Contacts of the helix formed by residues 212 - 224 (chain F) in PDB entry 5UQ9
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 ALA 212 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210F GLY 3.9 0.6 + - - -
211F MET* 1.3 75.0 - - - +
213F GLN* 1.3 57.1 + - - +
214F ASP* 3.5 2.0 - - + +
215F GLU* 3.6 22.2 + - + +
216F MET* 2.6 40.9 + - - +
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Residues in contact with GLN 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F TYR* 3.5 23.0 + - - -
206F LYS* 5.5 2.2 - - - +
212F ALA* 1.3 73.2 - - - +
214F ASP* 1.3 59.6 + - - +
216F MET* 3.0 16.0 + - + +
217F ALA* 2.9 28.4 + - - +
240F LEU* 3.5 39.3 - - - +
249F HIS* 3.8 35.7 - - + +
251F LEU* 4.6 4.6 - - - +
252F PRO* 3.9 28.9 - - + +
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Residues in contact with ASP 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F ALA* 3.5 2.1 - - + +
213F GLN* 1.3 78.2 - - - +
215F GLU* 1.3 62.1 + - - +
217F ALA* 3.5 7.1 + - - +
218F GLN* 3.2 20.6 + - - +
240F LEU 4.3 0.4 - - - +
241F LYS* 3.9 29.0 - - + +
243F GLN* 4.8 9.3 + - - -
249F HIS* 3.7 22.4 + - - -
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Residues in contact with GLU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F MET* 3.9 33.5 - - + +
212F ALA* 3.3 29.7 + - + +
213F GLN 3.2 0.6 - - - -
214F ASP* 1.3 77.1 - - - +
216F MET* 1.3 64.9 + - - +
218F GLN* 3.2 26.7 + - - +
219F ALA* 3.2 12.0 + - - +
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Residues in contact with MET 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F TYR* 3.5 31.9 - - + +
205F MET* 3.7 60.1 - - + +
206F LYS* 3.8 15.3 - - + -
211F MET* 3.9 12.5 - - + +
212F ALA 2.6 30.6 + - - +
213F GLN* 3.3 18.2 - - + +
215F GLU* 1.3 74.3 - - - +
217F ALA* 1.3 60.8 + - - +
219F ALA* 3.0 17.7 + - - +
220F PHE* 3.2 16.5 + - - -
240F LEU* 3.9 9.2 - - + -
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Residues in contact with ALA 217 (chain F).
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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213F GLN 2.9 11.1 + - - +
214F ASP* 3.8 4.7 - - - +
215F GLU 3.3 0.2 - - - -
216F MET* 1.3 76.0 - - - +
218F GLN* 1.3 56.6 + - - +
220F PHE* 3.5 0.8 + - - +
221F GLU* 2.9 33.3 + - - +
237F ALA* 3.4 32.5 - - - +
240F LEU* 3.7 18.7 - - + +
241F LYS* 3.6 22.2 - - + -
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Residues in contact with GLN 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F ASP 3.2 13.2 + - - +
215F GLU* 3.2 23.1 + - - +
216F MET 3.2 0.8 - - - -
217F ALA* 1.3 76.3 - - - +
219F ALA* 1.3 58.4 + - - +
221F GLU* 4.4 7.0 - - - -
222F ASP* 2.9 56.1 + - - +
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Residues in contact with ALA 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F MET* 3.7 25.6 - - - -
211F MET* 4.9 3.6 - - + -
215F GLU 3.2 9.8 + - - +
216F MET* 3.0 11.9 + - - +
218F GLN* 1.3 77.8 - - - +
220F PHE* 1.3 57.2 + - - +
222F ASP* 3.7 3.2 - - - -
223F TRP* 2.8 40.0 + - + +
320F LEU* 4.1 21.1 - - + -
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Residues in contact with PHE 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F ILE* 3.6 41.5 - - + -
201F ALA* 4.6 2.0 - - + -
202F TYR* 4.1 9.0 - - + -
205F MET* 3.5 27.1 - - + -
216F MET 3.2 18.1 + - - -
217F ALA 4.0 1.1 - - - +
219F ALA* 1.3 77.6 - - - +
221F GLU* 1.3 59.1 + - - +
223F TRP* 3.1 29.7 + + - +
224F ASN 2.8 25.1 + - - -
233F ILE* 3.2 36.5 - - + +
236F THR* 3.9 15.9 - - + -
237F ALA* 3.9 17.0 - - + -
240F LEU* 3.7 20.6 - - + -
327F LEU* 4.8 1.1 - - + -
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Residues in contact with GLU 221 (chain F).
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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217F ALA 2.9 19.2 + - - +
218F GLN* 4.0 7.2 - - - +
220F PHE* 1.3 76.4 - - - +
222F ASP* 1.3 64.6 + - - +
224F ASN* 3.4 19.8 + - + +
225F LYS* 3.6 22.7 + - - +
233F ILE* 5.3 0.2 - - - -
237F ALA* 4.1 10.2 - - + +
241F LYS* 4.4 19.8 - - - +
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Residues in contact with ASP 222 (chain F).
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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218F GLN* 2.9 42.1 + - - +
219F ALA* 3.8 4.2 - - - +
221F GLU* 1.3 83.1 - - - +
223F TRP* 1.3 69.1 + - + +
224F ASN 3.1 0.7 - - - -
225F LYS* 3.1 31.4 + - - +
226F THR* 3.8 8.3 - - - +
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Residues in contact with TRP 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F ALA* 4.0 11.2 - - + -
205F MET* 3.8 15.0 - - + -
219F ALA* 2.8 28.0 + - - +
220F PHE* 3.1 42.1 + + - +
222F ASP* 1.3 76.1 - - + +
224F ASN* 1.3 56.9 + - - +
225F LYS 3.0 3.2 + - - -
226F THR* 2.9 27.1 + - + -
228F LEU* 3.9 23.8 - - + +
233F ILE* 4.8 2.2 - - + -
320F LEU* 3.4 54.1 - - + +
321F GLU* 5.1 1.2 + - - -
323F ILE* 3.6 23.6 - - + -
324F ARG* 3.4 36.1 - - + +
327F LEU* 4.1 17.9 - - + -
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Residues in contact with ASN 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F PHE 2.8 9.9 + - - +
221F GLU* 3.4 16.7 - - + +
222F ASP 3.1 0.6 - - - -
223F TRP* 1.3 75.3 - - - +
225F LYS* 1.3 60.5 + - + +
226F THR 3.4 0.7 - - - -
229F ASP* 3.1 48.9 - - - +
230F SER 3.3 6.5 + - - +
233F ILE* 3.3 15.1 + - + +
234F GLU* 3.2 50.1 - - - +
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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