Contacts of the strand formed by residues 293 - 296 (chain R) in PDB entry 1U8F
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 293 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155R ASN 4.3 2.7 - - - -
156R CYS* 2.9 30.3 + - - -
159R PRO* 4.5 5.2 - - - -
160R LEU* 4.4 2.1 - - - +
273R ILE 3.0 5.7 + - - +
274R LEU* 3.1 21.3 - - - +
275R GLY 2.6 31.2 + - - -
291R HIS* 3.3 1.7 - - - +
292R SER* 1.3 80.9 - - - +
294R THR* 1.3 55.6 + - - +
312R SER* 2.4 27.5 + - - -
313R TRP 3.4 8.1 - - - -
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Residues in contact with THR 294 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275R GLY* 3.4 17.4 - - - -
276R TYR 4.1 3.1 - - - +
277R THR* 4.1 10.3 - - + +
286R PHE* 3.5 39.7 - - + -
289R ASP* 4.3 0.5 + - - -
291R HIS* 3.6 23.4 - - - +
293R SER* 1.3 75.9 + - - +
295R PHE* 1.3 71.0 + - - +
296R ASP 3.4 0.9 + - - -
312R SER* 3.1 5.3 + - - -
313R TRP* 2.9 40.4 + - - -
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Residues in contact with PHE 295 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160R LEU* 3.8 24.2 - - + -
255R TYR* 3.7 21.1 - + - -
258R ILE* 4.2 18.2 - - + -
259R LYS* 4.3 11.0 - - + -
262R VAL* 3.5 26.7 - - + -
274R LEU* 4.4 5.3 - - + +
275R GLY 2.9 12.0 + - - +
276R TYR* 3.6 30.1 - + + -
277R THR* 3.0 30.5 + - - +
293R SER 4.1 0.4 - - - -
294R THR* 1.3 71.3 - - - +
296R ASP* 1.3 58.3 + - - +
297R ALA* 3.6 21.7 + - + -
310R LEU* 4.0 26.5 - - + -
311R ILE 3.6 16.4 - - - -
312R SER* 3.7 4.8 + - - -
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Residues in contact with ASP 296 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197Q ARG* 2.8 30.8 + - - -
255R TYR* 4.0 2.6 + - - -
277R THR* 4.0 6.9 - - - +
279R HIS 4.4 2.9 - - - +
281R VAL* 3.4 8.7 - - - +
294R THR 3.4 0.8 + - - -
295R PHE* 1.3 72.1 - - - +
297R ALA* 1.3 63.7 + - - +
298R GLY 3.4 2.6 + - - -
299R ALA* 3.0 36.4 + - + +
300R GLY* 3.6 7.8 + - - -
311R ILE* 2.8 21.9 + - + +
313R TRP* 2.8 36.2 + - + +
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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