* 1.3 79.0 - - - +
463A LEU* 1.3 58.1 + - - +
465A ARG* 3.2 33.1 + - - -
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 4.0 9.3 - - + +
237A GLN* 3.7 18.4 - - + +
238A LEU* 3.6 42.4 - - + +
241A ALA* 3.5 28.0 - - + -
278A GLY* 3.6 1.9 - - - -
279A ALA* 3.3 31.8 + - + +
281A ILE* 3.9 21.1 - - + -
355A LEU* 4.0 6.1 - - + -
459A LEU* 2.6 28.6 + - + +
460A ASN* 4.5 1.6 - - - +
462A ALA* 1.3 72.0 - - - +
464A ASP* 1.3 61.6 + - - +
465A ARG* 3.3 13.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASN* 5.0 9.0 + - - -
278A GLY* 5.6 0.2 - - - -
279A ALA 3.2 17.2 + - - +
280A ASN* 4.3 14.3 - - - +
460A ASN* 2.6 35.7 + - + +
461A ARG* 3.6 12.1 - - - +
463A LEU* 1.3 70.2 - - - +
465A ARG* 1.3 73.7 + - - +
467A PRO* 5.3 6.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il