Contacts of the strand formed by residues 264 - 268 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199O PHE* 4.4 9.2 - - + -
237O GLY* 4.2 9.2 - - - -
238O HIS 3.0 53.7 - - - +
239O TYR* 3.5 31.0 - - + -
240O LEU* 3.3 7.5 + - - +
262O VAL* 3.6 5.6 + - - +
263O PRO* 1.3 81.7 - - + +
265O ILE* 1.3 78.1 + - - +
289O LEU* 4.1 1.7 - - - +
290O PHE* 3.6 29.2 - - + +
291O LEU 4.8 0.2 - - - +
292O HIS* 4.2 8.7 - - + +
325O HIS* 3.9 20.0 - - + +
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Residues in contact with ILE 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218O PHE* 5.3 1.3 - - + -
239O TYR* 4.3 2.5 - - - -
240O LEU* 3.2 19.7 - - + +
242O ALA* 4.2 8.1 - - + -
253O ARG 5.1 0.9 - - - +
254O ALA* 4.0 16.2 - - + -
257O ALA* 3.5 32.1 - - + -
264O ILE* 1.3 82.3 - - - +
266O MET* 1.3 61.6 + - - +
280O LEU* 3.9 29.6 - - + -
284O CYS* 3.7 22.9 - - - -
289O LEU* 4.4 8.7 - - + +
290O PHE 3.0 15.1 + - - +
291O LEU* 3.5 5.6 - - + -
292O HIS 2.8 23.9 + - - -
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Residues in contact with MET 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201O KCX 3.7 25.8 - - - +
202O ASP* 3.2 21.5 - - - +
204O GLU* 4.0 4.7 - - - -
239O TYR* 3.7 28.9 - - + +
240O LEU 2.9 7.1 + - - -
241O ASN* 3.3 37.0 + - - +
242O ALA* 2.9 30.0 + - - +
265O ILE* 1.3 75.0 - - - +
267O HIS* 1.3 63.4 + - - +
268O ASP* 3.8 17.0 - - - +
291O LEU* 4.2 3.4 - - - -
292O HIS* 3.0 17.3 - - + +
294O HIS* 4.0 13.7 - - + -
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Residues in contact with HIS 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243O THR* 3.5 23.5 + - + -
244O ALA 5.3 0.4 - - - -
250O MET* 3.9 19.1 - - + -
266O MET* 1.3 76.6 - - - +
268O ASP* 1.3 77.4 + - - +
269O TYR* 3.3 16.0 + - - -
272O GLY* 3.9 18.2 - - - -
273O GLY 4.1 1.0 + - - -
276O ALA* 4.3 2.4 - - + +
277O ASN* 2.8 54.5 + - + +
280O LEU* 3.5 24.0 - - + +
291O LEU* 4.0 4.7 - - + +
292O HIS 2.9 5.9 + - - -
293O ILE* 3.5 6.3 - - + +
294O HIS* 3.0 22.1 + - - -
275V THR* 5.0 2.2 - - - -
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Residues in contact with ASP 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204O GLU* 2.7 33.7 - - - +
241O ASN* 4.1 0.2 - - - +
243O THR* 2.8 30.3 + - + +
266O MET* 3.8 7.1 - - - +
267O HIS* 1.3 74.1 + - - +
269O TYR* 1.3 57.8 + - - +
270O LEU 3.3 2.9 - - - -
271O THR* 3.1 17.4 + - - +
272O GLY* 2.8 28.2 + - - -
294O HIS* 3.4 27.4 - - - +
296O ALA* 4.3 7.2 - - + -
118V THR* 3.2 15.9 + - - +
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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