Contacts of the helix formed by residues 227 - 236 (chain A) in PDB entry 3EU9
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 THR 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A MET* 4.5 0.7 - - - -
217A VAL 4.4 7.6 - - - -
218A ASN* 3.8 20.5 + - - +
219A LEU 3.3 22.0 - - - +
220A GLY* 4.3 3.1 - - - -
225A LYS 4.5 3.6 - - - +
226A ASN* 1.3 74.2 - - - +
228A ALA* 1.3 66.1 + - - +
229A LEU* 3.2 18.5 + - - +
230A HIS* 2.8 42.8 + - + +
231A TRP* 3.0 17.7 + - - -
249A ALA* 6.5 0.2 - - - -
250A ASN 5.2 1.4 + - - -
253A ALA* 4.1 17.4 - - + +
254A GLN 6.2 0.2 - - - +
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Residues in contact with ALA 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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194A LEU* 3.8 38.1 - - + +
195A MET* 4.1 13.1 - - + +
198A ALA* 3.3 18.9 - - + +
217A VAL* 4.4 7.7 + - + +
219A LEU 4.2 2.0 + - - -
227A THR* 1.3 74.7 - - - +
229A LEU* 1.3 56.5 + - - +
231A TRP* 3.4 8.8 + - - -
232A ALA* 3.0 25.1 + - - +
244A LEU* 3.8 14.8 - - + -
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Residues in contact with LEU 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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217A VAL 5.3 0.8 + - - -
218A ASN* 6.2 0.2 - - - +
227A THR* 3.0 12.0 + - - +
228A ALA* 1.3 76.6 - - - +
230A HIS* 1.3 66.3 + - - +
232A ALA* 3.2 1.6 + - - +
233A VAL* 3.0 31.3 + - + +
241A ILE* 4.1 26.9 - - + -
244A LEU* 3.9 16.4 - - + +
245A LEU* 4.0 19.7 - - + -
249A ALA* 3.6 32.7 - - + +
250A ASN 3.9 14.4 - - - +
251A VAL* 4.1 8.3 - - + -
261A ALA* 3.9 24.0 - - + -
277A LEU* 6.1 2.9 - - + -
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Residues in contact with HIS 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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225A LYS 4.5 2.5 - - - -
226A ASN* 3.6 29.2 - - + +
227A THR* 2.8 45.9 + - + +
229A LEU* 1.3 76.6 - - - +
231A TRP* 1.3 58.9 + - - +
233A VAL* 3.2 6.6 + - - +
234A LEU* 2.9 33.2 + - - +
250A ASN 5.6 0.2 - - - -
253A ALA* 3.0 34.3 + - + -
255A ASN* 3.9 11.4 + - - -
259A GLU 3.2 12.3 + - - -
260A SER 3.8 1.8 - - - -
261A ALA* 3.4 20.0 + - + -
264A LEU* 3.5 27.3 - - + +
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Residues in contact with TRP 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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191A MET* 3.5 34.8 - - + -
195A MET* 3.7 25.4 - - + +
198A ALA 4.3 1.8 - - - -
199A TYR* 3.6 44.4 - + + +
221A ASP* 3.5 22.2 + - - -
224A HIS* 3.8 17.0 - + - -
226A ASN* 3.1 36.4 + - + -
227A THR 3.0 26.3 + - - -
228A ALA* 3.7 4.7 - - - +
230A HIS* 1.3 75.8 - - - +
232A ALA* 1.3 64.4 + - - +
234A LEU* 3.3 16.1 + - + -
235A ALA* 2.9 25.8 + - - +
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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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198A ALA* 3.6 19.4 + - + +
228A ALA 3.0 14.5 + - - +
229A LEU* 3.5 8.7 - - - +
231A TRP* 1.3 76.2 - - - +
233A VAL* 1.3 58.7 + - - +
235A ALA 3.1 1.6 + - - -
236A GLY 2.8 23.7 + - - -
237A ASN* 2.9 16.7 + - - +
240A VAL* 4.4 1.1 - - + -
241A ILE* 3.5 25.5 - - + +
244A LEU* 4.0 14.4 - - + -
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Residues in contact with VAL 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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229A LEU* 3.0 21.0 + - + +
230A HIS* 3.4 7.6 - - - +
232A ALA* 1.3 76.7 - - - +
234A LEU* 1.3 58.2 + - + +
236A GLY* 2.7 24.9 + - - -
241A ILE* 4.2 8.3 - - + +
261A ALA* 3.8 22.0 - - + +
264A LEU* 3.7 28.9 - - + +
265A ALA* 3.8 18.2 - - + +
268A ARG* 5.5 1.6 - - + -
273A MET* 3.7 31.9 - - + +
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Residues in contact with LEU 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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199A TYR* 4.6 11.5 - - + -
226A ASN* 3.8 25.1 - - - +
230A HIS 2.9 24.8 + - - +
231A TRP* 3.7 23.6 - - + +
233A VAL* 1.3 73.2 - - + +
235A ALA* 1.3 58.6 + - - +
264A LEU* 4.0 29.4 - - + -
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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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198A ALA 4.1 4.5 - - - +
199A TYR* 3.5 38.4 - - + +
202A HIS* 3.4 17.5 + - + +
231A TRP 2.9 16.4 + - - +
232A ALA 3.7 3.8 - - - +
234A LEU* 1.3 78.0 - - - +
236A GLY* 1.3 64.7 + - - +
237A ASN 3.4 2.8 + - - +
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Residues in contact with GLY 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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202A HIS* 4.0 5.4 + - - -
232A ALA 2.8 0.6 + - - -
233A VAL 2.7 16.0 + - - -
234A LEU 3.4 0.2 - - - -
235A ALA* 1.3 80.0 - - - +
237A ASN* 1.3 58.9 + - - +
238A THR* 3.2 14.5 + - - +
270A ASN* 5.6 0.7 - - - -
273A MET* 4.0 19.1 - - - -
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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