Contacts of the helix formed by residues 371 - 395 (chain A) in PDB entry 2Y48
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 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ALA* 3.5 9.6 - - + +
370A VAL* 1.3 92.2 - - + +
372A LYS* 1.3 54.4 + - + +
373A GLU* 2.8 19.1 + - + +
374A LYS* 2.8 26.3 + - + +
375A ASP* 3.0 8.6 + - - -
524A ARG* 4.5 18.2 - - - +
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Residues in contact with LYS 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL 4.0 1.2 + - - -
371A PRO* 1.3 69.5 - - + +
373A GLU* 1.3 62.5 + - - +
374A LYS 3.3 0.2 - - - -
375A ASP* 4.0 8.5 - - - -
376A GLU* 3.2 41.9 + - - +
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 2.8 9.6 + - + +
372A LYS* 1.3 76.4 - - - +
374A LYS* 1.3 59.8 - - + +
376A GLU* 4.1 2.4 - - - +
377A MET* 3.3 44.9 + - - +
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL* 3.8 11.2 - - + -
371A PRO* 2.8 19.5 + - + +
373A GLU* 1.3 71.9 - - + +
375A ASP* 1.3 67.6 + - - +
376A GLU 2.9 1.1 - - - -
377A MET* 2.7 17.3 + - - -
378A VAL* 2.9 22.9 + - + +
522A SER* 4.4 3.0 + - - -
524A ARG* 3.5 31.8 - - - +
525A ASP* 2.7 44.5 + - - +
528A ILE* 4.3 14.1 - - + -
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Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A CYS 4.7 1.2 - - - +
361A PRO* 5.0 2.8 - - - +
362A LEU* 4.4 16.3 + - - +
370A VAL* 3.5 26.0 - - + +
371A PRO 3.0 13.2 + - - +
372A LYS* 4.0 11.1 - - - +
374A LYS* 1.3 78.2 - - - +
376A GLU* 1.3 62.4 + - + +
378A VAL* 4.4 2.7 - - - +
379A GLU* 3.5 21.5 + - - +
528A ILE* 5.6 3.1 - - - +
532A HIS* 5.0 1.7 + - - -
7C ARG* 2.8 43.8 + - - -
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LYS* 3.2 33.1 + - - +
373A GLU* 4.1 2.9 - - - +
374A LYS 2.9 1.2 - - - -
375A ASP* 1.3 83.5 - - + +
377A MET* 1.3 61.8 + - + +
378A VAL 3.4 0.4 - - - -
379A GLU* 4.1 5.5 - - - +
380A GLN* 3.2 27.1 + - - +
7C ARG* 5.9 0.7 - - - +
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 3.3 31.3 + - - +
374A LYS* 2.7 14.1 + - - +
376A GLU* 1.3 75.8 - - + +
378A VAL* 1.3 60.7 + - + +
380A GLN* 4.1 21.4 + - - +
381A GLU* 3.4 22.7 + - - +
521A LEU* 5.8 1.3 - - - +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LYS* 2.9 35.8 + - + +
375A ASP 4.4 1.1 - - - +
377A MET* 1.3 77.6 - - + +
379A GLU* 1.3 66.4 + - - +
381A GLU* 3.0 7.0 + - + +
382A PHE* 2.8 21.2 + - - +
521A LEU* 5.1 8.5 - - + -
525A ASP* 4.0 15.0 - - + +
528A ILE* 4.0 23.6 - - + +
529A LEU* 3.5 42.5 - - + +
532A HIS* 4.5 2.5 - - + -
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP 3.5 17.2 + - - +
376A GLU* 4.1 6.1 - - - +
378A VAL* 1.3 77.2 - - - +
380A GLN* 1.3 58.8 + - + +
382A PHE* 2.7 30.3 + - - +
383A ASN* 3.0 23.3 + - - +
532A HIS* 3.6 25.7 + - + -
7C ARG* 2.4 58.9 + - - +
8C LYS 5.4 0.2 - - - +
9C PRO* 5.4 4.9 - - - +
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Residues in contact with GLN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLU 3.2 16.3 + - - +
377A MET* 4.2 28.0 + - - +
378A VAL 3.3 0.4 - - - -
379A GLU* 1.3 82.8 - - + +
381A GLU* 1.3 58.7 + - - +
383A ASN* 4.0 6.4 - - - +
384A ARG* 3.0 62.6 + - + +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A MET 3.4 15.1 + - - +
378A VAL* 3.0 11.5 + - - +
380A GLN* 1.3 78.6 + - - +
382A PHE* 1.3 53.9 + - - +
384A ARG* 3.0 32.8 + - - +
385A LEU* 2.7 44.2 + - + +
419A GLN* 5.2 0.7 - - - +
520A TYR* 2.7 44.1 + - + +
521A LEU* 4.7 13.7 - - + -
529A LEU* 5.3 2.0 - - + -
313B GLY 5.6 0.3 - - - +
314B MET* 4.2 12.3 - - - +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL 2.8 11.0 + - - +
379A GLU 2.7 16.3 + - - +
381A GLU* 1.3 70.0 - - - +
383A ASN* 1.3 72.7 + - - -
385A LEU* 3.1 7.4 + - - +
386A LEU* 2.9 54.0 + - + +
412A LEU* 5.7 0.2 - - - +
529A LEU* 3.9 14.7 - - + +
532A HIS* 3.4 48.5 - - + -
533A PHE* 3.6 37.2 - + - -
535A ASN* 5.8 1.8 - - - -
536A LEU* 4.4 17.5 - - + -
5C LEU* 5.0 12.6 - - + -
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A GLU* 3.0 36.0 + - - +
380A GLN* 4.0 7.5 - - + +
382A PHE* 1.3 94.8 - - - +
384A ARG* 1.3 62.3 + - + +
386A LEU* 3.5 10.7 + - - +
387A GLU* 3.2 32.6 + - - +
7C ARG 5.6 0.8 + - - -
9C PRO* 3.1 36.5 - - + +
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Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A GLN* 3.0 51.6 + - + +
381A GLU* 3.0 29.4 + - - +
383A ASN* 1.3 76.0 - - + +
385A LEU* 1.3 57.7 + - - +
387A GLU* 3.5 8.4 + - - +
388A ALA* 3.1 27.0 + - - +
311B PRO* 3.8 9.0 - - + +
312B LYS* 2.2 42.6 + - - +
313B GLY* 3.2 25.5 + - - -
314B MET* 3.1 31.1 - - + +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A GLU* 2.7 21.0 + - + +
382A PHE* 3.3 8.1 - - - +
384A ARG* 1.3 71.3 - - - +
386A LEU* 1.3 66.1 + - - +
388A ALA* 3.3 6.2 - - - +
389A THR* 3.3 23.9 + - - +
412A LEU* 4.0 14.2 - - + +
415A VAL* 3.2 31.6 - - + +
416A ILE* 4.0 24.2 - - + +
419A GLN* 4.9 0.4 - - + -
520A TYR* 4.0 21.1 - - - +
529A LEU* 3.8 35.9 - - + -
533A PHE* 4.5 6.1 - - + -
314B MET* 4.3 6.7 - - - -
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PHE* 2.9 47.2 + - + +
383A ASN* 3.8 13.0 - - - +
384A ARG 3.5 0.2 - - - -
385A LEU* 1.3 71.1 - - - +
387A GLU* 1.3 56.5 + - - +
389A THR* 2.4 44.6 + - - +
390A SER* 3.2 4.4 + - - -
408A LEU* 4.4 9.4 - - + -
412A LEU* 4.7 8.4 - - + +
536A LEU* 4.1 21.8 - - + -
552A TRP* 4.1 24.0 - - + +
2C ARG* 3.9 24.9 - - - +
5C LEU* 5.1 4.9 - - + -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASN* 3.2 22.7 + - - +
384A ARG* 3.7 2.2 - - - +
386A LEU* 1.3 77.6 - - + +
388A ALA* 1.3 56.4 + - - +
390A SER* 3.4 11.9 + - - -
391A TYR* 3.0 27.2 + - - +
311B PRO* 3.7 27.8 - - + +
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ARG 3.1 14.9 + - - +
385A LEU* 3.3 11.9 - - - +
386A LEU 2.9 0.4 + - - -
387A GLU* 1.3 74.7 - - - +
389A THR* 1.3 59.5 + - - +
391A TYR* 3.0 6.9 + - - +
392A LEU* 2.8 33.4 + - - +
415A VAL* 3.8 25.6 - - + -
311B PRO* 4.1 9.4 - - - +
314B MET* 3.8 16.4 - - + -
316B LEU* 4.3 4.7 - - + +
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Residues in contact with THR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU 3.3 14.4 - - - +
386A LEU* 2.4 30.4 + - - +
388A ALA* 1.3 68.9 - - - +
390A SER* 1.3 66.2 + - - -
392A LEU* 3.1 12.4 + - - +
393A SER* 2.9 23.9 + - - -
408A LEU* 3.9 12.3 - - + +
411A ALA* 4.0 9.9 - - + +
412A LEU* 3.9 38.1 - - + +
415A VAL* 4.4 3.1 - - + -
549A LEU* 3.8 20.9 - - - +
552A TRP* 5.4 1.4 + - - -
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A LEU 3.2 3.5 + - - -
387A GLU* 3.4 15.9 - - - -
389A THR* 1.3 84.1 + - - +
391A TYR* 1.3 55.7 + - - +
393A SER* 3.2 5.3 + - - -
394A HIS* 3.0 50.0 + - - +
549A LEU* 5.6 0.7 - - - -
553A ASP* 6.0 1.8 - - - -
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Residues in contact with TYR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A GLU 3.0 13.4 + - - +
388A ALA* 3.0 9.8 + - - +
390A SER* 1.3 74.1 - - - +
392A LEU* 1.3 64.4 + - - +
393A SER 3.1 0.2 - - - -
395A GLN* 3.2 45.3 + - + +
396A LEU* 3.1 51.4 + - + +
308B ARG 3.9 9.4 + - - -
309B LYS* 3.6 33.3 - - - +
310B PRO* 3.5 29.5 - - + +
311B PRO* 5.0 1.3 - - + -
316B LEU* 3.6 28.8 + - + -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ALA 2.8 25.5 + - - +
389A THR* 3.1 10.1 + - - +
391A TYR* 1.3 72.9 - - - +
393A SER* 1.3 58.3 + - - +
396A LEU* 3.4 21.0 - - + +
397A ASP 3.1 10.0 + - - -
398A PHE* 2.9 65.5 + - + -
411A ALA* 4.5 10.8 - - + -
414A VAL* 4.1 17.3 - - + -
415A VAL* 3.6 24.9 - - + -
418A LEU* 6.1 0.2 - - + -
549A LEU* 4.9 2.9 - - + -
316B LEU* 3.7 18.8 - - + -
321B VAL* 4.5 5.8 - - + -
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR 2.9 15.1 + - - -
390A SER* 3.6 7.2 - - - -
391A TYR 3.1 0.2 - - - -
392A LEU* 1.3 76.7 - - - +
394A HIS* 1.3 69.1 + - - +
397A ASP* 3.1 26.9 + - - +
399A ASN* 3.1 33.5 + - - +
549A LEU* 3.8 17.9 - - - -
550A LYS* 3.6 23.2 - - - +
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Residues in contact with HIS 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.0 38.3 + - - +
393A SER* 1.3 87.7 - - - +
395A GLN* 1.3 75.9 + - + +
397A ASP* 4.4 4.7 + - - +
549A LEU 5.9 0.2 - - - -
550A LYS* 4.1 35.5 + - + +
553A ASP* 5.7 3.6 - - - -
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Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR* 3.2 49.8 + - + +
394A HIS* 1.3 88.1 + - + +
396A LEU* 1.3 67.7 + - + +
397A ASP* 3.4 1.4 + - - +
308B ARG* 3.2 46.3 + - - +
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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) + - + + + + + -
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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