Contacts of the strand formed by residues 243 - 250 (chain F) in PDB entry 1TYE
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 243 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F PRO 3.0 15.5 + - - -
112F VAL* 4.2 5.8 - - - +
113F ASP* 2.7 35.5 + - - +
242F ALA* 1.3 74.1 - - - +
244F HIS* 1.3 59.6 + - - +
245F LEU* 4.6 11.3 - - - +
305F ASN* 4.8 5.2 + - - -
351F ILE* 3.8 36.3 - - - +
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Residues in contact with HIS 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ASP* 3.1 25.9 + - + -
238F TRP* 3.4 35.3 - + + +
239F ARG 3.1 25.8 + - - -
240F ASN* 4.1 9.4 - - - -
242F ALA* 3.9 14.3 + - - +
243F SER* 1.3 76.8 + - - +
245F LEU* 1.3 61.9 + - - +
302F LYS 3.7 10.8 + - - -
303F ASN* 3.1 28.8 + - + +
304F ILE* 3.9 11.2 - - + +
305F ASN* 3.2 35.0 + - - +
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Residues in contact with LEU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F VAL* 4.1 14.1 - - + -
113F ASP 2.6 16.2 + - - +
114F ILE* 3.3 26.6 - - + -
115F TYR 2.9 27.5 + - - +
142F MET* 5.2 1.3 - - + -
238F TRP* 3.6 7.5 - - - -
243F SER* 4.6 7.2 - - - +
244F HIS* 1.3 82.4 - - - +
246F LEU* 1.3 61.4 + - - +
247F VAL* 4.1 4.4 + - + -
304F ILE* 4.7 0.2 - - - -
305F ASN* 3.9 23.3 - - + +
307F ILE* 4.6 10.8 - - + -
344F ILE* 4.0 25.8 - - + +
347F ALA* 4.3 25.4 - - + -
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Residues in contact with LEU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TYR* 3.2 39.0 - - + +
117F LEU* 4.1 17.5 - - + -
226F ILE* 4.0 18.6 - - + +
229F ALA* 4.4 5.8 - - + -
230F THR* 3.9 21.5 - - - +
238F TRP* 4.4 13.9 - - + -
245F LEU* 1.3 71.5 - - - +
247F VAL* 1.3 63.8 + - - +
248F PHE* 3.7 1.0 + - + -
299F LEU* 5.0 1.6 - - + -
304F ILE* 4.2 8.5 - - + -
305F ASN 3.1 15.9 + - - +
306F LEU* 3.8 22.5 - - + +
307F ILE* 3.0 29.2 + - - +
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Residues in contact with VAL 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ILE* 4.2 14.6 - - + -
115F TYR 3.1 6.6 + - - +
116F TYR* 3.8 27.7 - - + -
117F LEU* 2.8 34.9 + - - +
134F LEU* 4.8 0.7 - - + -
138F LEU* 4.0 20.9 - - + -
245F LEU* 5.1 1.8 - - + -
246F LEU* 1.3 75.1 - - - +
248F PHE* 1.3 58.5 + - - +
307F ILE* 3.6 14.1 - - + +
309F ALA* 4.0 21.5 - - + -
340F VAL* 4.6 11.4 - - + -
344F ILE* 4.4 17.5 - - + -
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Residues in contact with PHE 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LEU* 3.9 16.8 - - + -
156F PHE* 3.7 18.6 - + - -
222F GLY* 3.6 43.5 - - - -
223F PHE* 4.5 5.4 - + - -
226F ILE* 3.7 19.1 - - + -
246F LEU* 6.2 0.2 - - + -
247F VAL* 1.3 74.1 - - - +
249F THR* 1.3 61.4 + - - +
250F THR* 3.9 24.7 - - + -
254F THR* 5.4 2.0 - - - -
306F LEU* 4.6 8.7 - - + -
307F ILE 2.9 15.7 + - - +
308F PHE* 3.6 28.9 - + + -
309F ALA* 2.6 33.6 + - - +
310F VAL* 4.7 1.0 - - + +
318F TYR* 4.1 16.4 - + - -
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Residues in contact with THR 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F TYR* 3.7 28.1 + - + +
117F LEU 2.9 19.4 + - - -
118F MET* 3.5 11.8 - - - +
119F ASP* 3.1 23.7 + - - +
124F MET* 4.7 0.9 - - - -
131F ILE* 4.2 10.7 - - + +
134F LEU* 4.1 3.6 - - + -
156F PHE* 3.6 8.3 - - - -
248F PHE* 1.3 74.4 - - - +
250F THR* 1.3 65.3 + - - +
309F ALA* 3.2 31.2 - - + +
333F LEU* 3.8 17.3 - - + -
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Residues in contact with THR 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ASP* 2.8 26.2 + - - -
124F MET* 4.4 5.5 - - - +
156F PHE* 4.6 3.5 - - - -
220F GLU* 4.6 6.2 - - - +
248F PHE* 3.9 13.0 - - + -
249F THR* 1.3 78.7 - - - +
251F ASP* 1.3 60.2 + - - +
252F ALA 3.3 17.4 + - - +
253F LYS 4.9 0.3 + - - -
309F ALA 3.7 2.3 + - - +
310F VAL* 3.4 16.2 - - + +
311F THR* 3.3 22.2 + - - +
318F TYR* 3.4 33.3 + - + +
333F LEU* 4.5 1.7 - - - +
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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