Contacts of the strand formed by residues 271 - 276 (chain A) in PDB entry 1UEC
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 VAL 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A VAL* 5.8 3.3 - - + +
266A ILE* 5.1 0.7 - - - +
267A ARG* 3.4 2.6 - - - -
268A LYS* 3.0 43.6 + - + +
269A ASP* 3.0 10.9 + - + +
270A ASP* 1.3 85.2 - - + +
272A THR* 1.3 67.1 + - - +
325A ARG* 4.4 16.4 - - - +
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP* 5.6 0.5 - - - -
245A VAL* 4.6 4.0 - - - +
256A ILE* 5.0 4.0 - - + -
265A VAL* 4.1 9.9 - - + -
266A ILE 3.1 12.6 - - - +
267A ARG* 4.3 5.8 - - + -
271A VAL* 1.3 83.8 - - - +
273A GLY* 1.3 59.3 + - - +
321A GLN* 2.9 46.9 + - - +
324A TYR* 3.6 4.3 - - + +
325A ARG* 3.5 15.8 + - - +
328A SER* 3.8 32.1 - - - +
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Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASP 3.4 12.6 - - - -
245A VAL* 3.5 17.0 - - - +
265A VAL* 3.4 3.3 - - - -
266A ILE* 2.8 35.4 + - - +
272A THR* 1.3 77.6 - - - +
274A TYR* 1.3 62.8 + - - -
321A GLN* 3.2 10.4 + - - -
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 5.5 0.2 - - - -
243A ASP* 2.8 38.5 + - + +
244A GLU* 3.4 7.1 - - - +
245A VAL* 3.0 24.7 + - - +
259A LEU* 3.9 0.9 - - + -
263A TRP* 3.4 43.2 - - + -
264A TRP 3.2 8.3 - - - -
265A VAL* 3.6 20.9 - - + -
273A GLY* 1.3 72.6 - - - -
275A PHE* 1.3 61.9 + - - +
301A ARG* 3.2 30.7 - - - +
318A ARG* 3.0 48.8 + - - +
319A LEU 4.3 1.6 + - - -
321A GLN* 3.2 24.5 + - + -
324A TYR* 4.2 2.4 - - - -
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA* 4.4 2.0 - - + -
235A LYS 4.0 11.7 - - - -
237A TYR* 3.5 30.3 - + + -
245A VAL* 3.2 28.3 - - + -
247A LEU* 3.5 35.9 - - + -
263A TRP* 3.8 4.9 - - - -
264A TRP* 2.9 30.5 + - - +
266A ILE* 4.1 22.0 - - + -
274A TYR* 1.3 75.2 - - - +
276A PRO* 1.3 90.6 - - + +
277A SER 3.3 0.5 + - - -
279A TYR* 3.7 23.3 - - + -
280A LEU* 3.5 31.9 - - + +
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Residues in contact with PRO 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TYR* 4.2 7.9 - - + -
262A GLY 3.5 9.0 - - - +
263A TRP* 3.4 35.4 - - + +
275A PHE* 1.3 115.1 - - + +
277A SER* 1.3 66.2 + - - +
278A MET* 3.2 3.8 - - + +
279A TYR* 3.0 41.6 + - + +
280A LEU* 3.7 2.0 - - - +
298A ALA* 3.9 15.3 - - + -
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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
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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