Contacts of the helix formed by residues 225 - 239 (chain D) in PDB entry 4XH9
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 TYR 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221D ASP* 2.4 49.2 + - + +
222D LEU 4.9 0.2 + - - -
223D ASP 3.3 1.0 - - - -
224D SER* 1.3 92.0 - - - +
226D ILE* 1.3 64.1 + - - +
227D PRO* 3.3 3.6 - - - -
228D LEU* 3.0 29.8 - - + +
229D HIS* 3.1 12.7 - - - -
262D ALA* 3.5 39.8 + - + -
263D TYR* 3.8 40.7 + + + +
266D TYR* 5.4 0.9 - - + -
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Residues in contact with ILE 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ILE* 3.7 24.7 - - + +
193D LEU* 4.1 18.4 - - + +
194D LYS* 3.6 30.1 - - + -
223D ASP* 3.3 35.9 - - - +
224D SER 3.4 0.2 - - - -
225D TYR* 1.3 76.9 - - - +
227D PRO* 1.4 71.1 - - + +
229D HIS* 2.9 22.2 + - - +
230D GLU* 2.9 35.3 + - - +
263D TYR* 4.8 0.2 + - - -
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Residues in contact with PRO 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D ASP 5.1 0.4 - - - +
224D SER 3.7 13.0 - - - +
225D TYR* 3.5 4.0 - - - -
226D ILE* 1.4 94.6 - - + +
228D LEU* 1.3 55.1 + - - +
230D GLU* 3.6 18.6 - - + +
231D ASP* 2.8 31.1 + - - +
259D ARG* 5.7 0.7 - - - -
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D TYR* 3.0 33.3 + - + +
226D ILE 3.1 0.2 - - - -
227D PRO* 1.3 79.9 - - - +
229D HIS* 1.3 56.4 + - + +
231D ASP* 3.4 13.3 - - - +
232D LEU 3.4 0.3 + - - -
256D TRP* 2.8 49.3 + - + +
259D ARG* 3.4 74.3 - - + +
260D LEU* 4.3 14.6 - - + -
262D ALA* 4.5 6.3 - - + -
263D TYR* 4.7 3.1 - - + -
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Residues in contact with HIS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D GLU* 2.8 28.0 + - - +
189D LEU* 3.3 31.0 - - + +
190D ILE* 3.9 18.4 - - + -
193D LEU* 5.0 1.6 - - + -
225D TYR 3.1 25.8 + - - -
226D ILE* 2.9 10.3 + - - +
228D LEU* 1.3 73.4 - - + +
230D GLU* 1.3 65.6 + - - +
231D ASP 3.2 1.6 - - - -
232D LEU* 3.3 4.9 + - - +
233D LEU* 3.2 24.3 + - - +
256D TRP* 3.8 6.7 - + - -
260D LEU* 4.0 12.1 - - + -
263D TYR* 2.5 41.0 + + - -
314D ARG* 5.4 0.2 - - + -
318D TYR* 3.6 12.1 + + - -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ILE* 3.6 20.5 - - + +
194D LYS* 4.3 15.2 + - - -
226D ILE* 2.9 32.3 + - + +
227D PRO* 3.6 20.0 - - - +
229D HIS* 1.3 75.5 - - - +
231D ASP* 1.3 57.2 + - - +
233D LEU* 3.2 9.8 + - + +
234D THR* 2.9 33.0 + - - +
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Residues in contact with ASP 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PRO 2.8 18.1 + - - +
228D LEU* 3.4 7.6 - - - +
230D GLU* 1.3 77.4 - - - +
232D LEU* 1.3 61.1 + - - +
234D THR* 3.2 9.5 + - - +
235D ARG* 2.6 60.2 + - - +
256D TRP* 4.3 2.8 - - - -
259D ARG* 2.4 32.6 + - - +
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D MET* 5.1 4.9 - - + -
186D GLU* 3.8 24.2 - - + -
228D LEU 3.4 2.2 + - - -
229D HIS 3.3 10.2 + - - +
231D ASP* 1.3 79.2 - - - +
233D LEU* 1.3 57.7 + - + +
235D ARG* 3.4 3.0 + - - -
236D ILE* 3.0 52.7 + - + +
252D ILE* 3.8 25.1 - - + -
253D LEU* 4.3 13.7 - - + -
256D TRP* 3.6 62.3 - - + +
318D TYR* 5.1 2.2 - - + -
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Residues in contact with LEU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D SER* 3.5 38.1 - - - +
186D GLU* 3.7 12.1 - - + -
187D GLN* 3.8 29.6 - - + +
190D ILE* 3.7 28.7 - - + -
229D HIS 3.2 9.2 + - - +
230D GLU* 3.2 10.5 + - + +
232D LEU* 1.3 77.8 - - - +
234D THR* 1.3 58.4 + - - +
236D ILE* 3.9 6.4 - - + +
237D GLY* 2.9 24.1 + - - -
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Residues in contact with THR 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 2.9 16.2 + - - +
231D ASP* 3.2 14.4 + - - +
233D LEU* 1.3 77.9 - - - +
235D ARG* 1.3 59.5 + - + +
237D GLY* 3.1 3.0 + - - -
238D GLU* 2.9 49.9 + - + +
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ASP* 2.6 54.6 + - - +
232D LEU* 4.1 3.8 - - - +
234D THR* 1.3 74.4 - - + +
236D ILE* 1.3 60.8 + - - +
238D GLU* 3.3 18.8 + - - +
239D ALA* 3.0 29.3 + - - +
252D ILE* 3.7 29.1 - - + +
256D TRP* 5.6 5.7 - - - +
259D ARG* 3.9 6.3 - - - +
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ILE* 4.8 6.5 - - + -
182D MET* 4.4 8.5 - - + -
183D SER* 3.5 30.5 - - - +
232D LEU* 3.0 48.4 + - + +
233D LEU* 3.9 7.6 - - + +
235D ARG* 1.3 75.9 - - - +
237D GLY* 1.3 55.6 + - - +
239D ALA* 3.2 4.0 + - - +
240D THR* 2.6 37.3 + - - +
246D VAL* 4.6 14.2 - - + +
249D ILE* 4.2 26.5 - - + -
252D ILE* 4.4 8.5 - - + -
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Residues in contact with GLY 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D LEU 2.9 16.5 + - - -
234D THR* 3.1 5.6 + - - -
236D ILE* 1.3 78.2 - - - +
238D GLU* 1.3 59.9 + - - +
240D THR* 3.2 25.4 + - - +
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Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D THR* 2.9 39.6 + - + +
235D ARG* 3.8 18.4 + - - +
237D GLY* 1.3 76.3 - - - +
239D ALA* 1.3 58.1 + - - +
240D THR 3.2 6.1 + - - +
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ARG 3.0 17.3 + - - +
236D ILE* 3.5 6.5 - - - +
237D GLY 3.2 0.4 - - - -
238D GLU* 1.3 74.9 - - - +
240D THR* 1.3 60.7 + - - +
241D LYS* 3.8 4.7 + - - +
246D VAL* 3.8 20.3 - - + +
247D GLU* 4.2 4.9 + - - +
248D GLN 4.4 11.1 + - - +
251D HIS* 5.3 4.3 - - + +
252D ILE* 3.6 21.3 - - + -
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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