Contacts of the helix formed by residues 363 - 390 (chain C) in PDB entry 2JIF
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 PHE 363 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C GLY 5.4 1.6 - - - -
291C ASN* 3.9 38.8 - - + -
292C GLU* 4.7 3.4 - - + -
295C ILE* 4.1 8.7 - - + -
353C ALA 3.9 8.7 - - - +
356C LEU* 3.9 4.0 - - + -
357C LEU* 3.9 52.7 - - + +
361C LYS 3.3 11.1 + - - -
362C PRO* 1.3 75.1 - - + +
364C ILE* 1.3 65.5 + - + +
366C GLU* 3.2 12.2 + - - +
367C ALA* 2.7 41.6 + - + -
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Residues in contact with ILE 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ASN* 3.4 42.2 - - + +
362C PRO* 5.4 0.6 - - - +
363C PHE* 1.3 90.2 - - + +
365C LYS* 1.3 63.4 + - - +
366C GLU* 3.9 0.4 + - - -
367C ALA* 3.3 3.9 + - - +
368C SER* 3.0 24.1 + - - +
423C THR* 4.0 16.4 - - + -
427C HIS* 3.5 30.5 - - + +
1434C COS 4.0 16.4 - - + +
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Residues in contact with LYS 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE 3.4 0.4 - - - -
364C ILE* 1.3 78.4 - - - +
366C GLU* 1.3 82.2 + - - +
368C SER* 3.4 6.2 + - - -
369C MET* 2.9 62.3 + - + +
423C THR* 5.5 0.4 - - - -
424C ILE* 4.1 17.0 - - + +
427C HIS* 3.8 36.4 + - + +
428C ILE* 4.8 6.1 - - + +
431C GLU* 2.9 36.2 + - - +
344D GLU* 4.6 9.6 + - - -
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Residues in contact with GLU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C LEU* 4.6 3.8 - - + +
352C ASN* 4.8 2.5 - - - +
353C ALA* 3.9 13.3 - - + +
356C LEU* 3.4 32.8 - - + +
362C PRO* 3.5 8.5 - - - +
363C PHE* 3.4 22.9 + - - +
364C ILE 3.2 0.4 - - - -
365C LYS* 1.3 98.4 + - - +
367C ALA* 1.3 60.2 + - - +
369C MET* 3.4 8.4 + - - +
370C ALA* 2.9 30.0 + - - +
344D GLU* 3.8 24.0 - - + +
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ASN* 3.5 26.5 - - - +
294C ARG* 4.0 10.4 - - + +
295C ILE* 3.6 17.5 - - + -
353C ALA* 3.9 10.0 - - - +
363C PHE* 2.7 26.9 + - + +
364C ILE* 3.7 5.2 - - - +
366C GLU* 1.3 73.2 - - - +
368C SER* 1.3 57.5 + - - +
370C ALA* 3.4 3.3 + - - +
371C LYS* 3.0 28.9 + - - +
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Residues in contact with SER 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 4.2 9.3 + - - +
364C ILE* 3.0 18.4 + - - +
365C LYS 3.6 3.8 - - - -
367C ALA* 1.3 71.8 - - - +
369C MET* 1.3 60.8 + - - +
371C LYS* 4.5 0.7 - - - +
372C TYR* 2.9 33.4 + - - +
420C GLN* 3.3 31.2 + - - +
423C THR* 3.5 19.7 - - - +
424C ILE* 3.8 19.3 - - - -
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Residues in contact with MET 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C LEU* 4.6 8.3 - - + -
365C LYS* 2.9 50.1 + - + +
366C GLU* 3.5 9.0 - - - +
367C ALA 3.4 0.2 - - - -
368C SER* 1.3 75.0 - - - +
370C ALA* 1.3 57.1 + - - +
372C TYR* 3.9 1.3 - - - +
373C TYR* 3.0 34.4 + - - +
424C ILE* 3.7 18.1 - - + +
340D ALA* 3.7 39.3 - - + +
341D THR* 3.5 24.2 - - + +
344D GLU* 3.7 33.7 - - + +
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Residues in contact with ALA 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG 5.4 0.2 - - - +
295C ILE* 5.4 1.6 - - - -
298C ALA* 3.6 17.3 - - + -
346C ALA* 5.5 0.6 - - - +
349C LEU* 3.7 32.6 - - - +
350C THR* 3.8 11.0 - - - +
353C ALA* 4.6 4.5 - - + -
366C GLU 2.9 20.2 + - - +
367C ALA* 3.4 4.9 + - - +
369C MET* 1.3 71.8 - - - +
371C LYS* 1.3 58.3 + - - +
374C ALA* 2.9 35.2 + - - +
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Residues in contact with LYS 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 3.4 34.5 - - + +
297C ILE* 3.9 23.6 - - + -
298C ALA* 3.8 9.2 - - - +
301C MET* 5.4 0.2 - - - +
367C ALA 3.0 14.0 + - - +
368C SER 4.0 2.2 - - - +
370C ALA* 1.3 73.1 - - - +
372C TYR* 1.3 60.8 + - - +
374C ALA* 4.3 0.2 - - - +
375C SER* 2.8 38.8 + - - +
410C GLY 2.7 28.0 + - - +
411C THR* 4.1 7.7 - - - +
413C TYR 2.7 20.4 + - - -
414C GLU* 4.0 6.1 - - - -
415C GLY 2.6 25.9 + - - -
416C ALA* 4.4 1.8 - - - +
417C SER* 4.6 0.6 - - - +
420C GLN* 3.7 15.9 - - + +
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Residues in contact with TYR 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C SER 2.9 18.6 + - - +
369C MET* 3.9 1.3 - - - +
371C LYS* 1.3 77.5 - - - +
373C TYR* 1.3 66.3 + + + +
375C SER* 2.9 19.0 + - - -
376C GLU* 3.0 46.6 + - + +
417C SER* 3.9 22.9 - - - +
420C GLN* 3.9 15.9 - - + +
421C LEU* 3.7 41.0 - - + +
424C ILE* 4.7 1.8 - - + -
338D HIS* 2.7 40.3 + + - +
341D THR* 4.2 22.7 - - + -
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Residues in contact with TYR 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C GLN* 3.3 42.7 - - - +
345C ALA* 3.7 13.0 - - + +
346C ALA* 3.7 15.5 - - + -
349C LEU* 3.6 22.2 - - + -
369C MET 3.0 18.6 + - - +
370C ALA 4.2 0.2 - - - +
372C TYR* 1.3 84.9 - + - +
374C ALA* 1.3 54.4 + - - +
376C GLU* 3.3 3.6 + - + +
377C ILE* 2.8 56.8 + - + +
338D HIS* 6.3 2.0 - + - -
341D THR* 4.0 20.0 - - + -
342D GLN* 5.2 3.4 - - + -
345D ALA* 4.8 2.7 - - + -
373D TYR* 3.6 22.4 - - - -
1441D CL 3.6 23.4 - - + +
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Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C ALA* 3.6 31.6 - - + +
301C MET* 3.7 6.6 - - + +
302C LEU* 4.4 3.4 - - + +
346C ALA* 4.2 15.9 - - + +
350C THR* 4.5 3.8 - - - +
370C ALA 2.9 19.8 + - - +
373C TYR* 1.3 77.0 - - - +
375C SER* 1.3 57.2 + - - +
377C ILE* 3.7 10.6 - - - +
378C ALA* 2.9 31.7 + - - +
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Residues in contact with SER 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C MET* 3.7 21.6 - - - +
371C LYS* 2.8 27.1 + - - +
372C TYR* 2.9 12.1 + - - -
374C ALA* 1.3 75.9 - - - +
376C GLU* 1.3 61.3 + - - +
378C ALA* 3.4 3.3 + - - +
379C GLY* 3.2 17.8 + - - -
407C ALA 4.7 2.3 - - - +
410C GLY* 3.3 35.4 + - - -
411C THR* 3.7 17.5 - - - +
417C SER* 4.3 2.4 + - - -
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Residues in contact with GLU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LYS* 4.7 11.1 + - - -
387A GLU* 4.4 9.8 - - - +
372C TYR* 3.0 46.0 + - + +
373C TYR* 3.8 4.7 - - - +
375C SER* 1.3 81.9 + - - +
377C ILE* 1.3 64.3 + - + +
379C GLY* 3.3 4.3 + - - -
380C GLN* 3.2 36.2 + - - +
411C THR* 3.4 14.9 - - - +
417C SER* 2.7 30.6 + - - +
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Residues in contact with ILE 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 5.9 1.8 - - + -
305C ALA* 4.6 2.0 - - + -
342C GLN* 3.7 49.1 - - + +
343C LEU* 3.9 19.5 - - + +
346C ALA* 4.0 8.3 - - + -
373C TYR* 2.8 59.7 + - + +
374C ALA* 3.7 9.6 - - - +
376C GLU* 1.3 73.2 - - + +
378C ALA* 1.3 63.2 + - - +
380C GLN* 3.7 9.3 - - - +
381C THR* 2.7 44.7 + - - +
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Residues in contact with ALA 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C MET* 3.5 38.4 - - - +
304C LEU* 4.6 2.5 - - + -
305C ALA* 3.8 14.1 - - + -
374C ALA 2.9 23.2 + - - +
375C SER 3.7 4.9 - - - +
376C GLU 3.3 0.2 - - - -
377C ILE* 1.3 73.7 - - - +
379C GLY* 1.3 59.5 + - - +
382C THR* 2.8 33.1 + - - +
407C ALA* 3.8 8.1 - - + -
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Residues in contact with GLY 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C SER 3.2 12.9 + - - -
376C GLU* 3.3 4.0 + - - -
377C ILE 3.3 0.2 - - - -
378C ALA* 1.3 74.6 - - - +
380C GLN* 1.3 57.2 + - - +
382C THR* 3.2 6.2 + - - -
383C SER* 3.0 32.6 + - - -
404C PHE* 4.7 2.5 - - - -
407C ALA* 4.0 10.6 - - - +
408C LYS* 5.6 3.6 - - - -
411C THR* 6.4 0.2 - - - -
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Residues in contact with GLN 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C HIS* 4.9 2.9 + - - -
339C VAL* 5.2 2.0 - - + -
342C GLN* 3.2 32.2 + - - +
376C GLU* 3.2 28.4 + - - +
377C ILE* 3.2 12.0 + - - +
379C GLY* 1.3 75.0 - - - +
381C THR* 1.3 58.7 + - - +
383C SER* 3.7 5.1 - - - -
384C LYS* 2.9 38.6 + - + +
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Residues in contact with THR 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ALA* 3.6 32.9 - - + +
308C CYS* 5.0 0.9 - - + -
309C PHE* 4.4 5.4 - - + +
339C VAL* 3.6 36.0 + - + +
342C GLN* 5.1 2.1 + - - -
343C LEU* 4.3 3.2 - - + +
377C ILE* 2.7 39.2 + - - +
378C ALA 3.9 3.4 - - - -
380C GLN* 1.3 72.2 - - - +
382C THR* 1.3 57.9 + - - +
384C LYS* 3.3 4.2 + - - +
385C CYS* 2.9 40.1 + - - -
388C TRP* 5.2 0.2 - - - -
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Residues in contact with THR 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LEU* 3.5 28.9 - - + -
305C ALA* 4.7 3.1 - - - -
308C CYS* 3.9 18.2 - - + -
378C ALA 2.8 21.6 + - - +
379C GLY* 3.2 5.7 + - - -
381C THR* 1.3 72.7 - - - +
383C SER* 1.3 66.6 + - - +
385C CYS* 3.3 1.9 + - - +
386C ILE* 3.2 27.9 + - - +
400C VAL* 4.1 1.0 - - - +
403C TYR* 3.7 17.3 - - + +
404C PHE* 3.5 29.7 + - - -
407C ALA* 3.6 5.9 - - + +
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Residues in contact with SER 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LYS* 2.7 41.2 + - - +
379C GLY 3.0 20.6 + - - -
380C GLN* 3.7 5.2 - - - -
382C THR* 1.3 77.5 + - - +
384C LYS* 1.3 64.8 + - - +
386C ILE* 3.5 1.4 + - - +
387C GLU* 3.5 14.2 + - - +
404C PHE* 3.7 21.5 - - - -
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Residues in contact with LYS 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLU* 4.9 13.0 + - - -
335C GLN* 3.7 36.1 + - + +
339C VAL* 4.4 11.0 - - + -
380C GLN* 2.9 21.2 + - + +
381C THR 3.7 3.4 - - - +
383C SER* 1.3 77.2 - - - +
385C CYS* 1.3 61.4 + - - +
387C GLU* 3.1 29.2 + - - +
388C TRP* 3.0 52.7 + - + +
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Residues in contact with CYS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C CYS* 3.6 26.0 - - - -
309C PHE* 4.0 14.6 - - - -
312C THR* 3.4 27.1 - - - +
381C THR* 2.9 24.9 + - - +
382C THR 3.3 1.3 + - - +
384C LYS* 1.3 74.3 - - - +
386C ILE* 1.3 65.0 + - - +
388C TRP* 3.3 29.2 + - - +
389C MET* 3.0 28.6 + - - +
400C VAL* 3.8 3.8 - - + -
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Residues in contact with ILE 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.9 15.0 - - + -
408A LYS* 4.0 14.6 - - + -
412A ILE* 3.7 21.6 - - + +
382C THR 3.2 12.0 + - - +
383C SER 3.7 6.7 - - - +
384C LYS 3.3 0.2 - - - -
385C CYS* 1.3 75.5 - - - +
387C GLU* 1.3 63.7 + - - +
389C MET* 3.3 5.4 + - - +
390C GLY* 3.0 22.9 + - - +
393C GLY* 3.8 20.0 - - - +
394C TYR* 4.2 3.6 - - + +
400C VAL* 3.5 18.2 - - + +
401C GLU* 4.0 6.1 - - - -
404C PHE* 3.4 44.4 - - + -
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Residues in contact with GLU 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLU* 4.4 9.4 - - - +
408A LYS* 2.6 28.1 + - - +
411A THR* 2.9 38.6 + - - +
412A ILE* 4.5 11.2 - - + +
417A SER* 5.1 4.6 - - - -
1433A FAD 2.8 28.6 + - - +
335C GLN* 4.8 2.1 - - - +
383C SER* 3.5 10.1 + - - +
384C LYS* 3.1 37.2 + - - +
386C ILE* 1.3 77.3 - - - +
388C TRP* 1.3 62.5 + - + +
390C GLY* 3.1 11.4 + - - -
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Residues in contact with TRP 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ASN* 6.0 0.4 - - - -
1433A FAD 3.3 24.2 - - - +
309C PHE* 4.1 13.9 - + - -
312C THR* 3.8 19.3 - - + -
313C ILE* 4.5 2.7 - - + -
316C ILE* 3.6 31.7 - - + +
326C LEU* 3.8 3.3 - - - +
332C LEU* 4.0 18.9 - - + +
335C GLN* 3.0 53.4 + - + +
336C VAL* 3.6 32.5 - - + -
339C VAL* 3.8 22.2 - - + -
384C LYS* 3.0 34.7 + - + +
385C CYS* 3.3 25.8 + - - +
387C GLU* 1.3 78.8 - - + +
389C MET* 1.3 60.9 + - - +
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Residues in contact with MET 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433A FAD 4.2 6.7 + - - +
311C TYR* 3.9 19.5 - - + -
312C THR* 3.8 16.8 - - + -
315C TYR* 3.5 59.7 + - + -
385C CYS 3.0 18.8 + - - +
386C ILE 3.5 7.6 - - - +
387C GLU 3.2 0.2 - - - -
388C TRP* 1.3 75.9 - - - +
390C GLY* 1.3 60.0 + - - +
391C GLY 3.8 0.5 + - - -
392C VAL* 3.4 30.8 - - + +
393C GLY* 3.6 16.4 - - - +
398C TYR* 3.8 18.8 - - + -
400C VAL* 3.9 16.8 - - + -
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Residues in contact with GLY 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 3.9 20.6 - - - +
1433A FAD 3.8 18.2 - - - -
386C ILE 3.0 11.1 + - - +
387C GLU 3.1 13.6 + - - -
388C TRP 3.5 0.2 + - - -
389C MET* 1.3 76.1 - - - +
391C GLY* 1.3 66.4 + - - +
393C GLY* 2.9 15.8 + - - -
394C TYR 3.6 2.4 + - - -
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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).
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