Contacts of the helix formed by residues 299 - 321 (chain B) in PDB entry 3ZXR
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 SER 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B LEU 2.6 28.6 + - - -
289B MET 2.7 18.5 + - - -
290B TYR 3.8 11.9 - - - -
291B ASP* 3.5 15.3 - - - +
298B LEU* 1.3 75.9 - - - +
300B ASP* 1.3 59.3 + - - +
301B THR* 3.5 4.0 + - - -
302B ALA* 3.2 12.2 + - - +
303B ARG* 2.9 29.2 + - - +
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Residues in contact with ASP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ASP* 5.1 5.3 + - - +
299B SER* 1.3 71.7 - - - +
301B THR* 1.3 60.9 + - - +
303B ARG* 2.7 42.8 + - - +
304B HIS* 2.9 50.3 + - + +
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 4.6 7.4 - - + -
281B LEU* 4.6 10.8 - - + -
288B LEU* 4.1 23.9 + - + +
289B MET* 5.4 2.0 - - - -
299B SER* 3.3 9.0 + - - -
300B ASP* 1.3 78.6 - - - +
302B ALA* 1.3 63.7 + - - +
304B HIS* 3.4 4.2 + - - +
305B TYR* 3.0 21.7 + - - +
391B ILE* 3.6 37.5 - - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU 4.6 0.6 + - - -
289B MET* 3.5 55.0 - - + +
298B LEU* 3.8 17.5 - - + -
299B SER* 3.2 9.3 + - - +
301B THR* 1.3 78.9 - - - +
303B ARG* 1.3 63.4 + - - +
305B TYR* 3.0 5.3 + - - +
306B ILE* 2.9 28.9 + - + +
365B LEU* 4.5 0.5 - - - +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B TYR* 6.3 1.8 - - - -
298B LEU* 4.7 13.1 + - + +
299B SER 2.9 14.1 + - - +
300B ASP* 2.7 40.0 + - - +
302B ALA* 1.3 74.2 - - - +
304B HIS* 1.3 63.7 + - - +
306B ILE* 3.3 12.9 + - - +
307B GLY 2.9 21.8 + - - -
342B TYR* 4.0 18.4 - - + +
396B GLU* 3.0 36.8 + - - -
397B PRO* 3.5 25.1 - - + +
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASP* 2.9 38.9 + - + +
301B THR* 3.8 5.6 + - - +
303B ARG* 1.3 79.2 + - - +
305B TYR* 1.3 59.9 + - - +
307B GLY* 3.2 1.4 + - - -
308B GLY 2.9 24.1 + - - -
390B GLY* 3.4 24.7 - - - +
391B ILE* 3.8 12.9 + - + +
394B LYS* 3.6 41.0 + - + +
395B ILE 3.4 20.7 - - - +
396B GLU* 2.9 29.5 + - - -
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 4.4 3.6 - - - -
279B GLN* 2.8 38.8 + - + +
280B SER 6.3 0.7 - - - -
281B LEU* 3.8 24.7 - - + +
289B MET* 4.9 4.0 - - + -
301B THR 3.0 14.7 + - - +
302B ALA* 3.0 12.8 + - - +
304B HIS* 1.3 74.4 - - - +
306B ILE* 1.3 62.2 + - - +
308B GLY* 3.2 2.9 + - - -
309B LEU* 3.0 33.1 + - + +
365B LEU* 3.6 21.8 - - + -
383B MET 4.0 1.1 - - - -
384B LEU* 3.5 32.9 + - + +
387B GLY* 3.5 40.7 - - - -
388B LEU 4.3 0.2 - - - -
391B ILE* 3.8 14.7 - - + +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU* 3.9 19.3 - - + -
302B ALA 2.9 19.6 + - - +
303B ARG* 3.5 7.2 - - - +
305B TYR* 1.3 73.4 - - - +
307B GLY* 1.3 65.3 + - - +
309B LEU* 3.1 9.3 + - - +
310B LEU* 2.9 35.1 + - + +
342B TYR* 3.8 37.9 - - + -
351B VAL* 4.1 9.9 - - + -
353B ILE* 3.8 29.2 - - + -
365B LEU* 3.7 24.2 - - + -
397B PRO* 4.3 3.8 - - + -
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ARG 2.9 12.2 + - - -
304B HIS 3.2 5.3 + - - -
306B ILE* 1.3 76.7 - - - +
308B GLY* 1.3 55.9 + - - +
310B LEU* 3.6 1.6 + - - +
311B HIS* 2.9 33.1 + - - +
395B ILE* 3.6 24.7 - - - +
397B PRO* 3.8 19.7 - - - +
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Residues in contact with GLY 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B HIS 2.9 11.1 + - - -
305B TYR 3.2 2.8 + - - -
307B GLY* 1.3 72.8 - - - +
309B LEU* 1.3 55.5 + - - +
312B HIS* 2.8 40.9 + - - +
386B ALA 3.3 24.7 - - - -
390B GLY* 3.7 14.0 - - - -
395B ILE* 4.5 6.7 - - - -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLN* 4.5 0.7 - - - +
305B TYR* 3.0 30.0 + - + +
306B ILE* 3.1 9.4 + - - +
308B GLY* 1.3 73.5 - - - +
310B LEU* 1.3 61.8 + - + +
312B HIS 3.9 0.2 - - - -
313B ALA* 3.0 29.6 + - - +
316B LEU* 3.8 26.8 - - + +
351B VAL* 4.5 6.3 - - + -
365B LEU* 3.7 29.8 - - + -
367B PHE* 4.1 31.2 - - + -
383B MET* 3.6 33.9 - - + +
386B ALA* 4.2 3.0 + - + -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ILE* 2.9 33.6 + - + +
307B GLY* 4.3 2.9 - - - +
309B LEU* 1.3 75.7 - - - +
311B HIS* 1.3 66.6 + - - +
313B ALA* 3.6 14.3 - - + +
314B PRO* 4.3 0.5 - - - +
340B LEU* 3.6 42.9 - - + +
341B VAL* 3.8 17.5 - - - -
342B TYR* 3.8 9.2 - - + +
350B CYS* 3.8 34.3 - - + -
351B VAL* 4.0 13.7 - - + -
367B PHE* 4.9 1.3 - - + -
397B PRO* 4.6 9.6 - - + -
398B GLN* 5.7 3.4 - - + +
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Residues in contact with HIS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY 2.9 20.9 + - - +
308B GLY 3.8 1.6 - - - +
310B LEU* 1.3 78.4 - - - +
312B HIS* 1.3 92.8 + + - +
314B PRO* 3.4 12.6 - - - +
395B ILE* 3.9 28.0 - - + +
429B ARG* 5.3 3.1 + - - -
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Residues in contact with HIS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLY* 2.8 29.3 + - - +
309B LEU 4.6 0.2 - - - +
311B HIS* 1.3 96.3 + + - +
313B ALA* 1.3 64.6 + - - +
314B PRO* 3.2 4.7 - - - -
315B SER* 2.8 10.6 + - - -
316B LEU* 2.8 21.1 + - + -
386B ALA* 3.9 22.2 - - + -
389B ASP* 2.7 30.9 + - + -
395B ILE* 4.6 0.6 - - + +
429B ARG* 6.4 0.2 - - - +
433B ASP* 4.6 12.1 + - - -
436B TYR* 3.5 52.3 - + + +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LEU 3.0 18.2 + - - +
310B LEU* 3.6 12.6 - - + +
312B HIS* 1.3 74.9 - - - +
314B PRO* 1.4 68.8 - - + +
315B SER 3.0 1.4 + - - -
316B LEU* 3.9 7.6 - - + -
317B LEU* 3.1 39.5 + - + +
340B LEU* 3.6 27.1 - - + -
350B CYS* 5.8 0.2 - - - -
367B PHE* 5.6 3.8 - - + -
420B PRO* 5.2 1.3 - - + -
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Residues in contact with PRO 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B LEU 4.3 2.9 - - - +
311B HIS 3.4 13.5 - - - +
312B HIS 3.2 6.5 - - - -
313B ALA* 1.4 92.8 - - + +
315B SER* 1.3 55.6 + - - +
340B LEU* 4.6 11.2 - - + -
418B GLN 6.1 0.2 - - - +
420B PRO* 4.3 15.4 - - + +
425B ASP 4.9 0.2 - - - -
426B VAL* 3.5 29.6 - - - +
429B ARG* 3.5 45.0 - - + +
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B HIS* 2.8 6.7 + - - +
314B PRO* 1.3 76.7 - - - +
316B LEU* 1.3 67.4 + - - +
317B LEU 3.1 2.0 - - - -
318B ALA* 3.0 24.4 + - - +
319B PHE* 5.2 0.7 - - - -
426B VAL 4.3 4.0 - - - -
429B ARG* 3.9 11.6 - - - +
430B LEU* 3.8 22.6 - - - +
433B ASP* 3.6 20.1 + - - -
436B TYR* 2.7 39.1 + - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LEU* 3.8 38.4 - - + +
312B HIS* 2.8 24.4 + - + +
313B ALA* 3.9 3.6 - - - +
315B SER* 1.3 73.7 + - - +
317B LEU* 1.3 56.7 + - + +
319B PHE* 3.0 22.2 + - - +
320B THR* 3.2 21.8 + - + +
367B PHE* 3.9 21.1 - - + -
382B ALA* 3.5 42.6 - - + +
383B MET* 3.7 2.9 - - - +
386B ALA* 4.0 9.6 - - + -
436B TYR* 3.3 12.6 - - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ALA* 3.1 29.0 + - + +
315B SER 3.1 0.8 + - - -
316B LEU* 1.3 77.5 - - + +
318B ALA* 1.3 57.6 + - - +
319B PHE 3.1 0.4 - - - -
320B THR* 3.0 19.7 - - - +
321B ASN* 2.7 39.1 + - + +
327B TYR* 3.6 13.7 - - + +
330B LEU* 4.1 16.2 - - + -
340B LEU* 5.9 1.1 - - + -
367B PHE* 4.3 11.2 - - + -
369B SER* 3.3 30.3 - - - +
419B THR* 5.0 4.0 - - + -
420B PRO* 3.7 27.1 - - + -
426B VAL* 4.1 7.2 - - + -
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B SER 3.0 16.8 + - - +
317B LEU* 1.3 78.0 - - - +
319B PHE* 1.3 56.3 + - + +
321B ASN 4.9 0.4 - - - -
322B PRO* 3.4 17.1 - - - +
426B VAL* 3.6 28.3 - - + +
427B ILE* 4.0 10.9 - - + +
430B LEU* 3.8 27.6 - - + -
451B TRP* 2.9 21.9 + - - +
455B LYS* 5.3 0.2 - - - -
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B SER 5.2 1.1 - - - -
316B LEU* 3.0 6.8 + - - +
318B ALA* 1.3 79.5 - - + +
320B THR* 1.3 61.2 + - - +
321B ASN 3.5 0.4 - - - -
322B PRO* 3.9 12.1 - - - +
374B GLY* 5.5 0.2 - - - -
375B ASN 4.6 4.7 + - - +
378B LEU* 3.9 29.3 - - + +
379B ALA* 3.5 16.0 + - - +
382B ALA* 3.9 31.6 - - + -
430B LEU* 3.9 22.4 - - + -
437B LEU* 4.0 18.8 - - + -
443B PHE* 3.8 24.7 - + - -
447B LEU* 4.7 4.0 - - + -
448B ILE* 4.6 7.4 - - + -
451B TRP* 3.4 56.7 - + + -
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.2 21.0 + - + -
317B LEU* 3.0 24.3 - - - +
319B PHE* 1.3 78.9 - - + +
321B ASN* 1.3 76.8 + - - +
322B PRO* 3.6 6.2 - - - +
367B PHE* 4.2 4.5 - - + -
370B PRO* 3.4 13.7 - - - +
371B ASP 3.1 30.7 + - - +
379B ALA* 4.2 9.6 - - + +
383B MET* 3.7 38.8 - - + -
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Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 2.7 19.9 + - + +
320B THR* 1.3 101.6 + - - +
322B PRO* 1.3 59.8 - - - +
323B THR 3.3 0.5 + - - -
326B SER* 3.3 16.6 + - - -
327B TYR* 2.8 40.2 + - + +
329B ARG* 3.9 4.8 - - - +
330B LEU* 3.9 16.2 - - - +
369B SER* 2.7 42.9 + - - +
370B PRO* 4.2 0.2 - - - +
371B ASP* 3.5 14.9 + - - -
423B LEU* 4.0 1.0 - - - +
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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