Contacts of the helix formed by residues 212 - 222 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483B THR* 3.6 19.9 - - + +
484B GLU* 5.0 0.4 - - - -
487B LYS* 3.2 19.7 + - - -
521B TYR* 4.2 2.7 + - - -
173D ASN* 4.1 7.5 + - - -
176D ILE* 4.1 17.4 - - + +
177D PRO* 2.9 38.9 - - + +
180D LEU* 4.7 5.6 - - + +
208D ALA* 2.9 27.8 - - + +
209D LEU* 2.9 7.7 + - + +
211D LEU* 1.3 92.3 - - + +
213D ILE* 1.3 65.0 + - - +
214D ASP 3.4 2.0 - - - -
215D SER* 3.0 17.2 + - - -
216D PHE* 2.9 21.5 + - - +
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LEU* 3.1 11.3 + - + +
210D MET* 3.0 24.9 - - + +
211D LEU 3.8 0.9 - - - -
212D HIS* 1.3 76.4 - - - +
214D ASP* 1.3 66.2 + - - +
216D PHE* 2.8 10.8 + - + +
217D ILE* 2.6 48.8 + - + +
242D LEU* 4.6 13.9 - - + -
246D ARG* 2.8 61.7 - - + +
249D ARG* 3.8 13.5 - - + +
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Residues in contact with ASP 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D HIS 3.4 0.6 - - - -
213D ILE* 1.3 81.8 - - - +
215D SER* 1.3 57.9 + - - +
217D ILE* 4.1 6.7 - - - +
218D GLU* 2.9 47.1 + - - +
249D ARG* 3.0 37.4 + - - +
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Residues in contact with SER 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 3.6 12.6 - - - +
212D HIS* 3.0 21.0 + - - -
214D ASP* 1.3 77.7 - - - +
216D PHE* 1.3 54.8 + - - +
218D GLU* 3.6 10.7 - - - +
219D ASN* 2.5 48.8 + - - +
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Residues in contact with PHE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 3.6 27.3 - - + +
183D PHE* 4.0 12.3 - + - -
195D VAL* 5.1 0.2 - - + -
198D VAL* 3.7 19.1 - - + -
199D ASN* 3.6 22.2 - - - -
202D ILE* 4.0 17.7 - - + -
209D LEU* 3.9 20.9 - - + -
212D HIS 2.9 11.8 + - - +
213D ILE* 2.8 13.6 + - + +
215D SER* 1.3 72.4 - - - +
217D ILE* 1.3 60.9 + - + +
219D ASN* 2.9 5.1 + - - +
220D LEU* 2.8 56.4 + - + +
238D ALA* 3.8 2.5 - - + -
242D LEU* 3.7 34.3 - - + -
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Residues in contact with ILE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ILE* 2.6 33.6 + - + +
214D ASP* 4.1 6.5 - - - +
216D PHE* 1.3 71.7 - - + +
218D GLU* 1.3 63.9 + - + +
220D LEU* 3.1 11.5 + - + +
221D PHE* 3.0 54.4 + - + -
239D LEU* 5.6 0.7 - - + -
242D LEU* 4.3 20.4 - - + -
246D ARG 5.5 0.7 - - - +
249D ARG* 3.8 38.4 - - + +
250D LEU* 4.3 16.4 - - + +
253D HIS* 5.0 9.0 - - + +
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Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ASP* 2.9 39.3 + - - +
215D SER* 3.6 10.7 + - - +
217D ILE* 1.3 74.5 - - + +
219D ASN* 1.3 58.8 + - - +
221D PHE* 3.5 12.2 + - + +
222D ALA* 3.1 26.3 + - - +
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Residues in contact with ASN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 3.9 26.5 - - + +
183D PHE* 3.6 25.0 - - + +
184D LYS* 3.4 32.2 + - - +
215D SER* 2.5 43.8 + - - +
216D PHE* 2.9 10.3 + - - +
218D GLU* 1.3 70.7 - - - +
220D LEU* 1.3 65.6 + - - +
222D ALA* 3.6 5.1 + - - -
223D LEU* 3.5 27.7 + - - +
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D PHE* 4.4 4.9 - - + -
195D VAL* 4.1 10.8 - - + -
216D PHE* 2.8 48.0 + - + +
217D ILE* 3.1 11.2 + - - +
219D ASN* 1.3 74.8 - - - +
221D PHE* 1.3 69.9 - - + +
223D LEU* 2.9 15.8 + - - +
224D ALA* 3.1 10.1 + - - +
235D VAL* 3.8 35.1 - - + +
238D ALA* 3.7 27.8 - - + -
239D LEU* 4.3 13.5 - - + -
242D LEU* 3.9 17.5 - - + -
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Residues in contact with PHE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ILE* 3.0 41.9 + - + -
218D GLU* 3.7 12.1 - - + +
220D LEU* 1.3 79.2 - - + +
222D ALA* 1.3 56.9 + - - +
223D LEU 3.1 4.2 + - - -
224D ALA* 3.4 23.0 + - + +
235D VAL* 6.4 0.2 - - + -
239D LEU* 4.6 15.9 - - + -
250D LEU* 5.4 0.2 - - + -
253D HIS* 3.4 46.9 - + + -
256D ASN* 6.1 1.8 - - + -
257D ILE* 3.9 24.5 - - + -
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LYS* 5.2 13.2 - - - +
218D GLU 3.1 17.0 + - - +
219D ASN* 4.0 8.7 - - - +
220D LEU 3.2 0.6 - - - -
221D PHE* 1.3 74.3 - - - +
223D LEU* 1.3 67.3 + - + +
224D ALA 3.6 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