Contacts of the strand formed by residues 304 - 311 (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 ILE 304 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D THR* 3.5 44.0 - - + +
238D TRP* 3.8 27.4 - - + +
244D HIS* 3.7 15.0 - - + +
246D LEU* 3.8 29.4 - - + -
299D LEU* 2.9 40.2 + - + +
302D LYS* 3.5 17.0 - - + +
303D ASN* 1.3 78.4 - - - +
305D ASN* 1.3 69.1 + - - +
306D LEU 3.8 2.6 + - - -
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Residues in contact with ASN 305 (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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243D SER* 5.8 4.4 - - - -
244D HIS 2.8 22.1 + - - +
245D LEU* 3.5 20.4 - - + +
246D LEU 2.8 27.3 + - - -
303D ASN 5.7 1.4 + - - -
304D ILE* 1.3 77.5 - - - +
306D LEU* 1.3 62.3 + - - +
307D ILE* 3.7 4.1 + - + +
327D GLY* 4.0 16.1 - - - +
347D ALA* 5.7 3.3 - - + +
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Residues in contact with LEU 306 (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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226D ILE* 3.9 27.4 - - + -
246D LEU* 3.4 38.8 - - + +
248D PHE* 4.4 8.5 - - + -
295D MET* 5.9 1.3 - - - -
299D LEU* 4.0 25.5 - - + +
304D ILE 3.8 2.8 + - - -
305D ASN* 1.3 73.2 - - - +
307D ILE* 1.3 62.2 + - - +
308D PHE* 3.7 34.3 - - + -
325D ILE* 5.0 6.1 - - + -
327D GLY 4.4 2.1 + - - +
328D THR* 3.3 28.5 - - + +
329D THR 3.2 20.1 + - - -
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Residues in contact with ILE 307 (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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245D LEU* 4.2 22.7 - - + -
246D LEU 2.9 11.4 + - - +
247D VAL* 3.6 13.2 - - + -
248D PHE* 2.9 29.3 + - - +
305D ASN* 4.4 6.5 - - + +
306D LEU* 1.3 76.7 - - - +
308D PHE* 1.3 69.7 + - - +
309D ALA 3.7 1.2 + - - +
329D THR* 3.4 20.0 - - - +
340D VAL* 5.0 7.6 - - + -
343D LEU* 3.7 41.5 - - + +
344D ILE* 3.6 28.3 - - + -
347D ALA* 5.0 1.6 - - + -
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Residues in contact with PHE 308 (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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223D PHE* 4.5 15.5 - + - -
226D ILE* 4.2 7.2 - - + -
248D PHE* 3.5 32.8 - + + -
306D LEU* 3.7 29.6 - - + -
307D ILE* 1.3 73.8 - - - +
309D ALA* 1.3 56.6 + - - +
310D VAL* 3.6 7.5 + - + -
318D TYR* 3.9 33.0 - + + -
321D TYR* 4.5 4.7 - - + -
322D SER* 4.3 15.0 - - - -
325D ILE* 4.7 8.5 - - + -
328D THR* 4.6 7.0 - - - -
329D THR 2.7 13.9 + - - +
330D VAL* 3.4 30.9 - - + +
331D GLY 2.7 34.1 + - - +
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Residues in contact with ALA 309 (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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134D LEU* 4.1 4.0 - - + -
247D VAL* 4.1 17.7 - - + -
248D PHE 2.6 14.8 + - - +
249D THR* 3.1 40.5 - - + +
250D THR 3.6 1.0 + - - -
307D ILE* 3.7 1.2 + - + -
308D PHE* 1.3 71.0 - - - +
310D VAL* 1.3 60.2 + - - +
331D GLY 3.3 7.0 - - - -
333D LEU* 3.8 7.8 - - + +
340D VAL* 3.8 24.2 - - + -
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Residues in contact with VAL 310 (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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248D PHE* 4.7 2.9 - - + +
250D THR* 3.5 22.2 - - + +
308D PHE* 3.6 8.9 - - + -
309D ALA* 1.3 84.1 - - - +
311D THR* 1.3 61.2 + - - +
314D VAL* 3.8 14.4 - - + -
315D VAL* 3.8 31.9 - - + -
318D TYR* 3.6 30.7 - - + -
330D VAL* 4.4 7.6 - - + -
331D GLY 3.1 4.2 + - - +
332D VAL* 3.2 7.1 - - - +
333D LEU* 2.7 27.5 + - - -
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Residues in contact with THR 311 (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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127D ASP* 4.0 15.5 - - - +
250D THR 3.5 2.4 + - - +
251D ASP* 3.4 31.6 + - + +
310D VAL* 1.3 77.1 - - - +
312D GLU* 1.3 66.5 + - - +
313D ASN* 2.6 23.4 + - - -
314D VAL* 3.0 16.0 + - - +
315D VAL* 3.3 8.4 + - - +
333D LEU* 3.7 36.1 - - + +
334D SER* 6.0 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