Contacts of the helix formed by residues 268 - 285 (chain Z) in PDB entry 5UZV
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 268 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230Z LEU* 4.7 11.7 - - + -
266Z THR 3.4 9.8 - - - +
267Z VAL* 1.3 94.4 - - + +
269Z GLU* 1.3 63.2 + - - +
270Z ASP* 4.3 9.9 - - + +
271Z TYR* 3.2 21.0 + - + +
272Z ILE* 3.4 12.2 + - - +
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Residues in contact with GLU 269 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255Z LYS* 4.4 17.5 + - - -
267Z VAL 3.7 2.9 + - - +
268Z PRO* 1.3 70.4 - - - +
270Z ASP* 1.3 61.7 + - - +
272Z ILE* 3.0 26.5 + - - +
273Z ASN* 2.9 49.3 + - - +
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Residues in contact with ASP 270 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227Z LEU* 5.4 0.5 - - - +
268Z PRO* 3.2 7.3 - - + +
269Z GLU* 1.3 80.3 - - - +
271Z TYR* 1.3 56.9 + - - +
273Z ASN* 3.6 10.6 + - - +
274Z GLY* 2.9 24.6 + - - -
277Z ARG* 4.8 4.2 + - - -
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Residues in contact with TYR 271 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220Z ILE 4.4 0.5 + - - -
221Z LEU* 3.6 39.1 + - + +
227Z LEU* 3.5 30.6 - - + +
228Z SER 3.4 22.4 - - - -
229Z SER* 4.3 2.1 - - - -
230Z LEU* 3.7 45.1 + - + +
254Z ILE* 4.1 17.0 - - + -
267Z VAL* 3.9 20.2 - - + -
268Z PRO* 3.2 17.7 + - + +
269Z GLU 3.2 0.6 - - - -
270Z ASP* 1.3 76.5 - - - +
272Z ILE* 1.3 60.6 + - - +
274Z GLY* 3.8 1.7 - - - +
275Z PHE* 2.9 28.1 + + + +
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Residues in contact with ILE 272 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251Z VAL* 3.7 28.3 - - + +
254Z ILE* 3.7 36.3 - - + -
255Z LYS* 4.4 18.4 - - + -
267Z VAL* 3.7 13.2 - - + +
268Z PRO 3.5 12.8 - - - +
269Z GLU* 3.0 32.7 + - - +
271Z TYR* 1.3 76.0 - - - +
273Z ASN* 1.3 61.0 + - - +
275Z PHE* 3.0 6.7 + - + +
276Z ILE* 2.9 42.9 + - + +
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Residues in contact with ASN 273 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269Z GLU* 2.9 41.3 + - - +
270Z ASP* 3.9 10.9 - - - +
272Z ILE* 1.3 76.2 - - - +
274Z GLY* 1.3 57.5 + - - +
276Z ILE* 3.3 18.5 + - - +
277Z ARG* 2.9 43.9 + - + +
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Residues in contact with GLY 274 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226Z TYR 4.8 2.2 - - - +
227Z LEU* 3.8 19.6 - - - +
270Z ASP 2.9 18.9 + - - -
271Z TYR 3.8 1.8 - - - -
273Z ASN* 1.3 75.6 - - - +
275Z PHE* 1.3 57.3 + - - +
277Z ARG* 3.5 21.6 + - - +
278Z ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 275 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217Z TYR* 3.9 26.9 - + + -
220Z ILE* 3.6 30.2 - - + +
221Z LEU* 3.6 29.8 - - + -
227Z LEU* 3.6 11.2 - - + +
250Z ILE* 3.6 42.2 - - + -
251Z VAL* 5.8 2.2 - - + -
254Z ILE* 3.5 19.7 - - + -
271Z TYR* 2.9 21.3 + + + +
272Z ILE* 3.3 7.4 - - + +
274Z GLY* 1.3 74.5 - - - +
276Z ILE* 1.3 65.1 + - + +
278Z ALA* 3.3 2.7 + - - +
279Z ASN* 2.9 32.5 + - + +
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Residues in contact with ILE 276 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251Z VAL* 4.7 17.0 - - + -
272Z ILE* 2.9 31.8 + - + +
273Z ASN* 3.6 19.7 - - - +
275Z PHE* 1.3 82.0 - - + +
277Z ARG* 1.3 57.4 + - + +
279Z ASN* 3.5 4.6 + - - +
280Z ASN* 2.9 53.3 + - - +
312Z TYR* 5.0 1.1 - - - +
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Residues in contact with ARG 277 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Z SER* 5.8 5.3 - - - -
226Z TYR 5.3 6.1 + - - -
270Z ASP 4.8 4.0 + - - -
273Z ASN* 2.9 23.2 + - + +
274Z GLY* 3.8 24.1 + - - +
275Z PHE 3.3 0.2 - - - -
276Z ILE* 1.3 78.6 - - + +
278Z ALA* 1.3 52.6 + - - +
281Z THR* 2.5 38.0 + - - -
312Z TYR* 3.3 52.6 - - + +
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Residues in contact with ALA 278 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220Z ILE* 4.1 24.5 - - + -
224Z CYS* 4.6 0.7 - - - -
226Z TYR* 3.7 31.7 + - + -
227Z LEU* 4.2 6.5 - - + -
274Z GLY 2.9 19.0 + - - +
275Z PHE 3.7 4.3 - - - +
276Z ILE 3.3 0.2 - - - -
277Z ARG* 1.3 74.3 - - - +
279Z ASN* 1.3 58.8 + - - +
281Z THR* 3.1 4.9 + - - -
282Z PHE* 2.9 32.9 + - - -
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Residues in contact with ASN 279 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216Z ARG* 2.6 36.1 + - - +
217Z TYR* 3.6 29.0 + - - -
220Z ILE* 3.7 12.2 - - + +
250Z ILE* 5.6 2.2 - - - +
275Z PHE* 2.9 24.7 + - + +
276Z ILE* 3.8 5.8 - - - +
278Z ALA* 1.3 76.9 - - - +
280Z ASN* 1.3 60.9 + - - +
282Z PHE* 3.2 3.4 + - - +
283Z LEU* 2.9 48.6 + - - +
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Residues in contact with ASN 280 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276Z ILE* 2.9 38.1 + - - +
277Z ARG 3.7 0.9 - - - +
279Z ASN* 1.3 83.3 + - - +
281Z THR* 1.3 56.7 + - - +
283Z LEU* 3.8 2.2 - - - +
284Z TYR* 2.9 52.9 + - + +
305Z VAL* 5.1 5.1 - - - +
310Z LEU* 3.9 18.5 - - + +
312Z TYR* 3.1 28.7 + - + +
313Z ALA* 4.2 3.1 - - - +
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Residues in contact with THR 281 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Z LEU* 4.0 10.5 - - + -
177Z PHE* 4.5 0.3 - - - -
226Z TYR* 3.5 39.5 - - + +
277Z ARG 2.5 21.8 + - - -
278Z ALA* 3.1 6.8 + - - -
280Z ASN* 1.3 76.7 - - - +
282Z PHE* 1.3 63.4 + - - +
283Z LEU 3.2 0.4 - - - -
285Z GLN* 3.1 41.7 + - + +
312Z TYR* 3.4 19.3 + - - +
313Z ALA* 4.2 12.8 - - - -
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Residues in contact with PHE 282 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z ILE* 4.7 6.1 - - + -
173Z ASP* 4.5 4.9 - - + -
176Z ALA* 3.7 34.5 - - + +
177Z PHE* 3.5 47.0 - + - -
216Z ARG* 3.6 23.6 - - + -
219Z CYS* 5.6 0.4 - - + -
220Z ILE* 3.6 33.4 - - + -
224Z CYS* 4.0 18.6 - - + -
226Z TYR* 3.6 21.1 - + - -
278Z ALA 2.9 22.3 + - - -
279Z ASN 3.2 3.6 + - - +
281Z THR* 1.3 76.5 - - - +
283Z LEU* 1.3 59.3 + - - +
298Z LEU* 3.2 26.0 - - - +
299Z ASN* 4.2 1.7 + - - -
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Residues in contact with LEU 283 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Z GLU* 5.6 0.9 - - - +
216Z ARG* 3.5 38.4 - - - +
279Z ASN* 2.9 39.6 + - - +
280Z ASN* 4.6 2.0 - - - +
282Z PHE* 1.3 79.2 - - - +
284Z TYR* 1.3 94.6 + - + +
285Z GLN 3.7 0.7 - - - -
298Z LEU* 3.4 3.1 - - - +
299Z ASN* 2.9 51.2 + - + +
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Residues in contact with TYR 284 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280Z ASN* 2.9 41.8 + - - +
283Z LEU* 1.3 101.1 - - + +
285Z GLN* 1.3 66.9 + - - +
286Z LEU* 3.4 7.4 + - - +
297Z PRO* 3.8 13.4 - - + +
298Z LEU 4.0 1.8 - - - +
299Z ASN* 3.3 20.0 - - + -
300Z ALA 3.4 20.4 - - - -
301Z TYR* 3.6 31.7 + + + -
302Z GLU* 3.4 27.4 + - + +
304Z ASP* 5.1 0.5 + - - -
305Z VAL* 3.7 20.9 - - + +
310Z LEU* 3.9 19.5 - - + +
313Z ALA* 4.0 8.1 - - - +
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Residues in contact with GLN 285 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Z LEU* 4.0 12.4 - - + +
149Z TYR* 3.4 7.6 - - + +
150Z GLU* 3.1 55.1 + - - +
153Z ALA* 3.7 23.0 - - + +
177Z PHE* 4.1 3.4 - - + -
226Z TYR* 3.2 11.3 + - - -
280Z ASN 4.0 0.2 + - - -
281Z THR* 3.1 25.5 + - + +
283Z LEU 3.7 1.4 - - - -
284Z TYR* 1.3 75.8 - - - +
286Z LEU* 1.3 72.8 + - - +
287Z VAL* 3.5 2.3 + - - +
298Z LEU* 2.9 27.1 + - + +
313Z ALA* 3.3 20.2 - - - +
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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
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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