Contacts of the helix formed by residues 223 - 237 (chain A) in PDB entry 4JOQ
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ARG* 5.3 0.2 + - - -
197A TRP* 3.6 29.2 - - + +
221A ALA 3.1 1.1 + - - +
222A ALA* 1.3 80.3 - - - +
224A ASP* 1.3 61.9 + - - +
225A ASP* 3.3 14.8 + - - +
226A MSE 3.2 35.8 + - + +
227A ALA* 2.8 29.3 + - - +
247A GLY* 3.2 4.5 - - - -
248A GLY 3.4 16.3 - - - +
249A ALA* 4.8 3.1 - - - +
319A PHE* 5.9 1.9 - - - -
401A ACT 3.6 22.3 - - - +
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Residues in contact with ASP 224 (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* 1.3 72.4 + - - +
225A ASP* 1.3 65.4 + - - +
227A ALA* 3.2 6.6 + - - +
228A ILE* 3.0 26.0 + - - +
247A GLY* 3.6 4.7 - - - -
248A GLY 2.9 28.4 + - - +
250A GLY* 2.9 10.9 + - - -
251A MSE 2.6 51.2 + - + +
254A ILE* 3.8 18.8 - - + +
268A ASN* 2.8 24.4 + - - -
319A PHE* 5.2 2.0 - - + -
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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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197A TRP 4.2 8.7 - - - +
198A ASN* 3.9 3.8 - - - -
199A ARG* 2.6 79.6 + - - +
223A ASP* 3.3 11.8 + - - +
224A ASP* 1.3 76.0 - - - +
226A MSE 1.3 62.1 + - - +
228A ILE* 3.3 9.2 + - - +
229A GLY 3.3 9.0 + - - -
251A MSE 3.5 18.3 - - + +
319A PHE* 6.0 0.8 - - + -
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Residues in contact with MSE 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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163A LEU* 3.7 15.0 - - + +
164A ARG 3.2 38.1 - - - +
165A GLY 3.9 0.4 - - - +
195A GLY* 3.5 13.7 - - - -
197A TRP* 3.5 44.9 - - + +
198A ASN 3.9 6.7 - - - +
202A ALA* 3.5 19.9 - - + +
221A ALA* 3.1 35.9 - - - +
222A ALA* 4.3 4.0 - - + -
223A ASP* 3.2 18.5 + - + +
224A ASP 3.2 0.2 - - - -
225A ASP* 1.3 73.5 - - - +
227A ALA* 1.3 59.1 + - - +
229A GLY 3.3 1.9 + - - -
230A ALA* 2.9 27.7 + - - +
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Residues in contact with ALA 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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221A ALA* 3.6 20.8 - - + +
223A ASP 2.8 18.4 + - - +
224A ASP* 3.2 8.3 + - - +
226A MSE 1.3 77.7 - - - +
228A ILE* 1.3 57.2 + - - +
230A ALA* 3.5 3.1 + - - +
231A MSE 2.8 44.0 + - + +
245A VAL* 4.0 12.6 - - + -
247A GLY* 4.1 10.3 - - - -
254A ILE* 5.5 2.2 - - + -
265A LEU* 5.3 3.6 - - + -
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Residues in contact with ILE 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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199A ARG* 3.9 33.4 - - - +
224A ASP 3.0 20.1 + - - +
225A ASP 3.3 5.4 + - - +
226A MSE 3.3 0.2 - - - -
227A ALA* 1.3 73.5 - - - +
229A GLY* 1.3 62.9 + - - +
231A MSE 3.2 11.9 + - + +
232A GLU* 3.1 27.0 + - + +
251A MSE 3.7 23.8 - - - -
253A GLU* 3.7 33.4 - - + +
254A ILE* 4.1 17.0 - - + -
257A ARG* 5.9 1.1 - - - +
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Residues in contact with GLY 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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199A ARG* 3.6 26.0 - - - +
203A PHE* 3.5 15.6 - - - -
225A ASP 3.3 5.7 + - - -
226A MSE 3.3 5.2 + - - -
228A ILE* 1.3 74.1 - - - +
230A ALA* 1.3 67.3 + - - +
232A GLU* 3.1 29.3 - - - +
233A ALA 3.2 5.7 + - - -
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Residues in contact with ALA 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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163A LEU* 4.7 12.6 - - + -
202A ALA 4.3 0.2 + - - -
203A PHE 4.3 3.0 - - - +
206A MSE 3.8 36.3 - - + -
219A VAL* 4.9 3.4 - - + -
221A ALA* 4.8 4.0 - - + -
226A MSE 2.9 17.5 + - - +
227A ALA* 3.7 9.0 - - - +
229A GLY* 1.3 73.6 - - - +
231A MSE 1.3 61.0 + - - +
233A ALA* 3.1 5.2 + - - +
234A ILE* 2.9 31.9 + - + +
245A VAL* 5.1 2.9 - - + -
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Residues in contact with MSE 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 ALA* 2.8 34.1 + - + +
228A ILE* 3.2 14.3 + - + +
230A ALA* 1.3 72.6 - - - +
232A GLU* 1.3 57.4 + - - +
234A ILE* 3.5 6.8 + - - +
235A ALA* 2.9 30.0 + - - +
245A VAL* 4.1 15.5 - - + -
254A ILE* 4.0 19.1 - - + -
257A ARG* 3.6 27.6 - - - +
264A GLN* 3.4 41.2 + - - +
265A LEU* 3.9 21.5 - - + -
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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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199A ARG* 4.1 16.6 - - - +
200A ASP* 5.3 3.8 - - - +
203A PHE* 3.6 23.0 - - + +
228A ILE* 3.1 15.5 + - + +
229A GLY* 3.1 26.1 - - - +
231A MSE 1.3 74.1 - - - +
233A ALA* 1.3 59.6 + - - +
235A ALA* 3.2 6.5 + - - +
236A GLN* 2.9 41.3 + - + +
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Residues in contact with ALA 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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203A PHE* 3.5 42.4 - - + +
206A MSE 3.9 7.9 - - + -
207A GLN* 3.7 18.8 - - + +
210A LEU* 3.3 11.6 - - + +
229A GLY 3.2 4.8 + - - +
230A ALA 3.1 8.8 + - - +
232A GLU* 1.3 75.6 - - - +
234A ILE* 1.3 57.9 + - - +
236A GLN* 3.4 4.3 + - - +
237A ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 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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206A MSE 4.1 18.4 - - + -
210A LEU* 3.6 11.4 - - + -
219A VAL* 4.6 1.6 - - + -
230A ALA* 2.9 25.0 + - + +
231A MSE 3.7 9.0 - - - +
233A ALA* 1.3 77.2 - - - +
235A ALA* 1.3 60.6 + - - +
237A ALA* 3.4 3.6 + - - +
238A GLY 3.2 3.6 + - - -
239A ARG* 3.1 59.7 + - + +
240A THR* 3.6 9.2 - - - +
243A MSE 3.8 29.2 - - + -
245A VAL* 4.0 24.9 - - + -
264A GLN* 4.7 5.4 - - - +
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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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231A MSE 2.9 20.8 + - - +
232A GLU* 3.7 7.0 - - - +
234A ILE* 1.3 70.2 - - - +
236A GLN* 1.3 61.2 + - + +
238A GLY* 3.0 17.7 + - - +
240A THR* 3.4 18.6 - - - +
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Residues in contact with GLN 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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203A PHE* 3.5 35.8 - - - -
207A GLN* 4.5 6.2 + - - -
232A GLU* 2.9 25.4 + - + +
233A ALA* 3.8 4.9 - - - +
234A ILE 3.3 0.2 - - - -
235A ALA* 1.3 76.4 - - + +
237A ALA* 1.3 60.8 + - - +
238A GLY 3.2 1.1 + - - -
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Residues in contact with ALA 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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210A LEU* 3.9 20.2 - - + -
233A ALA 3.0 17.3 + - - +
234A ILE 3.5 6.1 - - - +
235A ALA 3.3 0.2 - - - -
236A GLN* 1.3 75.7 - - - +
238A GLY* 1.3 60.8 + - - +
239A ARG* 3.3 24.6 + - - +
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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