Contacts of the helix formed by residues 212 - 226 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211H MET* 1.3 75.9 - - - +
213H GLN* 1.3 80.7 + - - +
214H ASP* 3.3 2.9 - - + +
215H GLU* 3.0 30.6 + - + +
216H MET* 3.1 29.4 + - - +
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Residues in contact with GLN 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H ALA* 1.3 84.3 - - - +
214H ASP* 1.3 72.7 + - - +
215H GLU 3.4 0.2 + - - -
216H MET* 3.5 6.7 + - - +
217H ALA* 3.3 14.9 + - - +
240H LEU* 3.2 40.7 - - + +
249H HIS* 3.0 52.9 + - + +
251H LEU* 6.4 0.7 - - + -
252H PRO* 6.5 1.6 - - + -
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Residues in contact with ASP 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H ALA* 3.3 1.5 - - + +
213H GLN* 1.3 93.3 - - + +
215H GLU* 1.3 61.3 + - + +
217H ALA* 4.0 3.7 - - - +
218H GLN* 3.1 31.2 + - - +
241H LYS* 3.2 34.7 - - + +
249H HIS* 5.7 2.9 - - + -
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Residues in contact with GLU 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H GLY 5.4 0.3 - - - +
211H MET* 3.5 31.7 - - + +
212H ALA* 3.0 41.4 + - + +
214H ASP* 1.3 79.4 - - + +
216H MET* 1.3 59.7 + - - +
218H GLN* 3.4 6.9 + - - +
219H ALA* 3.0 22.9 + - - +
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Residues in contact with MET 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H TYR* 3.5 35.4 - - + +
205H MET* 3.9 24.2 - - + -
206H LYS* 3.6 30.5 - - + +
211H MET* 3.4 40.8 - - + +
212H ALA* 3.1 22.8 + - - +
213H GLN* 3.9 8.5 - - - +
215H GLU* 1.3 74.2 - - - +
217H ALA* 1.3 65.1 + - - +
219H ALA* 3.0 4.8 + - - +
220H PHE* 3.0 32.0 + - + -
240H LEU* 4.5 7.2 - - + -
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Residues in contact with ALA 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H GLN 3.3 9.2 + - - +
214H ASP 4.1 2.5 - - - +
216H MET* 1.3 77.6 - - - +
218H GLN* 1.3 62.0 + - - +
220H PHE* 3.3 10.3 + - - +
221H GLU* 3.3 20.8 + - - +
237H ALA* 3.3 33.3 - - - +
240H LEU* 3.6 17.4 - - + +
241H LYS* 3.6 24.7 - - + +
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Residues in contact with GLN 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H ASP* 3.1 24.7 + - - +
215H GLU* 3.6 7.9 - - - +
217H ALA* 1.3 77.9 - - - +
219H ALA* 1.3 55.7 + - - +
221H GLU* 3.2 29.7 + - - +
222H ASP* 2.7 44.9 + - - +
241H LYS* 5.5 3.3 - - + +
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H MET* 4.7 2.9 - - + -
211H MET* 4.6 1.8 - - + -
215H GLU 3.0 14.7 + - - +
216H MET* 3.0 11.8 + - - +
218H GLN* 1.3 79.0 - - - +
220H PHE* 1.3 61.7 + - - +
222H ASP* 3.3 17.4 + - - +
223H TRP* 3.4 11.6 + - - +
320H LEU* 4.4 23.5 - - + +
324H ARG* 3.9 22.5 + - - +
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Residues in contact with PHE 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198H ILE* 3.8 41.3 - - + -
201H ALA* 5.0 2.7 - - + -
202H TYR* 4.5 15.7 - + + -
205H MET* 4.2 22.2 - - + -
216H MET* 3.0 30.3 + - + -
217H ALA* 3.7 9.9 - - - +
218H GLN 3.3 0.4 - - - -
219H ALA* 1.3 74.6 - - - +
221H GLU* 1.3 64.3 + - - +
223H TRP* 4.1 0.7 - - - +
224H ASN* 3.1 23.4 + - - +
233H ILE* 4.2 27.3 - - + +
236H THR* 4.1 18.2 - - + -
237H ALA* 3.8 17.7 - - + +
240H LEU* 5.9 3.8 - - + -
324H ARG* 3.2 28.0 - - - +
327H LEU* 5.4 4.5 - - + -
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Residues in contact with GLU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H ALA* 3.3 15.6 - - - +
218H GLN* 3.2 25.0 + - - +
220H PHE* 1.3 78.0 - - - +
222H ASP* 1.3 65.8 + - - +
224H ASN* 3.4 19.3 + - - +
225H LYS* 3.6 10.2 + - - +
237H ALA* 4.1 12.8 - - + +
241H LYS* 3.6 26.9 - - - -
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Residues in contact with ASP 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H GLN* 2.7 38.5 + - - +
219H ALA* 3.3 10.3 + - - +
220H PHE 3.2 0.6 - - - -
221H GLU* 1.3 73.0 - - - +
223H TRP* 1.3 61.0 + - + +
224H ASN 3.0 4.3 - - - -
225H LYS* 2.9 22.5 + - - +
226H THR* 3.1 19.9 + - + +
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Residues in contact with TRP 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H ALA 3.4 6.0 + - - -
220H PHE 4.6 0.7 - - - +
222H ASP* 1.3 81.1 - - + +
224H ASN* 1.3 56.3 + - - +
225H LYS 3.3 0.2 - - - -
226H THR* 2.9 47.3 - - + +
227H GLU* 3.5 33.7 - - + -
229H ASP* 3.4 27.7 - - - +
233H ILE* 5.1 1.8 - - + -
320H LEU* 4.3 8.9 + - + +
321H GLU* 3.1 46.0 + - - -
324H ARG* 3.3 73.8 - - + +
325H LYS* 4.3 18.6 - - + -
328H TYR* 5.3 7.2 - - + -
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Residues in contact with ASN 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H PHE 3.1 20.8 + - - +
221H GLU* 3.4 11.9 + - - +
222H ASP 3.0 0.2 - - - -
223H TRP* 1.3 78.9 - - - +
225H LYS* 1.3 77.9 + - - +
226H THR 3.9 2.4 - - - +
227H GLU 5.1 0.7 - - - +
229H ASP* 3.3 19.8 + - - +
230H SER* 4.3 0.3 - - - -
233H ILE* 3.2 31.5 - - + +
234H GLU* 3.4 33.0 - - - +
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Residues in contact with LYS 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H GLU 3.6 8.3 + - - +
222H ASP* 2.9 9.3 + - - +
224H ASN* 1.3 94.4 + - + +
226H THR* 1.3 64.6 + - + +
227H GLU 4.0 4.7 + - - +
234H GLU* 5.9 1.0 + - - -
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Residues in contact with THR 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H ASP* 3.1 17.4 + - + +
223H TRP* 2.9 52.5 - - + +
224H ASN 3.9 1.9 - - - +
225H LYS* 1.3 77.6 - - + +
227H GLU* 1.3 74.6 + - - +
228H LEU 3.3 1.6 + - - -
229H ASP* 3.9 1.6 - - - +
321H GLU* 6.2 0.2 - - - +
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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