Contacts of the helix formed by residues 207 - 219 (chain C) in PDB entry 3BQM
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 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C PHE* 4.0 4.5 - - - -
174C SER 2.8 16.1 + - - +
175C THR* 2.9 36.0 + - - +
177C TYR* 3.4 15.5 + - + +
205C LEU* 4.6 6.2 - - - +
206C THR* 1.3 69.5 - - - +
208C THR* 1.3 58.5 + - - +
210C GLY 3.4 0.7 + - - -
211C ALA* 3.0 27.9 + - - +
243C THR* 3.0 19.7 + - - +
244C ASP* 3.3 33.4 + - - +
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Residues in contact with THR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 5.7 0.2 - - + -
173C PHE* 3.5 28.4 - - + -
206C THR* 3.0 20.5 + - - +
207C ASN* 1.3 68.3 - - - +
209C PHE* 1.3 66.2 + - - +
211C ALA* 3.6 1.5 - - + +
212C ILE* 3.0 38.8 + - + +
236C ILE* 4.5 11.0 - - + -
238C THR* 4.7 4.8 + - + +
240C GLY 4.9 1.0 + - - -
242C ALA* 3.6 19.3 + - - +
244C ASP* 3.2 2.2 + - - -
258C ILE* 5.1 2.0 - - + -
277C PHE* 4.0 23.7 - - + -
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Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C THR* 1.3 78.6 - - - +
210C GLY* 1.3 64.7 + - - +
212C ILE* 3.3 2.3 + - - +
213C ASN* 2.9 33.8 + - - +
242C ALA* 4.3 3.1 - - + -
244C ASP* 3.0 22.4 + - - +
245C SER* 3.6 32.8 - - - +
246C GLY* 3.3 22.9 - - - -
247C ASN* 3.5 31.4 - - - -
248C ILE* 3.9 12.1 - - + +
276C LYS* 3.7 31.9 - - + -
277C PHE* 3.5 26.7 - + - -
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Residues in contact with GLY 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C TYR* 3.2 27.0 - - - -
209C PHE* 1.3 72.8 - - - +
211C ALA* 1.3 51.7 + - - +
213C ASN* 3.5 8.3 + - - +
214C TYR* 2.8 34.8 + - - +
244C ASP* 2.8 16.3 + - - -
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Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 3.8 15.3 - - + +
173C PHE* 3.5 36.6 - - + -
177C TYR* 3.3 12.0 - - + -
207C ASN 3.0 18.2 + - - +
208C THR* 3.6 5.8 - - - +
210C GLY* 1.3 77.2 - - - +
212C ILE* 1.3 57.4 + - - +
214C TYR* 3.2 4.7 + - - +
215C VAL* 3.0 31.7 + - - +
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 3.8 19.7 - - + -
208C THR* 3.0 22.5 + - + +
209C PHE 3.3 3.1 + - - +
211C ALA* 1.3 75.3 - - - +
213C ASN* 1.3 64.5 + - - +
215C VAL* 3.2 6.0 + - - +
216C ALA* 3.0 21.8 + - - +
234C LEU* 4.4 10.0 - - + +
236C ILE* 3.7 24.7 - - + -
248C ILE* 3.7 20.9 - - + -
251C ALA* 3.6 26.0 - - + +
256C ARG* 4.9 1.3 - - - -
277C PHE* 3.6 38.1 - - + +
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Residues in contact with ASN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C PHE* 2.9 30.4 + - - +
210C GLY* 3.7 7.5 - - - +
212C ILE* 1.3 77.6 - - - +
214C TYR* 1.3 59.9 + - - +
216C ALA* 3.3 5.0 + - - +
217C THR* 2.9 34.9 + - + +
247C ASN* 3.0 29.5 + - - +
248C ILE* 4.5 5.2 - - - +
250C ALA* 3.5 25.2 + - - +
251C ALA* 5.2 0.4 + - - -
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Residues in contact with TYR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 3.7 22.4 - - + -
177C TYR* 3.7 42.7 + + + -
179C THR* 2.6 38.3 + - - -
210C GLY 2.8 21.7 + - - +
211C ALA 3.2 5.6 + - - +
213C ASN* 1.3 72.3 - - - +
215C VAL* 1.3 57.5 + - - +
217C THR* 4.1 4.7 - - - -
218C GLU* 2.7 66.7 + - + +
219C VAL* 3.5 13.4 + - + -
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL* 4.0 20.6 - - + -
135C LEU* 3.8 28.9 - - + -
171C VAL* 4.2 12.1 - - + -
211C ALA 3.0 17.6 + - - +
212C ILE* 3.2 8.9 + - - +
214C TYR* 1.3 75.7 - - - +
216C ALA* 1.3 63.3 + - - +
219C VAL* 3.0 25.7 + - + +
220C PHE* 3.1 37.6 + - + -
234C LEU* 3.9 20.4 - - + -
254C ILE* 4.9 0.9 - - + -
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ILE 3.0 15.8 + - - +
213C ASN* 3.3 4.2 + - - +
215C VAL* 1.3 77.9 - - - +
217C THR* 1.3 60.9 + - - +
220C PHE* 4.1 17.9 - - - +
250C ALA* 3.6 38.0 - - + +
251C ALA* 3.9 3.4 - - + -
254C ILE* 3.9 22.7 - - + -
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Residues in contact with THR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ASN* 2.9 26.9 + - + +
214C TYR* 4.1 0.5 - - - -
216C ALA* 1.3 79.9 - - - +
218C GLU* 1.3 78.1 + - - +
219C VAL 3.7 0.4 - - - -
221C ARG* 3.4 20.3 - - - +
250C ALA* 4.5 18.2 - - + -
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Residues in contact with GLU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C THR* 5.1 1.4 + - - -
214C TYR* 2.7 54.8 + - + +
217C THR* 1.3 90.8 - - - +
219C VAL* 1.3 60.9 + - - +
221C ARG* 3.8 21.3 + - - +
224C LEU* 3.1 22.5 - - - +
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 3.9 23.8 - - + -
169C ALA* 4.0 17.7 - - + -
171C VAL* 3.7 18.6 - - + -
179C THR* 3.8 13.0 - - + +
182C ASP* 5.5 2.0 - - + -
183C PHE* 3.7 14.4 - - + -
214C TYR* 3.7 27.8 - - + -
215C VAL* 3.0 20.6 + - + +
218C GLU* 1.3 84.3 - - - +
220C PHE* 1.3 62.2 + - - +
221C ARG* 2.8 12.4 + - - +
224C LEU* 4.2 12.2 - - + +
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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