Contacts of the helix formed by residues 289 - 296 (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 ILE 289 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLU 4.9 0.7 - - - +
60D SER* 1.2 83.6 - - - +
61D LYS* 2.9 46.4 - - + +
166F TYR* 3.8 4.9 - - + -
171F LEU* 3.7 26.0 - - + -
285F CYS* 4.4 6.1 - - + -
286F ASP* 2.8 29.2 + - + +
288F ASP* 1.4 67.4 - - - +
290F ARG* 1.3 54.2 + - - +
291F LYS 3.2 2.9 - - - -
292F ASP* 2.6 37.9 + - + +
293F LEU* 3.0 16.8 + - + +
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Residues in contact with ARG 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D THR* 2.6 39.6 + - - -
202D THR* 1.5 55.7 + - + +
205D GLU* 3.4 16.6 + - - +
244D ASP* 5.6 7.4 - - + -
270E GLU* 4.8 1.6 + - - -
282F ILE* 3.3 31.9 + - + +
283F MET* 2.8 43.9 + - - +
284F LYS 4.6 0.4 - - - -
285F CYS* 2.8 14.5 + - + -
286F ASP 3.5 1.0 + - - -
287F VAL 4.0 4.0 - - - +
288F ASP 3.7 0.4 - - - -
289F ILE* 1.3 75.1 - - - +
291F LYS* 1.3 65.4 + - - +
293F LEU* 2.9 12.8 + - - +
294F TYR* 2.9 35.4 + - + -
325F MET* 6.2 0.2 - - - -
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Residues in contact with LYS 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D SER* 4.8 0.2 - - - +
204D ALA* 3.0 20.6 - - + +
205D GLU* 4.0 4.8 + - - +
208D ILE* 5.0 3.8 - - - -
243D PRO* 3.4 44.8 - - + +
287F VAL 2.5 31.3 + - - -
288F ASP* 3.5 18.9 - - - +
289F ILE* 3.0 0.4 + - - -
290F ARG* 1.3 81.9 - - - +
292F ASP* 1.3 70.4 + - - +
294F TYR* 3.9 7.7 + - - +
295F ALA* 3.5 20.3 + - - +
325F MET* 4.8 4.9 - - - -
326F LYS 5.2 1.0 - - - +
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Residues in contact with ASP 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 4.7 15.0 - - - +
60D SER* 4.6 1.2 - - - -
149F THR* 4.4 24.6 - - + +
150F GLY* 4.5 1.3 - - - -
288F ASP 4.1 5.7 - - - +
289F ILE* 2.6 32.3 + - + +
291F LYS* 1.3 79.9 - - - +
293F LEU* 1.3 63.4 + - + +
295F ALA* 3.3 2.5 + - - +
296F ASN* 2.8 39.2 + - - +
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Residues in contact with LEU 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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61D LYS* 5.2 0.4 - - - +
149F THR* 5.0 4.3 - - + -
150F GLY* 3.0 38.8 - - - +
151F ILE* 3.4 10.2 - - + +
164F PRO* 3.8 10.5 - - + -
165F ILE 4.1 7.6 - - - +
282F ILE* 4.0 24.7 - - + -
285F CYS* 3.6 38.1 - - + -
289F ILE* 3.0 18.8 + - + +
290F ARG* 2.9 12.8 + - - +
292F ASP* 1.3 76.3 - - - +
294F TYR* 1.4 60.7 + - - +
296F ASN 3.3 11.6 + - - +
297F THR* 3.2 15.2 + - - -
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Residues in contact with TYR 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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244D ASP* 3.7 15.6 + - - -
279F PHE* 3.7 26.2 - + - -
282F ILE* 3.4 43.2 - - + +
283F MET* 4.6 1.7 - - - -
290F ARG* 2.9 38.8 + - + +
291F LYS* 4.3 4.3 - - - +
293F LEU* 1.4 71.6 - - - +
295F ALA* 1.3 58.9 + - - +
296F ASN 3.2 1.6 + - - -
297F THR* 3.8 7.7 + - - -
317F ILE* 4.0 15.9 - - + -
321F ALA* 3.7 21.3 - - + -
322F PRO* 3.9 3.1 - - + +
325F MET* 4.1 22.9 - - + -
326F LYS 3.9 13.0 - - - +
327F ILE* 3.4 22.7 - - + +
328F LYS 3.1 23.0 + - - +
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Residues in contact with ALA 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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147F ARG* 5.6 0.2 + - - -
291F LYS 3.5 12.3 + - - +
292F ASP* 3.3 5.4 + - - +
294F TYR* 1.3 77.9 - - - +
296F ASN* 1.3 76.3 + - - +
326F LYS* 4.0 25.5 + - + +
328F LYS* 3.1 35.7 - - + +
330F ILE* 3.7 2.1 - - - +
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Residues in contact with ASN 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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44D MET* 3.5 19.7 - - + +
147F ARG* 2.8 34.5 + - - +
149F THR* 3.9 8.9 + - - -
150F GLY* 3.4 0.5 - - - -
151F ILE 2.9 25.6 + - - +
292F ASP* 2.8 31.5 + - - +
293F LEU 3.3 5.7 - - - +
294F TYR 3.2 0.4 - - - -
295F ALA* 1.3 92.5 - - - +
297F THR* 1.3 60.6 + - - +
298F VAL* 3.7 1.8 - - - -
330F ILE* 3.7 8.3 - - - -
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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