Contacts of the strand formed by residues 243 - 250 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D PRO 3.0 12.1 + - - -
112D VAL* 3.5 8.5 - - - +
113D ASP 2.8 30.3 + - - +
242D ALA* 1.3 70.9 - - - +
244D HIS* 1.3 57.9 + - - +
245D LEU* 4.1 4.5 - - - -
305D ASN* 5.8 4.9 - - - -
351D ILE* 3.4 45.4 - - - +
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Residues in contact with HIS 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ASP* 3.4 17.7 - - + -
238D TRP* 3.3 43.1 - + + +
239D ARG 2.8 29.7 + - - -
240D ASN* 4.4 8.7 - - - -
242D ALA 3.2 17.1 + - - -
243D SER* 1.3 71.6 - - - +
245D LEU* 1.3 58.3 + - - +
302D LYS 3.8 10.4 + - - -
303D ASN* 2.8 29.2 + - + +
304D ILE* 3.7 9.5 - - + -
305D ASN* 2.8 39.6 + - - +
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D VAL* 4.5 12.6 - - + -
113D ASP 2.9 13.9 + - - +
114D ILE* 4.0 24.0 - - + -
115D TYR 3.2 22.2 + - - -
142D MET* 5.3 1.8 - - + -
238D TRP* 3.2 10.4 - - - -
243D SER* 5.0 4.3 - - - +
244D HIS* 1.3 76.3 - - - +
246D LEU* 1.3 59.9 + - - +
247D VAL* 4.1 1.6 - - + -
304D ILE* 4.7 0.2 - - - -
305D ASN* 3.5 26.7 - - + +
307D ILE* 4.2 13.7 - - + -
344D ILE* 3.9 33.4 - - + +
347D ALA* 3.8 28.7 - - + -
348D TYR 5.8 0.2 - - - +
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Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TYR* 3.5 36.6 - - + +
117D LEU* 4.0 16.2 - - + -
226D ILE* 4.1 17.0 - - + +
229D ALA* 4.3 7.2 - - + -
230D THR* 3.8 23.1 - - - +
238D TRP* 4.2 9.9 - - + -
245D LEU* 1.3 71.8 - - - +
247D VAL* 1.3 66.8 + - - +
299D LEU* 4.9 0.7 - - + -
304D ILE* 3.8 16.2 - - + -
305D ASN 2.8 14.8 + - - +
306D LEU* 3.4 23.2 - - + +
307D ILE* 2.9 27.7 + - - +
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ILE* 4.2 12.8 - - + -
115D TYR 2.9 7.8 + - - +
116D TYR* 3.7 26.4 - - + -
117D LEU* 2.7 35.3 + - - +
134D LEU* 4.5 5.6 - - + -
138D LEU* 4.0 19.7 - - + -
245D LEU* 5.2 0.9 - - + -
246D LEU* 1.3 73.6 - - - +
248D PHE* 1.3 58.6 - - - +
307D ILE* 3.6 12.6 - - + +
309D ALA* 4.1 20.6 - - + -
340D VAL* 4.6 7.9 - - + -
344D ILE* 4.0 23.1 - - + -
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Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.8 10.1 - - + -
156D PHE* 3.6 26.2 - + - -
222D GLY* 3.5 40.4 - - - -
223D PHE* 4.6 5.8 - + - -
226D ILE* 3.6 21.8 - - + -
247D VAL* 1.3 73.6 - - - +
249D THR* 1.3 60.6 + - - +
250D THR* 3.9 25.8 - - + -
254D THR* 5.4 2.0 - - - -
306D LEU* 4.4 10.8 - - + -
307D ILE 2.9 14.0 + - - +
308D PHE* 3.5 29.8 - + + -
309D ALA* 2.6 33.9 + - - +
310D VAL* 5.0 1.6 - - + -
318D TYR* 4.3 11.4 - + - -
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Residues in contact with THR 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D TYR* 3.9 21.1 - - + +
117D LEU 2.8 19.2 + - - -
118D MET* 3.5 10.9 - - - -
119D ASP* 3.0 23.0 + - - +
124D MET* 4.8 0.7 - - - -
131D ILE* 3.7 30.1 - - + +
134D LEU* 4.2 1.3 - - + -
156D PHE* 3.5 8.0 - - - -
248D PHE* 1.3 75.0 - - - +
250D THR* 1.3 63.5 + - - +
309D ALA* 3.1 29.4 - - + +
333D LEU* 3.9 7.9 - - + -
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Residues in contact with THR 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ASP* 2.7 25.7 + - - -
124D MET* 4.1 6.6 - - - +
156D PHE* 4.6 2.1 - - - -
220D GLU* 4.7 3.3 - - - +
248D PHE* 3.9 16.4 - - + -
249D THR* 1.3 76.6 - - - +
251D ASP* 1.3 63.3 + - - +
252D ALA* 3.4 25.7 + - - +
253D LYS 4.5 3.3 + - - -
309D ALA 3.6 3.1 + - - +
310D VAL* 3.5 17.5 - - + +
311D THR* 3.5 21.7 + - - +
318D TYR* 3.6 23.2 + - + +
333D LEU* 4.3 1.8 - - - +
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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
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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