Contacts of the helix formed by residues 212 - 224 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C GLY 3.9 0.6 + - - +
211C MET* 1.3 75.3 - - - +
213C GLN* 1.3 57.9 + - - +
214C ASP* 3.3 5.2 - - + +
215C GLU* 3.3 15.5 + - + +
216C MET* 2.8 39.2 + - - +
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Residues in contact with GLN 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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202C TYR* 3.2 22.2 + - - -
206C LYS* 4.8 11.1 - - - +
212C ALA* 1.3 75.4 - - - +
214C ASP* 1.3 58.9 + - - +
216C MET* 3.3 19.5 + - - +
217C ALA* 2.9 27.4 + - - +
240C LEU* 3.7 35.7 - - - +
249C HIS* 3.7 38.8 - - + +
251C LEU* 4.3 7.0 - - - +
252C PRO* 4.4 21.9 - - + +
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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 ALA* 3.3 3.0 - - + +
213C GLN* 1.3 76.5 - - - +
215C GLU* 1.3 63.3 + - - +
217C ALA* 3.3 8.0 + - - +
218C GLN* 3.1 32.2 + - - +
241C LYS* 3.6 17.7 - - + +
243C GLN* 4.9 2.3 + - - +
249C HIS* 3.4 30.1 + - - -
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Residues in contact with GLU 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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211C MET* 3.6 24.9 - - + +
212C ALA* 3.3 20.4 + - + +
214C ASP* 1.3 78.1 - - - +
216C MET* 1.3 62.1 + - - +
218C GLN* 3.2 17.0 + - - +
219C ALA* 3.1 21.0 + - - +
316C LYS* 3.1 42.1 + - - +
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Residues in contact with MET 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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202C TYR* 3.5 35.2 - - + -
205C MET* 3.6 39.0 - - + +
206C LYS* 3.9 20.4 - - + -
211C MET* 3.8 20.6 - - + +
212C ALA 2.8 27.9 + - - +
213C GLN* 3.3 31.2 + - - +
215C GLU* 1.3 74.0 - - - +
217C ALA* 1.3 61.9 + - - +
219C ALA* 3.3 2.3 + - - +
220C PHE* 3.1 29.3 + - - -
240C LEU* 3.8 9.6 - - + -
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Residues in contact with ALA 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 GLN 2.9 13.6 + - - +
214C ASP 3.6 8.7 - - - +
215C GLU 3.2 0.2 - - - -
216C MET* 1.3 76.7 - - - +
218C GLN* 1.3 62.4 + - + +
220C PHE 3.5 1.3 + - - +
221C GLU* 3.2 28.9 + - - +
237C ALA* 3.4 28.1 - - - +
240C LEU* 3.7 15.6 - - + +
241C LYS* 3.7 22.4 - - + +
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Residues in contact with GLN 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* 3.1 19.3 + - - +
215C GLU* 3.2 18.1 + - + +
217C ALA* 1.3 74.1 - - + +
219C ALA* 1.3 60.2 + - - +
221C GLU* 3.3 14.9 + - - +
222C ASP* 2.9 33.4 + - - +
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Residues in contact with ALA 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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205C MET* 3.8 19.1 - - + -
211C MET* 4.2 1.8 - - + -
215C GLU 3.1 13.3 + - - +
216C MET 3.6 9.4 - - - +
217C ALA 3.3 0.4 - - - -
218C GLN* 1.3 77.5 - - - +
220C PHE* 1.3 57.0 + - - +
222C ASP* 3.3 7.6 + - - +
223C TRP* 3.0 36.4 + - + -
320C LEU* 3.8 29.4 - - + -
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Residues in contact with PHE 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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198C ILE* 3.8 38.6 - - + -
201C ALA* 4.7 0.4 - - + -
202C TYR* 4.4 14.1 - - + -
205C MET* 3.6 21.5 - - + -
216C MET 3.1 20.8 + - - -
217C ALA 4.0 4.9 - - - +
219C ALA* 1.3 75.0 - - - +
221C GLU* 1.3 62.0 + - - +
223C TRP* 3.1 34.4 + + - +
224C ASN 2.9 23.7 + - - -
233C ILE* 3.2 34.1 - - + +
236C THR* 4.3 8.5 - - + -
237C ALA* 4.1 10.8 - - + -
240C LEU* 3.5 22.9 - - + -
327C LEU* 4.8 6.7 - - + -
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Residues in contact with GLU 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 ALA 3.2 16.5 + - - +
218C GLN* 3.6 17.0 - - - +
220C PHE* 1.3 75.2 - - - +
222C ASP* 1.3 63.8 + - - +
224C ASN* 3.4 19.2 + - - +
225C LYS* 3.9 17.4 - - - +
234C GLU* 6.2 0.9 - - - -
237C ALA* 3.5 13.5 - - + +
238C ASN* 4.6 2.1 - - - +
241C LYS* 2.1 37.7 + - - -
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Residues in contact with ASP 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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218C GLN* 2.9 17.1 + - - +
219C ALA* 3.5 11.8 - - - +
220C PHE 3.2 0.2 - - - -
221C GLU* 1.3 76.8 - - - +
223C TRP* 1.3 67.3 + - + +
224C ASN 3.3 0.5 + - - -
225C LYS* 3.4 23.7 + - - +
226C THR* 3.8 10.1 - - - +
320C LEU* 6.4 0.4 - - + -
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Residues in contact with TRP 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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201C ALA* 4.4 3.4 - - + -
205C MET* 3.5 22.2 - - + -
219C ALA* 3.0 18.4 + - + -
220C PHE* 3.1 46.2 + + - +
222C ASP* 1.3 81.1 - - + +
224C ASN* 1.3 56.6 + - - +
225C LYS 2.9 6.9 + - - -
226C THR* 3.2 20.3 + - - +
228C LEU* 3.7 29.1 - - + +
233C ILE* 4.7 4.5 - - + -
320C LEU* 3.4 50.8 - - + +
321C GLU* 5.1 1.6 + - - +
323C ILE* 3.8 17.0 - - + -
324C ARG* 3.4 37.0 - - + +
327C LEU* 4.1 22.2 - - + -
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Residues in contact with ASN 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 PHE 2.9 15.2 + - - +
221C GLU* 3.6 11.4 - - - +
222C ASP 3.2 1.4 - - - -
223C TRP* 1.3 73.6 - - - +
225C LYS* 1.3 60.7 + - + +
226C THR 3.6 0.7 - - - -
228C LEU 4.1 5.6 - - - -
229C ASP* 3.0 36.6 - - - +
230C SER 3.0 18.6 + - - +
233C ILE* 3.8 6.9 - - + +
234C GLU* 3.1 46.7 + - - +
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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