Contacts of the helix formed by residues 213 - 223 (chain G) in PDB entry 1QYY
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 ILE 213 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185G TYR 4.3 2.7 - - - +
186G THR* 4.0 25.1 - - - +
187G ILE 4.4 0.4 - - - +
207G TRP* 4.7 6.7 - - + -
208G LEU 3.6 18.2 - - - +
209G CYS* 3.6 17.0 - - + -
210G ASN 3.0 21.5 + - - +
212G GLU* 1.3 79.4 - - - +
214G LEU* 1.3 67.0 + - - +
215G TYR 3.2 2.5 - - - -
216G PHE* 3.3 31.8 + - + +
217G ARG* 3.1 16.1 + - - +
256G VAL* 3.8 19.5 - - + -
259G TYR* 3.6 24.2 - - + -
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Residues in contact with LEU 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 5.8 2.7 - - + -
211G CYS* 3.7 18.6 - - - +
212G GLU 3.5 1.0 - - - -
213G ILE* 1.3 79.6 - - - +
215G TYR* 1.3 57.9 + - - +
217G ARG* 3.0 38.1 + - - +
218G ARG* 2.9 27.4 + - - +
259G TYR* 3.6 32.1 - - + -
261G GLY* 4.0 5.6 - - - +
264G CYS* 3.4 29.8 - - + -
265G PRO 4.2 11.2 - - - +
266G THR* 4.3 8.5 - - + +
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Residues in contact with TYR 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G ILE* 4.1 15.5 - - + +
188G PRO 3.2 19.3 - - - -
189G LYS* 3.5 21.3 - - + -
190G GLY* 2.8 36.0 - - - -
191G PHE* 3.2 6.4 + - + -
192G PHE* 3.1 35.4 + + - +
193G GLY 3.6 7.0 + - - -
194G SER* 5.4 0.3 - - - -
212G GLU 5.0 4.6 + - - +
213G ILE* 3.2 1.0 - - - +
214G LEU* 1.3 79.4 - - - +
216G PHE* 1.3 62.0 + - - +
218G ARG* 3.2 44.1 + - - +
219G TRP* 3.1 25.5 + + + +
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Residues in contact with PHE 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G ILE* 3.5 31.4 + - + +
192G PHE* 3.7 26.9 - + - -
202G LEU* 3.3 39.9 - - + -
207G TRP* 3.7 17.0 - + - -
213G ILE* 3.3 34.5 + - + +
215G TYR* 1.3 79.7 - - - +
217G ARG* 1.3 61.1 + - - +
219G TRP* 3.9 5.6 - + - -
220G LEU* 3.0 44.3 + - + +
246G VAL* 3.7 20.4 - - + -
256G VAL* 4.8 2.2 - - + -
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Residues in contact with ARG 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLY 3.3 9.3 + - - -
234A VAL* 2.7 30.6 + - - +
235A ASP* 4.4 6.2 - - - +
236A VAL* 4.5 12.5 - - - +
213G ILE 3.1 12.4 + - - +
214G LEU* 3.0 40.4 + - - +
216G PHE* 1.3 75.6 - - - +
218G ARG* 1.3 66.1 + - - +
220G LEU* 3.5 10.0 + - - +
221G GLN* 3.0 37.9 + - - +
256G VAL* 3.5 24.4 - - + +
257G TYR* 3.8 13.0 - - - +
259G TYR* 2.6 42.4 + - + -
260G PRO 3.6 13.3 + - - -
261G GLY* 4.4 1.0 + - - -
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Residues in contact with ARG 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G LYS* 3.9 26.5 - - - +
214G LEU 2.9 12.3 + - - +
215G TYR* 3.2 40.3 - - - +
217G ARG* 1.3 79.2 - - - +
219G TRP* 1.3 63.9 + - - +
221G GLN* 3.3 9.9 + - - +
222G ASP* 2.9 36.0 + - - +
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Residues in contact with TRP 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G PHE* 3.2 66.8 - + + +
194G SER* 6.5 0.4 - - - -
195G HIS 3.7 11.2 + - - -
197G LEU* 4.1 21.1 - - + -
200G ALA* 4.3 17.3 - - + -
202G LEU* 3.9 21.8 - - + -
215G TYR* 3.1 19.9 + + + +
216G PHE* 3.5 17.9 - + - +
217G ARG 3.2 0.2 - - - -
218G ARG* 1.3 77.1 - - - +
220G LEU* 1.3 80.0 + - - +
222G ASP* 2.7 17.8 + - - -
223G ASN* 2.7 57.1 + - + +
226G ASN* 5.1 1.1 - - + -
227G VAL* 4.2 12.3 - - + -
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Residues in contact with LEU 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G LEU* 4.0 7.0 - - + -
216G PHE* 3.0 49.6 + - + +
217G ARG* 3.8 4.3 - - - +
219G TRP* 1.3 81.8 - - + +
221G GLN* 1.3 57.0 + - - +
223G ASN 3.4 1.5 - - - +
224G ALA* 2.9 31.2 + - - +
227G VAL* 4.2 5.6 - - + -
243G VAL* 3.6 23.6 - - + +
246G VAL* 3.7 32.8 - - + -
256G VAL* 3.7 36.1 - - + -
257G TYR* 4.1 12.3 - - + +
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Residues in contact with GLN 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLN 4.8 3.4 + - - -
233A GLY* 3.9 17.7 + - - +
234A VAL 5.2 0.2 - - - +
235A ASP* 4.1 15.6 + - - +
217G ARG* 3.0 32.8 + - - +
218G ARG* 3.5 8.2 - - - +
219G TRP 2.8 1.8 + - - -
220G LEU* 1.3 79.2 - - - +
222G ASP* 1.3 62.9 + - - +
223G ASN 3.2 0.3 + - - -
224G ALA* 3.4 14.0 + - - +
257G TYR* 3.7 40.2 + - + -
258G LYS* 5.9 1.2 - - - +
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Residues in contact with ASP 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G ARG* 2.9 30.3 + - - +
219G TRP* 2.7 12.0 + - - +
221G GLN* 1.3 75.4 - - - +
223G ASN* 1.3 66.5 + - - +
224G ALA 3.5 0.7 + - - -
225G GLU 5.4 0.2 + - - -
226G ASN* 4.9 0.7 + - - -
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Residues in contact with ASN 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G HIS 4.0 3.5 + - - +
196G LEU* 3.8 21.7 - - - +
197G LEU 4.2 0.2 + - - -
219G TRP* 2.7 73.9 + - + +
220G LEU 3.4 4.0 - - - -
222G ASP* 1.3 84.7 - - - +
224G ALA* 1.3 56.3 + - - -
225G GLU 3.2 3.6 - - - -
226G ASN* 2.9 47.8 + - - +
227G VAL* 3.7 9.2 - - - +
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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