Contacts of the helix formed by residues 291 - 302 (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 291 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312E LEU* 4.5 10.1 - - - -
324E GLU* 2.9 30.9 + - - -
353E TYR* 5.3 0.7 - - - -
355E ARG* 5.0 5.1 + - - -
256F ILE* 5.9 0.7 - - - +
257F ALA* 3.5 21.5 - - - +
269F ASN* 5.2 0.6 - - - +
290F PRO* 1.3 76.3 - - - +
292F LEU* 1.3 67.1 + - - +
294F LEU* 3.4 18.3 + - - +
295F MET* 3.2 22.6 + - - +
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Residues in contact with LEU 292 (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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285E MET 4.3 0.2 - - - +
286E ALA* 3.8 27.1 - - + +
314E MET* 4.2 15.9 - - + -
223F PHE* 3.9 16.4 - - + -
256F ILE* 5.3 2.9 - - + +
291F SER* 1.3 72.3 - - - +
293F GLY* 1.3 59.8 + - - +
295F MET* 3.0 29.4 + - + +
296F THR* 2.9 32.3 + - - +
321F TYR* 4.3 14.4 - - + -
324F LEU* 3.7 40.2 - - + -
325F ILE* 4.1 17.5 - - + +
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Residues in contact with GLY 293 (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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314E MET* 3.9 18.8 - - - -
324E GLU* 4.3 14.1 + - - -
353E TYR* 3.4 17.0 + - - -
291F SER 3.4 0.4 - - - -
292F LEU* 1.3 79.3 - - - +
294F LEU* 1.3 55.6 + - - +
296F THR* 3.3 8.1 + - - -
297F GLU* 2.9 26.2 + - - +
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Residues in contact with LEU 294 (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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353E TYR* 3.6 28.8 + - + +
227F MET* 3.9 16.6 - - + -
269F ASN* 3.8 35.0 - - + +
270F ASP 5.4 1.1 - - - +
271F GLY* 3.8 20.6 - - - +
290F PRO* 4.5 1.1 - - + -
291F SER* 3.4 24.8 + - - +
292F LEU 3.3 0.8 - - - -
293F GLY* 1.3 76.6 - - - +
295F MET* 1.3 62.0 + - - +
297F GLU* 3.6 6.5 + - - +
298F LYS* 3.2 52.1 + - - +
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Residues in contact with MET 295 (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* 3.3 58.8 - - + +
226F ILE* 4.7 15.7 - - + -
227F MET* 3.6 23.6 - - + -
290F PRO* 4.1 6.3 - - + +
291F SER 3.2 8.7 + - - +
292F LEU* 3.0 37.6 + - + +
294F LEU* 1.3 75.4 - - - +
296F THR* 1.3 59.6 + - - +
298F LYS* 3.2 3.9 + - - +
299F LEU* 2.8 43.1 + - + +
306F LEU* 5.9 1.3 - - - -
325F ILE* 4.2 11.2 - - + -
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Residues in contact with THR 296 (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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314E MET* 5.6 0.5 - - - -
292F LEU 2.9 16.1 + - - -
293F GLY* 3.5 10.3 - - - -
295F MET* 1.3 76.5 - - - +
297F GLU* 1.3 62.9 + - - +
299F LEU* 3.1 6.0 + - + +
300F SER* 3.0 33.2 + - - +
324F LEU 3.9 10.8 + - - +
325F ILE* 3.6 24.2 - - + +
326F PRO* 4.5 21.8 - - + +
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Residues in contact with GLU 297 (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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352E LEU* 4.2 9.4 - - - +
353E TYR* 3.0 40.0 + - - +
293F GLY 2.9 9.3 + - - +
294F LEU* 3.8 8.3 - - - +
295F MET 3.3 0.2 - - - -
296F THR* 1.3 77.6 - - - +
298F LYS* 1.3 82.3 + - + +
300F SER* 3.4 5.6 + - - -
301F GLN* 3.1 31.4 + - + +
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Residues in contact with LYS 298 (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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227F MET* 3.9 21.1 - - + -
230F THR* 3.5 16.1 - - + +
231F VAL* 3.9 23.3 - - + -
270F ASP 5.2 2.4 + - - -
271F GLY* 3.7 21.7 + - - -
272F GLN* 6.0 1.2 - - - +
294F LEU* 3.2 29.4 + - + +
295F MET 3.8 2.9 - - - +
297F GLU* 1.3 94.2 + - - +
299F LEU* 1.3 64.9 + - - +
301F GLN* 3.8 26.7 + - - +
302F LYS* 3.1 22.7 + - + +
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Residues in contact with LEU 299 (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* 4.7 10.1 - - + -
230F THR* 3.5 30.1 - - + +
246F LEU* 5.0 1.8 - - + -
295F MET* 2.8 30.7 + - + +
296F THR* 3.6 4.7 - - + +
298F LYS* 1.3 77.1 - - - +
300F SER* 1.3 57.3 + - - +
303F ASN* 3.2 4.3 + - - -
304F ILE* 2.8 56.7 + - + +
306F LEU* 4.0 30.7 - - + -
325F ILE* 4.0 26.7 - - + -
328F THR* 4.8 1.6 - - + -
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Residues in contact with SER 300 (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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296F THR* 3.0 22.1 + - - +
297F GLU* 3.7 6.2 - - - -
299F LEU* 1.3 76.2 - - - +
301F GLN* 1.3 67.2 + - - +
303F ASN* 3.1 21.8 + - - +
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Residues in contact with GLN 301 (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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297F GLU* 3.1 22.8 + - + +
298F LYS* 3.8 31.5 + - - +
299F LEU 3.5 0.2 - - - -
300F SER* 1.3 80.0 - - - +
302F LYS* 1.3 91.1 + - + +
303F ASN* 3.2 4.7 + - - +
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Residues in contact with LYS 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F THR* 3.2 22.2 - - + +
231F VAL* 4.1 25.4 + - + +
233F ASP* 2.9 37.2 + - - +
244F HIS* 3.7 11.1 + - - -
298F LYS* 3.1 17.9 + - - +
301F GLN* 1.3 101.1 - - + +
303F ASN* 1.3 72.0 + - - +
304F ILE* 3.5 15.4 - - + +
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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