Contacts of the helix formed by residues 209 - 222 (chain A) in PDB entry 1QO0
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 GLY 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PRO* 4.1 16.8 - - - -
186A LEU* 4.2 5.5 - - - +
205A VAL* 4.7 5.8 - - - -
208A THR* 1.3 79.4 - - - +
210A THR* 1.3 58.8 + - - +
211A ALA 4.5 0.4 - - - +
212A GLU* 3.0 26.1 + - - +
213A LEU* 2.9 30.2 + - - +
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 5.5 0.2 - - - +
205A VAL* 3.7 28.5 + - + +
207A GLY 2.7 31.6 + - - -
208A THR 3.8 0.2 + - - -
209A GLY* 1.3 76.0 - - - +
211A ALA* 1.3 62.2 + - - +
213A LEU* 3.3 3.2 + - - +
214A TYR* 3.1 53.5 + - + -
234A THR* 3.8 14.4 - - - +
238A GLU* 3.7 25.5 - - + +
242A MET* 4.2 2.9 - - + -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLY 3.4 0.6 - - - +
210A THR* 1.3 77.5 - - - +
212A GLU* 1.3 74.3 + - - +
214A TYR* 3.3 4.9 + - - +
215A ARG* 3.0 30.2 + - - +
238A GLU* 4.3 4.7 - - - +
241A LYS* 3.9 39.5 - - + +
242A MET* 4.2 22.4 - - + +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 4.1 18.4 - - + -
208A THR* 4.7 7.1 - - - +
209A GLY* 3.0 32.1 + - - +
211A ALA* 1.3 86.9 + - - +
213A LEU* 1.3 56.6 + - - +
215A ARG* 3.4 30.4 + - - +
216A ALA* 2.9 31.2 + - - +
241A LYS* 6.0 1.4 - - - +
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 4.2 22.9 - - + -
177A ILE* 4.9 1.3 - - + -
186A LEU* 4.0 22.5 - - + +
189A ALA* 5.2 1.6 - - + -
190A VAL* 4.0 16.8 - - + -
193A ILE* 4.6 8.1 - - + -
203A SER* 4.3 5.2 - - - +
205A VAL* 3.6 38.4 - - + -
209A GLY 2.9 15.5 + - - +
210A THR 3.3 8.0 + - - +
212A GLU* 1.3 76.2 - - - +
214A TYR* 1.3 65.6 + - + +
216A ALA* 3.3 3.9 + - - +
217A ILE* 3.0 46.8 + - + +
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 4.3 10.1 - - - -
210A THR* 3.1 35.8 + - + +
211A ALA 3.3 6.9 + - - +
213A LEU* 1.3 84.1 - - + +
215A ARG* 1.3 59.6 + - - +
217A ILE* 3.6 2.5 + - - +
218A ALA* 3.1 26.3 + - - +
226A ARG* 5.7 0.2 + - - -
229A ILE* 3.2 56.0 + - + +
231A SER* 3.5 9.4 - - - -
234A THR* 2.7 27.0 + - + -
239A VAL* 6.0 0.9 - - + -
242A MET* 3.3 29.6 - - + -
246A VAL* 3.5 14.0 - - + +
250A GLN* 4.0 29.3 + - + +
252A VAL* 5.2 2.3 - - + +
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Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ALA* 3.0 23.1 + - - +
212A GLU* 3.4 42.2 + - - +
214A TYR* 1.3 71.7 - - - +
216A ALA* 1.3 62.1 + - - +
218A ALA* 3.2 2.8 + - - +
219A ARG* 2.9 44.0 + - + +
241A LYS 4.2 16.4 + - - -
242A MET* 5.2 4.2 - - - +
243A GLU* 3.7 29.2 + - - +
246A VAL* 3.7 19.9 - - + +
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 5.5 5.6 - - + -
187A GLN* 4.1 17.5 + - - +
190A VAL* 3.6 21.3 - - + +
212A GLU 2.9 18.5 + - - +
213A LEU* 3.3 5.6 + - - +
215A ARG* 1.3 74.7 - - - +
217A ILE* 1.3 63.8 + - - +
219A ARG* 4.3 4.6 - - - +
220A ARG* 3.0 24.8 + - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 4.2 19.5 - - + -
193A ILE* 3.7 34.3 - - + -
201A VAL* 4.7 8.1 - - + -
213A LEU* 3.0 35.6 + - + +
214A TYR 3.9 4.9 - - - +
215A ARG 3.3 0.4 - - - -
216A ALA* 1.3 74.0 - - - +
218A ALA* 1.3 64.9 + - - +
220A ARG* 3.3 6.9 + - - +
221A TYR* 3.3 38.5 - - + -
226A ARG* 5.2 5.8 - - - +
227A PRO* 5.2 8.3 - - + +
229A ILE* 3.8 33.7 - - + -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TYR 3.1 16.1 + - - +
215A ARG 3.4 8.1 - - - +
217A ILE* 1.3 78.4 - - - +
219A ARG* 1.3 66.1 + - - +
221A TYR* 3.5 3.1 + - - +
222A GLY* 3.2 26.5 + - - +
226A ARG* 3.6 40.0 + - - +
246A VAL* 3.9 19.3 - - + -
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Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 2.9 29.9 + - + +
216A ALA* 4.3 4.9 - - - +
218A ALA* 1.3 85.0 + - - +
220A ARG* 1.3 64.8 + - - +
221A TYR 3.2 1.6 - - - -
222A GLY* 3.1 15.7 + - - +
226A ARG* 4.7 4.4 - - - +
243A GLU* 2.7 34.2 + - - -
245A ASP* 2.8 30.1 + - - -
246A VAL* 3.6 10.1 - - - +
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLN* 5.9 2.7 - - - +
190A VAL* 3.6 20.2 - - + -
191A GLU* 2.8 35.2 + - - +
194A TYR* 3.5 60.9 + - + +
195A GLN* 5.0 0.6 + - - -
216A ALA 3.0 19.0 + - - +
217A ILE* 3.3 6.7 + - - +
219A ARG* 1.3 76.5 - - - +
221A TYR* 1.3 60.3 + - + +
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Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL 5.9 0.2 - - - -
193A ILE* 3.9 12.1 + - + +
194A TYR* 3.5 56.3 + + + -
197A ARG* 4.7 11.1 - - + -
198A ALA 4.9 0.2 + - - -
217A ILE* 3.3 33.1 + - + -
218A ALA 4.0 5.2 - - - +
219A ARG 3.2 0.4 - - - -
220A ARG* 1.3 80.4 - - + +
222A GLY* 1.3 57.1 + - - +
223A ASP* 2.6 27.7 - - - +
224A GLY* 4.6 3.4 - - - +
225A ARG 3.7 19.7 - - - -
226A ARG* 3.7 22.0 - - + -
227A PRO* 3.4 34.5 - - + +
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA 3.2 13.8 + - - +
219A ARG* 3.1 20.0 + - - -
221A TYR* 1.3 78.9 - - - +
223A ASP* 1.3 60.6 + - - -
224A GLY 4.1 3.1 + - - +
226A ARG* 5.3 6.4 + - - -
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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