Contacts of the helix formed by residues 207 - 221 (chain I) in PDB entry 1QDU
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 THR 207 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175I LYS* 5.9 3.4 - - + -
206I CYS* 1.3 73.5 - - - +
208I VAL* 1.3 65.2 + - - +
209I GLU* 3.4 9.9 + - - +
210I GLN* 2.3 54.4 + - - +
211I ILE* 2.9 17.2 + - - +
245I GLY* 4.0 0.4 - - - -
246I THR* 3.5 17.0 - - + +
247I ASP* 3.5 30.7 - - + +
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Residues in contact with VAL 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207I THR* 1.3 72.4 - - - +
209I GLU* 1.3 65.9 + - - +
211I ILE* 2.9 21.0 + - + +
212I TYR* 3.1 39.1 + - + -
245I GLY* 3.6 10.9 - - - +
247I ASP* 3.2 6.1 + - - -
254I GLN* 3.2 51.4 - - + +
255I GLU 3.5 16.8 - - - +
256I ALA* 4.2 6.7 - - + +
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Residues in contact with GLU 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207I THR* 3.2 8.4 + - - +
208I VAL* 1.3 82.7 - - - +
210I GLN* 1.3 63.9 + - - +
212I TYR* 3.2 9.7 + - + +
213I GLU* 2.9 41.6 + - - +
247I ASP* 5.0 1.2 + - - +
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Residues in contact with GLN 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I HIS 5.8 0.2 - - - -
205I ASP 3.8 6.0 + - - +
206I CYS* 3.1 20.0 - - + +
207I THR* 2.3 64.7 + - - +
209I GLU* 1.3 77.4 - - - +
211I ILE* 1.3 58.7 + - - +
213I GLU* 3.3 16.1 + - - +
214I ILE* 2.9 39.9 + - + +
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Residues in contact with ILE 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ILE* 3.5 43.7 - - + -
170I ASN* 4.1 9.2 - - - +
206I CYS* 3.7 17.0 - - + +
207I THR 2.9 18.6 + - - +
208I VAL* 2.9 9.8 + - + +
210I GLN* 1.3 77.0 - - - +
212I TYR* 1.3 64.0 + - + +
214I ILE* 3.3 7.0 + - - +
215I LEU* 3.0 35.7 + - + +
234I ILE* 4.9 3.1 - - + -
243I ILE* 4.7 17.5 - - + -
245I GLY* 4.7 4.5 - - - -
261I LEU* 4.6 17.7 - - + -
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Residues in contact with TYR 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I VAL* 3.1 43.3 + - + -
209I GLU* 3.7 7.9 - - + +
211I ILE* 1.3 73.8 - - + +
213I GLU* 1.3 57.7 + - - +
215I LEU* 3.1 3.4 + - + +
216I LYS* 2.7 38.0 + - - +
255I GLU 5.0 1.1 + - - -
256I ALA* 3.6 14.8 - - + +
257I PRO* 3.9 1.7 - - - +
260I GLU* 3.1 40.3 + - + +
261I LEU* 3.4 27.1 - - + -
264I GLN* 4.0 21.9 + - - +
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Residues in contact with GLU 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I GLU* 2.9 33.8 + - + +
210I GLN* 3.4 21.2 - - - +
212I TYR* 1.3 78.7 - - - +
214I ILE* 1.3 62.5 + - + +
216I LYS* 3.3 9.7 + - - +
217I ILE* 3.2 24.8 + - + +
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Residues in contact with ILE 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I LEU* 3.8 23.6 - - + -
168I ILE* 4.7 11.7 - - + -
203I HIS* 3.3 54.5 - - + +
206I CYS* 4.3 13.9 - - - -
210I GLN* 2.9 25.8 + - + +
211I ILE* 3.5 5.2 - - - +
213I GLU* 1.3 75.0 - - + +
215I LEU* 1.3 66.7 + - - +
217I ILE* 3.0 27.6 + - + +
218I TYR* 3.3 12.3 - - + -
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Residues in contact with LEU 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I LEU* 4.0 13.5 - - + -
168I ILE* 4.6 5.6 - - + -
211I ILE* 3.0 29.0 + - + +
212I TYR* 3.8 3.8 - - - +
214I ILE* 1.3 75.5 - - - +
216I LYS* 1.3 53.0 + - - +
217I ILE 3.1 0.2 + - - -
218I TYR* 3.2 2.5 + - - +
219I GLN* 2.7 39.0 + - - +
232I CYS* 4.0 24.9 - - - -
234I ILE* 5.4 1.8 - - + -
261I LEU* 3.5 51.8 - - + +
264I GLN* 4.0 11.9 - - - +
265I PHE* 3.7 27.7 - - + -
280I PHE* 5.2 0.4 - - + -
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Residues in contact with LYS 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I TYR 2.7 17.7 + - - +
213I GLU* 3.4 9.2 - - + +
214I ILE 3.2 0.2 - - - -
215I LEU* 1.3 77.2 - - - +
217I ILE* 1.3 61.7 - - + +
219I GLN* 3.4 15.9 + - - +
220I LEU* 3.1 45.6 + - + +
264I GLN* 4.1 9.3 - - - +
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Residues in contact with ILE 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I HIS* 6.4 2.5 - - + -
213I GLU* 3.2 15.1 + - + +
214I ILE* 3.0 16.0 + - + +
215I LEU 3.0 0.8 - - - -
216I LYS* 1.3 76.9 - - + +
218I TYR* 1.3 71.4 + - + +
220I LEU* 2.8 28.3 + - - +
221I MET* 3.1 31.7 + - + +
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Residues in contact with TYR 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I TYR* 3.6 37.7 - + + -
166I LEU* 3.7 37.9 - - + -
201I LYS* 3.0 33.6 - - + +
203I HIS* 4.4 8.5 + + - -
214I ILE* 3.3 23.3 - - + -
215I LEU 3.2 2.8 + - - +
217I ILE* 1.3 90.0 - - + +
219I GLN* 1.3 60.6 + - - +
220I LEU 3.5 0.2 + - - -
221I MET* 3.6 25.6 + - + +
224I HIS* 2.7 28.6 + + - +
230I PHE* 4.1 10.3 - + + -
265I PHE* 3.7 19.9 - - + -
270I CYS* 4.5 0.3 - - - -
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Residues in contact with GLN 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LEU 2.7 19.3 + - - +
216I LYS* 3.4 19.1 - - - +
217I ILE 2.9 0.2 - - - -
218I TYR* 1.3 80.2 - - - +
220I LEU* 1.3 78.6 + - - +
221I MET 4.6 0.2 - - - +
264I GLN* 2.9 44.1 + - + +
265I PHE* 3.7 11.6 - - + -
269I LYS* 2.8 36.5 + - - +
270I CYS* 3.6 19.1 - - + +
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Residues in contact with LEU 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216I LYS* 3.1 42.6 - - + +
217I ILE* 2.8 8.8 + - - +
219I GLN* 1.3 97.5 - - - +
221I MET* 1.3 65.2 + - - +
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Residues in contact with MET 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I TYR* 3.4 38.4 - - + +
201I LYS* 6.0 2.0 - - - -
217I ILE* 3.1 28.9 + - + +
218I TYR* 3.6 26.0 + - + +
219I GLN 3.5 3.8 - - - +
220I LEU* 1.3 82.5 - - - +
222I ASP* 1.3 63.3 + - - +
224I HIS* 3.6 19.4 - - + +
270I CYS* 4.7 0.3 - - - -
272I SER* 2.9 17.2 + - - -
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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