Contacts of the strand formed by residues 278 - 282 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASP 3.3 7.4 + - - +
239A GLY* 3.1 4.0 - - - -
240A ALA 2.9 24.1 + - - -
276A ASP 3.6 7.2 + - - +
277A VAL* 1.3 75.9 - - - +
279A ILE* 1.3 58.9 + - - +
304A ASP* 3.3 17.8 + - + +
352A GLU* 3.0 39.2 + - - -
462A PHE* 3.5 10.4 - - + -
465A TYR* 5.3 1.3 - - + -
466A LEU* 3.6 30.7 - - + -
469A LEU* 4.2 17.1 - - + +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA* 3.3 13.5 - - + +
242A PHE* 4.0 23.8 - - + -
269A ILE* 3.7 25.4 - - + +
272A PHE* 4.0 17.5 - - + -
273A LYS* 3.5 28.7 - - + -
277A VAL* 4.0 8.3 - - + +
278A LYS* 1.3 79.1 - - - +
280A HIS* 1.3 66.3 + - - +
281A VAL* 4.5 0.2 - - + -
303A VAL* 3.8 23.5 - - + +
304A ASP* 2.7 22.8 + - - +
305A SER 2.8 29.3 + - - +
462A PHE* 4.2 2.2 - - - -
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Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA 2.9 6.7 + - - +
241A ILE* 3.3 16.4 - - + +
242A PHE 2.8 25.6 + - - +
279A ILE* 1.3 75.5 - - - +
281A VAL* 1.3 74.0 + - - +
282A GLU* 2.8 32.9 + - + -
305A SER* 2.7 38.5 + - - -
306A VAL 3.7 1.2 - - - -
307A GLY* 3.4 15.1 + - - -
355A GLN* 4.6 5.3 + - - +
458A SER* 3.6 17.0 + - - -
462A PHE* 3.7 39.2 - + + +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.1 23.8 - - + +
245A TYR* 4.1 15.9 - - + +
279A ILE 4.1 0.2 - - - -
280A HIS* 1.3 78.5 - - - +
282A GLU* 1.3 69.3 + - - +
283A PHE* 3.7 7.6 + - + +
295A ILE* 6.4 0.7 - - + -
299A ILE* 3.7 14.6 - - + -
300A LEU* 4.0 20.9 - - + -
303A VAL* 3.7 36.3 - - + -
305A SER 2.8 9.5 + - - +
306A VAL* 3.3 4.7 - - + +
307A GLY 3.0 25.1 + - - -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.5 17.0 + - - +
123A ILE* 5.0 5.4 - - + -
241A ILE* 5.0 7.6 - - + +
242A PHE 3.1 7.2 + - - +
243A SER* 3.6 23.1 - - - -
244A GLY 4.8 0.5 + - - -
245A TYR* 5.7 0.7 - - - -
246A GLN* 5.1 1.0 - - - +
280A HIS* 2.8 31.7 + - + +
281A VAL* 1.3 73.0 - - - +
283A PHE* 1.3 67.8 + - - +
284A ALA* 5.0 0.3 - - - +
307A GLY* 3.3 11.6 - - - +
312A GLU* 5.6 0.5 - - - +
357A HIS* 2.8 33.6 + - - -
454A GLY 3.7 4.7 - - - +
455A ASP* 3.5 23.2 - - - +
458A SER* 2.7 23.8 + - - -
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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