Contacts of the helix formed by residues 260 - 272 (chain A) in PDB entry 1AOX
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.7 11.4 - - - -
257A SER* 3.1 20.4 + - - -
258A HIS 3.6 2.2 - - - -
259A ASP* 1.3 72.3 - - - +
261A SER* 1.3 59.4 + - - +
262A MET 3.0 7.5 + - - -
263A LEU* 3.2 19.4 + - - +
299A GLU* 4.4 4.7 - - - -
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Residues in contact with SER 261 (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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259A ASP* 4.3 5.4 + - - -
260A GLY* 1.3 76.7 - - - +
262A MET* 1.3 60.5 + - - +
263A LEU 3.3 1.7 + - - -
264A LYS* 5.0 2.8 + - - +
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Residues in contact with MET 262 (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 PHE* 3.6 23.3 - - + +
225A GLY* 4.6 4.5 - - - +
228A GLN* 4.6 14.1 - - + +
259A ASP* 3.1 33.2 - - - +
260A GLY 3.0 1.4 - - - -
261A SER* 1.3 79.6 + - - +
263A LEU* 1.3 63.0 + - - +
264A LYS 3.4 2.5 - - - -
265A ALA* 3.6 10.5 + - + +
266A VAL* 3.1 44.1 + - + +
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Residues in contact with LEU 263 (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 PHE* 3.2 44.4 - - + -
260A GLY 3.2 17.7 + - - +
261A SER 3.3 1.2 - - - -
262A MET* 1.3 78.2 - - - +
264A LYS* 1.3 69.9 + - + +
266A VAL* 4.0 0.5 - - - +
267A ILE* 3.0 48.7 + - + +
299A GLU* 4.8 4.5 - - + +
302A ALA* 4.2 28.9 - - + +
303A ILE* 4.2 4.3 - - + -
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Residues in contact with LYS 264 (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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261A SER 5.0 1.0 + - - -
262A MET 3.4 0.4 - - - -
263A LEU* 1.3 86.7 - - + +
265A ALA* 1.3 61.1 + - - +
267A ILE* 4.3 1.7 - - - +
268A ASP* 2.8 65.7 + - - +
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Residues in contact with ALA 265 (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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228A GLN* 6.0 0.2 - - - +
262A MET* 3.6 12.8 + - + +
263A LEU 3.5 0.4 - - - -
264A LYS* 1.3 77.8 - - - +
266A VAL* 1.3 61.4 + - + +
268A ASP* 3.6 6.0 - - - +
269A GLN* 3.0 42.2 + - - +
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Residues in contact with VAL 266 (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 PHE* 4.1 17.3 - - + +
227A ILE* 3.5 35.2 - - + -
228A GLN* 4.0 27.8 - - - +
262A MET* 3.1 47.3 + - + +
263A LEU 4.1 1.8 - - - +
265A ALA* 1.3 73.9 - - + +
267A ILE* 1.3 62.9 + - + +
269A GLN* 3.3 8.3 + - - +
270A CYS* 3.0 27.5 + - - -
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Residues in contact with ILE 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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224A PHE* 4.4 9.0 - - + -
227A ILE* 4.6 6.3 - - + -
263A LEU* 3.0 34.7 + - + +
264A LYS* 4.3 2.5 - - - +
266A VAL* 1.3 87.6 - - + +
268A ASP* 1.3 66.3 + - - +
270A CYS* 3.8 5.6 - - - +
271A ASN* 3.1 29.7 + - - +
277A ARG* 3.9 39.9 - - - +
302A ALA 4.1 22.7 - - - +
303A ILE* 4.4 10.5 - - + -
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Residues in contact with ASP 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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264A LYS* 2.8 58.0 + - - +
265A ALA* 3.6 6.8 - - - +
267A ILE* 1.3 80.6 - - - +
269A GLN* 1.3 62.0 + - + +
271A ASN* 3.2 12.8 + - - +
272A HIS* 3.0 23.1 + - - +
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Residues in contact with GLN 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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228A GLN* 2.8 40.3 + - - +
231A ARG* 3.2 32.2 - - - +
265A ALA* 3.0 29.5 + - - +
266A VAL* 3.3 7.5 - - - +
268A ASP* 1.3 78.1 - - + +
270A CYS* 1.3 61.2 + - - +
272A HIS* 3.2 7.3 + - - +
273A ASP* 3.0 29.2 + - - +
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Residues in contact with CYS 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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227A ILE* 3.8 27.1 - - - -
231A ARG* 4.1 21.3 - - - +
249A MET* 4.7 4.9 - - - -
266A VAL* 3.0 22.5 + - - +
267A ILE* 3.8 7.2 - - - +
268A ASP 3.3 0.2 - - - -
269A GLN* 1.3 76.8 - - - +
271A ASN* 1.3 59.8 + - - +
273A ASP 3.3 1.8 + - - +
274A ASN 3.2 3.5 + - - -
275A ILE* 3.0 42.4 + - + +
277A ARG* 3.6 26.9 - - - +
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Residues in contact with ASN 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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267A ILE* 3.1 26.0 + - - +
268A ASP* 3.5 14.9 + - - +
270A CYS* 1.3 75.4 - - - +
272A HIS* 1.3 65.6 - - - +
274A ASN* 3.0 20.5 + - - +
275A ILE 4.9 1.5 - - - +
277A ARG* 2.8 32.1 + - - +
305A SER* 5.3 0.2 + - - -
306A ILE* 5.9 5.1 - - - +
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Residues in contact with HIS 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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268A ASP 3.0 12.8 + - - +
269A GLN* 3.5 12.1 - - - +
271A ASN* 1.3 77.6 - - - +
273A ASP* 1.3 75.9 + - - +
274A ASN* 3.3 9.2 + - - +
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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