Contacts of the helix formed by residues 203 - 222 (chain A) in PDB entry 5JNQ
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 ILE 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.4 33.7 - - + +
76A ILE* 4.4 2.2 - - - +
79A VAL* 3.8 13.9 - - + -
196A ALA* 4.0 11.4 - - + -
201A MET* 3.7 5.3 - - + -
202A GLY* 1.3 79.0 - - - +
204A SER* 1.3 66.2 + - - +
205A PRO* 3.4 4.0 - - - -
206A ILE* 3.2 15.1 - - + +
207A THR* 3.1 30.8 + - + +
244A SER* 3.8 28.5 - - - +
247A MET* 4.3 9.6 - - + -
248A MET* 3.6 37.5 - - + -
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.3 9.5 - - - +
5A THR* 2.7 34.9 + - - +
73A TYR* 4.4 2.9 - - - -
193A THR 4.2 2.0 - - - -
196A ALA* 3.7 20.6 + - - +
197A ILE* 3.7 26.2 - - - +
201A MET 5.3 1.1 + - - -
202A GLY* 3.7 0.6 - - - -
203A ILE* 1.3 75.3 - - - +
205A PRO* 1.4 65.4 - - - +
207A THR* 3.0 9.1 + - - -
208A GLY 2.9 25.5 + - - -
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Residues in contact with PRO 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU 5.3 0.2 - - - +
5A THR* 4.7 7.0 - - + +
8A ALA* 3.7 14.7 - - + +
65A THR* 5.1 0.5 - - - +
66A SER* 5.8 1.7 - - - -
69A TYR* 3.6 32.8 - - + -
73A TYR* 3.7 48.5 - - + -
76A ILE* 3.9 11.0 - - + -
203A ILE* 3.5 4.9 - - - -
204A SER* 1.4 94.7 - - - +
206A ILE* 1.4 51.1 + - - +
209A ALA* 2.8 32.6 + - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.8 14.1 - - + -
66A SER* 3.8 10.5 - - - -
76A ILE* 3.8 30.8 - - + +
79A VAL* 4.0 27.4 - - + -
80A LEU* 3.8 48.5 - - + +
83A THR* 5.5 2.7 - - + -
203A ILE* 3.2 22.0 + - + +
205A PRO* 1.4 74.1 - - - +
207A THR* 1.4 61.6 + - + +
208A GLY 3.2 1.3 - - - -
209A ALA* 3.2 5.1 + - - +
210A VAL* 2.9 34.2 + - + +
240A PHE* 4.5 2.0 - - + -
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Residues in contact with THR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 3.7 10.6 - - - +
192A LEU* 3.9 14.3 - - + +
193A THR* 2.8 28.3 + - - -
203A ILE* 3.1 35.2 + - + +
204A SER* 3.0 19.4 + - - -
206A ILE* 1.4 75.6 - - + +
208A GLY* 1.3 58.2 + - - +
210A VAL* 3.5 4.7 + - - +
211A VAL* 3.3 23.2 + - - +
240A PHE* 3.7 25.8 - - + -
244A SER* 3.8 4.3 - - - +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 4.6 3.1 - - - -
9A ILE* 3.2 32.9 - - - +
193A THR* 3.2 9.8 + - - -
204A SER 2.9 16.4 + - - -
205A PRO 3.7 1.6 - - - -
207A THR* 1.3 75.5 + - - +
209A ALA* 1.4 56.9 + - - +
211A VAL* 3.1 5.2 + - - -
212A GLY 3.0 24.4 + - - -
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 4.2 4.7 - - - +
12A ALA* 3.3 12.4 - - + +
62A ILE* 4.3 17.3 - - + +
65A THR* 4.1 24.9 - - + -
66A SER 5.0 2.5 - - - +
205A PRO 2.8 21.9 + - - +
206A ILE* 3.2 11.2 + - + +
208A GLY* 1.4 72.2 - - - +
210A VAL* 1.4 52.8 + - - +
212A GLY 3.4 0.2 + - - -
213A SER* 2.8 37.8 + - - -
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.7 30.7 - - + -
83A THR* 6.0 1.1 - - + -
185A THR* 4.7 0.7 - - + -
189A ALA* 3.9 6.3 - - + -
206A ILE* 2.9 18.8 + - + +
207A THR 3.6 8.3 - - - +
208A GLY 3.2 0.2 - - - -
209A ALA* 1.4 72.9 - - - +
211A VAL* 1.4 58.3 + - - +
214A LEU* 2.9 51.3 + - + +
237A LEU* 3.9 13.5 - - + -
240A PHE* 3.7 45.1 - - + -
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.3 14.8 - - + -
186A ILE* 4.0 12.9 - - + +
189A ALA* 3.6 8.5 - - + +
190A THR* 3.6 43.7 - - - +
193A THR* 4.2 4.9 - - - +
207A THR 3.3 16.9 + - - +
208A GLY* 3.1 10.0 + - - +
210A VAL* 1.4 74.4 - - - +
212A GLY* 1.3 58.3 + - - +
214A LEU* 3.8 3.5 - - - +
215A LEU* 3.0 51.2 + - + +
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.2 33.8 - - - +
12A ALA* 4.2 0.2 - - - -
13A PHE* 3.2 22.4 - - - +
208A GLY 3.0 11.0 + - - -
209A ALA 3.8 2.2 - - - -
211A VAL* 1.3 76.0 - - - +
213A SER* 1.3 61.1 + - - +
215A LEU* 3.3 3.7 + - - +
216A GLY 3.2 17.8 + - - -
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.6 12.5 - - - +
16A SER* 2.7 24.5 + - - -
58A ILE* 2.8 41.5 + - - +
61A SER* 3.4 13.5 - - - -
62A ILE* 3.9 12.3 - - - -
209A ALA 2.8 22.2 + - - -
210A VAL 3.9 2.7 - - - -
212A GLY* 1.3 69.9 - - - +
214A LEU* 1.3 63.0 + - - +
216A GLY 3.4 0.2 + - - -
217A PHE* 3.2 8.3 + - - +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.9 26.9 - - + -
182A THR* 3.3 30.0 - - + +
185A THR* 3.8 31.0 - - + -
186A ILE* 3.5 25.6 - - + +
210A VAL* 2.9 37.0 + - + +
213A SER* 1.3 73.6 - - - +
215A LEU* 1.3 60.2 + - - +
217A PHE* 3.7 2.0 - - + +
218A LEU* 2.9 26.5 + - - +
237A LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 215 (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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9A ILE* 4.6 10.8 - - + -
13A PHE* 3.7 16.4 - - + -
186A ILE* 4.1 26.7 - - + -
211A VAL* 3.0 39.6 + - + +
212A GLY* 3.3 6.0 + - - +
214A LEU* 1.3 75.8 - - - +
216A GLY* 1.3 60.5 + - - +
218A LEU* 3.7 10.6 + - + +
219A LEU* 3.6 21.1 + - - +
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Residues in contact with GLY 216 (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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13A PHE* 3.4 18.3 - - - -
16A SER* 3.7 20.2 - - - -
17A ALA 4.0 8.7 - - - -
212A GLY 3.2 10.3 + - - -
213A SER 3.4 0.4 + - - -
214A LEU 3.3 0.2 - - - -
215A LEU* 1.3 76.1 - - - +
217A PHE* 1.4 60.1 + - - +
219A LEU* 3.4 23.2 + - - +
220A PHE* 3.5 11.3 - - - -
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Residues in contact with PHE 217 (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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16A SER* 3.3 5.8 + - - +
20A CYS* 4.2 18.8 - - - -
54A GLY* 3.4 25.4 - - - -
57A ILE* 4.9 3.6 - - + -
58A ILE* 3.7 33.0 - - + -
182A THR* 3.8 15.0 - - + -
213A SER 3.2 16.1 + - - +
214A LEU* 3.7 5.6 - - - +
216A GLY* 1.4 73.3 - - - +
218A LEU* 1.4 51.1 + - - +
220A PHE* 3.0 9.6 + - + +
221A ASN* 2.9 61.1 + - + -
227A VAL* 4.2 15.9 - - + -
228A PHE* 3.9 4.3 - - - -
229A MET* 3.9 34.5 - - + -
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Residues in contact with LEU 218 (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 GLY* 3.8 17.0 - - - +
182A THR* 3.8 22.9 - - + +
183A SER* 3.6 25.4 - - - +
186A ILE* 3.7 19.3 - - + -
214A LEU 2.9 19.6 + - - +
215A LEU* 3.8 13.5 - - + +
216A GLY 3.4 0.4 - - - -
217A PHE* 1.4 72.6 - - - +
219A LEU* 1.4 64.6 + - - +
221A ASN* 4.2 3.8 - - - +
222A VAL* 3.1 37.1 + - + +
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Residues in contact with LEU 219 (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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13A PHE* 3.8 29.4 - - + -
17A ALA* 3.9 15.9 - - + -
215A LEU 3.6 8.2 + - - +
216A GLY 3.4 16.6 + - - +
217A PHE 3.2 0.4 - - - -
218A LEU* 1.4 77.1 - - - +
220A PHE* 1.4 72.4 + - + +
221A ASN 4.0 0.2 + - - -
222A VAL* 4.3 12.2 - - - +
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Residues in contact with PHE 220 (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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17A ALA* 3.6 29.4 - - + -
20A CYS* 3.5 31.4 - - + -
21A PRO* 3.8 22.4 - - + -
24A ILE* 5.3 4.9 - - + -
216A GLY 3.5 19.3 - - - -
217A PHE* 3.0 6.7 + - + +
219A LEU* 1.4 87.0 - - + +
221A ASN* 1.3 59.1 + - - +
222A VAL 3.7 2.6 - - - +
224A PRO 4.8 0.2 - - - +
225A ALA* 4.0 0.2 - - - -
226A LYS* 2.8 49.1 + - + +
227A VAL* 3.7 10.4 + - + -
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Residues in contact with ASN 221 (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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175A ASP* 5.7 0.7 + - - +
178A ASP* 3.5 6.4 - - - +
179A GLY* 2.8 32.8 + - - -
182A THR* 3.7 7.2 + - - +
217A PHE* 2.9 48.2 + - + +
218A LEU* 3.3 4.4 + - - -
220A PHE* 1.3 77.4 - - - +
222A VAL* 1.3 66.9 + - - +
225A ALA* 3.2 16.4 - - - +
227A VAL 3.0 25.9 + - - -
228A PHE* 4.2 3.2 - - - +
229A MET* 4.7 2.4 - - - +
401A TUM 3.6 17.1 + - - +
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP 5.6 0.7 - - - +
179A GLY* 4.4 11.1 - - - +
183A SER* 5.8 0.4 - - - +
218A LEU* 3.1 34.9 + - + +
219A LEU* 4.3 10.3 - - - +
220A PHE 4.5 2.1 - - - +
221A ASN* 1.3 80.6 - - - +
223A TYR* 1.3 73.3 + - - +
224A PRO* 3.2 12.6 - - - +
225A ALA* 3.6 0.3 - - - -
304A VAL* 6.1 3.8 - - + -
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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
------------------------------------------------------------
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