Contacts of the strand formed by residues 264 - 268 (chain R) in PDB entry 1UW9
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 264 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199R PHE* 4.3 9.0 - - + -
237R GLY* 4.2 8.7 - - - -
238R HIS 3.0 47.7 - - - +
239R TYR* 3.5 36.1 - - + -
240R LEU* 3.3 7.9 + - - +
262R VAL* 3.6 5.6 + - - +
263R PRO* 1.3 83.4 - - + +
265R ILE* 1.3 78.9 + - - +
289R LEU* 4.1 1.3 - - - +
290R PHE* 3.6 30.5 - - + +
291R LEU 4.9 0.2 - - - -
292R HIS* 4.2 7.9 - - + +
325R HIS* 3.9 20.0 - - + +
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Residues in contact with ILE 265 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218R PHE* 5.3 0.9 - - + -
239R TYR* 4.3 1.8 - - - -
240R LEU* 3.2 20.4 - - + +
242R ALA* 4.2 8.1 - - + -
253R ARG 5.1 1.1 - - - +
254R ALA* 4.0 16.2 - - + -
257R ALA* 3.5 32.8 - - + -
264R ILE* 1.3 82.4 - - - +
266R MET* 1.3 54.9 + - - +
280R LEU* 3.9 29.8 - - + -
284R CYS* 3.7 25.6 - - - -
289R LEU* 4.4 8.7 - - + +
290R PHE 3.1 14.6 + - - +
291R LEU* 4.1 2.7 - - + -
292R HIS 2.8 29.8 + - - -
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Residues in contact with MET 266 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201R KCX 3.6 20.0 - - - +
202R ASP* 3.2 29.4 - - - +
204R GLU* 4.0 4.9 - - - -
239R TYR* 3.6 30.3 - - + +
240R LEU 2.9 7.5 + - - -
241R ASN* 3.4 38.5 + - - +
242R ALA* 3.0 29.1 + - - +
265R ILE* 1.3 75.6 - - - +
267R HIS* 1.3 62.9 + - - +
268R ASP* 3.9 16.6 - - - +
291R LEU* 4.2 3.1 - - - +
292R HIS* 3.0 18.2 - - + +
294R HIS* 4.0 13.5 - - + -
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Residues in contact with HIS 267 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H THR* 4.9 2.7 - - - -
243R THR* 3.5 23.9 + - - -
244R ALA 5.3 0.2 - - - -
250R MET* 3.9 18.3 - - - -
266R MET* 1.3 75.8 - - - +
268R ASP* 1.3 77.7 + - - +
269R TYR* 3.3 13.6 + - - -
272R GLY* 3.9 15.7 - - - -
273R GLY 4.0 5.7 + - - -
276R ALA* 4.3 2.4 - - + +
277R ASN* 2.7 54.3 + - + +
280R LEU* 3.6 23.0 - - + +
291R LEU* 4.0 6.0 - - + +
292R HIS 2.9 6.5 + - - -
293R ILE* 3.4 6.6 - - + +
294R HIS* 3.0 21.9 + - - -
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Residues in contact with ASP 268 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H THR* 3.3 14.3 - - - +
204R GLU* 2.7 36.0 - - - +
241R ASN* 4.1 0.2 - - - +
243R THR* 2.9 30.5 + - + +
266R MET* 3.9 5.5 - - - +
267R HIS* 1.3 72.7 + - - +
269R TYR* 1.3 59.7 + - - +
270R LEU 3.3 2.6 + - - -
271R THR* 3.2 17.5 - - - +
272R GLY* 2.8 28.2 + - - -
294R HIS* 3.4 27.8 - - - +
296R ALA* 4.4 7.4 - - + -
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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