Contacts of the strand formed by residues 278 - 282 (chain B) in PDB entry 1U2X
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 LYS 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ASP 3.3 6.2 + - - +
239B GLY* 3.2 3.5 - - - -
240B ALA 3.0 22.7 + - - -
276B ASP 3.7 7.1 + - - +
277B VAL* 1.3 76.6 - - - +
279B ILE* 1.3 60.0 + - - +
304B ASP* 3.3 17.8 + - + +
352B GLU* 2.8 30.9 + - - -
462B PHE* 3.5 11.4 - - + -
465B TYR* 5.5 1.1 - - + -
466B LEU* 3.7 27.8 - - + -
469B LEU* 3.7 28.7 - - + -
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ALA* 3.4 18.2 - - + +
242B PHE* 4.0 21.1 - - + -
269B ILE* 3.8 26.7 - - + +
272B PHE* 4.0 14.6 - - + -
273B LYS* 3.6 26.7 - - + -
277B VAL 4.0 8.1 - - - +
278B LYS* 1.3 78.7 - - - +
280B HIS* 1.3 70.1 + - - +
281B VAL* 4.6 0.4 - - + -
303B VAL* 3.9 22.6 - - + +
304B ASP* 2.8 39.0 + - - +
305B SER 2.9 10.8 + - - +
462B PHE* 4.1 2.7 - - - -
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Residues in contact with HIS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ALA 2.9 7.6 + - - +
241B ILE* 3.3 15.8 - - + +
242B PHE* 2.7 32.1 + - - -
279B ILE* 1.3 76.7 - - - +
281B VAL* 1.3 68.6 + - - +
282B GLU* 2.8 32.7 + - + -
305B SER* 2.7 40.5 + - - -
306B VAL 3.8 0.6 + - - -
307B GLY* 3.4 14.9 + - - -
355B GLN* 4.6 4.0 + - - +
458B SER* 3.7 17.2 + - - -
462B PHE* 3.6 38.1 - + + +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 3.2 22.4 - - + +
245B TYR* 4.1 17.7 - - + +
279B ILE* 4.6 0.2 - - + -
280B HIS* 1.3 77.3 - - - +
282B GLU* 1.3 65.4 + - - +
283B PHE* 3.8 8.1 + - + +
295B ILE* 6.0 0.2 - - + -
299B ILE* 3.8 13.0 - - + -
300B LEU* 4.0 21.3 - - + -
303B VAL* 3.7 38.1 - - + -
305B SER 2.9 7.0 + - - +
306B VAL* 3.2 5.0 - - + +
307B GLY 2.8 31.0 + - - -
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 3.4 23.8 + - - +
123B ILE* 4.9 10.8 - - + -
241B ILE* 5.0 1.8 - - + +
242B PHE 3.2 5.5 + - - -
243B SER* 3.6 26.7 - - - -
244B GLY 5.0 0.3 + - - -
245B TYR* 5.7 0.3 - - - -
246B GLN* 5.2 1.2 - - - +
280B HIS* 2.8 24.8 + - + +
281B VAL* 1.3 74.4 - - - +
283B PHE* 1.3 67.4 + - - +
284B ALA* 5.1 0.2 - - - +
307B GLY* 3.4 11.8 - - - +
308B ILE* 5.0 0.3 - - - -
312B GLU* 5.6 0.5 - - - +
357B HIS* 3.2 21.7 + - - -
454B GLY 3.9 4.4 - - - +
455B ASP* 3.4 14.3 - - - +
458B SER* 2.7 33.3 + - - -
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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
------------------------------------------------------------
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