Contacts of the strand formed by residues 305 - 311 (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 ASN 305 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243F SER* 4.8 6.5 + - - -
244F HIS 3.2 25.7 + - - +
245F LEU* 3.9 19.0 - - + +
246F LEU* 3.1 24.8 + - - +
303F ASN* 5.5 5.3 + - - +
304F ILE* 1.3 80.1 - - - +
306F LEU* 1.3 62.3 + - - +
307F ILE* 4.1 3.9 + - + +
327F GLY* 4.7 12.4 - - - +
347F ALA* 6.2 0.9 - - - +
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Residues in contact with LEU 306 (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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226F ILE* 4.2 22.9 - - + -
246F LEU* 3.8 38.4 - - + +
248F PHE* 4.6 7.2 - - + -
295F MET* 5.9 2.2 - - - -
299F LEU* 4.0 25.8 - - + +
304F ILE 3.9 1.2 + - - -
305F ASN* 1.3 75.0 - - - +
307F ILE* 1.3 65.4 + - - +
308F PHE* 3.5 38.1 - - + -
325F ILE* 4.7 6.5 - - + -
327F GLY 4.3 2.8 + - - +
328F THR* 3.5 27.0 - - + +
329F THR* 3.3 21.0 + - - -
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Residues in contact with ILE 307 (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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245F LEU* 4.6 17.0 - - + -
246F LEU 3.0 13.5 + - - +
247F VAL* 3.6 16.0 - - + -
248F PHE* 2.9 29.5 + - - +
305F ASN* 5.0 5.8 - - + +
306F LEU* 1.3 80.5 - - - +
308F PHE* 1.3 70.4 + - - +
309F ALA 3.6 0.8 + - - +
329F THR* 3.4 20.2 - - - +
340F VAL* 5.1 8.7 - - + +
343F LEU* 4.0 42.6 - - + +
344F ILE* 4.1 21.8 - - + -
347F ALA* 5.2 2.0 - - + -
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Residues in contact with PHE 308 (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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223F PHE* 4.8 9.0 - + - -
226F ILE* 4.3 7.4 - - + -
248F PHE* 3.6 33.7 - + + -
306F LEU* 3.5 33.2 - - + -
307F ILE* 1.3 72.8 - - - +
309F ALA* 1.3 56.9 + - - +
310F VAL* 3.6 12.4 + - + -
318F TYR* 3.8 42.6 - + + -
321F TYR* 4.4 12.6 - - + -
322F SER* 4.2 6.5 - - - -
325F ILE* 4.6 10.3 - - + -
328F THR* 4.6 11.0 - - - -
329F THR 2.8 13.4 + - - +
330F VAL* 3.4 16.3 - - + +
331F GLY* 2.6 35.0 + - - +
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Residues in contact with ALA 309 (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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134F LEU* 4.0 7.6 - - + -
247F VAL* 4.0 9.0 - - + -
248F PHE 2.6 22.2 + - - +
249F THR* 3.2 32.6 - - + +
307F ILE* 3.6 1.4 + - + -
308F PHE* 1.3 69.5 - - - +
310F VAL* 1.3 58.7 + - - +
331F GLY* 3.1 9.4 - - - +
333F LEU* 3.5 9.4 - - + +
340F VAL* 3.9 28.3 - - + -
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Residues in contact with VAL 310 (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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248F PHE* 4.7 2.9 - - + +
250F THR* 3.4 21.8 - - + +
308F PHE* 3.6 13.2 - - + -
309F ALA* 1.3 78.3 - - - +
311F THR* 1.3 68.0 + - - +
314F VAL* 3.6 27.1 - - + +
315F VAL* 3.8 14.5 - - + +
318F TYR* 3.6 27.6 - - + -
330F VAL* 4.1 13.5 - - + -
331F GLY 3.1 3.2 + - - +
332F VAL* 3.3 6.2 - - - -
333F LEU* 2.7 27.6 + - - -
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Residues in contact with THR 311 (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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127F ASP* 4.4 15.5 - - + +
250F THR 3.3 5.4 + - - +
251F ASP* 3.2 35.5 + - + +
310F VAL* 1.3 78.9 - - - +
312F GLU* 1.3 67.4 + - - +
313F ASN* 2.6 24.5 + - - -
314F VAL* 3.1 15.4 + - - +
315F VAL* 3.3 6.6 - - - +
333F LEU* 3.7 28.3 - - + +
334F 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