Contacts of the helix formed by residues 266 - 274 (chain A) in PDB entry 3A3K
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 GLN 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ARG* 3.9 7.5 - - - +
221A ASN* 5.4 1.8 + - - -
224A LEU* 3.7 24.2 - - + +
264A ASP* 2.9 31.5 + - - +
265A GLY* 1.3 77.4 - - - +
267A ASP* 1.3 54.9 + - - +
268A ARG 3.3 2.7 - - - -
269A SER* 3.1 5.2 + - - -
270A ALA* 2.7 33.8 + - - +
501A SO4 4.0 0.7 - - - -
194B ASP 4.5 8.5 + - - -
197B PRO* 3.5 26.6 - - - +
198B LYS* 3.7 34.2 + - - +
201B ARG* 3.5 30.2 + - - +
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Residues in contact with ASP 267 (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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220A ARG* 3.0 16.9 + - - +
260A TRP* 3.6 17.2 - - + +
261A GLU* 3.3 19.4 - - - +
262A ARG 2.9 21.8 + - - -
263A GLY* 2.8 28.5 + - - -
264A ASP* 3.4 1.3 - - - +
266A GLN* 1.3 78.2 - - - +
268A ARG* 1.3 56.3 + - - +
270A ALA* 3.6 2.6 - - - +
271A ARG* 2.8 31.9 + - - +
501A SO4 3.1 20.7 + - - +
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Residues in contact with ARG 268 (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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267A ASP* 1.3 76.4 - - - +
269A SER* 1.3 63.5 + - - +
271A ARG* 3.4 7.7 + - - +
272A GLN* 3.1 24.6 + - - +
501A SO4 3.0 41.3 + - - +
201B ARG* 6.2 0.2 - - - +
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Residues in contact with SER 269 (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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224A LEU* 3.8 15.0 - - - -
227A LEU* 3.5 19.1 - - - +
266A GLN 3.1 6.0 + - - -
268A ARG* 1.3 75.3 - - - +
270A ALA* 1.3 60.6 + - - +
272A GLN* 3.2 6.3 + - - +
273A ALA* 2.8 29.5 + - - +
201B ARG* 2.8 38.3 + - - +
205B ARG* 3.7 12.0 + - - -
509B SO4 5.0 2.6 + - - -
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Residues in contact with ALA 270 (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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220A ARG* 3.8 19.1 - - + +
224A LEU* 3.6 13.2 - - + +
260A TRP* 3.3 33.2 - - + +
266A GLN 2.7 20.3 + - - +
267A ASP 3.6 2.5 - - - +
269A SER* 1.3 74.0 - - - +
271A ARG* 1.3 52.9 + - - +
273A ALA* 3.0 4.4 + - - +
274A PHE* 2.7 40.3 + - + -
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Residues in contact with ARG 271 (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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260A TRP* 3.9 40.2 - - + +
267A ASP 2.8 20.9 + - - +
268A ARG* 3.7 7.9 - - - +
270A ALA* 1.3 73.2 - - - +
272A GLN* 1.3 63.2 + - - +
274A PHE 3.3 6.8 + - - -
275A GLN* 3.4 18.8 + - - +
381A MET* 3.5 21.7 - - + +
383A PRO 3.1 26.3 + - - -
384A GLU 3.2 18.8 + - - -
385A THR 3.5 11.9 + - - -
386A GLY* 3.6 12.9 - - - +
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Residues in contact with GLN 272 (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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227A LEU* 4.1 29.0 - - + +
268A ARG 3.1 14.5 + - - +
269A SER* 3.5 12.4 + - - +
271A ARG* 1.3 76.8 - - - +
273A ALA* 1.3 62.1 + - - +
275A GLN* 3.5 32.4 + - - +
276A ALA* 5.7 0.3 - - - +
509B SO4 4.6 15.7 + - - -
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Residues in contact with ALA 273 (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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223A MET* 3.5 43.7 - - + +
224A LEU* 4.2 3.1 - - + +
227A LEU* 4.0 16.5 - - + +
269A SER 2.8 17.6 + - - +
270A ALA* 3.4 11.0 - - - +
272A GLN* 1.3 74.5 - - - +
274A PHE* 1.3 57.3 + - + +
275A GLN 3.1 5.6 + - - -
276A ALA* 3.2 21.5 + - - +
277A ALA 4.2 0.7 + - - -
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Residues in contact with PHE 274 (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 PRO 5.6 0.7 - - - -
219A PHE* 3.8 28.7 - + - -
220A ARG* 4.0 26.5 - - + -
223A MET* 3.9 21.5 - - + -
247A SER* 6.4 0.4 - - - -
259A PRO* 4.3 14.4 - - + -
260A TRP* 3.7 33.0 - + + -
270A ALA* 2.7 24.9 + - + +
271A ARG 3.3 5.6 + - - +
273A ALA* 1.3 71.6 - - + +
275A GLN* 1.3 63.0 + - - +
276A ALA 3.0 1.8 - - - -
277A ALA* 3.1 31.2 + - + +
279A ILE* 5.2 4.7 - - + -
381A MET* 3.9 16.5 - - + +
388A PHE* 3.7 29.1 - + + -
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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