Contacts of the helix formed by residues 272 - 279 (chain A) in PDB entry 3EBV
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR 3.2 15.3 - - - -
12A GLN* 2.8 33.4 + - - -
225A ALA* 3.6 4.7 - - - +
270A THR* 3.7 8.7 - - - -
271A TRP* 1.3 87.0 + - - +
273A THR* 1.3 65.3 + - - +
274A ASN 3.3 3.0 + - - -
275A TRP* 3.1 21.3 + - - +
276A ASP* 2.9 23.3 + - - +
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Residues in contact with THR 273 (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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9A GLY* 3.9 21.3 - - - +
10A TYR 2.8 23.3 + - - +
11A TRP* 3.6 13.0 - - + +
21A GLN* 2.8 27.5 + - - +
26A VAL* 4.1 18.8 - - + -
27A PRO* 4.9 1.8 - - - +
30A TYR* 3.9 27.8 - - + -
33A ILE* 5.5 0.7 - - + -
272A SER* 1.3 71.0 - - - +
274A ASN* 1.3 62.4 + - - +
276A ASP* 3.2 10.2 + - - +
277A ALA* 2.9 26.7 + - - +
281A ASN* 4.8 0.7 - - - +
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Residues in contact with ASN 274 (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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10A TYR 4.1 0.3 - - - +
11A TRP* 3.9 2.5 - - - +
12A GLN* 2.9 57.6 + - - +
14A PHE 5.4 1.0 + - - -
18A ALA* 3.5 17.3 - - + -
19A THR 2.9 29.7 + - - +
20A VAL* 4.2 2.0 - - - +
21A GLN* 3.7 28.8 + - - +
56A LEU* 6.0 0.8 - - - +
272A SER* 3.1 0.9 + - - -
273A THR* 1.3 83.2 + - - +
275A TRP* 1.3 57.5 + - - +
277A ALA* 3.2 4.3 + - - +
278A THR* 3.0 28.8 + - - -
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Residues in contact with TRP 275 (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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12A GLN* 3.7 2.2 - - - -
16A ASN* 3.4 39.3 - - + +
17A GLY 4.0 4.9 - - - -
18A ALA* 3.5 31.6 - - + -
225A ALA* 4.1 3.6 - - + -
226A SER* 4.1 8.2 + - - +
228A ARG* 3.8 49.1 - - + -
229A ALA* 3.5 36.1 + - + +
271A TRP* 4.0 10.9 - - - +
272A SER* 3.1 29.2 + - - +
274A ASN* 1.3 72.4 - - - +
276A ASP* 1.3 66.9 + - - +
278A THR* 3.2 16.3 + - + -
279A ALA* 3.1 23.4 + - - +
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Residues in contact with ASP 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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27A PRO* 4.2 0.5 - - - +
30A TYR* 2.7 27.6 + - - +
225A ALA* 3.6 13.1 - - + +
272A SER 2.9 13.9 + - - +
273A THR 3.2 8.4 + - - +
275A TRP* 1.3 75.8 - - - +
277A ALA* 1.3 52.6 + - - +
279A ALA* 3.0 17.3 + - - +
281A ASN* 2.8 47.3 + - - +
283A TRP* 3.4 12.8 + - - +
284A SER* 2.6 43.2 + - - -
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Residues in contact with ALA 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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19A THR* 3.9 19.6 + - + -
21A GLN* 3.5 28.5 - - - +
273A THR 2.9 6.0 + - - +
274A ASN 3.5 8.3 - - - +
275A TRP 3.2 0.2 - - - -
276A ASP* 1.3 73.8 - - - +
278A THR* 1.3 65.2 + - - +
280A GLY* 3.0 13.5 + - - -
281A ASN* 3.3 16.8 + - - +
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Residues in contact with THR 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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17A GLY 4.8 0.7 + - - -
18A ALA* 3.7 4.5 - - - -
19A THR* 2.7 38.9 + - - -
228A ARG* 4.4 26.0 - - - +
274A ASN 3.0 7.9 + - - -
275A TRP* 3.2 19.7 + - + +
277A ALA* 1.3 75.8 - - - +
279A ALA* 1.3 57.0 - - + +
280A GLY 3.5 2.4 + - - -
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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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225A ALA 4.8 4.0 - - - +
226A SER* 4.0 21.1 - - - -
275A TRP 3.1 14.0 + - - +
276A ASP* 3.0 12.5 + - - +
278A THR* 1.3 77.8 - - + +
280A GLY* 1.3 59.4 + - - +
281A ASN 3.2 0.7 + - - -
282A ALA* 3.3 20.4 + - + +
283A TRP 6.0 0.7 - - - +
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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