Contacts of the strand formed by residues 291 - 298 (chain A) in PDB entry 5AQX
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A PHE* 3.9 20.4 - - + -
249A HIS* 3.4 48.2 - - + +
251A LYS* 4.9 10.1 - - + -
286A SER* 4.0 0.4 - - - +
287A LEU* 2.9 24.3 + - - +
288A PHE 3.2 21.6 + - - +
289A GLU* 3.8 16.2 - - + +
290A GLY* 1.4 76.3 - - - +
292A ASP* 1.3 70.0 + - - +
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Residues in contact with ASP 292 (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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249A HIS* 4.6 3.8 + - - -
284A ILE 3.4 5.8 - - - +
285A ASP* 3.5 8.0 - - - +
286A SER* 2.8 28.1 + - - +
290A GLY 3.6 5.0 + - - +
291A ILE* 1.3 87.5 - - - +
293A PHE* 1.3 60.8 + - - +
294A TYR* 3.7 26.8 + - + -
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Residues in contact with PHE 293 (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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241A PHE* 3.7 48.7 - + + -
244A GLU* 3.8 25.6 - - + -
245A PHE* 3.8 24.2 - + + -
248A LYS* 4.4 10.3 - - + -
249A HIS* 5.0 5.2 - - - -
263A LEU* 4.1 3.6 - - + -
282A LEU* 3.6 8.7 - - + +
284A ILE* 2.8 45.1 + - + +
287A LEU* 3.6 36.3 - - + -
291A ILE 3.8 0.8 + - - -
292A ASP* 1.3 73.4 - - - +
294A TYR* 1.3 61.8 + - - +
295A THR* 3.7 21.2 + - + -
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Residues in contact with TYR 294 (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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248A LYS* 4.6 5.2 + - - -
282A LEU 3.3 4.5 - - - +
283A GLU* 3.5 42.8 + - + +
284A ILE 3.7 13.9 - - - -
285A ASP* 2.6 32.1 + - - -
292A ASP* 3.7 25.3 + - + -
293A PHE* 1.3 75.8 - - - +
295A THR* 1.3 60.6 + - - +
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Residues in contact with THR 295 (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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241A PHE* 3.6 21.9 - - + -
244A GLU* 2.4 32.5 + - - +
248A LYS* 3.1 12.1 + - - +
281A SER* 3.2 8.0 - - - -
282A LEU* 2.8 39.1 + - + +
293A PHE* 3.7 22.7 - - + -
294A TYR* 1.3 75.3 - - - +
296A SER* 1.3 70.7 + - - +
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Residues in contact with SER 296 (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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240A HIS* 5.5 1.4 + - - -
241A PHE* 4.5 6.9 - - - -
244A GLU* 5.0 3.3 - - - +
279A GLN* 5.7 4.5 - - - -
280A ALA 3.3 11.9 - - - -
281A SER* 4.4 8.1 - - - -
282A LEU 4.7 0.4 - - - +
295A THR* 1.3 88.0 + - - +
297A ILE* 1.3 63.2 + - - +
298A THR* 6.0 1.0 - - - +
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Residues in contact with ILE 297 (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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237A LEU* 3.2 31.2 - - + -
240A HIS* 4.0 15.9 - - + +
241A PHE* 3.8 19.3 - - + -
270A ALA* 4.7 6.5 - - + -
274A LEU* 4.1 16.4 - - + +
279A GLN* 3.4 4.4 - - - +
280A ALA* 2.8 43.7 + - + +
282A LEU* 5.1 0.7 - - + -
296A SER* 1.3 76.0 - - - +
298A THR* 1.3 76.3 - - - +
301A ARG* 4.0 11.2 - - + -
302A PHE* 4.1 9.2 - - + +
305A LEU* 3.6 19.3 - - + -
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Residues in contact with THR 298 (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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274A LEU* 3.8 3.6 - - - -
278A THR* 3.2 9.2 - - - +
279A GLN* 4.4 6.5 - - + +
296A SER* 5.9 1.8 - - - +
297A ILE* 1.3 83.9 - - - +
299A ARG* 1.3 65.7 + - - +
300A ALA* 3.6 9.8 + - - +
301A ARG* 3.0 25.6 + - + +
302A PHE* 2.9 20.8 + - - +
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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