Contacts of the helix formed by residues 293 - 304 (chain F) in PDB entry 4DEM
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 THR 293 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291F ARG 3.6 3.1 + - - +
292F ALA* 1.3 74.7 - - - +
294F PRO* 1.3 71.3 - - + +
295F GLU* 3.6 7.5 + - - +
296F GLN* 2.7 44.5 + - - +
297F TYR* 2.8 25.4 + - - +
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Residues in contact with PRO 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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292F ALA 4.5 0.9 - - - +
293F THR* 1.3 88.0 - - + +
295F GLU* 1.3 61.0 + - - +
297F TYR* 3.4 9.8 + - + +
298F GLN* 3.2 24.3 + - - +
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Residues in contact with GLU 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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293F THR* 3.2 8.7 + - - +
294F PRO* 1.3 78.1 - - - +
296F GLN* 1.3 59.5 + - + +
298F GLN* 3.3 8.4 + - - +
299F ILE* 3.0 31.1 + - + +
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Residues in contact with GLN 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ARG 4.1 0.3 - - - +
292F ALA* 3.5 14.8 - - + -
293F THR* 2.7 48.8 + - - +
295F GLU* 1.3 77.1 - - + +
297F TYR* 1.3 58.5 + - - +
299F ILE* 3.1 9.9 + - + +
300F LEU* 2.9 29.3 + - - +
318F LEU* 3.6 29.9 - - + +
321F GLU* 4.7 13.5 - - - +
322F LEU* 3.7 23.0 - - - +
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Residues in contact with TYR 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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197F VAL* 5.7 1.4 - - - +
199F LEU* 3.7 27.0 - - + +
200F VAL* 4.8 6.8 + - - +
289F LEU* 3.6 32.3 - - + -
292F ALA* 3.9 11.1 - - + +
293F THR 2.8 16.6 + - - +
294F PRO* 3.5 13.7 - - + +
296F GLN* 1.3 71.1 - - - +
298F GLN* 1.3 70.6 + - - +
300F LEU* 3.2 7.8 + - - +
301F LYS* 2.8 38.9 + - + +
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Residues in contact with GLN 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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294F PRO 3.2 11.0 + - - +
295F GLU* 3.4 11.7 - - - +
296F GLN 3.2 0.4 - - - -
297F TYR* 1.3 86.1 - - - +
299F ILE* 1.3 68.2 + - + +
301F LYS* 3.3 35.6 + - - +
302F GLU* 3.0 25.8 + - + +
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Residues in contact with ILE 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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295F GLU* 3.0 21.9 + - + +
296F GLN* 3.1 11.4 + - + +
298F GLN* 1.3 75.1 - - - +
300F LEU* 1.3 65.2 + - - +
302F GLU* 5.0 1.3 - - + -
303F ASN* 2.8 46.1 + - + +
314F ARG* 3.8 50.3 - - + +
315F VAL* 5.8 0.4 - - - -
318F LEU* 4.5 11.7 - - + -
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Residues in contact with LEU 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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199F LEU* 3.8 16.8 - - + -
285F VAL* 3.9 10.5 - - + -
288F CYS* 3.8 27.4 - - - -
289F LEU* 3.6 34.5 - - + -
292F ALA* 5.9 0.7 - - + -
296F GLN 2.9 12.9 + - - +
297F TYR* 3.4 9.6 - - - +
299F ILE* 1.3 80.0 - - - +
301F LYS* 1.3 63.9 + - - +
303F ASN* 3.2 1.5 + - - -
304F TYR* 2.9 54.2 + - + +
315F VAL* 3.9 20.0 - - + +
318F LEU* 4.1 8.9 - - + +
319F TYR* 4.3 0.4 - - + -
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Residues in contact with LYS 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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197F VAL* 4.2 43.4 - - + +
199F LEU* 3.7 16.5 - - + +
297F TYR* 2.8 30.9 + - + +
298F GLN* 3.3 31.6 + - - +
300F LEU* 1.3 76.8 - - - +
302F GLU* 1.3 60.2 + - - +
303F ASN 3.5 0.2 + - - -
304F TYR* 4.3 6.3 + - - +
306F GLN* 4.4 4.5 + - - -
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Residues in contact with GLU 302 (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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298F GLN* 3.0 17.4 + - + +
299F ILE* 3.2 1.3 + - + -
300F LEU 3.2 0.2 - - - -
301F LYS* 1.3 77.6 - - + +
303F ASN* 1.4 69.8 + - - +
306F GLN* 3.1 15.6 + - - +
311F LYS* 3.5 19.7 + - - +
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Residues in contact with ASN 303 (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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276F ILE* 4.7 2.3 - - - +
299F ILE* 2.8 43.4 + - + +
302F GLU* 1.4 90.2 - - - +
304F TYR* 1.3 64.9 + - - +
305F GLY 3.9 0.3 + - - -
306F GLN* 3.6 8.9 + - - +
310F GLU* 4.5 2.8 - - - +
311F LYS* 3.4 56.1 + - - +
312F VAL 4.5 0.3 + - - -
314F ARG* 3.7 19.4 - - + +
315F VAL* 3.6 15.5 - - + +
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Residues in contact with TYR 304 (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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199F LEU* 4.6 6.7 - - + -
202F PHE* 3.7 15.5 - + - -
275F ASP* 3.7 10.2 + - - +
276F ILE* 3.9 30.7 - - + +
279F ASN* 3.3 37.1 - - - +
280F LYS 2.6 29.3 + - - -
282F SER* 4.2 6.9 - - - -
285F VAL* 3.7 16.0 - - + +
300F LEU* 2.9 38.5 + - + +
301F LYS* 4.3 4.5 + - - +
302F GLU 3.9 0.2 - - - -
303F ASN* 1.3 77.5 - - - +
305F GLY* 1.3 64.2 + - - +
306F GLN* 2.9 18.5 + - - +
315F VAL* 3.9 6.1 - - + +
319F TYR* 3.3 21.0 + - - -
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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