Contacts of the helix formed by residues 364 - 388 (chain F) in PDB entry 5I4V
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 PRO 364 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362F SER 4.3 2.0 - - - +
363F LEU* 1.3 98.8 - - + +
365F LEU* 1.3 61.2 + - - +
366F ASP* 4.5 4.0 - - + +
367F ASP* 3.0 22.4 + - + +
368F GLN* 2.9 25.1 + - - +
455F SER* 3.8 19.3 - - - +
459F GLU* 4.4 12.8 - - - +
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Residues in contact with LEU 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F LEU 3.5 1.8 + - - -
364F PRO* 1.3 70.3 - - - +
366F ASP* 1.3 64.2 - - - +
368F GLN* 3.2 13.8 + - - +
369F VAL* 3.1 29.0 + - + +
539F HIS* 4.1 27.4 - - + +
542F LEU* 3.8 42.2 - - + +
543F GLN* 3.8 17.0 - - - +
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Residues in contact with ASP 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F PRO* 3.3 3.5 - - + +
365F LEU* 1.3 78.1 - - - +
367F ASP* 1.3 63.3 + - - +
369F VAL* 3.4 8.7 - - - +
370F ILE* 3.1 34.3 + - + +
539F HIS* 4.6 15.4 + - - -
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Residues in contact with ASP 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363F LEU* 4.7 9.3 - - + +
364F PRO* 3.0 27.1 + - + +
366F ASP* 1.3 79.3 - - - +
368F GLN* 1.3 64.7 + - - +
369F VAL 3.1 1.3 - - - -
370F ILE* 3.1 9.7 + - - +
371F LEU* 3.0 30.5 + - + +
453F GLY 4.3 0.2 - - - +
454F LEU* 3.7 19.3 - - + +
455F SER* 2.7 48.4 + - - -
456F ASN* 3.7 9.2 + - - +
459F GLU* 5.6 0.5 - - - +
460F VAL* 5.3 3.0 - - + +
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Residues in contact with GLN 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355F LYS* 5.9 1.2 - - - +
360F PHE* 3.4 51.1 - - + +
361F SER* 2.8 29.6 + - - +
363F LEU* 2.6 29.9 + - + +
364F PRO 2.9 13.9 + - - +
365F LEU* 3.5 13.7 - - - +
367F ASP* 1.3 76.7 - - - +
369F VAL* 1.3 61.8 + - - +
371F LEU* 3.7 1.2 + - - +
372F LEU* 3.3 22.6 + - - +
542F LEU* 3.8 28.7 - - + +
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Residues in contact with VAL 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F LEU* 3.1 20.1 + - + +
366F ASP* 3.4 11.0 - - - +
368F GLN* 1.3 76.5 - - - +
370F ILE* 1.3 65.9 + - + +
372F LEU* 3.3 3.8 + - - +
373F ARG* 3.0 28.3 + - - +
535F HIS* 4.7 20.0 - - + +
538F LEU* 3.8 21.1 - - + +
539F HIS* 3.9 28.5 - - + +
542F LEU* 3.6 22.4 - - + -
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Residues in contact with ILE 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366F ASP* 3.1 22.7 + - + +
367F ASP* 3.1 17.2 + - - +
369F VAL* 1.3 80.1 - - + +
371F LEU* 1.3 58.4 + - - +
373F ARG* 3.4 8.0 + - - +
374F ALA* 3.0 26.9 + - + +
451F ALA* 4.0 18.4 - - + -
452F LYS 3.3 20.9 - - - +
453F GLY* 3.1 31.9 - - - +
454F LEU* 4.0 11.0 - - + +
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Residues in contact with LEU 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360F PHE* 4.1 11.2 - - + -
363F LEU* 3.9 28.9 - - + -
367F ASP 3.0 19.1 + - - +
368F GLN 4.0 3.6 - - - +
370F ILE* 1.3 77.3 - - - +
372F LEU* 1.3 57.2 + - - +
374F ALA* 3.3 4.3 + - - +
375F GLY* 2.9 26.7 + - - -
446F LEU* 3.6 34.6 - - + +
447F PHE* 4.3 11.2 - - + -
448F ASN* 3.5 30.2 - - + +
451F ALA* 4.4 4.9 - - + -
454F LEU* 4.1 15.3 - - + -
460F VAL* 4.2 10.3 - - + -
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Residues in contact with LEU 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F LEU* 3.9 34.3 - - + +
351F VAL* 4.5 9.6 - - + +
354F ALA* 4.1 17.5 - - + -
360F PHE* 3.9 19.7 - - + -
368F GLN 3.3 16.0 + - - +
369F VAL 3.3 4.3 + - - +
371F LEU* 1.3 76.8 - - - +
373F ARG* 1.3 60.5 + - - +
375F GLY* 5.1 0.2 - - - -
376F TRP* 3.0 37.0 + - + +
379F LEU* 4.5 3.6 - - + -
446F LEU* 4.4 10.8 - - + -
525F MET* 4.8 2.9 - - - +
538F LEU* 4.2 21.8 - - + -
542F LEU* 4.0 20.0 - - + -
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Residues in contact with ARG 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369F VAL* 3.0 23.8 + - - +
370F ILE* 3.8 7.4 - - - +
372F LEU* 1.3 79.1 - - - +
374F ALA* 1.3 57.9 + - - +
376F TRP* 3.1 24.6 + - - -
525F MET* 4.1 29.4 + - - +
527F GLU 2.7 29.3 + - - -
528F ALA* 3.8 18.8 + - - +
535F HIS* 3.3 43.9 + - - -
538F LEU* 4.9 2.2 - - + +
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Residues in contact with ALA 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F ILE* 3.0 17.2 + - + +
371F LEU* 3.8 3.8 - - - +
372F LEU 3.3 0.2 - - - -
373F ARG* 1.3 76.2 - - - +
375F GLY* 1.3 59.6 + - - +
376F TRP* 3.8 0.6 - - - -
377F ASN* 5.0 3.6 + - - +
378F GLU* 3.9 11.1 - - - +
448F ASN* 4.8 13.5 + - + +
451F ALA* 3.8 24.7 - - + -
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Residues in contact with GLY 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F LEU 2.9 15.4 + - - -
374F ALA* 1.3 78.4 - - - +
376F TRP* 1.3 66.0 + - - +
377F ASN 2.9 5.0 + - - -
378F GLU* 3.1 12.0 + - - +
379F LEU* 3.0 33.0 + - - +
445F ILE* 4.6 12.6 - - - -
446F LEU* 5.7 0.7 - - - -
448F ASN* 6.3 0.7 - - - -
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Residues in contact with TRP 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F ALA* 5.3 2.7 - - + -
347F LEU* 3.9 23.6 - - + -
350F LEU* 3.7 26.9 - - + -
372F LEU 3.0 19.5 + - - +
373F ARG* 3.1 32.7 + - - -
375F GLY* 1.3 74.9 - - - +
377F ASN* 1.3 89.2 + - + +
379F LEU* 3.6 3.1 - - - +
380F LEU* 3.0 42.7 + - + +
504F LEU* 4.3 18.8 - - + +
507F LEU* 3.9 21.3 - - + -
522F LEU* 3.7 27.4 - - + -
525F MET* 3.6 36.6 + - + +
526F LEU* 4.6 8.1 - - + -
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Residues in contact with ASN 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374F ALA 5.0 3.6 + - - +
375F GLY 2.9 2.5 + - - -
376F TRP* 1.3 104.5 - - + +
378F GLU* 1.3 67.5 + - + +
380F LEU* 3.2 2.1 + - - +
381F ILE* 3.2 35.1 + - - +
500F GLY* 2.7 44.5 + - - -
503F CYS* 4.3 3.1 - - - +
504F LEU* 4.1 19.7 - - + +
507F LEU* 4.1 17.7 - - - +
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Residues in contact with GLU 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E VAL* 5.3 0.3 - - - +
374F ALA 3.9 17.2 - - - +
375F GLY* 3.1 6.6 + - - +
377F ASN* 1.3 80.8 + - - +
379F LEU* 1.3 62.4 + - - +
381F ILE* 3.3 9.4 + - - +
382F ALA* 3.0 24.6 + - - +
445F ILE* 3.9 24.4 - - + +
493F LEU 5.5 0.2 - - - +
496F LEU* 4.0 34.5 - - + +
497F ARG* 2.7 47.3 + - - +
500F GLY* 4.6 10.3 - - - -
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Residues in contact with LEU 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F LEU* 3.8 34.1 - - + -
353F TRP* 4.0 15.3 - - + -
371F LEU 5.6 0.2 - - - +
372F LEU* 4.5 4.0 - - + -
375F GLY* 3.0 30.2 + - - +
376F TRP 3.6 4.5 - - - +
378F GLU* 1.3 77.0 - - - +
380F LEU* 1.3 62.0 + - - +
382F ALA* 3.4 3.3 + - - +
383F SER 3.2 16.8 + - - -
442F ARG* 3.2 60.5 + - + +
445F ILE* 4.0 13.5 - - + -
446F LEU* 4.1 17.9 - - + +
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Residues in contact with LEU 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F ALA* 4.2 29.8 - - + +
346F GLN* 3.8 31.4 - - + +
347F LEU* 4.3 6.7 - - + -
350F LEU* 4.5 19.3 - - + -
376F TRP* 3.0 42.9 + - + +
377F ASN* 3.8 3.6 - - - +
379F LEU* 1.3 73.8 - - - +
381F ILE* 1.3 68.2 + - + +
383F SER* 3.3 10.6 + - - +
384F PHE* 3.0 32.8 + - + +
442F ARG* 5.0 1.6 - - - +
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Residues in contact with ILE 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F ASN* 3.2 42.7 + - - +
378F GLU* 3.7 7.4 - - - +
380F LEU* 1.3 77.4 - - + +
382F ALA* 1.3 58.9 + - - +
384F PHE* 3.5 27.1 - - + -
385F SER* 2.8 36.1 + - - +
420F VAL* 4.9 2.5 - - + -
424F LEU* 3.7 26.7 - - + -
496F LEU* 3.7 9.4 - - + -
499F ILE* 4.4 7.0 - - + -
500F GLY* 4.0 17.3 - - - +
503F CYS* 4.0 19.1 - - + -
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Residues in contact with ALA 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F GLU 3.0 17.0 + - - +
379F LEU* 3.7 4.9 - - - +
381F ILE* 1.3 80.7 - - - +
383F SER* 1.3 62.3 + - - +
385F SER* 3.4 5.5 + - - -
386F HIS* 3.1 24.3 + - - +
424F LEU* 5.7 1.3 - - - -
428F MET* 3.7 9.5 - - + +
438F LEU* 3.9 8.8 - - + +
441F LEU* 6.5 0.7 - - + -
442F ARG* 4.2 19.5 - - + -
445F ILE* 4.9 2.7 - - + -
496F LEU* 4.3 17.0 - - + -
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Residues in contact with SER 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F GLU* 5.3 1.3 - - - -
346F GLN* 4.7 6.6 + - - +
379F LEU 3.2 11.6 + - - -
380F LEU* 3.3 14.2 + - - +
382F ALA* 1.3 80.9 - - - +
384F PHE* 1.3 59.4 + - - +
386F HIS* 3.5 2.8 + - - +
387F ARG* 3.0 43.6 + - - +
438F LEU* 4.6 10.4 - - - +
442F ARG* 3.9 23.5 + - - +
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Residues in contact with PHE 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F ILE* 6.1 5.2 - - + -
380F LEU* 3.0 23.6 + - + +
381F ILE* 3.5 38.8 - - + -
383F SER* 1.3 77.8 + - - +
385F SER* 1.3 68.7 + - - +
387F ARG* 3.1 32.2 - - - +
388F SER* 2.5 35.0 + - - -
395F ILE* 3.6 34.5 - - + -
396F LEU 4.1 5.6 - - - +
397F LEU* 5.2 7.6 - - + -
420F VAL* 4.2 18.2 - - + -
503F CYS* 6.0 2.5 - - - -
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Residues in contact with SER 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F ILE* 2.8 25.9 + - - +
382F ALA 3.7 4.3 - - - -
383F SER 3.3 0.2 - - - -
384F PHE* 1.3 80.2 - - - +
386F HIS* 1.3 62.8 + - - +
388F SER* 3.1 11.6 + - - -
389F ILE* 3.7 4.5 + - - +
420F VAL* 3.7 12.1 - - - +
424F LEU* 3.5 30.4 - - - +
425F VAL* 3.5 25.3 - - - +
428F MET* 3.8 18.4 - - - -
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Residues in contact with HIS 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F ALA 3.1 14.4 + - - +
383F SER 3.8 1.8 - - - +
385F SER* 1.3 78.8 - - - +
387F ARG* 1.3 63.7 + - - +
389F ILE* 3.2 36.4 + - + +
428F MET* 3.6 8.5 - - + -
433F MET* 2.9 48.0 + - + -
434F ASP* 3.7 8.3 + - - -
435F LYS* 4.1 33.3 - - + +
438F LEU* 3.6 29.4 - - + +
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Residues in contact with ARG 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F GLN* 3.6 24.5 - - - +
383F SER* 3.0 30.1 + - - +
384F PHE* 3.1 32.6 - - - +
386F HIS* 1.3 79.5 + - - +
388F SER* 1.3 57.9 + - - +
389F ILE 3.3 3.4 + - - -
390F ASP* 4.6 6.9 + - - +
391F VAL* 5.1 0.9 - - - +
396F LEU* 3.1 39.6 + - + +
397F LEU* 4.0 5.1 - - - +
398F ALA* 3.3 31.2 - - - +
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Residues in contact with SER 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384F PHE 2.5 23.2 + - - -
385F SER 3.1 9.8 + - - -
387F ARG* 1.3 74.3 - - - +
389F ILE* 1.3 63.2 + - - +
390F ASP 3.1 3.4 - - - -
391F VAL* 3.1 26.4 + - - +
394F GLY 3.9 5.2 - - - +
395F ILE* 3.3 25.9 - - - +
396F LEU* 3.0 19.5 + - - +
425F VAL* 3.6 17.2 - - - +
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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