Contacts of the helix formed by residues 212 - 222 (chain A) in PDB entry 1QAS
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 ALA 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A GLN 3.7 4.9 + - - -
211A ARG* 1.3 67.7 - - - +
213A GLU* 1.3 60.9 + - + +
215A ASP* 2.9 30.5 + - - +
216A ARG* 3.0 13.1 + - - +
683A ARG* 6.3 2.9 - - - -
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Residues in contact with GLU 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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211A ARG* 3.0 40.3 + - - +
212A ALA* 1.3 76.7 + - + +
214A ILE* 1.3 69.8 + - - +
216A ARG* 3.6 11.1 - - + +
217A ALA* 3.1 24.6 + - - +
636A ILE* 3.7 25.4 - - + -
637A SER* 3.6 20.7 + - - -
683A ARG* 4.9 11.4 - - + -
685A ASP* 5.2 2.7 - - - +
749A PHE* 3.1 28.2 - - + -
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Residues in contact with ILE 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 ARG* 2.9 52.7 + - + +
213A GLU* 1.3 78.0 + - - +
215A ASP* 1.3 57.7 + - - +
217A ALA* 4.2 2.0 - - - -
218A PHE* 3.1 26.3 + - - +
272A LYS* 4.3 20.2 - - + -
275A PHE* 3.7 10.3 - - + -
276A LEU* 3.4 35.7 - - + -
279A LEU* 3.9 25.1 - - + -
732A HIS* 4.2 1.6 - - + -
749A PHE* 4.1 12.1 - - + -
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Residues in contact with ASP 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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210A GLN* 4.6 4.9 - - - -
211A ARG 2.9 23.1 + - - +
212A ALA* 2.9 15.1 + - - +
214A ILE* 1.3 77.8 - - - +
216A ARG* 1.3 65.6 + - - +
219A GLU* 2.9 45.5 + - - +
272A LYS* 2.8 41.3 + - - +
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Residues in contact with ARG 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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212A ALA 3.0 11.3 + - - +
213A GLU* 3.6 15.0 - - + +
215A ASP* 1.3 78.2 - - - +
217A ALA* 1.3 58.6 + - - +
219A GLU* 4.0 9.3 - - - +
220A GLU* 3.1 68.5 + - - +
730A TYR* 3.1 16.8 + - - -
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Residues in contact with ALA 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 GLU 3.1 15.9 + - - +
214A ILE* 4.2 3.8 - - - +
216A ARG* 1.3 80.5 - - - +
218A PHE* 1.3 64.7 + - - +
220A GLU* 3.4 14.3 - - - +
221A ALA* 3.3 19.9 + - - +
236A PHE* 4.8 0.9 - - - -
275A PHE* 3.8 14.5 - - + -
730A TYR* 4.0 37.0 - - + +
749A PHE* 5.0 4.3 - - + -
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Residues in contact with PHE 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 ILE 3.1 20.4 + - - +
215A ASP 3.1 3.3 + - - +
217A ALA* 1.3 74.2 - - - +
219A GLU* 1.3 61.1 + - + +
221A ALA* 3.0 4.7 + - - +
222A ALA* 2.6 50.6 + - + +
225A ALA 5.1 0.4 - - - -
226A GLU* 3.7 22.2 - - + -
227A THR* 4.2 4.0 - - - -
228A LEU* 3.8 14.6 - - + -
270A MET 3.1 28.0 - - - -
271A THR 3.5 10.8 - - - -
272A LYS* 3.5 41.1 - - + -
275A PHE* 3.3 36.3 - + + -
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Residues in contact with GLU 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 ASP* 2.9 35.3 + - - +
216A ARG* 4.0 7.1 - - - +
218A PHE* 1.3 76.4 - - + +
220A GLU* 1.3 59.7 + - - +
221A ALA 2.9 5.4 - - - -
222A ALA* 4.0 5.4 - - + +
223A GLY* 2.7 43.6 + - - +
272A LYS* 5.6 3.3 - - - -
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Residues in contact with GLU 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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216A ARG* 3.1 56.3 + - - +
217A ALA 3.4 10.1 - - - +
219A GLU* 1.3 77.7 - - - +
221A ALA* 1.3 57.0 + - - +
223A GLY* 4.7 0.4 - - - -
232A ARG* 4.6 9.4 + - - -
236A PHE* 5.0 1.2 - - - -
240A GLN* 3.9 23.5 - - - +
730A TYR* 3.1 30.2 + - - -
751A LYS* 4.2 3.8 + - - -
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Residues in contact with ALA 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 ALA 3.3 10.3 + - - +
218A PHE* 3.0 8.7 + - - +
219A GLU 2.9 0.4 - - - -
220A GLU* 1.3 83.5 - - - +
222A ALA* 1.3 59.0 + - - +
223A GLY 3.5 0.2 - - - -
228A LEU* 3.4 23.6 - - + +
232A ARG* 3.3 31.8 + - - +
236A PHE* 3.9 32.8 - - + -
240A GLN* 5.9 0.2 - - + -
275A PHE* 4.8 0.9 - - + -
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Residues in contact with ALA 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 PHE* 2.6 38.4 + - + +
219A GLU* 4.3 2.7 - - + -
221A ALA* 1.3 74.4 - - - +
223A GLY* 1.3 62.0 + - - +
224A SER 3.5 3.1 + - - -
225A ALA* 3.5 32.7 - - - +
227A THR 3.9 15.0 - - - +
228A LEU* 3.7 11.2 - - + -
232A ARG* 4.1 13.2 + - - +
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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