Contacts of the helix formed by residues 212 - 225 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B PRO* 3.9 26.4 - - + +
180B LEU* 3.7 25.4 - - + +
208B ALA* 3.1 25.6 - - - +
209B LEU* 2.8 10.8 + - - +
211B LEU* 1.3 97.2 + - + +
213B ILE* 1.3 49.6 + - - +
214B ASP 3.4 2.7 - - - -
215B SER* 3.1 15.6 + - - +
216B PHE* 2.7 34.8 + - - +
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B LEU* 3.0 8.2 + - + +
210B MET* 3.2 41.1 - - + +
211B LEU 3.7 1.1 - - - -
212B HIS* 1.3 72.5 - - - +
214B ASP* 1.3 64.3 + - - +
216B PHE* 2.9 10.4 + - + +
217B ILE* 2.6 46.9 + - + +
242B LEU* 5.1 9.4 - - + -
246B ARG* 3.3 56.8 - - + +
249B ARG* 3.8 20.4 - - + +
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Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B HIS 3.4 0.4 - - - -
213B ILE* 1.3 83.5 - - - +
215B SER* 1.3 56.9 + - - +
217B ILE* 3.8 5.6 - - - +
218B GLU* 2.9 46.7 + - - +
249B ARG* 2.8 40.2 + - - -
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.5 7.6 - - - +
212B HIS* 3.1 25.1 + - - -
213B ILE 3.1 0.4 - - - -
214B ASP* 1.3 77.3 - - - +
216B PHE* 1.3 62.7 + - - +
218B GLU* 4.1 8.7 - - - +
219B ASN* 3.1 41.3 + - - -
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 3.5 27.8 - - + +
183B PHE* 3.6 21.8 - + - -
195B VAL* 5.1 0.7 - - + -
198B VAL* 3.6 21.5 - - + -
199B ASN* 3.8 19.3 - - - -
202B ILE* 3.8 23.3 - - + -
209B LEU* 4.2 17.5 - - + -
212B HIS 2.7 16.8 + - - +
213B ILE* 3.3 13.2 - - + +
215B SER* 1.3 70.4 - - - +
217B ILE* 1.3 61.2 + - + +
219B ASN* 3.3 3.0 + - - +
220B LEU* 2.9 49.9 + - + +
238B ALA* 4.1 0.4 - - + -
242B LEU* 4.0 20.4 - - + -
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ILE* 2.6 30.4 + - + +
214B ASP* 3.8 5.2 - - - +
216B PHE* 1.3 73.7 - - + +
218B GLU* 1.3 60.1 + - + +
220B LEU* 2.8 25.0 + - + +
221B PHE* 2.9 46.0 + - + -
239B LEU* 6.1 0.4 - - + -
242B LEU* 3.9 28.5 - - + -
249B ARG* 3.5 42.2 - - + +
250B LEU* 4.7 8.3 - - + -
253B HIS* 5.0 8.1 - - + +
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ASP* 2.9 33.8 + - - +
215B SER* 4.2 7.2 - - - +
217B ILE* 1.3 75.5 - - + +
219B ASN* 1.3 57.8 + - - +
221B PHE* 3.6 11.0 + - + +
222B ALA* 3.0 30.5 + - - +
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 3.7 22.8 + - - +
183B PHE* 3.4 28.4 - - + +
184B LYS* 3.3 35.7 + - - +
215B SER* 3.1 33.0 + - - +
216B PHE* 3.7 3.4 - - - +
217B ILE 3.2 0.8 - - - -
218B GLU* 1.3 76.1 - - - +
220B LEU* 1.3 63.8 + - - +
222B ALA* 3.9 8.2 - - - +
223B LEU* 3.3 28.1 + - - +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PHE* 4.3 4.9 - - + -
195B VAL* 4.1 16.4 - - + -
216B PHE* 2.9 40.9 + - + +
217B ILE* 2.8 12.5 + - + +
219B ASN* 1.3 74.9 - - - +
221B PHE* 1.3 63.9 + - + +
223B LEU* 2.9 19.7 + - + +
224B ALA 3.0 10.0 + - - -
235B VAL* 3.8 28.1 - - + +
238B ALA* 3.7 33.7 - - + -
239B LEU* 4.5 14.1 - - + -
242B LEU* 3.8 20.6 - - + -
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Residues in contact with PHE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ILE* 2.9 39.5 + - + -
218B GLU* 3.9 11.4 - - + +
220B LEU* 1.3 77.2 - - + +
222B ALA* 1.3 59.1 + - - +
224B ALA* 3.0 30.3 + - + +
225B GLY 4.6 0.5 + - - -
239B LEU* 4.3 19.7 - - + -
250B LEU* 4.9 2.9 - - + -
253B HIS* 3.5 49.8 - + + -
256B ASN* 6.5 0.9 - - + -
257B ILE* 4.2 22.4 - - + -
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LYS* 6.2 1.6 - - - -
218B GLU 3.0 19.3 + - - +
219B ASN* 3.9 12.8 - - - +
220B LEU 3.3 0.2 - - - -
221B PHE* 1.3 74.2 - - - +
223B LEU* 1.3 60.9 + - + +
225B GLY 5.2 1.9 + - - -
226B ASP 5.6 0.2 + - - -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PHE* 3.7 39.9 - - + +
191B ARG* 4.0 19.5 - - + +
195B VAL* 3.8 19.1 - - + -
219B ASN 3.3 17.8 + - - +
220B LEU* 2.9 7.8 + - - +
222B ALA* 1.3 80.2 - - + +
224B ALA* 1.3 67.0 + - - +
225B GLY 3.3 2.0 - - - -
226B ASP* 3.0 47.9 + - - +
231B VAL* 3.8 9.8 - - + +
232B ARG* 5.2 0.5 - - - +
235B VAL* 4.1 16.4 - - + +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B LEU 3.0 7.8 + - - +
221B PHE* 3.0 22.7 + - + +
223B LEU* 1.3 76.5 - - - +
225B GLY* 1.3 59.1 + - - +
226B ASP 3.0 5.7 + - - -
232B ARG* 3.6 10.7 - - - +
235B VAL* 4.5 4.9 - - + -
260B TYR* 3.2 50.8 + - + -
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B PHE 4.6 0.6 + - - -
222B ALA 5.2 1.6 + - - -
223B LEU 3.3 0.8 - - - -
224B ALA* 1.3 77.6 - - - +
226B ASP* 1.3 64.7 + - - +
227B GLU* 3.4 3.8 + - - +
232B ARG* 5.4 0.8 + - - -
260B TYR* 5.5 0.9 - - - -
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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