Contacts of the strand formed by residues 255 - 265 (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 HIS 255 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247L ASP* 6.3 2.2 - - + -
248L LEU 3.5 7.2 - - - +
249L THR* 3.2 23.1 + - - +
253L ASN* 3.3 46.3 + - - -
254L THR* 1.3 75.8 - - - +
256L ARG* 1.3 64.7 + - - +
257L TYR* 5.7 1.0 - - - -
283L ASP* 4.4 2.6 - - - +
379L MET* 5.2 6.0 - - - +
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Residues in contact with ARG 256 (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* 3.8 2.3 - - - +
248L LEU* 3.2 29.7 + - - +
254L THR* 3.9 13.3 + - + +
255L HIS* 1.3 77.3 - - - +
257L TYR* 1.3 63.9 + - - +
283L ASP* 2.8 48.1 + - - +
284L ALA* 4.0 10.1 - - + -
370L TRP* 3.1 55.8 - - + +
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Residues in contact with TYR 257 (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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245L ARG* 3.7 19.0 + - - -
246L ILE 3.2 13.5 - - - +
247L ASP* 3.6 15.5 - - - +
255L HIS 5.7 0.9 - - - -
256L ARG* 1.3 76.7 - - - +
258L ALA* 1.3 57.6 + - - +
259L ASP* 2.8 40.4 - - - -
281L ASP* 2.5 26.7 + - + -
282L GLY* 3.1 36.9 - - - -
283L ASP* 2.9 31.7 + - - -
284L ALA* 3.1 18.8 + - - -
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Residues in contact with ALA 258 (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 3.8 0.2 - - - +
245L ARG* 3.4 1.0 - - - -
246L ILE* 2.9 35.4 + - + +
248L LEU* 5.3 0.2 - - + -
257L TYR* 1.3 75.1 - - - +
259L ASP* 1.3 68.7 + - - +
260L TYR* 4.0 11.7 - - + -
279L TYR* 4.1 9.4 - - + -
281L ASP 3.9 5.6 - - - -
282L GLY* 4.3 0.4 - - - -
284L ALA* 4.2 2.5 - - + -
367L TRP* 4.0 36.3 - - + +
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Residues in contact with ASP 259 (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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243L ARG* 3.1 22.2 + - + +
244L LEU 3.3 8.7 - - - +
245L ARG* 3.0 33.2 + - - +
257L TYR* 2.8 29.5 - - - -
258L ALA* 1.3 91.0 - - - +
260L TYR* 1.3 71.4 + - - +
279L TYR* 3.4 5.0 - - - -
280L LEU* 3.0 35.4 + - + -
281L ASP* 3.1 16.8 + - + +
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Residues in contact with TYR 260 (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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242L TYR 3.9 0.5 - - - +
243L ARG* 3.4 2.4 - - - -
244L LEU* 2.7 56.9 + - + +
246L ILE* 4.4 2.5 - - + -
258L ALA* 4.0 20.9 - - + -
259L ASP* 1.3 92.2 - - - +
261L GLY* 1.3 62.5 + - - +
263L PHE* 3.9 0.9 - - + +
276L TYR* 3.3 41.3 - + + -
278L MET 3.4 8.7 - - - -
279L TYR* 3.6 7.9 - + - -
280L LEU* 3.8 1.8 - - - -
286L ASN* 3.1 47.5 + - - -
287L ALA 3.5 1.2 + - - -
288L PHE* 3.2 50.1 + + + -
367L TRP* 3.9 4.2 - + - -
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Residues in contact with GLY 261 (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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260L TYR* 1.3 69.7 - - - +
262L HIS* 1.3 57.8 + - - -
263L PHE 2.8 12.2 + - - -
276L TYR* 3.1 4.5 - - - +
277L SER* 2.8 31.6 + - - -
278L MET 3.2 3.4 + - - -
280L LEU* 2.9 27.7 - - - +
387L MET* 3.4 17.7 - - - -
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Residues in contact with HIS 262 (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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241L ALA* 3.8 19.3 - - + +
242L TYR 3.0 15.6 + - - +
261L GLY* 1.3 71.1 - - - +
263L PHE* 1.3 66.1 + - - +
264L LYS* 3.5 5.9 + - - +
275L PHE* 3.6 23.5 - - + -
276L TYR* 4.0 0.7 - - - -
277L SER* 2.9 38.6 - - - +
280L LEU* 5.9 0.2 - - + -
387L MET* 3.2 28.1 - - + +
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Residues in contact with PHE 263 (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* 5.6 2.7 - - + -
233L ILE* 4.2 13.5 - - + -
237L THR* 3.6 30.7 - - + +
242L TYR* 2.8 20.2 + - - +
244L LEU* 3.3 46.9 - - + +
260L TYR 3.9 4.3 - - - +
261L GLY 2.8 4.6 + - - -
262L HIS* 1.3 79.7 - - - +
264L LYS* 1.3 69.1 + - - +
265L LEU* 3.9 17.9 - - + -
274L LEU* 3.2 29.6 - - + -
275L PHE 3.2 9.2 - - - -
276L TYR* 4.1 7.4 - + + -
288L PHE* 5.3 1.1 - + - -
333L TRP* 4.6 9.6 - + - -
382L MET* 4.7 9.2 - - + -
384L LEU* 3.8 19.1 - - + -
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Residues in contact with LYS 264 (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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237L THR* 3.4 25.6 - - - +
238L GLY* 4.9 11.4 - - - +
262L HIS 3.7 3.4 - - - +
263L PHE* 1.3 83.4 - - - +
265L LEU* 1.3 87.9 + - - +
266L THR* 4.9 10.6 - - + +
273L ARG 3.7 0.2 - - - +
274L LEU* 4.2 0.7 - - - +
275L PHE* 2.9 59.8 + - + +
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Residues in contact with LEU 265 (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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230L ASN* 4.4 15.9 - - - +
233L ILE* 3.5 32.3 - - + -
234L HIS* 2.5 39.8 + - + -
237L THR* 3.4 5.0 + - - -
238L GLY* 5.7 0.5 + - - -
263L PHE* 3.9 8.7 - - + -
264L LYS* 1.3 95.0 - - - +
266L THR* 1.3 60.5 + - - +
272L TYR* 4.3 17.5 - - + +
273L ARG 3.1 13.9 - - - +
274L LEU* 3.8 4.7 - - - -
333L TRP* 3.3 42.0 - - + +
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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