Contacts of the helix formed by residues 283 - 304 (chain B) in PDB entry 4HNE
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 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PRO* 3.9 30.4 - - + +
376A PHE 5.0 6.1 - - - +
377A SER* 5.6 4.0 - - - -
437A ASN* 6.6 0.2 - - + -
280B GLU* 5.9 1.1 - - - +
281B PRO 4.4 0.7 - - - +
282B LEU* 1.3 93.5 - - + +
284B GLU* 1.3 66.6 + - - +
285B ASN* 4.6 4.0 - - + +
286B THR* 3.1 18.4 + - - +
287B ASN 3.0 17.2 + - - -
318B TYR* 4.5 7.9 - - - +
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 2.2 33.1 - - - +
287A ASN* 4.1 3.3 - - - +
288A ARG* 3.9 27.9 - - + +
291A LEU* 3.2 38.5 - - + +
292A LEU* 6.4 1.8 - - + -
374A VAL* 4.0 13.8 - - + +
375A PRO 4.9 1.6 + - - +
377A SER* 5.8 9.5 - - - +
282B LEU 3.5 2.0 + - - +
283B PRO* 1.3 71.8 - - - +
285B ASN* 1.3 58.4 + - - +
287B ASN* 3.1 17.5 + - - +
288B ARG* 2.8 29.5 + - - +
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 3.0 30.3 + - - +
377A SER* 5.4 3.3 - - - -
378A GLN* 5.3 5.1 - - - +
379A GLU* 2.9 33.5 + - - -
283B PRO* 3.3 3.6 - - + +
284B GLU* 1.3 79.2 - - - +
286B THR* 1.3 62.2 + - - +
288B ARG* 3.5 8.9 + - - +
289B GLN* 3.2 29.9 + - - +
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 3.9 16.2 - - + -
283B PRO* 3.1 23.5 + - - +
285B ASN* 1.3 78.0 - - - +
287B ASN* 1.3 58.5 + - - +
289B GLN* 3.0 11.7 + - + +
290B LEU* 2.9 25.8 + - - +
318B TYR* 3.8 28.0 + - + -
338B PRO* 4.2 17.2 + - - +
340B ILE* 3.7 21.5 - - + +
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Residues in contact with ASN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 4.0 2.4 - - - +
287A ASN* 5.4 0.5 - - - +
277B PHE* 6.4 0.2 - - - +
282B LEU* 3.9 27.6 - - + +
283B PRO 3.0 13.4 + - - +
284B GLU* 3.4 30.6 - - - +
286B THR* 1.3 75.7 - - - +
288B ARG* 1.3 61.3 - - - +
290B LEU* 3.2 15.0 + - - +
291B LEU* 3.0 37.9 + - - +
371B GLN* 5.4 6.5 - - - +
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 3.9 29.1 - - + +
285A ASN* 2.8 25.1 + - - +
288A ARG* 4.0 24.7 - - - +
284B GLU* 2.8 20.7 + - - +
285B ASN* 3.6 10.7 + - - +
287B ASN* 1.3 73.0 + - - +
289B GLN* 1.3 85.8 + - - +
291B LEU* 3.3 2.9 + - - +
292B LEU* 3.0 43.1 + - + +
379B GLU* 3.0 25.9 + - - +
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 3.2 14.7 + - - +
286B THR* 3.0 14.4 + - + +
288B ARG* 1.3 103.4 - - - +
290B LEU* 1.3 63.3 - - - +
292B LEU* 3.2 15.0 + - + +
293B GLN* 3.1 26.8 + - + +
339B VAL* 5.5 9.1 - - + +
340B ILE* 3.5 26.0 - - + +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 5.0 5.6 - - + -
277B PHE* 4.7 4.9 - - + -
282B LEU* 4.5 6.5 - - + -
286B THR 2.9 11.2 + - - +
287B ASN* 3.4 20.9 - - - +
289B GLN* 1.3 76.1 - - - +
291B LEU* 1.3 53.5 + - + +
293B GLN* 3.3 7.0 + - + +
294B PHE* 2.8 38.8 + - + +
314B TRP* 5.2 4.5 - - + -
316B ILE* 4.2 22.9 - - + -
340B ILE* 3.8 33.1 - - + +
342B VAL* 4.5 14.1 - - + -
371B GLN* 4.0 32.3 - - + +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 3.2 44.6 - - + +
287B ASN* 3.0 25.1 + - - +
288B ARG 3.3 6.7 + - - +
290B LEU* 1.3 74.4 - - + +
292B LEU* 1.3 67.4 + - + +
294B PHE* 3.2 10.6 + - + +
295B GLU* 2.9 34.1 + - + +
371B GLN* 3.6 48.9 - - + +
374B VAL* 4.3 17.5 - - + -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 6.2 3.1 - - + -
288B ARG* 3.0 54.7 + - + +
289B GLN* 3.3 18.6 - - - +
291B LEU* 1.3 77.9 - - + +
293B GLN* 1.3 64.1 + - + +
295B GLU* 3.6 10.8 + - - +
296B ARG* 3.4 29.8 + - - +
377B SER* 3.7 28.7 - - - +
379B GLU* 4.2 20.6 - - + +
380B ILE* 5.2 0.9 - - - +
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Residues in contact with GLN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU 5.1 0.2 + - - -
207B ILE* 4.6 4.5 - - - +
289B GLN* 3.1 15.6 + - + +
290B LEU* 3.4 7.6 - - - +
292B LEU* 1.3 75.5 - - + +
294B PHE* 1.3 65.4 + - - +
296B ARG* 2.9 39.6 + - - +
297B LEU* 3.2 10.4 + - - +
340B ILE 4.2 12.6 - - - +
341B LYS* 3.0 34.3 + - - +
342B VAL* 2.9 51.7 + - + +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 2.8 28.0 + - + +
291B LEU* 3.5 14.1 - - + +
293B GLN* 1.3 71.6 - - - +
295B GLU* 1.3 65.1 + - + +
297B LEU* 3.2 14.1 + - + +
298B VAL* 3.1 37.0 + - + +
314B TRP* 4.0 21.3 - + + -
342B VAL* 4.2 5.1 - - - +
366B TRP* 3.7 44.9 - + + -
369B LEU* 4.3 10.1 - - + -
371B GLN* 3.5 43.7 - - + -
372B ALA* 3.7 12.1 - - + -
440B PRO* 4.6 4.3 - - + -
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 6.2 0.2 - - - +
291B LEU* 2.9 23.5 + - + +
292B LEU* 3.6 18.8 - - - +
294B PHE* 1.3 74.6 - - + +
296B ARG* 1.3 65.5 + - - +
298B VAL* 3.2 11.6 + - - +
299B VAL* 3.0 28.7 + - - +
374B VAL* 5.3 3.3 - - - +
375B PRO 3.9 4.0 - - - +
376B PHE* 3.3 23.3 - - + -
377B SER* 2.7 50.1 + - - -
380B ILE* 3.8 19.6 + - + +
440B PRO* 5.4 4.0 - - + -
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Residues in contact with ARG 296 (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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204B GLU 3.1 20.2 + - - -
205B LEU* 3.0 49.1 + - + +
206B ASN* 4.6 4.6 - - - +
207B ILE* 3.7 14.1 - - + -
292B LEU* 3.4 20.3 + - - +
293B GLN* 2.9 26.4 + - - +
295B GLU* 1.3 76.5 - - - +
297B LEU* 1.3 58.1 + - - +
299B VAL* 3.6 1.0 + - - +
300B LEU* 3.1 28.9 + - - +
380B ILE* 4.0 17.1 - - + +
383B LEU* 4.0 17.7 - - - +
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Residues in contact with LEU 297 (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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207B ILE* 3.5 12.0 - - + +
293B GLN 3.2 8.4 + - - +
294B PHE* 3.2 16.9 + - + +
296B ARG* 1.3 75.4 - - - +
298B VAL* 1.3 60.2 + - - +
300B LEU* 4.8 0.9 - - + -
301B ASP* 2.9 48.5 + - - +
309B ARG* 4.0 9.0 - - - +
314B TRP* 3.4 49.4 - - + -
342B VAL* 4.6 6.7 - - + -
344B ALA* 3.8 27.8 - - + -
366B TRP* 4.0 17.0 - - + +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 3.1 27.6 + - + +
295B GLU* 3.2 9.8 + - - +
297B LEU* 1.3 75.9 - - + +
299B VAL* 1.3 56.7 + - - +
301B ASP* 3.8 0.9 - - - +
302B TYR* 2.8 34.1 + - - +
366B TRP* 3.7 37.9 - - + -
376B PHE* 4.0 16.8 - - + -
440B PRO* 3.8 35.4 - - + -
443B LEU* 4.1 11.9 - - + -
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 4.4 8.1 - - + -
205B LEU* 4.5 4.7 - - + -
295B GLU 3.0 19.3 + - - +
296B ARG* 3.9 6.5 - - - +
297B LEU 3.3 0.2 - - - -
298B VAL* 1.3 74.7 - - - +
300B LEU* 1.3 65.5 + - - +
302B TYR* 3.9 2.8 - - - +
303B ILE* 3.0 46.2 + - + +
376B PHE* 4.8 8.1 - - + -
380B ILE* 4.0 22.9 - - + -
384B ILE* 3.9 24.9 - - + -
430B LEU* 4.0 24.0 - - + -
434B LEU* 5.4 1.3 - - + -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ALA* 3.9 22.7 - - + +
199B VAL* 4.1 20.4 - - + -
200B ASP 4.4 4.5 - - - +
205B LEU* 3.6 13.7 - - + -
207B ILE* 4.0 7.6 - - + -
208B VAL* 4.2 22.2 - - + -
296B ARG 3.1 18.4 + - - +
297B LEU 3.7 3.6 - - - +
298B VAL 3.3 0.2 - - - -
299B VAL* 1.3 80.0 - - - +
301B ASP* 1.3 80.6 + - - +
302B TYR 3.2 0.2 + - - -
303B ILE* 4.0 1.9 - - - +
304B ILE* 3.2 43.2 + - + +
309B ARG* 4.1 11.9 - - - +
344B ALA* 4.6 3.4 - - + -
347B ASN* 4.9 2.0 - - - +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 2.9 27.3 + - - +
300B LEU* 1.3 78.8 - - - +
302B TYR* 1.3 57.5 + - - +
304B ILE* 4.2 3.2 - - - +
305B ARG* 3.0 21.8 + - - -
306B ASN* 3.0 28.7 + - + +
309B ARG* 2.9 45.1 + - - +
364B PHE* 3.5 9.5 - - + -
366B TRP* 2.9 35.7 + - + +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B VAL* 2.8 20.2 + - + +
299B VAL* 3.9 3.8 - - - +
300B LEU 3.2 0.2 - - - -
301B ASP* 1.3 77.2 - - - +
303B ILE* 1.3 64.8 + - - +
305B ARG 3.1 5.0 + - - -
364B PHE* 4.2 22.9 - + - -
366B TRP* 4.9 2.4 - + + -
426B GLN* 2.8 81.1 + - + +
429B ASN* 3.0 31.0 + - + +
430B LEU* 4.2 10.1 - - + -
443B LEU* 3.8 48.7 + - + -
444B VAL* 4.4 12.3 - - + -
446B MET 4.8 3.3 + - - -
448B PRO* 5.6 1.0 - - - +
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Residues in contact with ILE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 4.4 10.5 - - + -
203B LEU* 3.7 26.7 - - + -
299B VAL* 3.0 31.4 + - + +
300B LEU 4.1 1.8 - - - +
302B TYR* 1.3 76.9 - - + +
304B ILE* 1.3 63.8 + - + +
305B ARG* 3.3 1.6 + - - +
388B ILE* 4.5 14.1 - - + -
397B LEU* 5.2 1.8 - - + -
423B MET* 3.5 49.2 - - + +
426B GLN* 3.9 14.1 - - - +
427B ILE* 4.3 20.0 - - + +
430B LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ALA* 4.2 15.5 - - + -
199B VAL* 4.0 24.9 - - + -
300B LEU* 3.2 41.2 + - + +
301B ASP* 3.9 7.0 - - - +
303B ILE* 1.3 76.5 - - + +
305B ARG* 1.3 71.3 + - - +
306B ASN* 3.9 9.2 - - + +
347B ASN* 5.1 4.3 - - + -
350B ALA* 3.7 21.1 - - + -
351B PHE* 2.9 63.1 + - + -
352B PRO* 3.6 0.2 - - - +
423B MET* 5.3 1.3 - - + -
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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