Contacts of the helix formed by residues 296 - 306 (chain Y) in PDB entry 3UBT
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 SER 296 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198Y LYS 5.6 0.4 - - - -
199Y ASN* 3.6 9.9 - - - -
200Y LYS* 3.9 21.5 + - - -
294Y TYR* 3.4 10.0 - - - -
295Y GLU* 1.3 78.2 - - - +
297Y LEU* 1.3 67.2 + - - +
298Y ASN* 3.1 11.5 + - - -
299Y ASP* 3.1 29.5 + - - +
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Residues in contact with LEU 297 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Y ALA* 3.6 21.5 - - + -
199Y ASN* 3.2 14.8 + - + +
200Y LYS 3.6 29.2 - - - +
201Y THR* 3.7 2.9 - - - -
212Y GLU* 3.6 38.6 - - + +
213Y TYR 3.7 23.1 - - - -
214Y PHE* 3.8 13.2 - - + +
277Y VAL* 4.2 5.0 - - + +
294Y TYR* 3.8 13.5 - - + -
296Y SER* 1.3 70.5 - - - +
298Y ASN* 1.3 58.2 + - - +
300Y GLY* 2.8 19.8 + - - -
301Y TYR* 3.0 27.9 + - + -
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Residues in contact with ASN 298 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Y ASN* 5.7 0.6 - - - +
214Y PHE* 4.8 14.8 - - + -
240Y ALA 5.5 0.4 + - - -
241Y SER* 3.9 7.8 + - - +
242Y GLY* 3.1 25.1 + - - -
243Y ARG 4.6 1.6 + - - -
296Y SER* 3.1 8.6 + - - -
297Y LEU* 1.3 79.1 - - - +
299Y ASP* 1.3 58.7 + - - +
301Y TYR* 3.1 8.1 + - - +
302Y LYS* 2.9 49.9 + - - +
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Residues in contact with ASP 299 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y SER* 4.0 33.2 + - - +
294Y TYR* 4.2 11.3 - - + +
295Y GLU 5.4 1.0 + - - -
296Y SER* 3.1 25.1 + - - +
298Y ASN* 1.3 78.6 + - - +
300Y GLY* 1.3 59.3 + - - +
302Y LYS* 3.8 19.6 + - - +
303Y MET* 3.0 34.2 + - + +
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Residues in contact with GLY 300 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277Y VAL* 4.7 5.6 - - - -
292Y PHE* 5.5 1.8 - - - -
294Y TYR* 3.9 26.4 - - - -
296Y SER 3.8 2.2 + - - -
297Y LEU 2.8 12.3 + - - -
299Y ASP* 1.3 76.6 - - - +
301Y TYR* 1.3 62.7 + - - -
302Y LYS 3.3 0.2 + - - -
303Y MET* 3.4 8.3 + - - +
304Y ILE* 3.2 32.8 + - - +
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Residues in contact with TYR 301 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213Y TYR* 3.7 4.7 - - - -
214Y PHE* 3.2 38.3 + + + +
238Y VAL* 5.2 1.5 - - + +
239Y GLN 3.8 5.4 - - - +
240Y ALA* 3.7 5.7 - - - -
241Y SER 3.8 9.2 - - - +
242Y GLY* 3.5 29.4 - - - +
245Y CYS* 3.9 15.7 - - + -
275Y LEU 2.7 29.9 + - - -
276Y THR* 3.8 5.8 - - - -
277Y VAL* 3.8 15.4 + - + +
280Y CYS* 3.9 22.4 - - + -
297Y LEU* 3.0 42.6 + - + -
298Y ASN* 3.1 5.8 + - - +
300Y GLY* 1.3 76.1 - - - +
302Y LYS* 1.3 57.4 + - - +
304Y ILE* 3.5 5.7 + - + +
305Y GLY* 2.8 27.9 + - - -
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Residues in contact with LYS 302 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Y ASP* 4.8 12.6 + - - -
240Y ALA* 3.3 31.9 - - + +
298Y ASN* 2.9 37.0 + - - +
299Y ASP* 3.8 18.8 + - - +
300Y GLY 3.2 0.2 - - - -
301Y TYR* 1.3 74.1 - - - +
303Y MET* 1.3 65.9 + - + +
306Y ASN* 3.0 41.7 + - - +
333Y ATP 6.0 0.2 + - - -
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Residues in contact with MET 303 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y GLY* 6.4 0.2 - - - -
10Y ALA* 3.9 24.6 + - + +
33Y SER* 4.1 16.8 - - - +
34Y ILE* 4.0 31.4 - - + -
37Y THR* 3.3 46.7 - - + +
292Y PHE* 3.6 16.2 - - + -
293Y HIS 4.6 6.3 - - - +
294Y TYR* 5.5 0.4 - - - -
299Y ASP* 3.0 26.6 + - + +
300Y GLY* 3.4 8.9 + - - +
302Y LYS* 1.3 77.5 - - + +
304Y ILE* 1.3 63.6 + - + +
306Y ASN* 4.2 2.7 - - - +
307Y ALA* 3.6 19.4 + - - +
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Residues in contact with ILE 304 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238Y VAL* 4.6 2.0 - - + -
277Y VAL* 3.4 40.6 - - + +
280Y CYS* 3.8 25.1 - - + +
281Y ALA* 3.9 13.9 - - + +
284Y GLN* 2.7 55.9 + - + -
286Y PHE* 4.5 4.9 - - + -
292Y PHE* 3.7 25.6 - - + -
300Y GLY 3.2 18.3 + - - +
301Y TYR* 4.0 4.0 - - - +
302Y LYS 3.2 0.4 - - - -
303Y MET* 1.3 74.7 - - - +
305Y GLY* 1.3 56.5 + - - +
307Y ALA* 3.2 10.4 + - - +
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Residues in contact with GLY 305 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Y ARG* 2.6 30.7 + - - -
155Y ARG* 5.1 0.5 + - - -
238Y VAL* 3.4 28.8 - - - +
239Y GLN 3.9 9.2 - - - -
240Y ALA* 4.0 3.7 + - - -
284Y GLN* 4.3 0.4 - - - -
301Y TYR 2.8 22.8 + - - -
302Y LYS 3.8 0.2 - - - -
304Y ILE* 1.3 73.2 - - - +
306Y ASN* 1.3 56.1 + - - +
307Y ALA 3.3 0.2 - - - -
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Residues in contact with ASN 306 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Y GLU* 4.9 7.3 - - - +
153Y ARG* 4.3 4.1 + - - +
155Y ARG* 5.9 0.4 + - - +
240Y ALA* 3.5 21.3 - - - +
302Y LYS* 3.0 34.1 + - - +
303Y MET* 4.2 3.4 - - - +
305Y GLY* 1.3 76.4 - - - +
307Y ALA* 1.3 61.8 + - - +
308Y VAL* 3.9 1.4 + - - +
333Y ATP 5.5 4.6 + - - -
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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