Contacts of the helix formed by residues 273 - 283 (chain F) in PDB entry 3LUE
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 GLY 273 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178F LEU* 4.9 0.2 - - - -
261F LEU 3.1 15.0 - - - -
262F PHE 3.4 18.6 + - - -
264F PRO* 3.7 9.3 - - - +
272F CYS* 1.3 77.0 - - - +
274F ILE* 1.3 61.2 + - - -
275F HIS* 2.8 15.7 + - - -
276F GLU* 2.9 16.8 + - - +
277F THR* 3.3 10.8 + - - -
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Residues in contact with ILE 274 (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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153F MET* 3.5 30.9 - - + +
155F SER* 5.7 0.4 - - - +
160F THR* 3.4 25.6 - - + +
162F THR* 4.9 0.4 - - + +
178F LEU* 3.3 29.8 - - + -
261F LEU* 2.9 32.1 + - + +
262F PHE* 3.6 32.3 - - + -
273F GLY* 1.3 71.0 - - - -
275F HIS* 1.3 60.4 + - - +
276F GLU 3.4 0.4 - - - -
277F THR* 4.0 6.8 - - + -
278F THR* 3.1 27.7 + - - -
309F ILE* 5.5 3.1 - - + -
313F MET* 4.0 15.3 - - + +
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Residues in contact with HIS 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F PHE* 3.1 54.9 + + + -
273F GLY* 2.8 7.0 + - - -
274F ILE* 1.3 75.8 - - - +
276F GLU* 1.3 88.1 + - + +
278F THR* 4.1 0.7 + - - -
279F PHE* 3.6 18.9 + - - +
312F ARG* 5.6 0.2 - - - -
313F MET* 4.1 13.0 - - - -
316F GLU* 3.7 43.2 + - + -
317F ILE* 4.1 8.7 - - + +
320F LEU* 3.9 16.4 - - + +
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Residues in contact with GLU 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F CYS* 3.9 30.7 - - + +
273F GLY 2.9 7.9 + - - +
275F HIS* 1.3 105.9 + - + +
277F THR* 1.3 59.7 + - - +
279F PHE* 3.4 6.3 + - - +
280F ASN* 2.9 39.5 + - - +
320F LEU* 3.5 25.3 - - + +
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Residues in contact with THR 277 (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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160F THR* 6.2 0.9 - - + -
161F HIS* 6.0 0.4 - - - -
162F THR* 3.4 25.4 - - + +
176F LEU* 3.7 21.6 - - + +
177F ARG 5.3 1.3 - - - +
178F LEU* 3.8 30.1 - - + +
272F CYS* 3.9 12.1 - - - +
273F GLY 3.3 12.8 + - - -
274F ILE* 4.1 6.3 - - + -
275F HIS 3.5 0.2 - - - -
276F GLU* 1.3 72.8 - - - +
278F THR* 1.4 65.9 + - - +
280F ASN* 2.9 18.2 + - - -
281F SER* 3.1 14.6 + - - -
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Residues in contact with THR 278 (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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151F ILE* 4.0 14.6 - - + +
153F MET* 3.5 12.0 - - + +
162F THR* 3.4 23.7 - - - +
274F ILE 3.1 16.9 + - - -
275F HIS 4.1 5.2 - - - -
277F THR* 1.4 74.1 - - - +
279F PHE* 1.3 63.1 + - - +
281F SER* 3.1 10.2 + - - -
282F ILE* 3.2 26.4 + - + +
297F THR* 3.9 18.8 - - + +
313F MET* 3.9 2.7 - - + +
317F ILE* 3.6 27.1 - - + -
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Residues in contact with PHE 279 (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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244D ASP* 5.4 0.2 - - - -
275F HIS 3.6 13.0 + - - +
276F GLU* 3.4 9.6 + - - +
277F THR 3.2 0.6 - - - -
278F THR* 1.3 80.3 - - - +
280F ASN* 1.3 76.7 + - - +
282F ILE* 3.8 8.5 - - - +
283F MET* 3.0 52.3 + - + +
294F TYR* 3.7 27.4 - + + -
317F ILE* 5.4 6.5 - - + +
320F LEU* 3.4 57.9 - - + -
321F ALA* 4.4 2.0 - - - -
322F PRO* 5.1 2.5 - - + -
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Residues in contact with ASN 280 (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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176F LEU* 3.7 17.1 - - + +
272F CYS* 4.7 13.9 - - - -
276F GLU* 2.9 33.4 + - - +
277F THR* 2.9 3.7 + - - +
279F PHE* 1.3 91.8 - - - +
281F SER* 1.3 63.3 + - - +
283F MET* 3.8 9.9 + - - +
284F LYS* 3.6 21.8 + - + +
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Residues in contact with SER 281 (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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151F ILE* 3.7 22.2 - - - -
162F THR* 3.0 24.0 + - - -
164F PRO* 3.8 6.1 - - - -
174F ALA* 2.7 27.4 + - - +
176F LEU* 3.1 9.7 - - - +
277F THR 3.1 5.1 + - - -
278F THR 3.7 2.5 - - - -
280F ASN* 1.3 73.4 - - - +
282F ILE* 1.3 65.8 + - - +
284F LYS* 2.8 20.3 + - - +
285F CYS* 3.4 11.1 - - - -
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Residues in contact with ILE 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ILE* 4.3 14.3 - - + +
278F THR* 3.2 26.1 + - + +
279F PHE* 3.8 5.4 - - - +
281F SER* 1.3 76.8 - - - +
283F MET* 1.3 67.4 + - + +
284F LYS 3.2 0.9 + - - -
285F CYS* 3.3 16.2 + - - +
290F ARG* 3.3 25.5 + - + +
293F LEU* 4.0 22.4 - - + +
294F TYR* 3.4 67.5 - - + +
297F THR* 5.1 1.6 - - - +
317F ILE* 5.8 1.1 - - + -
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Residues in contact with MET 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D SER* 6.1 4.0 - - - -
201D THR* 4.2 8.2 + - - +
244D ASP* 4.5 15.5 - - - +
268E GLY 5.1 2.8 - - - +
279F PHE* 3.0 47.0 + - + +
280F ASN* 4.0 8.1 - - - +
281F SER 3.1 2.0 + - - -
282F ILE* 1.3 80.8 - - + +
284F LYS* 1.3 54.5 - - + +
285F CYS 3.4 0.7 - - - -
290F ARG* 2.8 45.1 + - - +
294F TYR* 4.6 5.6 - - - -
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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