Contacts of the helix formed by residues 225 - 239 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ASP* 2.8 42.5 + - - +
223A ASP 3.1 1.6 - - - -
224A SER* 1.3 92.6 - - - +
226A ILE* 1.3 64.6 + - - +
227A PRO* 3.3 3.6 - - - -
228A LEU* 3.1 23.8 + - + +
229A HIS* 3.0 20.3 - - - -
262A ALA* 3.4 44.5 + - + -
263A TYR* 3.7 40.3 + + + +
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Residues in contact with ILE 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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189A LEU* 4.7 0.7 - - + -
190A ILE* 3.7 37.2 - - + +
193A LEU* 3.6 36.1 - - + +
194A LYS* 4.3 15.5 - - + -
223A ASP* 3.2 24.0 - - + +
224A SER 3.4 0.2 - - - -
225A TYR* 1.3 76.9 - - - +
227A PRO* 1.4 69.3 - - + +
229A HIS* 3.1 8.2 + - - +
230A GLU* 2.9 44.0 + - - +
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Residues in contact with PRO 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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223A ASP 5.0 0.2 - - - +
224A SER 3.7 13.2 - - - +
225A TYR* 3.4 4.3 - - - -
226A ILE* 1.4 95.5 - - + +
228A LEU* 1.3 55.3 + - - +
230A GLU* 3.6 17.1 - - + +
231A ASP* 2.8 31.0 + - - +
259A ARG* 5.3 0.7 - - - -
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Residues in contact with LEU 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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225A TYR* 3.1 28.7 + - + +
227A PRO* 1.3 78.6 - - - +
229A HIS* 1.3 62.7 + - + +
231A ASP* 3.3 3.5 - - - +
232A LEU 3.3 8.1 + - - -
256A TRP* 2.8 49.0 + - + +
259A ARG* 3.4 69.8 - - + +
260A LEU* 3.8 24.0 - - + -
262A ALA* 4.7 3.1 - - + -
263A TYR* 4.6 6.1 - - + -
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Residues in contact with HIS 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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186A GLU* 2.8 29.4 + - - +
189A LEU* 3.4 27.6 - - + +
190A ILE* 3.9 18.6 - - + -
193A LEU* 5.0 0.4 - - + -
225A TYR 3.0 25.6 - - - -
226A ILE* 3.1 7.2 + - - +
228A LEU* 1.3 77.0 - - + +
230A GLU* 1.3 65.5 + - - +
232A LEU* 3.3 4.9 + - - +
233A LEU* 3.3 24.4 + - - +
256A TRP* 3.9 6.3 - + - -
260A LEU* 4.1 10.3 - - + -
263A TYR* 2.5 40.7 + + - -
314A ARG* 5.2 1.8 - - + -
318A TYR* 3.5 18.0 + + - -
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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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190A ILE* 3.8 20.5 - - + +
194A LYS* 4.2 13.3 + - - -
226A ILE* 2.9 31.3 + - - +
227A PRO* 3.6 21.0 - - + +
229A HIS* 1.3 74.2 - - - +
231A ASP* 1.3 64.7 + - - +
233A LEU* 3.2 8.6 + - + +
234A THR* 3.0 28.2 + - - +
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Residues in contact with ASP 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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227A PRO 2.8 17.7 + - - +
228A LEU 3.3 7.9 - - - +
230A GLU* 1.3 76.3 - - - +
232A LEU* 1.3 61.2 + - - +
234A THR* 3.4 9.2 + - - +
235A ARG* 3.1 54.7 + - - +
256A TRP* 4.3 1.6 - - - -
259A ARG* 3.0 34.6 + - - +
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Residues in contact with LEU 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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182A MET* 5.1 7.6 - - + -
186A GLU* 3.7 24.5 - - + -
228A LEU 3.3 1.8 + - - -
229A HIS 3.3 8.4 + - - +
230A GLU 3.2 0.8 - - - -
231A ASP* 1.3 80.0 - - - +
233A LEU* 1.3 59.1 + - - +
235A ARG* 3.2 5.1 + - - +
236A ILE* 3.0 50.3 + - + +
249A ILE* 6.2 0.2 - - + -
252A ILE* 3.7 26.2 - - + -
253A LEU* 4.4 12.1 - - + -
256A TRP* 3.4 61.4 - - + +
318A TYR* 5.2 0.2 - - + -
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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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183A SER* 3.4 40.2 - - - +
186A GLU* 3.9 10.5 - - + -
187A GLN* 3.6 34.1 - - + +
190A ILE* 3.7 28.3 - - + -
229A HIS 3.3 7.5 + - - +
230A GLU* 3.2 9.9 + - + +
232A LEU* 1.3 79.1 - - - +
234A THR* 1.3 57.7 + - - +
236A ILE* 3.8 7.4 - - + +
237A GLY* 2.9 26.3 + - - -
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Residues in contact with THR 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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230A GLU* 3.0 16.1 + - - +
231A ASP* 3.5 14.6 - - - +
232A LEU 3.2 0.2 - - - -
233A LEU* 1.3 77.2 - - - +
235A ARG* 1.3 59.6 + - + +
237A GLY* 3.3 2.1 + - - -
238A GLU* 2.9 50.1 + - + +
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Residues in contact with ARG 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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231A ASP* 3.1 48.1 + - - +
232A LEU* 3.7 7.4 - - - +
234A THR* 1.3 76.5 - - + +
236A ILE* 1.3 65.4 + - - +
238A GLU* 3.4 10.0 + - - +
239A ALA* 3.0 24.8 + - - +
252A ILE* 3.7 32.3 + - + +
255A SER* 4.7 12.7 + - - -
256A TRP* 4.5 17.8 - - - +
259A ARG* 4.0 13.5 - - - +
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Residues in contact with ILE 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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179A ILE* 4.7 6.7 - - + -
182A MET* 4.5 8.3 - - + -
183A SER* 3.4 33.2 - - - +
232A LEU* 3.0 46.1 + - + +
233A LEU* 3.9 7.6 - - + +
235A ARG* 1.3 76.3 - - - +
237A GLY* 1.3 56.2 + - - +
239A ALA* 3.2 5.3 + - - +
240A THR* 2.6 37.6 + - - +
246A VAL* 4.6 14.0 - - + +
249A ILE* 4.1 26.7 - - + -
252A ILE* 4.4 7.4 - - + -
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Residues in contact with GLY 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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233A LEU 2.9 18.3 + - - -
234A THR* 3.6 2.0 - - - -
235A ARG 3.2 0.2 - - - -
236A ILE* 1.3 77.6 - - - +
238A GLU* 1.3 56.4 + - - +
240A THR* 3.1 28.8 + - - +
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Residues in contact with GLU 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 THR* 2.9 37.2 + - + +
235A ARG* 4.0 9.8 - - - +
237A GLY* 1.3 76.2 - - - +
239A ALA* 1.3 58.0 + - - +
240A THR 3.2 5.7 + - - +
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Residues in contact with ALA 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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235A ARG 3.0 16.8 + - - +
236A ILE* 3.6 7.0 - - - +
237A GLY 3.2 0.4 - - - -
238A GLU* 1.3 76.6 - - - +
240A THR* 1.3 58.6 + - - +
241A LYS* 4.0 5.6 + - - +
245A THR 4.0 5.4 - - - +
246A VAL* 4.1 15.1 - - + +
247A GLU* 4.5 3.3 + - - +
248A GLN 4.4 11.6 + - - +
251A HIS* 5.6 3.1 - - + +
252A ILE* 4.0 18.2 - - + -
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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