Contacts of the helix formed by residues 225 - 240 (chain A) in PDB entry 2E9D
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 ASP 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.3 29.1 + - - +
223A ASP 3.2 5.7 + - - +
224A PHE* 1.3 75.2 - - - +
226A GLU* 1.3 55.3 + - - +
227A GLN* 3.2 27.7 + - - +
228A ASP* 2.5 47.0 + - - +
229A PHE* 2.7 18.6 + - - +
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Residues in contact with GLU 226 (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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52A ARG* 3.1 44.0 + - + +
55A SER* 4.8 6.6 - - - -
56A PHE* 3.5 38.8 + - + +
59A ASN* 5.9 0.9 + - - -
225A ASP* 1.3 78.4 - - - +
227A GLN* 1.3 67.1 + - - +
229A PHE* 3.2 5.4 + - - +
230A GLU* 2.8 39.3 + - - +
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Residues in contact with GLN 227 (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 ASP* 3.1 23.2 - - - +
226A GLU* 1.3 87.5 + - - +
228A ASP* 1.3 58.1 + - - +
230A GLU* 3.8 15.2 - - - +
231A GLY* 3.1 21.1 + - - -
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Residues in contact with ASP 228 (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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215A TYR* 5.2 2.3 + - - -
219A VAL* 4.2 18.8 - - - +
223A ASP 3.1 25.3 - - - +
224A PHE* 3.5 31.8 - - + -
225A ASP* 2.5 30.0 + - - +
227A GLN* 1.3 71.1 - - - +
229A PHE* 1.3 62.3 + - - +
230A GLU 3.1 1.8 - - - -
231A GLY* 3.2 2.9 + - - -
232A ALA* 3.2 19.4 + - - +
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Residues in contact with PHE 229 (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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21A VAL* 3.8 37.9 - - + -
23A ILE* 4.1 14.1 - - + -
53A ALA* 3.5 33.2 - - + -
56A PHE* 3.7 27.8 - + + -
57A ALA* 4.7 4.5 - - + -
62A ILE* 4.3 15.5 - - + -
65A LEU* 4.6 6.1 - - + -
193A ILE* 4.1 14.4 - - + -
224A PHE* 3.6 20.1 - + + -
225A ASP 2.7 13.9 + - - +
226A GLU* 3.7 10.5 - - - +
228A ASP* 1.3 73.0 - - - +
230A GLU* 1.3 61.1 + - - +
232A ALA* 3.5 1.9 + - - +
233A LEU* 3.2 29.8 + - + +
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Residues in contact with GLU 230 (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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56A PHE* 3.1 38.8 - - + -
60A ASN* 5.0 1.7 - - - +
226A GLU* 2.8 21.6 + - - +
227A GLN* 3.8 14.2 - - - +
229A PHE* 1.3 76.2 - - - +
231A GLY* 1.3 66.9 + - - +
233A LEU* 3.1 5.1 + - - -
234A ASN* 2.9 36.9 + - - +
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Residues in contact with GLY 231 (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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215A TYR* 4.3 9.5 + - - -
227A GLN 3.1 16.2 + - - -
228A ASP* 3.2 5.5 + - - -
230A GLU* 1.3 75.7 - - - +
232A ALA* 1.3 56.5 + - - +
234A ASN* 3.7 6.9 - - - +
235A ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 232 (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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191A LEU* 4.1 7.9 - - + +
193A ILE* 3.6 31.6 - - + -
215A TYR* 3.7 35.0 - - + -
224A PHE* 5.4 0.2 - - + -
228A ASP 3.2 9.8 + - - +
229A PHE 4.0 4.3 - - - +
230A GLU 3.1 0.8 - - - -
231A GLY* 1.3 74.5 - - - +
233A LEU* 1.3 55.2 + - - +
235A ALA* 3.2 2.1 + - - +
236A PHE* 2.7 34.5 + - - +
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Residues in contact with LEU 233 (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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16A HIS* 4.2 25.6 - - + +
18A CYS* 3.3 39.7 - - + -
21A VAL* 4.4 6.7 - - + -
56A PHE* 3.7 22.9 - - + -
60A ASN* 5.3 1.8 - - + +
62A ILE* 3.6 25.6 - - + -
191A LEU* 3.6 14.4 - - + -
229A PHE* 3.2 16.3 + - + +
230A GLU* 3.1 6.5 + - - +
232A ALA* 1.3 76.0 - - - +
234A ASN* 1.3 62.8 + - - +
236A PHE* 3.7 2.6 - - + +
237A ALA* 2.8 31.0 + - - +
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Residues in contact with ASN 234 (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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16A HIS* 6.0 0.7 - - - +
230A GLU* 2.9 26.6 + - - +
231A GLY* 3.7 6.0 - - - +
233A LEU* 1.3 80.9 - - - +
235A ALA* 1.3 59.7 + - - +
237A ALA* 4.3 4.5 - - - -
238A ASN* 2.8 44.8 + - - +
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Residues in contact with ALA 235 (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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213A GLU* 5.7 0.4 - - - -
215A TYR* 3.5 27.8 - - + -
231A GLY 2.9 18.1 + - - +
232A ALA 3.5 5.4 - - - +
234A ASN* 1.3 78.2 - - - +
236A PHE* 1.3 53.1 + - - +
238A ASN* 3.9 4.0 - - - +
239A ARG* 2.7 46.3 + - + +
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Residues in contact with PHE 236 (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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16A HIS 3.2 16.2 - - - -
17A GLY 2.9 31.6 - - - -
18A CYS* 3.7 9.6 - - + -
190A ASP* 3.3 37.5 - - + -
191A LEU* 4.1 21.1 - - + -
213A GLU* 3.7 28.7 - - + +
215A TYR* 5.7 0.2 - - - -
232A ALA 2.7 21.0 + - - +
233A LEU* 3.7 4.9 - - - +
235A ALA* 1.3 73.4 - - - +
237A ALA* 1.3 67.8 + - - +
239A ARG* 3.0 16.4 + - - +
240A GLU* 3.0 14.8 + - - -
200B ARG* 4.5 12.7 + - - -
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Residues in contact with ALA 237 (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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16A HIS* 3.7 27.4 - - + +
233A LEU 2.8 22.7 + - - +
234A ASN* 3.8 6.1 - - - +
236A PHE* 1.3 80.3 - - - +
238A ASN* 1.3 66.0 + - - +
240A GLU* 3.3 19.0 + - - +
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Residues in contact with ASN 238 (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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234A ASN* 2.8 35.0 + - - +
235A ALA* 4.1 3.4 - - - +
237A ALA* 1.3 72.6 - - - +
239A ARG* 1.3 58.0 + - + +
240A GLU* 3.0 25.9 + - - +
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Residues in contact with ARG 239 (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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213A GLU* 3.4 31.6 + - - +
235A ALA* 2.7 35.0 + - + +
236A PHE 3.0 5.4 + - - +
238A ASN* 1.3 74.8 - - + +
240A GLU* 1.3 71.5 + - - +
197B GLY 2.5 31.9 + - - -
198B GLU* 3.5 30.6 + - - +
199B HIS* 3.2 31.2 + - - -
200B ARG* 4.3 0.5 + - - -
218B ASP* 4.2 10.7 + - - -
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Residues in contact with GLU 240 (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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236A PHE* 3.0 13.1 + - - -
237A ALA* 3.3 13.9 + - - +
238A ASN* 3.0 13.5 - - - +
239A ARG* 1.3 88.6 - - - +
200B ARG* 4.1 23.2 + - - -
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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
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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