Contacts of the helix formed by residues 289 - 296 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLU 4.9 0.7 - - - +
60F SER* 1.2 83.2 - - - +
61F LYS* 2.9 46.2 - - + +
64F ILE* 4.1 0.2 - - + -
166H TYR* 3.8 4.7 - - + -
171H LEU* 3.7 25.6 - - + -
285H CYS* 4.4 6.3 - - + -
286H ASP* 2.8 29.4 + - + +
288H ASP* 1.4 68.8 - - - +
290H ARG* 1.3 55.7 + - - +
291H LYS 3.2 2.9 - - - -
292H ASP* 2.6 37.4 + - + +
293H LEU* 3.0 16.8 + - + -
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Residues in contact with ARG 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F THR* 2.6 39.8 + - - -
202F THR* 1.5 55.7 + - + +
205F GLU* 3.4 15.1 + - - +
244F ASP* 5.6 6.5 - - + -
270G GLU* 4.8 1.8 + - - -
282H ILE* 3.3 31.3 + - + +
283H MET* 2.8 42.2 + - - +
284H LYS 4.6 0.2 - - - -
285H CYS* 2.8 14.1 + - + +
286H ASP 3.5 0.8 + - - -
287H VAL 3.9 3.8 + - - +
288H ASP 3.7 0.6 - - - -
289H ILE* 1.3 75.6 - - - +
291H LYS* 1.3 66.2 + - - +
293H LEU* 2.9 12.5 + - - +
294H TYR* 2.9 34.9 + - + -
325H MET* 6.2 0.2 - - - -
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Residues in contact with LYS 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F ALA* 3.0 20.1 - - + +
205F GLU* 4.0 4.4 + - - +
208F ILE* 5.0 3.4 - - - -
243F PRO* 3.4 46.6 - - + +
287H VAL 2.5 31.5 + - - -
288H ASP* 3.5 19.4 - - - +
289H ILE* 3.0 0.4 + - - -
290H ARG* 1.3 82.4 - - - +
292H ASP* 1.3 70.0 + - - +
294H TYR* 3.9 8.1 + - - +
295H ALA* 3.5 19.6 + - - +
325H MET* 4.8 4.7 - - - -
326H LYS 5.2 1.2 - - - +
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Residues in contact with ASP 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F GLU* 4.7 14.4 - - - +
60F SER* 4.6 1.4 - - - -
149H THR* 4.4 24.0 - - + +
150H GLY* 5.0 1.1 - - - -
288H ASP 4.1 5.4 - - - +
289H ILE* 2.6 32.4 + - + +
291H LYS* 1.3 79.7 - - - +
293H LEU* 1.3 62.3 + - - +
295H ALA* 3.3 2.1 + - - -
296H ASN* 2.8 38.4 + - - +
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Residues in contact with LEU 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F LYS* 5.2 0.2 - - - +
149H THR* 5.1 4.7 - - + -
150H GLY* 3.0 38.1 - - - +
151H ILE* 3.4 10.4 - - + +
164H PRO* 3.8 11.4 - - + -
165H ILE 4.1 7.4 - - - +
171H LEU* 5.9 0.2 - - + -
282H ILE* 4.0 24.7 - - + -
285H CYS* 3.6 37.9 - - + -
289H ILE* 3.0 19.7 + - + +
290H ARG* 2.9 12.5 + - - +
292H ASP* 1.3 76.5 - - - +
294H TYR* 1.4 59.2 + - - +
296H ASN 3.3 12.0 + - - +
297H THR* 3.2 15.2 + - - -
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Residues in contact with TYR 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F ASP* 3.7 15.7 + - - -
279H PHE* 3.7 27.4 - + - -
282H ILE* 3.4 42.9 - - + +
283H MET* 4.6 1.4 - - - -
290H ARG* 2.9 38.7 + - + +
291H LYS* 4.3 4.5 - - - +
292H ASP 3.4 0.2 - - - -
293H LEU* 1.4 72.1 - - - +
295H ALA* 1.3 57.9 + - - +
296H ASN 3.2 1.2 + - - -
297H THR* 3.8 7.1 + - - -
317H ILE* 4.0 15.7 - - + -
321H ALA* 3.7 21.3 - - + -
322H PRO* 3.9 2.9 - - + +
325H MET* 4.1 24.0 - - + -
326H LYS 3.9 13.0 - - - +
327H ILE* 3.4 22.3 - - + +
328H LYS 3.1 23.2 + - - +
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Residues in contact with ALA 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291H LYS 3.5 12.3 + - - +
292H ASP* 3.3 5.6 + - - +
294H TYR* 1.3 77.9 - - - +
296H ASN* 1.3 77.3 + - - +
326H LYS* 4.0 24.6 + - + +
328H LYS* 3.1 36.2 - - - +
330H ILE* 3.7 1.9 - - - +
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Residues in contact with ASN 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F MET* 3.5 20.9 - - + +
147H ARG* 2.8 34.7 + - - +
149H THR* 3.9 8.3 + - - -
150H GLY* 3.4 0.3 - - - -
151H ILE 2.9 25.8 + - - +
292H ASP* 2.8 31.1 + - - +
293H LEU 3.3 5.5 - - - +
294H TYR 3.2 0.4 - - - -
295H ALA* 1.3 92.0 - - - +
297H THR* 1.3 60.8 + - - +
298H VAL* 3.7 1.3 + - - -
330H ILE* 3.7 7.9 - - - -
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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
------------------------------------------------------------
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