Contacts of the helix formed by residues 212 - 225 (chain C) in PDB entry 2QMR
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 HIS 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C PRO* 3.8 28.1 - - + +
180C LEU* 3.7 25.2 - - + +
208C ALA* 3.1 25.6 - - - +
209C LEU* 2.8 10.6 + - - +
211C LEU* 1.3 96.1 + - + +
213C ILE* 1.3 51.1 + - - +
214C ASP 3.4 2.0 - - - -
215C SER* 3.1 16.8 + - - -
216C PHE* 2.7 34.5 + - - +
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Residues in contact with ILE 213 (chain C).
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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209C LEU* 3.0 9.4 + - + +
210C MET* 3.2 41.7 - - + +
211C LEU 4.9 0.4 - - - -
212C HIS* 1.3 72.3 - - - +
214C ASP* 1.3 71.0 + - - +
216C PHE* 2.9 10.5 + - + +
217C ILE* 2.7 47.0 + - + +
242C LEU* 5.1 8.1 - - + -
246C ARG* 3.3 57.2 - - + +
249C ARG* 3.9 14.6 - - + +
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Residues in contact with ASP 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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212C HIS 3.4 0.4 - - - -
213C ILE* 1.3 84.2 - - - +
215C SER* 1.3 57.5 + - - +
217C ILE* 3.8 6.4 - - - +
218C GLU* 2.9 47.3 + - - +
249C ARG* 2.9 40.5 + - - -
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Residues in contact with SER 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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180C LEU* 4.5 7.5 - - - +
212C HIS* 3.1 25.7 + - - +
214C ASP* 1.3 77.5 - - - +
216C PHE* 1.3 63.7 + - - +
218C GLU* 3.7 9.7 + - - +
219C ASN* 3.1 40.6 + - - -
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Residues in contact with PHE 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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180C LEU* 3.5 28.4 - - + +
183C PHE* 3.6 21.5 - + - -
195C VAL* 5.1 0.4 - - + -
198C VAL* 3.6 21.8 - - + -
199C ASN* 3.8 19.1 - - - -
202C ILE* 3.8 24.0 - - + -
209C LEU* 4.2 17.5 - - + -
212C HIS 2.7 16.5 + - - +
213C ILE* 2.9 13.7 + - + +
215C SER* 1.3 69.5 - - - +
217C ILE* 1.3 62.8 + - + +
219C ASN* 3.3 3.3 + - - +
220C LEU* 2.9 49.1 + - + +
238C ALA* 4.1 0.2 - - + -
242C LEU* 4.0 20.6 - - + -
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Residues in contact with ILE 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 ILE* 2.7 30.0 + - + +
214C ASP* 3.9 4.9 - - - +
216C PHE* 1.3 75.5 - - + +
218C GLU* 1.3 56.7 + - + +
220C LEU* 2.8 27.7 + - + +
221C PHE* 2.9 47.2 + - + -
239C LEU* 6.1 0.7 - - + -
242C LEU* 3.9 29.2 - - + -
246C ARG* 5.7 0.2 - - + -
249C ARG* 3.5 43.5 - - + +
250C LEU* 4.7 7.2 - - + -
253C HIS* 4.9 7.0 - - + +
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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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214C ASP* 2.9 34.1 + - - +
215C SER* 4.2 7.4 - - - +
217C ILE* 1.3 75.4 - - + +
219C ASN* 1.3 58.2 - - - +
221C PHE* 3.5 11.2 + - + +
222C ALA* 2.9 31.2 + - - +
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Residues in contact with ASN 219 (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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180C LEU* 3.8 22.8 + - - +
183C PHE* 3.4 28.0 - - + +
184C LYS* 3.2 36.4 + - - +
215C SER* 3.1 32.9 + - - +
216C PHE* 3.6 2.7 - - - +
218C GLU* 1.3 76.4 - - - +
220C LEU* 1.3 63.5 + - - +
222C ALA* 3.7 7.1 + - - +
223C LEU* 3.2 28.6 + - - +
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Residues in contact with LEU 220 (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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183C PHE* 4.3 5.6 - - + -
195C VAL* 4.1 10.8 - - + -
216C PHE* 2.9 39.6 + - + +
217C ILE* 2.8 12.9 + - + +
219C ASN* 1.3 73.9 - - - +
221C PHE* 1.3 64.2 + - + +
223C LEU* 2.9 19.8 + - - +
224C ALA* 3.0 9.9 + - - -
235C VAL* 3.8 33.1 - - + +
238C ALA* 3.7 33.9 - - + -
239C LEU* 4.5 14.1 - - + -
242C LEU* 3.8 21.1 - - + -
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Residues in contact with PHE 221 (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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217C ILE* 2.9 39.1 + - + -
218C GLU* 3.9 11.4 - - + +
220C LEU* 1.3 78.6 - - + +
222C ALA* 1.3 58.7 + - - +
224C ALA* 2.9 32.5 + - + +
225C GLY 4.5 0.9 + - - -
239C LEU* 4.3 18.8 - - + -
250C LEU* 4.9 2.9 - - + -
253C HIS* 3.5 50.9 - + + -
256C ASN* 6.4 0.7 - - + -
257C ILE* 4.1 22.7 - - + -
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Residues in contact with ALA 222 (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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184C LYS* 6.2 2.0 - - - -
218C GLU 2.9 20.1 + - - +
219C ASN* 3.8 12.6 - - - +
221C PHE* 1.3 74.8 - - - +
223C LEU* 1.3 60.9 + - + +
224C ALA 3.6 0.2 - - - -
225C GLY 5.2 1.5 + - - -
226C ASP 5.6 0.2 + - - -
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Residues in contact with LEU 223 (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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183C PHE* 3.7 38.1 - - + +
191C ARG* 4.0 18.6 - - + +
195C VAL* 3.8 19.5 - - + -
219C ASN 3.2 17.6 + - - +
220C LEU* 2.9 9.2 + - - +
222C ALA* 1.3 81.6 - - - +
224C ALA* 1.3 65.4 + - - +
225C GLY 3.3 2.2 - - - -
226C ASP* 2.9 47.8 + - + +
231C VAL* 3.8 10.5 - - + +
232C ARG* 5.2 0.3 - - - +
235C VAL* 4.1 16.1 - - + +
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Residues in contact with ALA 224 (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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220C LEU 3.0 7.5 + - - +
221C PHE* 2.9 22.3 + - + +
223C LEU* 1.3 76.6 - - - +
225C GLY* 1.3 58.4 + - - +
226C ASP 3.0 6.4 + - - -
232C ARG* 3.7 11.1 - - - +
235C VAL* 4.5 5.2 - - + -
260C TYR* 3.3 49.9 + - + -
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Residues in contact with GLY 225 (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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221C PHE 4.5 0.6 + - - -
222C ALA 5.2 1.0 + - - -
223C LEU 3.3 0.8 - - - -
224C ALA* 1.3 77.9 - - - +
226C ASP* 1.3 63.5 + - - +
227C GLU* 3.4 3.3 + - - +
232C ARG* 5.5 1.3 - - - -
260C TYR* 5.5 1.1 - - - -
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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