Contacts of the helix formed by residues 224 - 238 (chain A) in PDB entry 2YHS
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.4 18.1 + - + +
223A ILE* 1.3 76.9 - - - +
225A ASP* 1.3 64.4 + - - +
226A ASP* 3.2 16.1 + - - +
227A LEU* 2.9 33.5 + - - +
228A PHE* 3.2 19.5 + - - -
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Residues in contact with ASP 225 (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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224A ASP* 1.3 74.7 - - - +
226A ASP* 1.3 66.5 + - - +
228A PHE* 3.3 11.1 + - - +
229A GLU* 3.0 37.7 + - + +
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Residues in contact with ASP 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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224A ASP* 3.2 15.3 + - - +
225A ASP* 1.3 79.8 - - - +
227A LEU* 1.3 57.7 + - - +
229A GLU* 3.2 16.0 + - - +
230A GLU* 2.9 38.7 + - + +
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Residues in contact with LEU 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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217A LEU* 4.4 4.7 - - + +
218A PHE* 4.1 16.6 - - + -
221A LYS* 3.8 29.2 - - + -
222A LYS 3.6 12.3 - - - +
223A ILE* 3.7 10.8 - - + -
224A ASP* 2.9 22.5 + - - +
226A ASP* 1.3 76.7 - - - +
228A PHE* 1.3 60.4 + - + +
230A GLU* 3.0 13.2 + - - +
231A LEU* 2.9 27.0 + - + +
264A ALA* 3.2 33.0 - - + -
267A LEU* 3.5 23.8 - - + -
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Residues in contact with PHE 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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223A ILE* 3.4 32.5 - - + -
224A ASP* 3.2 21.7 + - - -
225A ASP* 3.9 11.2 - - - +
227A LEU* 1.3 80.3 - - + +
229A GLU* 1.3 57.6 + - + +
231A LEU* 3.4 9.6 + - + +
232A GLU* 2.9 29.3 + - - +
249A ILE* 4.0 22.5 - - + +
252A LEU* 3.9 31.0 - - + -
253A THR* 3.8 37.9 - - + -
256A ALA* 4.8 4.0 - - + -
267A LEU* 4.2 16.8 - - + -
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Residues in contact with GLU 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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225A ASP* 3.0 30.2 + - + +
226A ASP* 3.4 17.4 - - - +
228A PHE* 1.3 75.0 - - + +
230A GLU* 1.3 65.0 + - + +
232A GLU* 3.4 14.8 + - - +
233A GLU* 3.0 23.3 + - - +
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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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217A LEU* 3.8 15.8 - - + +
221A LYS* 2.8 39.6 + - - +
226A ASP* 2.9 24.3 + - + +
227A LEU* 3.5 10.1 - - - +
229A GLU* 1.3 72.6 - - + +
231A LEU* 1.3 66.5 + - - +
233A GLU* 3.3 14.1 + - - +
234A GLN* 3.0 21.8 + - - +
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Residues in contact with LEU 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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214A PHE* 3.8 34.3 - - + -
217A LEU* 3.8 19.5 - - + +
218A PHE* 4.1 12.6 - - + -
227A LEU* 2.9 12.5 + - + +
228A PHE* 3.6 12.8 - - + +
230A GLU* 1.3 74.3 - - - +
232A GLU* 1.3 65.6 + - - +
234A GLN* 3.1 2.6 + - + +
235A LEU* 2.9 29.3 + - + +
249A ILE* 3.5 17.9 - - + -
252A LEU* 3.4 33.9 - - + -
267A LEU* 5.4 0.7 - - + -
271A LEU* 3.9 16.2 - - + -
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Residues in contact with GLU 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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228A PHE 2.9 17.4 + - - +
229A GLU* 3.6 14.4 - - - +
230A GLU 3.3 0.2 - - - -
231A LEU* 1.3 76.5 - - - +
233A GLU* 1.3 64.2 + - - +
235A LEU* 3.2 2.6 + - - +
236A LEU* 2.9 40.0 + - + +
242A VAL* 5.7 3.3 - - - +
245A THR* 3.8 25.2 - - + +
246A ARG* 5.4 7.4 + - - +
249A ILE* 4.1 12.5 - - + +
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Residues in contact with GLU 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 GLU 3.0 14.2 + - - +
230A GLU* 3.6 16.4 - - - +
231A LEU 3.3 0.2 - - - -
232A GLU* 1.3 77.0 - - - +
234A GLN* 1.3 56.8 + - - +
236A LEU* 3.3 8.9 + - + +
237A ILE* 3.0 54.1 + - + +
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Residues in contact with GLN 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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208A GLU 4.7 1.0 + - - -
209A ASN* 2.8 45.7 + - + +
213A GLY 3.3 23.3 + - - +
214A PHE* 3.6 14.5 - - + +
217A LEU* 3.6 28.8 - - + +
230A GLU 3.0 12.9 + - - +
231A LEU* 3.1 9.8 + - + +
233A GLU* 1.3 76.4 - - - +
235A LEU* 1.3 62.8 + - - +
237A ILE* 3.5 10.7 + - + +
238A ALA* 3.2 22.7 + - - +
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Residues in contact with LEU 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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210A LEU* 3.8 25.4 - - + -
214A PHE* 3.9 15.3 - - + -
231A LEU* 2.9 26.4 + - + +
232A GLU 3.5 6.3 - - - +
234A GLN* 1.3 76.1 - - - +
236A LEU* 1.3 62.1 + - - +
238A ALA* 3.2 6.4 + - - -
240A VAL* 3.1 36.6 + - + +
245A THR* 3.5 31.9 - - + +
248A ILE* 4.3 19.5 - - + -
249A ILE* 3.9 20.9 - - + -
271A LEU* 5.4 0.4 - - + -
275A MET* 4.3 11.0 - - + -
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Residues in contact with LEU 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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232A GLU* 2.9 41.0 + - + +
233A GLU* 3.7 7.6 - - - +
235A LEU* 1.3 73.8 - - - +
237A ILE* 1.3 61.5 + - + +
239A ASP* 2.8 25.5 + - - +
240A VAL 4.6 1.8 - - - +
241A GLY* 3.9 3.3 + - - +
242A VAL* 3.7 40.6 - - + +
245A THR* 3.7 20.2 - - + +
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Residues in contact with ILE 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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209A ASN* 5.3 12.3 - - - +
233A GLU* 3.0 44.9 + - + +
234A GLN* 3.8 9.0 - - + +
235A LEU 3.4 0.2 - - - -
236A LEU* 1.3 75.1 - - + +
238A ALA* 1.3 55.7 + - - +
239A ASP* 3.2 2.0 + - - +
453A LYS* 2.8 47.6 + - + +
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Residues in contact with ALA 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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209A ASN* 4.1 13.7 - - + +
210A LEU* 3.7 33.0 - - + -
234A GLN 3.2 15.7 + - - +
235A LEU 3.7 4.7 - - - +
236A LEU 3.1 1.0 - - - -
237A ILE* 1.3 75.9 - - - +
239A ASP* 1.3 60.5 + - - +
240A VAL* 3.4 1.1 - - + -
452A ALA 4.9 0.4 - - - +
453A LYS* 3.2 19.3 - - - +
454A GLY 4.4 0.2 - - - +
455A GLY 2.6 31.4 + - - -
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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