Contacts of the helix formed by residues 364 - 388 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B SER 4.3 2.2 - - - +
363B LEU* 1.3 93.1 - - + +
365B LEU* 1.3 60.1 + - - +
366B ASP* 4.5 3.8 - - + +
367B ASP* 3.0 22.2 + - + +
368B GLN* 2.9 25.8 + - - +
455B SER* 3.8 19.1 - - - +
459B GLU* 4.4 15.0 - - - +
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU 3.5 2.0 + - - -
364B PRO* 1.3 70.9 - - - +
366B ASP* 1.3 68.3 + - - +
368B GLN* 3.2 14.6 + - - +
369B VAL* 3.0 29.1 + - + +
539B HIS* 4.5 17.7 - - + +
542B LEU* 3.3 42.0 - - + +
543B GLN* 3.3 31.0 - - + +
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Residues in contact with ASP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B PRO* 3.3 3.0 - - + +
365B LEU* 1.3 79.0 - - - +
367B ASP* 1.3 63.3 + - - +
369B VAL* 3.4 9.7 - - - +
370B ILE* 3.1 35.0 + - + +
539B HIS* 4.2 17.3 + - - -
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Residues in contact with ASP 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 4.7 9.9 - - + +
364B PRO* 3.0 26.8 + - + +
366B ASP* 1.3 78.6 - - - +
368B GLN* 1.3 65.1 + - - +
369B VAL 3.1 1.1 - - - -
370B ILE* 3.1 9.8 + - - +
371B LEU* 3.0 30.5 + - - +
453B GLY 4.2 0.5 - - - +
454B LEU* 3.7 19.6 - - + +
455B SER* 2.7 48.8 + - - -
456B ASN* 3.7 8.8 + - - +
459B GLU* 5.5 0.9 - - - +
460B VAL* 5.3 2.7 - - + +
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Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LYS* 5.8 1.4 - - - +
360B PHE* 3.5 52.2 - - + +
361B SER* 2.8 28.7 + - - +
363B LEU* 2.6 29.9 + - + +
364B PRO 2.9 14.0 + - - +
365B LEU* 3.2 14.0 + - - +
367B ASP* 1.3 74.9 - - - +
369B VAL* 1.3 61.1 + - - +
371B LEU* 3.6 1.0 + - - +
372B LEU* 3.3 21.5 + - - +
542B LEU* 3.9 32.1 - - + +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 3.0 27.2 + - + +
366B ASP* 3.4 10.8 - - - +
367B ASP 3.1 0.2 - - - -
368B GLN* 1.3 77.2 - - - +
370B ILE* 1.3 66.9 + - + +
372B LEU* 3.2 3.8 + - - +
373B ARG* 3.0 35.1 + - - +
538B LEU* 3.8 31.1 - - + +
539B HIS* 4.0 34.1 - - + +
542B LEU* 4.5 7.0 - - + -
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ASP* 3.1 22.2 + - + +
367B ASP* 3.1 18.5 + - - +
369B VAL* 1.3 78.9 - - + +
371B LEU* 1.3 59.1 + - - +
373B ARG* 3.4 7.5 + - - +
374B ALA* 3.0 27.5 + - + +
451B ALA* 4.0 18.2 - - + -
452B LYS 3.4 21.3 - - - +
453B GLY* 3.1 31.9 - - - +
454B LEU* 4.0 10.8 - - + +
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PHE* 4.1 12.3 - - + -
363B LEU* 3.8 28.0 - - + -
367B ASP 3.0 18.7 + - - +
368B GLN 4.0 4.0 - - - +
370B ILE* 1.3 76.7 - - - +
372B LEU* 1.3 56.3 + - - +
374B ALA* 3.4 4.1 + - - +
375B GLY* 2.9 27.2 + - - -
446B LEU* 3.6 36.0 - - + +
447B PHE* 4.4 11.4 - - + -
448B ASN* 3.5 29.7 - - + +
451B ALA* 4.4 4.9 - - + -
454B LEU* 4.1 16.2 - - + -
460B VAL* 4.2 10.8 - - + -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.9 34.1 - - + +
351B VAL* 4.5 9.9 - - + -
354B ALA* 4.1 17.7 - - + -
360B PHE* 3.9 15.3 - - + -
368B GLN 3.3 16.5 + - - +
369B VAL 3.2 4.4 + - - +
371B LEU* 1.3 76.9 - - - +
373B ARG* 1.3 62.0 + - - +
375B GLY 4.5 0.2 - - - +
376B TRP* 3.0 36.5 + - - +
379B LEU* 4.5 3.6 - - + -
446B LEU* 4.4 11.2 - - + -
525B MET* 4.2 6.0 - - + +
538B LEU* 4.2 21.3 - - + -
542B LEU* 3.8 25.1 - - + -
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Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B VAL* 3.0 33.0 + - - +
370B ILE* 3.7 7.0 - - - +
371B LEU 3.3 0.2 - - - -
372B LEU* 1.3 77.4 - - - +
374B ALA* 1.3 57.8 + - - +
376B TRP* 3.1 25.5 + - - -
524B GLU* 3.1 29.3 + - - +
525B MET* 3.8 27.6 + - - +
527B GLU* 2.9 23.4 + - - -
528B ALA* 3.2 19.4 + - - +
538B LEU* 4.3 6.5 - - + -
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE* 3.0 18.1 + - + +
371B LEU 3.8 3.8 - - - +
373B ARG* 1.3 78.9 - - - +
375B GLY* 1.3 58.4 + - - +
377B ASN* 5.0 4.0 + - - +
378B GLU* 3.9 11.4 - - - +
448B ASN* 4.7 13.3 + - + +
451B ALA* 3.9 24.9 - - + -
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Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU 2.9 14.8 + - - -
374B ALA* 1.3 79.1 - - - +
376B TRP* 1.3 66.8 + - - +
377B ASN 2.9 4.4 + - - -
378B GLU* 3.1 13.0 + - - +
379B LEU* 3.0 33.5 + - - +
445B ILE* 4.6 12.1 - - - -
446B LEU* 5.7 1.1 - - - -
448B ASN* 6.3 1.1 - - - -
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Residues in contact with TRP 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ALA* 5.3 2.5 - - + -
347B LEU* 3.9 23.8 - - + -
350B LEU* 3.7 26.5 - - + -
372B LEU 3.0 18.4 + - - +
373B ARG* 3.1 32.5 + - - +
374B ALA 5.0 0.2 - - - -
375B GLY* 1.3 75.7 - - - +
377B ASN* 1.3 90.7 + - + +
379B LEU* 3.7 2.1 - - - +
380B LEU* 3.0 43.2 + - + +
504B LEU* 4.3 13.4 - - + +
507B LEU* 3.9 22.2 - - + -
522B LEU* 3.7 26.9 - - + -
525B MET* 3.6 31.8 + - + +
526B LEU* 3.9 19.1 - - + -
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Residues in contact with ASN 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ALA 5.4 3.1 - - - +
375B GLY 2.9 2.3 + - - -
376B TRP* 1.3 106.3 - - + +
378B GLU* 1.3 65.3 + - + +
380B LEU* 3.2 2.6 + - - +
381B ILE* 3.2 35.7 + - - +
500B GLY* 2.6 44.3 + - - -
503B CYS* 4.4 2.9 - - - +
504B LEU* 4.1 18.3 - - + +
507B LEU* 4.1 18.4 - - - +
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Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 5.3 0.3 - - - +
374B ALA 3.9 17.7 - - - +
375B GLY* 3.1 6.9 + - - +
377B ASN* 1.3 80.3 - - - +
379B LEU* 1.3 62.9 + - - +
381B ILE* 3.4 9.2 + - - +
382B ALA* 3.0 24.8 + - - +
445B ILE* 3.9 24.8 - - + +
493B LEU 5.5 0.2 - - - +
496B LEU* 4.0 37.1 - - + +
497B ARG* 2.7 49.9 + - - +
500B GLY* 4.6 9.0 - - - -
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.8 34.3 - - + -
353B TRP* 4.0 15.3 - - + -
372B LEU* 4.5 4.3 - - + -
375B GLY* 3.0 30.9 + - - +
376B TRP* 3.7 4.0 - - - +
378B GLU* 1.3 77.4 - - - +
380B LEU* 1.3 61.4 + - - +
382B ALA* 3.4 2.9 + - - +
383B SER 3.2 16.6 + - - -
442B ARG* 3.2 59.7 + - + +
445B ILE* 4.0 13.9 - - + -
446B LEU* 4.1 18.6 - - + +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ALA* 4.2 30.1 - - + +
346B GLN* 3.8 32.5 - - + +
347B LEU* 4.4 7.2 - - + -
350B LEU* 4.5 19.7 - - + -
376B TRP* 3.0 43.8 + - + +
377B ASN* 3.8 3.4 - - - +
379B LEU* 1.3 74.8 - - - +
381B ILE* 1.3 68.0 + - + +
383B SER* 3.3 10.9 + - - +
384B PHE* 3.0 32.2 + - + +
442B ARG* 5.0 1.8 - - - +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASN* 3.2 42.9 + - - +
378B GLU* 3.7 7.6 - - - +
380B LEU* 1.3 77.9 - - + +
382B ALA* 1.3 58.5 + - - +
384B PHE* 3.5 27.1 - - + -
385B SER* 2.8 36.4 + - - +
420B VAL* 4.9 3.4 - - + -
424B LEU* 3.7 26.7 - - + -
496B LEU* 3.7 8.5 - - + -
499B ILE* 4.4 6.5 - - + -
500B GLY* 4.0 17.0 - - - +
503B CYS* 4.0 19.1 - - + -
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU 3.0 17.7 + - - +
379B LEU 3.7 4.3 - - - +
380B LEU 3.2 0.2 - - - -
381B ILE* 1.3 79.8 - - - +
383B SER* 1.3 62.9 + - - +
385B SER* 3.4 5.1 + - - -
386B HIS* 3.2 24.4 + - - +
424B LEU* 5.7 1.6 - - - -
428B MET* 3.7 9.7 - - + +
438B LEU* 3.9 9.5 - - + +
441B LEU* 6.5 0.4 - - + -
442B ARG* 4.2 19.7 - - + -
445B ILE* 4.9 2.2 - - + -
496B LEU* 4.3 15.9 - - + -
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 5.4 1.3 - - - -
346B GLN* 4.7 6.6 + - - +
379B LEU 3.2 11.5 + - - -
380B LEU* 3.3 14.6 + - - +
382B ALA* 1.3 81.4 - - - +
384B PHE* 1.3 59.5 + - - +
386B HIS* 3.8 2.4 - - - +
387B ARG* 3.0 43.7 + - - +
438B LEU* 4.7 10.8 - - - +
442B ARG* 3.9 22.8 + - - +
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Residues in contact with PHE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 6.1 5.2 - - + -
380B LEU* 3.0 22.9 + - + +
381B ILE* 3.5 39.9 - - + -
383B SER* 1.3 79.3 + - - +
385B SER* 1.3 67.7 + - - +
387B ARG* 3.1 31.7 + - - +
388B SER* 2.5 35.3 + - - -
395B ILE* 3.6 34.5 - - + -
396B LEU 4.1 5.8 - - - +
397B LEU* 5.3 7.0 - - + -
420B VAL* 4.2 17.7 - - + -
503B CYS* 6.0 2.7 - - - -
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Residues in contact with SER 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 2.8 23.9 + - - +
382B ALA* 3.7 4.9 - - - -
383B SER 3.3 0.2 - - - -
384B PHE* 1.3 79.8 - - - +
386B HIS* 1.3 63.2 + - - +
388B SER* 3.0 12.1 + - - -
389B ILE* 3.7 4.5 + - - +
420B VAL* 3.7 12.0 - - - +
424B LEU* 3.5 30.7 - - - +
425B VAL* 3.5 25.2 - - - +
428B MET* 3.8 17.5 - - - -
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Residues in contact with HIS 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ALA 3.2 14.0 + - - +
383B SER 3.8 1.8 - - - +
385B SER* 1.3 79.0 - - - +
387B ARG* 1.3 61.5 + - - +
389B ILE* 3.2 35.9 + - + +
428B MET* 3.6 10.2 - - + -
433B MET* 2.9 41.7 + - + -
434B ASP* 3.8 9.4 + - - -
435B LYS* 3.6 40.0 + - + -
438B LEU* 3.6 33.8 - - + +
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLN* 3.6 24.7 - - - +
383B SER* 3.0 30.5 + - - +
384B PHE* 3.1 32.1 - - - +
386B HIS* 1.3 78.8 + - - +
388B SER* 1.3 55.7 - - - +
389B ILE 3.3 3.9 + - - -
390B ASP* 4.6 7.1 + - - +
391B VAL* 5.1 1.0 - - - +
396B LEU* 3.1 39.1 + - + +
397B LEU* 4.0 5.5 - - - +
398B ALA* 3.3 30.2 - - - +
435B LYS* 5.7 3.4 - - - +
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B PHE 2.5 23.2 + - - -
385B SER 3.0 9.4 + - - -
387B ARG* 1.3 75.6 - - - +
389B ILE* 1.3 62.7 + - - +
390B ASP 3.1 4.0 + - - -
391B VAL* 3.1 24.3 + - - +
394B GLY 3.9 5.0 - - - +
395B ILE* 3.3 26.1 - - - +
396B LEU 3.0 18.4 + - - +
425B VAL* 3.6 17.3 - - - +
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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