Contacts of the helix formed by residues 277 - 292 (chain A) in PDB entry 2E52
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 MET 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A LEU* 6.0 1.6 - - + -
272A LEU* 4.0 12.0 + - + +
275A ILE* 2.9 35.9 + - + +
276A ASN* 1.3 71.4 + - - +
278A SER* 1.3 62.3 + - - +
280A LYS* 3.3 12.3 + - - +
281A ILE* 3.2 26.9 + - - +
252B TRP* 3.7 28.9 - - + +
255B GLN* 3.8 13.9 - - + +
256B ILE* 3.7 46.2 - - + -
259B ILE* 3.7 27.8 - - + -
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Residues in contact with SER 278 (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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276A ASN* 3.5 9.0 + - - -
277A MET* 1.3 77.5 - - - +
279A SER* 1.3 64.2 + - - +
281A ILE* 3.3 11.2 + - - +
282A GLU* 3.1 33.8 + - - +
256B ILE* 3.8 20.7 - - - +
260B LYS* 5.9 0.9 - - - -
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Residues in contact with SER 279 (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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276A ASN* 3.3 32.9 + - - -
278A SER* 1.3 79.7 + - - +
280A LYS* 1.3 60.9 + - - +
282A GLU* 3.3 15.5 + - - +
283A THR* 2.8 37.5 + - - -
9G T 4.0 13.2 + - - -
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Residues in contact with LYS 280 (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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275A ILE* 4.3 17.9 - - - +
276A ASN 3.2 22.8 + - - +
277A MET* 3.3 7.6 + - - +
279A SER* 1.3 75.4 - - - +
281A ILE* 1.3 63.7 + - - +
283A THR* 3.3 6.1 + - - -
284A ILE* 3.1 29.1 + - - +
115B SER* 3.7 24.7 + - - +
252B TRP* 3.4 50.0 - - + +
7G C 4.8 1.2 + - - -
8G T 3.5 29.6 + - - +
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Residues in contact with ILE 281 (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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277A MET 3.2 17.3 + - - +
278A SER* 3.6 11.2 - - - +
279A SER 3.3 0.2 - - - -
280A LYS* 1.3 76.9 - - - +
282A GLU* 1.3 58.7 + - + +
284A ILE* 3.3 6.2 + - - +
285A ASP* 3.0 41.4 + - - +
249B LYS* 4.0 29.6 - - + +
252B TRP* 3.7 20.2 - - + +
253B LYS* 3.8 36.3 - - + +
256B ILE* 4.7 8.1 - - + -
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Residues in contact with GLU 282 (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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278A SER* 3.1 24.8 + - - +
279A SER* 3.6 16.0 + - - +
281A ILE* 1.3 75.8 - - + +
283A THR* 1.3 60.4 + - - +
285A ASP* 3.3 8.1 + - - +
286A SER* 2.8 36.0 + - - +
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Residues in contact with THR 283 (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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279A SER* 2.8 26.4 + - - -
280A LYS* 3.5 6.0 - - - -
281A ILE 3.3 0.2 - - - -
282A GLU* 1.3 76.5 - - - +
284A ILE* 1.3 56.6 + - - +
286A SER* 3.3 5.9 + - - -
287A PHE* 2.8 30.5 + - + +
114B LEU 3.6 12.6 - - - +
115B SER* 3.5 24.7 + - - +
116B ARG 3.6 13.5 - - - +
117B THR* 4.3 12.3 - - + +
119B LYS* 5.8 0.2 - - - +
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Residues in contact with ILE 284 (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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280A LYS 3.1 16.6 + - - +
281A ILE* 3.3 6.9 + - - +
283A THR* 1.3 74.6 - - - +
285A ASP* 1.3 59.1 + - - +
287A PHE* 3.4 3.5 + - - +
288A ILE* 3.0 31.0 + - + +
51B GLU* 3.9 21.5 - - + +
114B LEU* 3.7 16.6 - - + -
115B SER* 3.7 18.8 - - - +
245B SER* 4.0 28.0 - - - +
248B GLU* 4.0 10.3 - - + +
249B LYS* 4.0 38.1 - - + +
252B TRP* 4.3 6.5 - - + -
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Residues in contact with ASP 285 (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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281A ILE* 3.0 27.1 + - - +
282A GLU* 3.6 8.2 - - - +
283A THR 3.3 0.2 - - - -
284A ILE* 1.3 78.0 - - - +
286A SER* 1.3 57.0 + - - +
288A ILE* 3.5 5.4 + - - +
289A LYS* 2.9 32.0 + - - +
249B LYS* 2.8 40.6 + - - +
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Residues in contact with SER 286 (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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282A GLU* 2.8 25.3 + - - +
283A THR* 3.7 6.1 - - - -
285A ASP* 1.3 69.9 - - - +
287A PHE* 1.3 60.0 + - - +
289A LYS* 3.8 7.3 - - - +
290A GLY* 2.9 26.3 + - - -
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Residues in contact with PHE 287 (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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283A THR* 2.8 23.1 + - + +
284A ILE* 3.5 6.7 - - - +
286A SER* 1.3 72.6 - - - +
288A ILE* 1.3 70.9 + - + +
290A GLY* 3.2 3.5 + - - -
291A ILE* 3.0 43.7 + - + +
296A ARG* 5.1 2.5 + - - -
114B LEU* 3.6 35.0 - - + +
119B LYS* 5.7 0.4 - - - -
144B PRO* 6.2 0.7 - - + -
146B PHE* 3.5 41.1 - + + -
147B GLN* 3.6 34.1 - - + -
241B ILE* 3.9 20.4 - - + -
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Residues in contact with ILE 288 (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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284A ILE* 3.0 19.7 + - + +
285A ASP* 3.9 5.4 - - - +
287A PHE* 1.3 92.3 - - + +
289A LYS* 1.3 65.9 + - - +
291A ILE* 3.5 10.6 + - + +
292A LYS* 3.3 31.6 + - + +
114B LEU* 4.9 1.1 - - + -
241B ILE* 3.8 22.2 - - + +
242B GLU* 3.8 34.5 - - + +
245B SER* 3.6 32.8 - - - +
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Residues in contact with LYS 289 (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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285A ASP 2.9 19.7 + - - +
286A SER* 3.8 8.1 - - - +
288A ILE* 1.3 79.5 - - - +
290A GLY* 1.3 62.8 + - - +
292A LYS* 3.4 16.7 + - - +
293A SER* 3.7 9.4 + - - -
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Residues in contact with GLY 290 (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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286A SER 2.9 15.3 + - - -
287A PHE* 3.2 4.2 + - - -
289A LYS* 1.3 76.9 - - - +
291A ILE* 1.3 61.0 + - - +
292A LYS 3.2 1.0 + - - -
293A SER* 3.3 17.1 + - - -
296A ARG* 3.3 31.6 - - - +
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Residues in contact with ILE 291 (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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287A PHE* 3.0 24.9 + - + +
288A ILE* 3.5 23.6 - - + +
290A GLY* 1.3 75.1 - - - +
292A LYS* 1.3 61.6 + - + +
293A SER 3.3 7.2 + - - +
296A ARG* 3.9 19.0 - - - +
297A LEU* 6.0 0.2 - - - +
146B PHE* 3.5 39.7 - - + -
238B ILE* 3.5 43.3 - - + +
241B ILE* 3.8 40.8 - - + -
242B GLU* 5.8 0.7 - - + -
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Residues in contact with LYS 292 (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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288A ILE* 3.3 25.2 + - + +
289A LYS* 3.9 8.7 - - - +
290A GLY 3.2 2.0 - - - -
291A ILE* 1.3 76.4 - - + +
293A SER* 1.3 63.6 + - - +
294A ASN* 3.6 2.1 + - - -
235B GLN* 5.3 7.7 + - - +
238B ILE* 4.2 20.3 - - + +
242B GLU* 2.8 40.7 + - - +
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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
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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