Contacts of the helix formed by residues 222 - 230 (chain D) in PDB entry 3QNQ
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 GLU 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217D GLY 3.1 24.5 + - - +
218D LYS* 3.4 39.3 + - + +
220D LEU 2.9 1.2 + - - -
221D GLN* 1.3 79.5 - - + +
223D PRO* 1.3 73.2 - - + +
225D SER* 3.4 4.1 + - - -
226D ILE* 3.2 31.2 + - + +
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Residues in contact with PRO 223 (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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218D LYS 3.9 10.8 - - - +
219D LEU* 3.8 20.6 - - - +
220D LEU* 3.2 13.5 - - - +
222D GLU* 1.3 95.2 - - + +
224D LEU* 1.3 60.0 + - + +
226D ILE* 2.9 29.9 + - + +
227D LEU* 3.2 15.7 + - + +
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Residues in contact with LEU 224 (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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147D PHE* 4.1 14.8 - - + -
219D LEU 5.5 0.4 - - - +
220D LEU* 2.8 50.2 + - + +
223D PRO* 1.3 77.1 - - + +
225D SER* 1.3 60.1 + - - +
227D LEU* 3.3 22.1 + - + +
228D GLY 3.2 16.6 + - - -
262D ILE* 3.6 24.4 - - + +
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Residues in contact with SER 225 (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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147D PHE* 6.2 0.2 - - - -
221D GLN* 2.7 28.6 + - - -
222D GLU* 3.4 6.2 + - - -
223D PRO 3.1 0.6 - - - -
224D LEU* 1.3 79.9 - - - +
226D ILE* 1.3 61.4 + - - +
227D LEU 3.4 0.2 - - - -
228D GLY* 3.5 2.1 + - - -
229D ALA* 3.4 20.8 + - - +
262D ILE* 3.7 17.5 - - - +
265D SER* 4.4 9.6 + - - -
266D LEU* 3.3 27.2 - - - +
269D GLN* 5.1 2.3 + - - -
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Residues in contact with ILE 226 (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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222D GLU* 3.2 21.5 + - + +
223D PRO* 2.9 15.1 + - + +
225D SER* 1.3 76.7 - - - +
227D LEU* 1.3 64.8 + - + +
228D GLY 3.2 0.4 - - - -
229D ALA* 3.4 13.8 + - + +
230D SER* 3.5 10.2 + - - -
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Residues in contact with LEU 227 (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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223D PRO* 3.2 12.7 + - + +
224D LEU* 3.6 25.8 - - + +
226D ILE* 1.3 80.6 - - + +
228D GLY* 1.3 58.5 + - - +
230D SER* 3.0 28.2 - - - -
233D GLY* 3.6 11.8 - - - -
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Residues in contact with GLY 228 (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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224D LEU 3.2 10.0 + - - -
225D SER 3.5 4.9 + - - -
226D ILE 3.2 0.8 - - - -
227D LEU* 1.3 75.1 - - - +
229D ALA* 1.3 57.6 + - - +
230D SER 3.2 8.5 + - - +
233D GLY* 4.6 2.9 - - - -
234D ALA 4.4 4.7 + - - -
259D MET* 4.2 15.3 - - - -
262D ILE* 4.0 16.2 - - - -
263D TRP* 4.0 6.1 + - - -
266D LEU* 4.2 3.6 - - - -
284D ILE* 3.1 22.0 - - - +
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Residues in contact with ALA 229 (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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225D SER 3.4 11.7 + - - +
226D ILE* 3.4 7.8 + - - +
227D LEU 3.3 0.6 - - - -
228D GLY* 1.3 74.4 - - - +
230D SER* 1.3 69.4 + - - +
266D LEU* 3.7 23.8 - - + +
282D ASN* 4.8 14.6 - - + +
283D THR* 5.8 0.5 - - - -
284D ILE* 3.8 16.2 + - + +
364D TYR* 4.2 10.4 + - - -
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Residues in contact with SER 230 (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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226D ILE 3.5 8.1 + - - -
227D LEU* 3.0 28.8 + - - +
228D GLY 3.2 1.0 - - - +
229D ALA* 1.3 85.0 - - - +
231D LEU* 1.3 71.4 + - - +
232D TRP* 2.8 21.1 + - - +
233D GLY 3.2 5.0 + - - -
234D ALA* 3.4 20.3 + - - +
284D ILE* 4.1 1.2 - - - +
364D TYR* 4.3 3.0 - - - -
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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