Contacts of the strand formed by residues 290 - 293 (chain Q) in PDB entry 3K9Q
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 SER 290 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154Q ASN 3.6 8.3 - - - -
155Q SER* 2.6 30.2 + - - +
158Q PRO* 3.7 5.2 - - - -
270Q SER 3.0 3.7 + - - +
271Q PHE* 3.3 27.5 - - - -
272Q GLY 2.7 31.5 + - - -
288Q TYR* 3.1 6.0 + - - +
289Q GLY* 1.3 80.5 - - - +
291Q LEU* 1.3 55.6 + - - +
292Q PHE 3.9 0.7 - - - -
312Q ALA* 3.6 7.3 - - - +
313Q TRP 3.6 7.6 - - - -
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Residues in contact with LEU 291 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53O ARG* 4.2 14.1 - - - +
272Q GLY* 3.4 29.2 - - - -
273Q TYR 3.6 14.6 - - - +
274Q THR* 4.0 13.9 - - + +
278Q ILE* 3.6 30.7 - - + -
283Q VAL* 4.1 11.7 - - + -
286Q MET* 3.6 23.8 - - + -
288Q TYR* 4.0 15.3 - - + -
290Q SER* 1.3 73.9 + - - +
292Q PHE* 1.3 63.9 + - - +
293Q ASP 3.4 1.0 + - - -
312Q ALA* 3.2 3.0 - - - -
313Q TRP* 2.8 41.4 + - + +
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Residues in contact with PHE 292 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159Q VAL* 4.2 12.8 - - + -
259Q VAL* 4.5 1.3 - - + -
260Q ASN* 3.3 22.4 - - - -
263Q MET* 3.5 49.8 - - + -
271Q PHE* 3.7 15.7 - - + -
272Q GLY 2.8 19.3 + - - +
273Q TYR* 4.0 12.1 - + + -
274Q THR* 2.8 31.6 + - - +
290Q SER 3.9 1.8 - - - -
291Q LEU* 1.3 71.7 - - - +
293Q ASP* 1.3 61.3 + - - +
294Q ALA* 3.8 11.7 - - + -
297Q THR* 3.4 19.5 - - - -
310Q VAL* 3.6 32.3 - - + -
311Q ALA 4.1 9.4 - - - -
312Q ALA* 4.2 2.5 - - - -
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Residues in contact with ASP 293 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274Q THR* 3.8 11.1 - - + +
276Q ASP 4.1 3.8 - - - +
278Q ILE* 4.4 1.0 - - - +
291Q LEU 3.4 0.6 + - - -
292Q PHE* 1.3 75.8 - - - +
294Q ALA* 1.3 63.6 + - - +
295Q THR* 2.6 30.3 + - - +
296Q GLN* 3.0 33.7 + - - +
297Q THR* 4.0 5.9 + - - -
311Q ALA 3.1 21.7 + - - +
313Q TRP* 2.9 35.2 + - + +
197R ARG* 3.1 14.9 + - - -
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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