Contacts of the helix formed by residues 275 - 285 (chain A) in PDB entry 5ON2
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 ASN 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A ALA 3.3 17.8 + - - +
272A ALA 3.0 19.1 - - - +
273A GLU 5.0 0.2 - - - -
274A ASN* 1.3 76.9 - - - +
276A PRO* 1.4 73.3 - - - +
277A GLU* 3.2 17.2 + - - +
278A LEU* 3.3 23.2 + - + +
279A ALA* 3.5 9.0 + - - +
303A VAL* 5.6 2.3 - - - +
304A ASP 4.1 13.9 + - - -
305A THR 4.1 9.4 + - - +
306A GLY* 5.7 0.4 - - - -
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Residues in contact with PRO 276 (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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274A ASN 3.4 9.4 - - - +
275A ASN* 1.4 89.6 - - - +
277A GLU* 1.3 64.7 + - + +
279A ALA* 3.5 7.3 + - + +
280A ALA* 3.3 19.4 + - - +
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Residues in contact with GLU 277 (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 ASN* 3.2 8.1 + - - +
276A PRO* 1.3 78.8 - - + +
278A LEU* 1.3 61.4 + - - +
280A ALA* 3.3 9.8 + - + +
281A PHE* 3.1 24.9 + - - +
303A VAL* 4.2 25.8 - - + +
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Residues in contact with LEU 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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268A ALA* 4.1 6.3 - - + +
271A ALA* 3.4 42.4 - - + +
272A ALA* 3.9 2.9 - - - +
275A ASN* 3.3 22.4 + - + +
277A GLU* 1.3 74.9 - - - +
279A ALA* 1.3 63.4 + - - +
281A PHE* 3.3 8.0 + - + +
282A ILE* 3.2 32.4 + - + +
303A VAL* 4.1 15.8 - - + +
304A ASP 4.1 13.0 - - - +
305A THR* 3.7 20.6 - - + +
322A ALA* 4.0 26.7 - - + -
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Residues in contact with ALA 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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272A ALA* 3.6 32.2 - - + +
275A ASN 3.5 5.7 + - - +
276A PRO* 3.5 12.1 + - + +
277A GLU 3.3 0.4 - - - -
278A LEU* 1.3 79.2 - - - +
280A ALA* 1.3 58.9 + - - +
282A ILE* 3.4 4.5 + - - +
283A ASP* 3.0 34.1 + - - +
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Residues in contact with ALA 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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276A PRO 3.3 11.4 + - - +
277A GLU* 3.3 13.9 + - + +
279A ALA* 1.3 78.5 - - - +
281A PHE* 1.3 58.1 + - - +
283A ASP* 3.7 5.9 + - - +
284A GLU* 3.0 28.7 + - - +
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Residues in contact with PHE 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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263A ALA* 5.6 2.5 - - + -
277A GLU 3.1 12.5 + - - +
278A LEU* 3.6 11.9 - - + +
279A ALA 3.3 0.4 - - - -
280A ALA* 1.3 74.6 - - - +
282A ILE* 1.3 62.4 + - + +
284A GLU* 3.4 22.5 + - - +
285A CYS* 3.1 51.9 + - - -
301A LYS* 4.0 20.2 - - + -
302A GLY* 3.9 28.9 - - - -
303A VAL* 3.7 23.3 - - + -
322A ALA* 3.9 29.2 - - + -
323A ALA* 4.0 15.7 - - - -
324A ASN* 4.4 7.0 - - + -
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Residues in contact with ILE 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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263A ALA* 4.3 18.4 - - - +
268A ALA* 3.4 41.3 - - + +
269A GLN* 3.6 22.7 - - - +
272A ALA* 3.6 20.6 - - + -
278A LEU* 3.2 17.2 + - + +
279A ALA* 3.9 4.5 - - - +
280A ALA 3.4 0.2 - - - -
281A PHE* 1.3 80.9 - - + +
283A ASP* 1.3 65.4 + - - +
285A CYS* 3.2 21.7 + - + +
286A ARG* 3.6 9.1 + - - +
322A ALA* 5.9 1.6 - - + -
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Residues in contact with ASP 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 ALA* 3.0 24.8 + - - +
280A ALA* 4.1 5.6 - - - +
282A ILE* 1.3 76.8 - - - +
284A GLU* 1.3 63.6 + - - +
286A ARG* 3.1 56.1 + - - +
287A ASN* 4.4 4.7 - - - +
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Residues in contact with GLU 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 ALA 3.0 18.5 + - - +
281A PHE* 3.4 28.3 - - - +
282A ILE 3.3 0.2 - - - -
283A ASP* 1.3 75.1 - - - +
285A CYS* 1.3 57.4 + - - +
286A ARG 3.2 2.2 - - - -
287A ASN* 3.2 32.2 + - + +
288A THR* 4.1 1.9 + - - -
301A LYS* 3.8 24.9 + - - +
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Residues in contact with CYS 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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185A ARG* 3.4 12.0 - - - -
263A ALA* 3.5 34.8 - - + -
281A PHE* 3.1 47.5 + - - -
282A ILE* 3.2 12.3 + - - +
284A GLU* 1.3 75.1 - - - +
286A ARG* 1.3 61.4 + - - +
287A ASN 3.3 0.2 - - - -
288A THR* 3.1 30.9 + - - +
324A ASN* 4.6 11.7 - - - -
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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