Contacts of the strand formed by residues 229 - 236 (chain A) in PDB entry 1UCU
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 TYR 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 4.6 5.6 - - + -
220A LEU* 4.5 7.6 - - + -
221A LYS 3.4 7.2 - - - +
222A PHE* 3.6 21.8 - + + -
227A GLY 3.3 20.6 - - - -
228A LYS* 1.3 76.2 - - - +
230A TYR* 1.3 60.9 - - - +
246A GLU* 3.5 10.1 - - - +
247A VAL* 2.9 46.0 + - + +
249A VAL* 3.7 33.7 - - + -
251A LYS* 2.8 32.0 + - - -
278A VAL* 4.1 23.8 - - + -
280A ASN 4.6 0.7 - - - -
281A VAL* 4.0 2.3 - - - +
282A GLN* 3.1 30.5 + - + +
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Residues in contact with TYR 230 (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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220A LEU* 3.5 6.2 - - - +
221A LYS* 2.8 34.3 + - - +
223A ASP* 3.9 14.5 + - + -
226A THR* 4.1 1.7 + - - +
228A LYS* 3.3 49.4 - - + +
229A TYR* 1.3 73.1 - - - +
231A ALA* 1.3 64.1 + - - +
244A TYR* 5.0 2.0 - - + -
245A TYR 3.1 7.0 - - - +
246A GLU* 3.8 24.6 + - + +
247A VAL* 4.2 2.5 - - - -
266A LEU* 3.5 33.7 - - + -
270A LEU* 3.6 20.0 - - + -
271A PRO* 3.5 27.4 - - + +
274A ALA* 3.8 15.5 - - + -
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Residues in contact with ALA 231 (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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216A ILE* 3.7 30.5 - - + -
220A LEU* 4.3 4.9 - - + +
221A LYS* 5.0 2.5 - - - +
230A TYR* 1.3 77.9 - - - +
232A LYS* 1.3 61.9 + - - +
233A VAL* 3.4 9.8 + - + +
243A GLY 3.5 0.9 - - - +
244A TYR* 3.6 7.1 - - - -
245A TYR 2.7 33.8 + - - +
247A VAL* 3.8 23.6 - - + -
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Residues in contact with LYS 232 (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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216A ILE* 3.2 9.6 - - - +
217A ASP* 2.8 66.3 + - + +
221A LYS* 3.6 22.1 - - - +
231A ALA* 1.3 72.7 - - - +
233A VAL* 1.3 61.4 + - - +
234A THR* 4.3 3.4 + - - -
243A GLY* 3.7 6.5 - - - +
244A TYR* 3.7 28.8 - - + +
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Residues in contact with VAL 233 (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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202A PHE* 3.5 41.7 - - + -
209A LEU* 4.8 2.0 - - + -
214A GLN* 4.6 1.3 - - + -
215A LYS 3.6 5.8 - - - +
216A ILE* 4.7 0.9 - - + -
217A ASP* 4.1 1.6 - - - -
231A ALA* 3.5 13.0 - - + +
232A LYS* 1.3 80.6 - - - +
234A THR* 1.3 64.6 + - - +
235A VAL* 3.7 22.6 + - + -
242A ASP* 3.3 26.2 - - - +
243A GLY 3.0 12.8 + - - -
245A TYR* 3.4 35.4 - - + -
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Residues in contact with THR 234 (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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213A ASP 3.3 0.5 - - - +
215A LYS* 2.8 64.8 + - - +
217A ASP* 2.6 33.1 + - - -
232A LYS* 4.3 3.5 + - - -
233A VAL* 1.3 72.2 + - - +
235A VAL* 1.3 62.1 + - - +
236A THR* 4.3 8.3 - - - +
242A ASP* 3.7 15.6 + - - +
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Residues in contact with VAL 235 (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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209A LEU* 4.2 15.0 - - + +
210A GLY 3.2 29.6 - - - +
213A ASP 3.3 3.1 - - - +
214A GLN* 3.7 12.1 - - + +
233A VAL* 3.7 20.6 - - + -
234A THR* 1.3 72.9 - - - +
236A THR* 1.4 58.3 + - - +
237A GLY 3.3 0.5 + - - -
238A GLY* 3.1 27.0 + - - +
241A LYS* 3.7 35.4 - - + +
242A ASP* 2.8 21.2 + - - +
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Residues in contact with THR 236 (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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211A GLY 3.6 0.9 - - - -
212A THR* 2.6 45.2 + - + +
213A ASP* 2.7 27.0 + - + +
215A LYS* 2.9 26.3 + - - -
234A THR* 3.6 6.1 + - - +
235A VAL* 1.4 69.1 - - - +
237A GLY* 1.3 55.0 + - - +
238A GLY 3.4 0.2 - - - -
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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