Contacts of the helix formed by residues 226 - 238 (chain A) in PDB entry 4IRP
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 ARG 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A TYR* 5.1 13.3 - - - -
196A TYR* 2.8 37.5 + - - -
199A TYR* 5.8 0.4 - - - -
221A PHE* 4.2 9.3 - - - -
224A TRP 3.9 0.2 + - - -
225A GLY* 1.3 75.0 - - - +
227A GLU* 1.3 64.3 + - - +
228A ASP* 3.1 6.1 + - + +
229A ASP* 2.9 28.4 + - + +
230A GLU* 3.2 19.9 + - - +
233A ARG* 5.0 3.1 + - - +
279A PHE 4.8 3.0 - - - +
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Residues in contact with GLU 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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140A ASN* 4.4 4.0 - - - +
141A ARG* 3.4 34.5 + - - +
142A ALA* 3.0 42.3 + - + +
217A MET* 4.0 4.4 - - + +
218A SER* 5.7 1.9 + - - +
221A PHE* 3.5 46.2 - - + +
223A GLY* 4.2 14.4 + - - -
224A TRP 4.8 1.1 + - - +
225A GLY 3.9 2.8 + - - -
226A ARG* 1.3 73.0 - - - +
228A ASP* 1.3 61.1 + - - +
230A GLU* 3.5 4.7 + - - +
231A PHE* 3.1 25.1 + - - +
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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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141A ARG* 2.8 40.8 + - - -
161A MET* 5.0 1.0 - - - +
196A TYR* 5.9 0.4 - - - +
199A TYR* 5.2 3.3 - - + -
200A VAL* 3.1 29.1 - - + +
201A GLY* 3.7 21.2 - - - +
202A GLY 5.0 0.2 + - - -
217A MET* 3.8 8.1 - - - +
226A ARG* 3.1 3.5 - - + +
227A GLU* 1.3 75.5 - - - +
229A ASP* 1.3 61.8 + - - +
230A GLU 3.2 1.3 - - - -
231A PHE* 2.9 8.6 + - - +
232A TYR 2.8 23.9 + - - -
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Residues in contact with ASP 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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196A TYR* 2.9 26.8 + - - -
198A THR* 3.7 10.3 - - - +
200A VAL* 3.6 14.3 - - - +
226A ARG* 2.9 40.8 + - + +
228A ASP* 1.3 75.4 - - - +
230A GLU* 1.3 66.3 + - - +
232A TYR* 3.3 7.6 + - + +
233A ARG* 3.1 43.1 + - - +
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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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218A SER* 3.9 13.4 + - - -
221A PHE* 3.7 29.2 - - + -
226A ARG 3.2 4.2 + - - +
227A GLU 3.7 9.4 - - - +
228A ASP 3.2 0.6 - - - -
229A ASP* 1.3 79.1 - - - +
231A PHE* 1.3 63.4 + - - +
233A ARG* 3.2 31.2 + - + +
234A ARG* 2.8 62.2 + - - +
281A VAL* 5.8 2.7 - - + -
283A ARG* 4.3 21.8 + - + +
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Residues in contact with PHE 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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161A MET* 4.1 4.9 - - + -
200A VAL* 4.6 0.9 - - + -
204A LEU* 3.6 33.0 - - + -
206A LEU* 3.6 30.5 - - + -
211A TYR* 3.9 12.6 - + - -
214A CYS* 3.9 14.1 - - + -
216A GLY 3.3 33.2 - - - -
217A MET* 3.6 27.4 - - + -
227A GLU 3.1 12.9 + - - +
228A ASP* 2.9 10.6 + - - +
230A GLU* 1.3 77.3 - - - +
232A TYR* 1.3 66.4 + - - +
234A ARG* 2.9 11.8 + - - +
235A ILE* 2.9 37.5 + - + +
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Residues in contact with TYR 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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197A LYS 5.9 0.2 - - - -
198A THR* 3.9 41.8 - - + +
200A VAL* 4.0 18.5 - - + +
228A ASP 2.8 12.2 + - - +
229A ASP* 3.3 11.9 + - + +
231A PHE* 1.3 76.5 - - - +
233A ARG* 1.3 68.5 + - + +
235A ILE* 3.2 22.5 + - + +
236A LYS* 3.2 50.3 + - + +
242A LEU* 3.9 36.1 - - + -
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Residues in contact with ARG 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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221A PHE* 5.6 1.2 - - - -
226A ARG* 5.0 3.2 + - - +
229A ASP* 3.1 39.7 + - - +
230A GLU* 3.2 37.5 + - + +
232A TYR* 1.3 82.4 - - + +
234A ARG* 1.3 55.8 + - + +
236A LYS* 3.6 4.8 + - - +
237A GLY* 2.9 26.3 + - - -
283A ARG* 4.7 21.6 - - - +
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Residues in contact with ARG 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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214A CYS* 3.6 27.3 + - + +
215A ASN* 3.0 30.7 + - - +
216A GLY 3.1 16.6 + - - -
217A MET 3.8 3.6 - - - -
218A SER* 3.7 23.0 + - - +
230A GLU* 2.8 38.8 + - - +
231A PHE* 2.9 14.1 + - + +
233A ARG* 1.3 74.9 - - + +
235A ILE* 1.3 63.3 + - - +
237A GLY* 3.3 2.1 + - - -
238A ALA* 3.0 25.3 + - - +
283A ARG 3.1 21.0 + - - -
284A GLU 4.6 0.4 - - - -
285A GLY 2.7 26.8 + - - -
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Residues in contact with ILE 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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182A PRO* 3.9 30.1 - - + -
200A VAL* 5.2 1.1 - - + -
204A LEU* 4.4 7.4 - - + -
214A CYS* 3.9 21.5 - - - -
231A PHE* 2.9 43.2 + - + +
232A TYR* 3.2 16.4 + - + +
234A ARG* 1.3 75.6 - - - +
236A LYS* 1.3 65.9 + - + +
238A ALA* 3.3 5.4 + - - +
240A LEU* 3.1 50.4 + - + +
241A GLN 4.5 7.4 - - - +
242A LEU* 4.6 13.2 - - + +
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Residues in contact with LYS 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 TYR* 3.2 53.9 + - + +
233A ARG* 4.1 4.7 - - - +
235A ILE* 1.3 76.4 - - + +
237A GLY* 1.3 65.9 + - - +
238A ALA 3.0 1.8 - - - -
239A GLY* 3.0 15.6 + - - -
240A LEU 3.0 23.1 + - - +
241A GLN* 3.6 20.0 - - - +
242A LEU 4.8 2.0 - - - +
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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 ARG 2.9 18.5 + - - -
234A ARG* 3.3 3.3 + - - -
236A LYS* 1.3 76.6 - - - +
238A ALA* 1.3 58.8 + - - +
239A GLY* 3.2 1.1 + - - -
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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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213A LEU* 3.8 46.9 - - + +
214A CYS* 4.3 12.1 - - - -
234A ARG 3.0 16.9 + - - +
235A ILE 3.8 5.4 - - - +
236A LYS 3.0 1.0 - - - -
237A GLY* 1.3 76.9 - - - +
239A GLY* 1.3 57.9 + - - +
240A LEU* 3.3 5.1 + - + -
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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