Contacts of the strand formed by residues 290 - 294 (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 PHE 290 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M LEU* 3.6 38.4 - - + -
153R HIS* 3.5 28.3 - + + -
158R GLU* 3.4 48.9 - - + +
161R LYS* 3.8 14.6 - - + -
162R LEU* 3.7 22.9 - - + -
199R PHE* 5.4 1.3 - + - -
263R PRO* 2.9 18.5 + - + +
264R ILE* 3.6 26.5 - - + -
265R ILE* 3.1 29.8 + - - +
288R GLY 4.2 0.6 + - - -
289R LEU* 1.3 76.0 - - - +
291R LEU* 1.3 58.8 + - - +
324R ASP* 3.3 11.0 - - + +
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Residues in contact with LEU 291 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R PRO* 4.1 10.8 - - + -
264R ILE* 4.9 1.3 - - - -
265R ILE* 3.5 15.5 - - + +
267R HIS* 4.0 15.3 - - + +
277R ASN* 4.5 4.3 - - - +
280R LEU* 3.7 28.7 - - + -
281R ALA* 3.7 34.1 - - + +
284R CYS* 4.0 9.9 - - - -
290R PHE* 1.3 74.3 - - - +
292R HIS* 1.3 63.4 + - - +
293R ILE* 3.6 14.1 + - + -
322R GLY 3.8 19.1 - - - +
323R GLY* 3.8 1.3 - - - -
324R ASP* 2.8 39.7 + - - +
325R HIS 3.3 4.2 + - - -
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Residues in contact with HIS 292 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201R KCX 3.7 7.6 - - - -
239R TYR* 3.1 45.4 - + + -
264R ILE* 4.2 2.8 - - + +
265R ILE 2.8 17.1 + - - +
266R MET* 3.0 17.7 - - + +
267R HIS 2.9 25.8 + - - -
290R PHE 4.1 0.4 - - - -
291R LEU* 1.3 73.5 - - - +
293R ILE* 1.3 65.5 + - - +
294R HIS* 4.1 1.5 + - - -
325R HIS* 3.1 34.3 + - + +
327R HIS* 2.9 41.3 + + - -
377R VAL* 3.7 16.6 - - + -
401R GLN* 4.0 2.5 - - - -
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Residues in contact with ILE 293 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267R HIS* 3.4 8.5 - - + +
269R TYR* 3.1 39.9 - - + -
277R ASN* 3.2 28.5 - - - +
291R LEU* 3.6 23.6 - - + -
292R HIS* 1.3 80.8 + - - +
294R HIS* 1.3 59.2 + - - +
318R LEU* 3.7 13.2 - - + -
322R GLY 4.0 1.3 - - - +
323R GLY* 3.7 20.6 - - - -
325R HIS 2.9 22.6 + - - +
326R LEU* 3.5 9.0 - - + +
327R HIS* 3.4 27.5 + - - -
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Residues in contact with HIS 294 (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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123H ASN* 3.3 23.3 - - - -
201R KCX 3.3 28.7 - - - -
204R GLU* 3.1 24.4 + - + +
266R MET* 4.0 10.3 - - + -
267R HIS 3.0 6.1 + - - -
268R ASP* 3.4 19.2 - - - +
269R TYR* 3.4 26.2 + - - -
292R HIS* 3.9 2.2 + - - +
293R ILE* 1.3 74.5 - - - +
295R ARG* 1.3 60.0 + - - +
296R ALA* 2.9 35.6 + - + +
327R HIS* 3.7 16.4 - + - +
1476R CAP 2.9 29.6 + - - -
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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
------------------------------------------------------------
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