Contacts of the helix formed by residues 289 - 296 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H GLU 4.9 0.7 - - - +
60H SER* 1.2 83.6 + - - +
61H LYS* 2.9 46.7 - - + +
166J TYR* 3.8 4.7 - - + -
171J LEU* 3.7 26.2 - - + -
285J CYS* 4.4 6.1 - - + -
286J ASP* 2.8 28.6 + - + +
288J ASP* 1.4 67.6 - - - +
290J ARG* 1.3 54.9 + - - +
291J LYS 3.2 3.1 - - - -
292J ASP* 2.6 38.4 + - + +
293J LEU* 3.0 17.2 + - + +
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Residues in contact with ARG 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H THR* 2.6 39.2 + - - -
202H THR* 1.5 55.3 + - + +
205H GLU* 3.4 14.9 + - - +
244H ASP* 5.6 7.4 - - + +
268I GLY 5.8 0.4 + - - -
270I GLU* 4.8 2.0 + - - -
282J ILE* 3.3 32.1 + - + +
283J MET* 2.8 43.3 + - - +
284J LYS 4.6 0.4 - - - -
285J CYS* 2.8 14.3 + - + -
286J ASP 3.5 0.6 + - - -
287J VAL 4.0 4.0 - - - +
288J ASP 3.7 0.8 - - - -
289J ILE* 1.3 74.2 - - - +
291J LYS* 1.3 65.5 + - - +
293J LEU* 2.9 13.2 + - - +
294J TYR* 2.9 35.6 + - + -
325J MET* 6.2 0.2 - - - -
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Residues in contact with LYS 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H ALA* 3.0 20.2 - - + +
205H GLU* 4.0 5.2 + - - +
208H ILE* 5.0 3.8 - - - -
243H PRO* 3.4 44.8 - - + +
287J VAL 2.5 30.9 + - - -
288J ASP* 3.5 19.2 - - - +
289J ILE* 3.0 0.4 + - - -
290J ARG* 1.3 82.2 - - - +
292J ASP* 1.3 70.8 + - - +
294J TYR* 3.9 8.1 + - - +
295J ALA* 3.5 20.1 + - - +
325J MET* 4.8 4.7 - - - -
326J LYS 5.2 1.0 - - - +
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Residues in contact with ASP 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H GLU* 4.7 15.1 - - - +
60H SER* 4.6 1.4 - - - -
149J THR* 4.4 24.9 - - + +
150J GLY* 4.5 1.1 - - - -
288J ASP 4.1 5.9 - - - +
289J ILE* 2.6 31.6 + - - +
291J LYS* 1.3 80.1 - - - +
293J LEU* 1.3 63.4 + - + +
295J ALA* 3.3 2.5 + - - +
296J ASN* 2.8 38.9 + - - +
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Residues in contact with LEU 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H LYS* 5.2 0.7 - - - +
149J THR* 5.1 4.5 - - + -
150J GLY* 3.0 38.6 - - - +
151J ILE* 3.4 10.6 - - + +
164J PRO* 3.8 11.2 - - + -
165J ILE 4.1 7.6 - - - +
282J ILE* 4.0 25.1 - - + -
285J CYS* 3.6 37.2 - - + -
289J ILE* 3.6 18.8 - - + +
290J ARG* 2.9 12.1 + - - +
292J ASP* 1.3 75.9 - - - +
294J TYR* 1.4 60.9 + - - +
296J ASN 3.3 11.6 + - - +
297J THR* 3.2 15.1 + - - -
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Residues in contact with TYR 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H ASP* 3.7 15.6 + - - -
279J PHE* 3.7 26.4 - + - -
282J ILE* 3.4 43.2 - - + +
283J MET* 4.6 1.7 - - - -
290J ARG* 2.9 38.3 + - + +
291J LYS* 4.3 4.0 - - - +
293J LEU* 1.4 71.8 - - - +
295J ALA* 1.3 57.8 + - - +
296J ASN 3.2 1.5 + - - -
297J THR* 3.8 7.2 + - - -
317J ILE* 4.1 16.4 - - + -
321J ALA* 3.7 20.9 - - + -
322J PRO* 3.9 3.1 - - + +
325J MET* 4.1 24.0 - - + -
326J LYS 3.9 13.0 - - - +
327J ILE* 3.4 23.0 - - + +
328J LYS 3.1 22.9 + - - +
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Residues in contact with ALA 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J ARG* 5.6 0.2 + - - -
291J LYS 3.5 12.7 + - - +
292J ASP* 3.3 5.8 + - - +
294J TYR* 1.3 77.9 - - - +
296J ASN* 1.3 75.6 + - - +
326J LYS* 4.0 25.3 + - + +
328J LYS* 3.1 35.4 - - + +
330J ILE* 3.7 1.9 - - - +
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Residues in contact with ASN 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H MET* 3.5 19.8 - - + +
147J ARG* 2.8 34.5 + - - +
149J THR* 3.9 9.4 + - - -
150J GLY* 3.4 0.3 - - - -
151J ILE 2.9 25.5 + - - +
292J ASP* 2.8 31.3 + - - +
293J LEU 3.3 6.3 - - - +
294J TYR 3.2 0.8 - - - -
295J ALA* 1.3 93.2 - - - +
297J THR* 1.3 59.9 + - - +
298J VAL* 3.7 1.8 - - - -
330J 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
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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