Contacts of the helix formed by residues 224 - 241 (chain A) in PDB entry 4QNR
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 GLY 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.5 31.0 - - - +
39A GLY* 3.6 4.5 - - - -
223A PRO* 1.3 76.1 - - - +
225A ASN* 1.3 71.3 + - - +
226A ILE 3.4 1.0 + - - -
227A ARG* 3.5 6.6 + - - +
228A GLU* 2.9 33.9 + - - -
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Residues in contact with ASN 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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37A GLU* 3.2 30.7 + - - +
38A ARG 2.9 23.3 + - - +
39A GLY 3.5 7.6 - - - +
40A THR* 3.6 11.0 - - + -
178A PRO* 3.4 7.3 - - - +
179A LEU* 2.8 40.0 + - + +
180A ARG* 4.6 0.7 + - - -
222A TRP* 2.9 26.6 + - - +
223A PRO 3.4 5.5 + - - -
224A GLY* 1.3 77.6 - - - +
226A ILE* 1.3 61.1 + - + +
228A GLU* 3.6 1.3 + - - +
229A LEU* 2.9 28.1 + - - +
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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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39A GLY 2.9 14.3 + - - +
40A THR* 4.7 6.5 - - + -
179A LEU* 3.6 29.4 - - + +
182A ARG* 4.7 9.4 - - - +
189A MET* 3.5 33.9 - - + -
193A PHE* 3.8 18.2 - - + -
225A ASN* 1.3 77.8 - - + +
227A ARG* 1.3 66.7 + - - +
229A LEU* 3.3 3.6 + - - +
230A LYS* 3.0 22.9 + - - +
301A ATP 3.4 46.9 - - + +
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Residues in contact with ARG 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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38A ARG* 4.4 7.9 - - - +
39A GLY* 3.5 21.6 + - - +
224A GLY* 3.5 6.4 + - - +
225A ASN 3.4 0.4 - - - -
226A ILE* 1.3 78.1 - - - +
228A GLU* 1.3 61.2 + - - +
230A LYS* 3.5 6.8 + - - +
231A ASN* 3.2 22.2 + - + +
301A ATP 3.1 86.0 + - + +
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Residues in contact with GLU 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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38A ARG* 5.6 1.3 - - - -
220A TYR* 2.6 33.8 + - - -
222A TRP* 3.5 11.6 - - + -
223A PRO* 3.3 14.7 - - - +
224A GLY* 2.9 41.2 + - - -
225A ASN 3.2 1.9 + - - +
226A ILE 3.2 0.2 - - - -
227A ARG* 1.3 78.8 - - - +
229A LEU* 1.3 60.5 + - - +
231A ASN* 3.2 5.8 + - + +
232A VAL* 2.9 41.4 + - + +
252A ILE* 4.6 6.2 - - - +
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Residues in contact with LEU 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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179A LEU* 3.9 21.1 - - + -
186A ILE* 3.9 16.8 - - + +
189A MET* 3.6 34.5 - - + -
190A ALA* 4.0 7.4 - - + +
193A PHE* 4.1 9.6 - - + -
217A LEU* 4.1 6.3 - - + -
222A TRP* 3.4 38.7 - - + -
225A ASN 2.9 16.3 + - - +
226A ILE* 3.3 5.6 + - + +
228A GLU* 1.3 75.1 - - - +
230A LYS* 1.3 63.5 + - - +
232A VAL* 3.4 0.5 + - - +
233A VAL* 2.9 44.5 + - + +
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Residues in contact with LYS 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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193A PHE* 3.6 44.4 - - + -
226A ILE* 3.0 17.6 + - + +
227A ARG* 3.7 6.5 - - - +
229A LEU* 1.3 77.5 - - - +
231A ASN* 1.3 57.6 + - - +
233A VAL* 3.9 1.0 - - - +
234A GLU* 2.9 70.4 + - - +
301A ATP 5.0 16.4 - - + +
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Residues in contact with ASN 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 ARG* 3.2 13.0 + - + +
228A GLU* 3.2 7.4 + - + +
230A LYS* 1.3 79.7 - - - +
232A VAL* 1.3 63.9 + - + +
234A GLU* 3.9 9.9 - - - +
235A ARG* 3.0 49.1 + - - +
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Residues in contact with VAL 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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217A LEU* 4.9 1.6 - - + -
222A TRP* 3.8 26.0 - - + -
228A GLU* 2.9 29.3 + - + +
229A LEU 3.9 2.9 - - - +
231A ASN* 1.3 76.6 - - + +
233A VAL* 1.3 57.2 + - - +
235A ARG* 3.5 23.7 + - - +
236A SER* 2.7 36.6 + - - -
250A ILE* 3.6 30.3 - - + -
251A ILE 3.7 11.4 - - - +
252A ILE* 3.9 16.4 - - + +
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Residues in contact with VAL 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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190A ALA* 3.5 24.9 - - + +
193A PHE* 3.9 6.7 - - + -
194A ALA* 3.5 39.5 - - + +
209A PHE* 4.5 9.2 - - + -
217A LEU* 4.5 10.5 - - + -
229A LEU* 2.9 40.9 + - + +
230A LYS 4.0 2.5 - - - +
232A VAL* 1.3 74.5 - - + +
234A GLU* 1.3 62.0 + - - +
236A SER* 3.2 5.6 + - - -
237A VAL* 2.9 30.2 + - + +
250A ILE* 5.6 2.2 - - + -
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Residues in contact with GLU 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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193A PHE* 4.5 10.2 - - + +
196A GLN* 5.4 4.7 - - - +
197A MET* 3.6 49.5 + - + +
200A GLU* 4.7 7.3 - - - +
230A LYS* 2.9 61.1 + - + +
231A ASN* 3.9 9.6 - - - +
233A VAL* 1.3 77.1 - - - +
235A ARG* 1.3 62.8 + - - +
237A VAL 3.4 0.2 + - - -
238A TYR* 3.0 24.1 + - - +
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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 ASN* 3.0 44.2 + - - +
232A VAL* 3.6 18.2 - - - +
234A GLU* 1.3 76.4 - - - +
236A SER* 1.3 57.8 + - - +
238A TYR* 3.3 10.3 + - + +
239A ARG* 2.9 48.2 + - + +
251A ILE* 2.9 47.6 + - + +
252A ILE 3.2 17.8 + - - -
254A PRO* 3.7 33.8 - - - +
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Residues in contact with SER 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 VAL* 2.7 25.1 + - - +
233A VAL* 3.7 5.2 - - - -
235A ARG* 1.3 76.1 - - - +
237A VAL* 1.3 63.0 + - - +
239A ARG* 3.5 1.8 + - - +
240A HIS* 3.0 25.5 + - - +
247A LEU* 4.1 13.9 - - - +
249A ASP 3.7 18.4 - - - +
250A ILE* 3.5 10.6 - - - +
251A ILE* 2.9 32.7 + - - -
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Residues in contact with VAL 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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194A ALA* 3.8 32.1 - - + +
197A MET* 3.8 18.6 - - + -
198A CYS* 4.0 23.8 - - - +
201A ILE* 4.1 11.9 - - + +
203A LEU* 4.4 4.3 - - + +
206A PHE* 4.3 5.2 - - + -
233A VAL* 2.9 20.7 + - + +
234A GLU 3.8 3.6 - - - +
236A SER* 1.3 75.0 - - - +
238A TYR* 1.3 59.2 + - - +
240A HIS* 3.3 4.7 + - + +
241A GLY* 2.8 27.7 + - - -
247A LEU* 3.8 18.6 - - + -
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A MET* 3.9 16.1 - - + +
201A ILE* 4.1 21.2 - - + +
234A GLU 3.0 17.7 + - - +
235A ARG* 3.6 9.0 - - + +
237A VAL* 1.3 78.9 - - - +
239A ARG* 1.3 81.7 + - + +
240A HIS 3.3 0.7 + - - -
241A GLY* 3.4 12.0 + - - -
303A GOL 3.8 35.3 + - - -
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Residues in contact with ARG 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* 2.9 38.8 + - + +
236A SER* 4.0 5.2 - - - +
238A TYR* 1.3 92.1 - - + +
240A HIS* 1.3 61.7 + - - +
251A ILE* 3.8 43.5 - - + +
254A PRO* 4.1 19.8 + - - +
256A LYS 5.0 7.1 + - - -
303A GOL 3.1 29.8 - - - +
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Residues in contact with HIS 240 (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 LEU* 6.0 0.9 - - + -
207A PRO* 4.3 4.7 - - + -
236A SER 3.0 18.4 + - - +
237A VAL* 3.5 7.4 - - + +
239A ARG* 1.3 79.5 - - - +
241A GLY* 1.3 61.6 + - - +
242A THR* 3.3 35.7 + - + +
245A TYR* 2.7 50.9 + + - -
246A PRO 3.2 22.4 + - - -
247A LEU* 3.8 22.8 - - + -
248A ASP* 4.6 3.9 + - + -
249A ASP* 5.7 1.8 + - - +
303A GOL 4.3 4.4 - - - -
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Residues in contact with GLY 241 (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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201A ILE* 4.8 5.2 - - - -
203A LEU* 4.0 16.8 - - - +
237A VAL 2.8 16.9 + - - -
238A TYR 3.4 13.7 + - - -
240A HIS* 1.3 73.6 - - - +
242A THR* 1.3 59.8 + - - +
303A GOL 3.9 17.2 + - - -
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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