Contacts of the helix formed by residues 213 - 223 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TYR 4.6 4.7 - - - +
186A THR* 4.6 6.5 - - - +
187A ILE 5.8 0.7 - - - -
207A TRP* 4.1 15.7 - - + -
208A LEU 3.5 24.0 - - - +
209A CYS* 3.5 27.6 - - + -
210A ASN 2.8 20.8 + - - +
211A CYS 2.8 0.4 + - - -
212A GLU* 1.3 79.4 - - - +
214A LEU* 1.3 60.5 + - - +
215A TYR 3.3 2.5 - - - -
216A PHE* 3.6 24.2 + - + +
217A ARG* 3.1 20.6 + - - +
256A VAL* 3.7 21.8 - - + -
259A TYR* 3.7 17.7 - - + -
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Residues in contact with LEU 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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211A CYS* 3.1 19.1 + - + +
212A GLU 3.5 0.2 - - - -
213A ILE* 1.3 77.5 - - - +
215A TYR* 1.3 64.7 + - - +
216A PHE 3.4 0.2 - - - -
217A ARG* 3.5 36.8 + - - +
218A ARG* 3.1 22.9 + - - +
259A TYR* 3.8 28.7 - - + -
261A GLY* 4.4 4.3 - - - +
264A CYS* 3.4 30.7 - - + -
265A PRO* 3.7 15.3 - - + +
266A THR 5.9 0.7 - - - -
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Residues in contact with TYR 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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187A ILE* 3.9 23.1 - - + +
188A PRO 3.5 14.1 - - - -
189A LYS* 3.9 17.3 - - + -
190A GLY* 3.1 39.3 - - - -
191A PHE 3.4 9.4 - - - -
192A PHE* 3.2 31.4 + + - +
193A GLY 3.6 11.3 + - - -
212A GLU 5.1 3.0 - - - +
213A ILE 3.3 1.0 - - - -
214A LEU* 1.3 79.9 - - - +
216A PHE* 1.3 65.4 + - - +
218A ARG* 3.3 11.1 + - + +
219A TRP* 3.0 26.6 + + + +
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Residues in contact with PHE 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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187A ILE* 3.7 25.3 + - + +
192A PHE* 3.6 36.1 - + - -
202A LEU* 3.7 27.4 - - + -
207A TRP* 3.9 21.1 - + - -
213A ILE* 3.6 32.2 + - + +
214A LEU 3.4 0.2 - - - -
215A TYR* 1.3 85.3 - - - +
217A ARG* 1.3 51.9 + - - +
219A TRP* 3.2 5.4 + + - +
220A LEU* 2.7 65.4 + - + +
246A VAL* 3.5 23.8 - - + -
256A VAL* 5.0 0.2 - - + -
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Residues in contact with ARG 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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213A ILE 3.1 16.0 + - - +
214A LEU* 3.5 36.9 + - + +
215A TYR 3.1 0.2 - - - -
216A PHE* 1.3 72.9 - - - +
218A ARG* 1.3 68.3 + - - +
220A LEU* 3.1 9.1 + - - +
221A GLN* 3.0 44.7 + - - +
256A VAL* 3.5 27.8 - - + +
257A TYR* 3.9 8.3 - - - -
259A TYR* 2.7 40.3 + - + -
260A PRO* 3.1 19.0 + - - +
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Residues in contact with ARG 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 LEU 3.1 10.2 + - - +
215A TYR* 3.8 13.5 - - + +
217A ARG* 1.3 80.3 - - - +
219A TRP* 1.3 59.5 + - - +
221A GLN* 2.9 16.8 + - + +
222A ASP* 2.8 55.5 + - - +
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Residues in contact with TRP 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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192A PHE* 3.3 62.2 - + + +
193A GLY 5.4 3.1 - - - -
195A HIS 5.4 4.8 + - - -
197A LEU* 4.4 18.7 - - + +
200A ALA* 3.7 24.9 - - + -
202A LEU* 3.6 22.9 - - + -
215A TYR* 3.0 22.8 + + + +
216A PHE* 3.3 15.5 - + - +
218A ARG* 1.3 77.5 - - - +
220A LEU* 1.3 69.2 + - + +
222A ASP* 3.0 7.7 + - - -
223A ASN* 2.7 77.5 + - + +
226A ASN* 5.4 0.9 - - + -
227A VAL* 4.0 15.7 - - + -
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Residues in contact with LEU 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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202A LEU* 4.4 0.2 - - + -
216A PHE* 2.7 51.2 + - + +
217A ARG* 3.3 7.9 - - - +
219A TRP* 1.3 86.4 - - + +
221A GLN* 1.3 54.1 + - - +
223A ASN 4.9 0.2 - - - -
224A ALA* 2.6 39.0 + - - +
227A VAL* 4.1 2.0 - - + -
243A VAL* 3.5 18.3 - - + +
246A VAL* 3.9 29.6 - - + -
256A VAL* 3.4 42.2 - - + -
257A TYR* 3.9 12.3 - - + +
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Residues in contact with GLN 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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217A ARG* 3.0 41.0 + - - +
218A ARG* 2.9 15.0 + - + +
220A LEU* 1.3 75.0 - - - +
222A ASP* 1.3 68.2 + - - +
223A ASN 3.1 0.9 + - - -
224A ALA* 3.3 18.2 + - - +
225A GLU* 5.6 1.2 - - - +
257A TYR* 3.7 28.1 - - + +
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Residues in contact with ASP 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 ARG* 2.8 53.1 + - - +
219A TRP* 3.6 3.4 + - - +
221A GLN* 1.3 72.9 - - - +
223A ASN* 1.3 74.7 + - - +
224A ALA 3.6 0.4 + - - -
225A GLU* 5.2 5.4 - - - +
226A ASN* 4.9 1.0 + - - -
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Residues in contact with ASN 223 (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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195A HIS 5.4 2.1 - - - +
196A LEU* 4.3 12.6 - - - +
197A LEU 4.8 3.6 + - - +
219A TRP* 2.7 79.4 + - + +
220A LEU 3.3 2.7 - - - -
222A ASP* 1.3 88.0 - - - +
224A ALA* 1.3 50.9 + - - -
225A GLU* 2.9 7.2 - - - -
226A ASN* 2.5 53.1 + - + +
227A VAL* 3.5 6.6 + - - +
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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