Contacts of the helix formed by residues 370 - 390 (chain N) in PDB entry 2JA7
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 370 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364N ILE* 5.2 3.4 - - + -
365N THR* 3.6 33.9 - - + +
367N LEU* 3.8 27.1 - - + -
368N GLU 2.6 11.6 + - - +
369N GLY* 1.3 88.3 - - - -
371N GLU* 1.3 58.2 + - - +
372N SER* 3.0 5.6 - - - +
373N ARG* 2.7 73.5 + - + +
374N LYS* 3.1 16.1 + - + +
567N GLU* 3.7 13.7 - - - -
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Residues in contact with GLU 371 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288N ALA 5.6 0.4 - - - +
289N LEU* 3.5 40.7 - - + +
327N ARG* 3.7 27.0 + - - +
356N LEU 5.7 1.0 - - - +
357N GLN* 4.8 13.7 + - - +
368N GLU* 2.7 30.2 - - - +
369N GLY* 3.8 4.6 - - - -
370N PHE* 1.3 76.1 + - - +
372N SER* 1.3 57.5 + - - +
374N LYS* 4.0 8.5 + - - +
375N ALA* 3.1 28.4 + - - +
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Residues in contact with SER 372 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291N ILE* 5.5 3.6 - - - -
300N HIS* 5.9 0.9 - - - -
370N PHE* 3.0 2.3 - - - -
371N GLU* 1.3 77.8 - - - +
373N ARG* 1.3 61.0 + - - +
374N LYS 3.4 0.2 - - - -
375N ALA* 4.0 6.5 - - - -
376N PHE* 2.9 40.0 + - - -
566N LEU* 4.6 2.6 - - - +
567N GLU* 4.0 38.0 + - - -
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Residues in contact with ARG 373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364N ILE* 4.1 26.0 + - + +
370N PHE* 2.7 55.2 + - + +
372N SER* 1.3 78.9 + - - +
374N LYS* 1.3 64.4 + - - +
376N PHE 4.1 0.2 - - - -
377N PHE* 3.7 17.0 + - - +
565N PRO* 5.6 4.9 - - - +
566N LEU* 3.6 37.4 - - + +
567N GLU* 3.6 17.2 + - - +
585N VAL* 5.9 1.8 - - - +
586N TRP 3.9 12.3 + - - +
587N HIS* 3.8 38.0 + - - +
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Residues in contact with LYS 374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289N LEU* 4.4 12.1 - - + -
356N LEU 2.7 27.9 + - - +
357N GLN* 3.0 24.2 + - - +
360N PHE* 3.1 40.8 + - + +
361N LEU* 3.8 16.2 - - + +
362N PRO* 5.0 0.6 - - - +
363N HIS 4.7 1.1 - - - -
364N ILE* 4.5 12.3 - - + -
365N THR* 3.0 23.5 + - - -
370N PHE* 3.1 16.6 + - + +
371N GLU* 4.3 10.3 + - - +
373N ARG* 1.3 75.1 - - - +
375N ALA* 1.3 61.5 + - - +
376N PHE 3.3 0.7 - - - -
377N PHE* 3.2 7.0 + - - +
378N LEU* 3.0 28.9 + - - +
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Residues in contact with ALA 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286N PHE* 3.2 17.0 - - + -
289N LEU* 3.6 17.5 - - + +
291N ILE* 3.3 33.2 - - + -
300N HIS* 4.2 4.2 - - + +
371N GLU 3.1 21.0 + - - +
372N SER* 4.3 5.8 - - - +
373N ARG 3.4 0.2 - - - -
374N LYS* 1.3 79.5 - - - +
376N PHE* 1.3 61.8 + - - +
378N LEU* 3.6 0.6 + - - +
379N GLY* 3.1 17.0 + - - -
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Residues in contact with PHE 376 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299N GLU 5.1 3.4 - - - -
300N HIS* 3.0 49.5 - + - +
303N TYR* 3.9 4.0 + + - -
372N SER* 2.9 32.1 + - - +
373N ARG 3.9 0.4 + - - +
374N LYS 3.3 0.4 - - - -
375N ALA* 1.3 79.8 - - - +
377N PHE* 1.3 56.2 - - - +
379N GLY* 3.6 2.1 + - - +
380N TYR 2.9 18.5 + - - -
566N LEU* 4.0 22.4 - - + -
567N GLU 5.0 3.6 - - - -
569N TYR* 3.0 57.0 - + + -
571N PRO* 5.1 3.1 - - + -
586N TRP* 2.9 41.8 - + + -
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Residues in contact with PHE 377 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221N ASN 5.7 0.2 - - - -
222N ILE* 6.3 0.2 - - - -
223N VAL* 4.9 6.5 - - + -
240N ILE* 3.4 33.7 - - + -
361N LEU* 3.1 33.4 - - + -
363N HIS* 3.9 5.6 - + - -
364N ILE* 4.3 8.3 - - + -
373N ARG 3.7 10.6 + - - +
374N LYS 3.2 4.6 + - - +
375N ALA 3.1 0.6 - - - -
376N PHE* 1.3 76.2 - - - +
378N LEU* 1.3 60.2 + - - +
379N GLY 2.8 1.1 - - - -
380N TYR* 2.6 35.6 + + - +
381N MET* 2.8 31.1 + - + +
581N PHE* 3.7 26.9 - + - -
584N GLY 3.9 19.3 - - - -
586N TRP* 4.1 23.1 - + + -
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Residues in contact with LEU 378 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254N LEU* 5.8 1.8 - - + -
256N VAL* 4.6 15.0 - - + -
271N ALA* 5.3 4.5 - - + -
282N ILE* 4.1 13.2 - - + +
285N ILE* 3.4 42.6 - - + -
286N PHE* 4.1 12.6 - - + -
289N LEU* 4.8 1.8 - - + -
360N PHE* 3.7 20.6 - - + -
361N LEU* 4.5 0.6 - - - +
374N LYS 3.0 16.1 + - - +
375N ALA* 4.0 4.0 - - - +
377N PHE* 1.3 75.5 - - - +
379N GLY* 1.3 60.9 + - - +
381N MET* 3.3 12.1 + - + +
382N ILE* 2.8 54.3 + - + +
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Residues in contact with GLY 379 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286N PHE* 3.9 11.0 - - - -
300N HIS 3.3 26.1 - - - +
301N ILE* 4.2 3.9 - - - -
303N TYR* 4.4 0.7 - - - -
375N ALA 3.1 12.3 + - - -
376N PHE 3.8 1.8 - - - -
377N PHE 2.8 1.0 - - - -
378N LEU* 1.3 79.2 - - - +
380N TYR* 1.3 56.5 + - - +
381N MET 2.9 0.7 + - - -
382N ILE* 3.0 7.5 + - - +
383N ASN* 2.8 30.0 + - - +
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Residues in contact with TYR 380 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223N VAL* 3.5 32.8 - - + +
303N TYR* 3.9 10.4 + + - -
376N PHE 2.9 15.3 + - - +
377N PHE* 2.6 27.3 + + - +
379N GLY* 1.3 70.1 - - - +
381N MET* 1.3 55.5 + - - -
383N ASN* 3.8 9.4 - - - +
384N ARG* 3.2 41.4 + - + +
579N ARG* 3.7 24.9 - - - -
581N PHE* 3.3 34.1 - + - -
586N TRP* 4.1 7.9 - + + -
623N GLU* 2.6 37.3 + - - -
625N LYS* 4.6 6.0 + - - -
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Residues in contact with MET 381 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223N VAL* 3.1 26.2 - - + -
238N ALA* 4.5 10.8 - - + +
240N ILE* 3.9 18.8 - - + -
254N LEU* 3.3 27.8 - - + -
256N VAL* 3.6 30.7 - - + -
361N LEU* 3.5 9.6 - - + -
377N PHE* 2.8 41.1 + - + +
378N LEU* 3.6 12.1 - - - +
380N TYR* 1.3 75.8 - - + +
382N ILE* 1.3 57.4 + - - +
383N ASN 2.9 2.4 + - - -
384N ARG* 3.0 7.3 + - - +
385N LEU* 2.7 35.9 + - - +
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Residues in contact with ILE 382 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256N VAL* 3.9 6.7 - - + -
269N ILE* 3.8 22.7 - - + -
282N ILE* 3.3 45.5 - - + -
286N PHE* 3.8 15.7 - - + -
301N ILE* 4.1 17.7 - - + -
314N LEU* 4.7 0.9 - - + -
378N LEU* 2.8 44.6 - - + +
379N GLY* 3.0 4.0 + - - +
381N MET* 1.3 74.5 - - - +
383N ASN* 1.3 64.3 + - - +
385N LEU* 3.4 8.0 - - + +
386N LEU* 3.1 27.2 + - + +
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Residues in contact with ASN 383 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301N ILE* 3.4 20.2 - - - +
302N CYS* 5.1 0.2 - - - -
303N TYR* 5.2 13.2 + - - +
310N MET* 3.0 20.4 - - - +
379N GLY 2.8 16.1 + - - +
380N TYR* 3.8 14.8 + - + +
381N MET 2.9 0.4 + - - -
382N ILE* 1.3 71.8 - - - +
384N ARG* 1.3 75.8 + - - +
386N LEU* 2.6 17.7 + - - -
387N LEU* 2.9 49.7 + - - +
579N ARG* 4.8 12.7 - - - +
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Residues in contact with ARG 384 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223N VAL* 5.0 17.5 + - + +
224N GLN* 5.8 0.4 - - - +
225N VAL* 4.1 26.5 - - + +
380N TYR* 3.2 46.9 + - + +
381N MET* 3.0 9.1 + - - +
383N ASN* 1.3 81.8 - - - +
385N LEU* 1.3 67.0 + - - +
387N LEU* 3.2 24.9 + - - +
388N CYS* 3.2 11.3 + - - +
393N LYS* 4.2 35.9 - - - +
394N ASP 4.7 4.0 + - - -
396N ASP* 3.9 20.0 + - - -
621N GLU* 5.1 10.5 - - - +
623N GLU* 5.1 5.1 + - - -
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Residues in contact with LEU 385 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N VAL* 3.7 10.8 - - + +
236N HIS* 3.8 24.4 + - + +
237N VAL* 3.8 14.6 - - - +
238N ALA* 4.1 4.3 - - + +
256N VAL* 3.6 24.9 - - + +
257N LYS 3.3 21.3 - - - +
258N LEU* 3.9 17.5 - - + -
269N ILE* 4.1 25.8 - - + -
381N MET 2.7 16.7 + - - +
382N ILE* 3.4 12.1 - - + +
383N ASN 2.8 1.4 + - - -
384N ARG* 1.3 73.9 - - - +
386N LEU* 1.3 66.4 + - + +
388N CYS* 3.3 9.7 + - - +
389N ALA* 3.3 10.4 + - - +
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Residues in contact with LEU 386 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258N LEU* 4.6 2.9 - - + -
269N ILE* 3.6 24.5 - - + -
301N ILE* 4.6 4.3 - - + -
310N MET* 3.7 41.5 - - + +
313N MET* 3.3 30.3 - - + -
314N LEU* 4.3 21.5 - - + -
382N ILE 3.1 13.9 - - - +
383N ASN 2.6 10.5 + - - +
385N LEU* 1.3 77.7 - - + +
387N LEU* 1.3 53.9 + - - +
388N CYS 2.4 19.4 + - - -
389N ALA* 2.6 17.0 + - - +
390N LEU* 3.0 20.1 + - + +
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Residues in contact with LEU 387 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310N MET* 3.1 23.1 - - + +
383N ASN* 2.9 58.8 + - - +
384N ARG* 3.2 19.9 + - - +
386N LEU* 1.3 71.1 - - - +
388N CYS* 1.3 58.1 + - - +
390N LEU* 3.7 3.0 + - - -
391N ASP 3.7 1.2 + - - -
392N ARG* 2.9 55.8 + - + +
393N LYS* 3.4 20.8 + - + -
579N ARG* 5.9 0.2 - - - +
621N GLU* 4.1 20.2 - - - +
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Residues in contact with CYS 388 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N VAL* 4.1 28.0 - - + -
226N PHE 6.2 0.2 - - - -
227N LYS* 5.2 9.1 - - - -
236N HIS* 4.0 18.9 - - - +
384N ARG 3.2 6.4 + - - +
385N LEU 3.3 9.9 - - - +
386N LEU 2.4 7.3 + - - -
387N LEU* 1.3 73.4 - - - +
389N ALA* 1.3 53.8 + - - +
390N LEU 2.5 5.3 + - - -
391N ASP* 2.5 32.4 + - - +
393N LYS* 3.4 26.4 - - + +
394N ASP 4.3 3.6 - - - -
395N GLN* 4.3 11.9 - - - -
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Residues in contact with ALA 389 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236N HIS* 3.5 26.6 + - + +
258N LEU* 3.9 24.0 - - + -
267N ARG* 4.5 20.1 + - - +
313N MET* 4.3 14.8 - - + -
385N LEU 3.3 4.2 + - - +
386N LEU* 2.6 12.5 + - - +
388N CYS* 1.3 73.7 - - - +
390N LEU* 1.3 62.6 + - - +
391N ASP* 3.4 8.4 - - - +
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Residues in contact with LEU 390 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267N ARG* 5.6 2.0 - - - +
309N GLN* 4.6 14.5 - - + +
310N MET* 3.9 26.5 - - + +
313N MET* 3.8 32.5 - - + -
386N LEU* 3.0 22.0 + - + +
387N LEU 4.1 3.4 - - - +
388N CYS 2.5 5.9 + - - -
389N ALA* 1.3 82.7 - - - +
391N ASP* 1.3 73.2 + - - +
392N ARG* 3.4 43.8 + - - +
90U GLN* 5.1 2.1 - - - +
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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