Contacts of the strand formed by residues 242 - 249 (chain L) in PDB entry 1LWU
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 TYR 242 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153L ASP* 2.4 40.5 + - + +
192L THR* 4.7 4.3 - - + -
236L LEU* 3.0 33.8 - - + +
237L THR* 3.7 15.7 - - - -
239L GLN* 3.0 18.4 + - - -
240L GLN* 3.4 25.8 + - + -
241L ALA* 1.3 77.6 - - - +
243L ARG* 1.3 60.4 + - - +
244L LEU 3.8 0.2 - - - -
262L HIS* 3.0 9.1 + - - +
263L PHE* 2.8 43.2 + - + +
384L LEU* 4.0 24.7 - - + -
385L LEU* 3.3 24.9 - - - -
386L PRO* 3.6 13.2 - - + -
387L MET* 4.0 1.8 - - - -
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Residues in contact with ARG 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L TRP* 3.7 23.1 - - - -
242L TYR* 1.3 71.8 - - - +
244L LEU* 1.3 67.9 + - - +
245L ARG* 4.4 4.0 - - - +
259L ASP* 3.1 27.2 + - + +
260L TYR 3.4 9.6 - - - +
280L LEU* 4.0 28.1 + - - +
281L ASP* 5.4 4.0 - - - +
384L LEU* 3.6 1.8 - - - -
385L LEU* 2.6 40.4 + - + +
386L PRO 4.9 1.3 - - - +
387L MET* 3.1 52.9 + - + +
389L ARG 4.8 8.3 + - - -
390L ASP* 5.1 14.4 + - - +
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Residues in contact with LEU 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L ILE* 5.8 0.2 - - + -
242L TYR 3.7 2.2 + - - -
243L ARG* 1.3 74.0 - - - +
245L ARG* 1.3 75.9 + - - +
246L ILE* 4.2 12.3 - - + -
259L ASP* 3.3 7.4 - - - +
260L TYR* 2.7 42.7 + - + +
263L PHE* 3.3 47.8 - - + -
288L PHE* 4.2 22.2 - - + -
382L MET* 4.0 27.1 - - + -
383L LYS 3.4 11.4 - - - +
384L LEU* 3.5 15.7 - - + -
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Residues in contact with ARG 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L GLU* 4.6 11.1 + - - -
191L TRP* 3.6 33.0 - - + -
243L ARG* 3.8 5.5 + - - +
244L LEU* 1.3 75.5 - - - +
246L ILE* 1.3 69.1 + - - +
247L ASP* 3.4 26.5 - - - +
257L TYR* 3.7 18.9 + - + -
258L ALA 3.4 3.1 - - - +
259L ASP* 3.0 33.8 + - - +
381L THR 3.4 1.0 - - - +
382L MET* 3.3 4.9 - - - -
383L LYS* 2.7 63.1 + - + +
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Residues in contact with ILE 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L LEU* 4.2 17.9 - - + -
245L ARG* 1.3 78.1 - - - +
247L ASP* 1.3 61.5 + - - +
248L LEU* 3.3 35.7 - - + +
257L TYR* 3.2 9.0 - - - +
258L ALA* 2.9 33.1 + - + +
260L TYR* 4.4 7.4 - - + -
288L PHE* 3.9 19.5 - - + -
342L LEU* 3.6 20.0 - - + -
367L TRP* 3.6 35.4 - - + -
381L THR 3.3 5.4 - - - +
382L MET* 4.4 6.1 - - + -
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Residues in contact with ASP 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L GLU* 4.9 0.5 - - - +
245L ARG* 3.4 23.7 - - - +
246L ILE* 1.3 73.2 - - - +
248L LEU* 1.3 63.6 + - - +
249L THR* 4.9 2.3 + - - +
255L HIS* 6.3 2.5 - - + -
256L ARG 3.8 4.2 - - - +
257L TYR* 3.6 10.6 - - - +
379L MET* 4.3 0.3 - - - +
380L THR* 3.3 6.8 + - - -
381L THR* 3.0 45.1 + - + +
383L LYS* 3.0 34.6 + - - +
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Residues in contact with LEU 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L ILE* 3.3 43.3 - - + +
247L ASP* 1.3 78.1 - - - +
249L THR* 1.3 69.1 + - - +
254L THR 3.5 0.6 - - - +
255L HIS* 3.5 20.1 - - - +
256L ARG 3.2 13.9 + - - +
284L ALA* 4.3 9.9 - - + -
342L LEU* 3.5 23.3 - - + -
367L TRP* 4.3 25.4 - - + +
370L TRP* 3.9 13.9 - - + -
377L LEU* 3.5 22.7 - - + -
379L MET 3.8 2.0 - - - -
380L THR* 3.8 11.0 - - + +
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Residues in contact with THR 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L ASP* 4.9 2.3 + - - +
248L LEU* 1.3 82.1 + - - +
250L ASP* 1.3 67.5 + - - +
253L ASN* 4.0 7.4 - - - +
254L THR 3.1 10.5 - - - +
255L HIS* 3.2 32.4 - - - +
377L LEU* 3.6 6.9 - - - +
378L LYS* 2.8 48.3 + - - +
379L MET* 3.3 34.2 + - + +
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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