Contacts of the helix formed by residues 206 - 221 (chain A) in PDB entry 3BRQ
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 ASN 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A TRP* 3.1 47.3 + - + +
204A ALA* 3.6 3.5 - - - +
205A SER* 1.3 78.4 - - - +
207A ASP* 1.3 65.8 + - - +
208A ASP* 3.8 12.0 + - - +
209A MSE 2.9 30.7 + - - +
210A ALA* 3.0 18.4 + - - +
232A GLY* 4.2 0.9 - - - -
233A PHE 3.2 13.5 - - - +
234A ASP* 3.3 21.5 + - - +
701A FRU 4.4 11.7 - - - +
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Residues in contact with ASP 207 (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 ASN* 1.3 73.0 - - - +
208A ASP* 1.3 64.4 + - - +
210A ALA* 2.8 5.0 + - - +
211A ILE* 2.8 27.2 + - - +
232A GLY* 3.3 4.9 - - - -
233A PHE 2.9 24.2 + - - +
234A ASP* 3.9 1.7 + - - +
235A ASP* 2.9 7.5 + - - -
236A ILE* 2.8 53.5 + - + +
239A ALA* 4.3 1.0 - - - +
246A LEU* 3.6 21.9 - - + +
248A SER* 2.5 25.9 + - - -
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TRP 3.5 21.3 - - - +
182A PRO* 3.3 28.5 - - + +
206A ASN* 3.3 8.4 + - - +
207A ASP* 1.3 77.3 - - - +
209A MSE 1.3 61.3 + - - +
211A ILE* 3.3 3.7 + - - +
212A GLY 3.1 17.3 + - - -
234A ASP* 5.3 0.6 + - - -
236A ILE* 4.1 16.5 - - - +
701A FRU 6.1 1.2 - - - -
237B ALA* 5.6 2.4 - - - +
238B ILE* 3.5 23.4 - - - +
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Residues in contact with MSE 209 (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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143A LEU* 3.7 24.7 - - + +
144A THR 3.2 23.8 - - - +
145A GLY* 4.3 1.8 - - - -
178A GLY* 3.5 17.5 - - - -
180A TRP* 3.5 24.2 - - - -
181A THR 3.3 19.7 - - - +
184A SER* 3.4 26.0 - - - +
185A GLY* 3.4 10.3 - - - -
188A GLY* 6.0 0.2 - - - -
204A ALA* 4.0 10.1 - - + -
205A SER 4.9 3.1 - - - -
206A ASN* 2.9 26.3 + - - +
208A ASP* 1.3 72.3 - - - +
210A ALA* 1.3 55.1 + - - +
212A GLY 3.2 1.0 + - - -
213A ALA* 2.8 35.0 + - - +
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Residues in contact with ALA 210 (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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204A ALA* 3.4 17.8 - - + +
206A ASN 3.0 13.2 + - - +
207A ASP* 2.8 11.3 + - - +
209A MSE 1.3 75.9 - - - +
211A ILE* 1.3 57.8 + - - +
213A ALA* 3.2 6.5 + - - +
214A MSE 2.9 35.2 + - - +
230A VAL* 4.0 8.2 - - + +
232A GLY* 4.0 5.2 - - - -
246A LEU* 3.7 28.5 - - + -
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Residues in contact with ILE 211 (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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207A ASP 2.8 20.3 + - - +
208A ASP 3.7 6.1 - - - +
210A ALA* 1.3 70.3 - - - +
212A GLY* 1.3 64.6 + - - +
214A MSE 3.4 12.7 + - + +
215A LYS* 3.1 21.1 + - - +
236A ILE* 4.0 14.8 - - + -
238A ILE* 3.4 31.9 - - + -
242A THR* 3.9 22.0 - - + -
246A LEU* 4.1 13.9 - - + -
238B ILE* 4.3 21.1 - - + -
241B TYR* 3.9 27.4 - - + +
242B THR* 4.9 3.4 - - + +
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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
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182A PRO* 3.3 23.3 - - - +
186A ALA* 3.4 16.7 - - - +
208A ASP 3.1 11.5 + - - -
209A MSE 3.2 0.8 + - - -
211A ILE* 1.3 77.6 - - - +
213A ALA* 1.3 62.2 + - - +
215A LYS* 3.3 3.5 + - - +
216A ALA 3.1 17.7 + - - -
241B TYR* 4.1 18.4 - - - -
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Residues in contact with ALA 213 (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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143A LEU* 4.0 10.5 - - + -
185A GLY 3.6 13.8 - - - +
186A ALA* 4.4 0.7 - - - +
189A VAL* 3.5 22.1 - - + +
202A LEU* 4.1 12.8 - - + -
209A MSE 2.8 17.2 + - - +
210A ALA* 3.4 7.0 - - - +
211A ILE 3.2 0.2 - - - -
212A GLY* 1.3 76.0 - - - +
214A MSE 1.3 57.9 + - - +
216A ALA* 3.2 3.3 + - - +
217A LEU* 3.0 35.6 + - + +
230A VAL* 5.2 1.6 - - + -
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Residues in contact with MSE 214 (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 ALA 2.9 13.1 + - - +
211A ILE* 3.9 23.1 - - + +
212A GLY 3.4 0.2 - - - -
213A ALA* 1.3 76.1 - - - +
215A LYS* 1.3 58.2 + - - +
217A LEU* 3.5 7.8 + - - +
218A HIS* 2.9 29.5 + - - +
224A VAL* 4.3 9.8 - - + +
230A VAL* 3.9 21.8 - - + -
242A THR* 3.8 28.9 - - - +
243A VAL 5.2 4.0 - - - +
244A PRO* 3.9 36.6 - - + +
246A LEU* 4.0 20.9 - - + -
288A SER* 4.1 15.3 - - - -
243B VAL* 5.2 3.7 - - + +
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Residues in contact with LYS 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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186A ALA* 5.8 0.9 - - + -
211A ILE 3.1 8.1 + - - +
212A GLY 3.4 11.0 - - - +
214A MSE 1.3 74.8 - - - +
216A ALA* 1.3 58.2 + - - +
218A HIS* 3.3 13.9 + - + +
219A GLU* 2.9 56.7 + - + +
240B PRO 3.6 14.8 - - - -
241B TYR* 3.4 44.4 - - + +
242B THR 3.1 20.9 + - - +
243B VAL* 4.2 15.9 - - + +
244B PRO* 4.6 1.8 - - - +
245B ALA* 4.0 13.1 - - - +
287B ASP* 5.1 5.1 + - - -
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Residues in contact with ALA 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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186A ALA* 3.7 30.7 - - + +
189A VAL* 3.7 16.6 - - + -
190A GLU* 4.4 13.0 - - + +
212A GLY 3.1 13.4 + - - +
213A ALA 3.2 3.3 + - - +
215A LYS* 1.3 76.0 - - - +
217A LEU* 1.3 63.3 + - - +
219A GLU* 3.4 12.2 + - - +
220A ARG* 3.1 27.9 + - + +
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Residues in contact with LEU 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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189A VAL* 4.0 24.5 - - + -
193A LEU* 4.7 9.6 - - + -
199A PHE* 5.1 4.5 - - + -
202A LEU* 5.2 1.8 - - + -
213A ALA* 3.0 23.0 + - + +
214A MSE 3.8 4.9 - - - +
215A LYS 3.3 0.4 - - - -
216A ALA* 1.3 73.3 - - - +
218A HIS* 1.3 61.7 + - - +
220A ARG* 3.2 4.9 + - - -
221A GLY 3.0 4.5 + - - -
222A VAL* 2.7 67.0 + - + +
224A VAL* 3.7 22.2 - - + -
228A VAL* 4.1 17.3 - - + -
230A VAL* 3.9 20.0 - - + -
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Residues in contact with HIS 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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214A MSE 2.9 17.3 + - - +
215A LYS* 3.5 16.4 - - - +
217A LEU* 1.3 77.3 - - - +
219A GLU* 1.3 59.1 + - + +
221A GLY* 2.8 23.5 + - - +
222A VAL 4.0 6.2 + - - +
224A VAL* 5.4 0.6 - - - +
243B VAL* 4.0 36.2 - - + +
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Residues in contact with GLU 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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186A ALA* 5.9 1.0 - - - +
190A GLU* 4.7 7.4 - - - +
215A LYS* 2.9 50.9 + - + +
216A ALA* 3.6 14.9 - - - +
217A LEU 3.3 0.2 - - - -
218A HIS* 1.3 79.0 - - + +
220A ARG* 1.3 70.9 + - - +
221A GLY* 3.3 1.0 + - - -
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Residues in contact with ARG 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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190A GLU* 5.2 16.9 - - + +
193A LEU* 3.4 33.1 - - + +
216A ALA* 3.1 18.8 + - + +
217A LEU 3.2 4.5 + - - +
219A GLU* 1.3 83.1 + - - +
221A GLY* 1.3 64.0 + - - +
222A VAL* 4.2 7.8 - - + +
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Residues in contact with GLY 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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218A HIS 2.8 17.3 + - - -
219A GLU 3.1 2.4 + - - -
220A ARG* 1.3 80.0 - - - +
222A VAL* 1.3 62.7 + - - +
223A ALA 4.0 0.4 + - - -
227A GLN* 3.9 6.4 - - - +
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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