Contacts of the strand formed by residues 255 - 265 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C ASP* 6.3 2.2 - - + -
248C LEU 3.5 7.0 - - - +
249C THR* 3.2 24.0 + - - +
253C ASN* 3.3 47.3 + - - -
254C THR* 1.3 75.3 - - - +
256C ARG* 1.3 64.2 + - - +
257C TYR* 5.7 1.0 - - - -
283C ASP* 4.4 2.9 - - - +
379C MET* 5.2 6.1 - - - +
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Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C ASP* 3.8 2.8 - - - +
248C LEU* 3.2 30.1 + - - +
254C THR* 3.9 12.6 + - + +
255C HIS* 1.3 78.1 - - - +
257C TYR* 1.3 62.5 + - - +
283C ASP* 2.8 47.1 + - - +
284C ALA* 4.0 9.6 - - + -
370C TRP* 3.1 56.9 - - + +
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Residues in contact with TYR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ARG* 3.7 19.0 + - - -
246C ILE 3.1 12.6 - - - +
247C ASP* 3.5 14.8 - - - +
255C HIS 5.7 0.7 - - - -
256C ARG* 1.3 79.4 - - - +
258C ALA* 1.3 57.2 + - - +
259C ASP* 2.8 39.5 - - - -
281C ASP* 2.5 27.5 + - + -
282C GLY* 3.1 29.7 - - - -
283C ASP* 2.9 30.4 + - - -
284C ALA* 3.0 26.3 + - - +
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Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C LEU 3.8 0.3 - - - +
245C ARG* 3.4 0.5 - - - -
246C ILE* 2.9 36.8 + - + +
248C LEU* 5.3 0.2 - - + -
257C TYR* 1.3 76.3 - - - +
259C ASP* 1.3 70.3 + - - +
260C TYR* 4.0 10.1 - - + -
279C TYR* 4.1 10.3 - - + -
281C ASP 3.9 5.6 - - - -
282C GLY* 4.3 0.4 - - - -
284C ALA* 3.9 2.7 - - + +
367C TRP* 4.0 36.1 - - + +
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Residues in contact with ASP 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ARG* 3.1 21.5 + - - +
244C LEU 3.3 8.1 - - - +
245C ARG* 3.0 32.5 + - - +
257C TYR* 2.8 30.3 - - - -
258C ALA* 1.3 91.6 - - - +
260C TYR* 1.3 73.0 + - - +
279C TYR* 3.4 5.0 - - - -
280C LEU* 3.0 34.6 + - + -
281C ASP* 3.0 18.0 + - - +
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Residues in contact with TYR 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C TYR 3.9 0.3 - - - +
243C ARG* 3.4 2.0 - - - -
244C LEU* 2.7 56.4 + - + +
246C ILE* 4.4 2.5 - - + -
258C ALA* 4.0 16.6 - - + -
259C ASP* 1.3 93.3 - - - +
261C GLY* 1.3 62.6 + - - +
263C PHE* 4.0 1.5 - - + +
276C TYR* 3.4 41.7 - + + -
278C MET 3.4 8.5 - - - -
279C TYR* 3.6 11.7 - + - -
280C LEU* 3.8 2.0 - - - -
286C ASN* 3.1 45.2 + - - -
287C ALA 3.5 1.4 + - - -
288C PHE* 3.2 49.8 + + + -
367C TRP* 3.9 4.7 - + - -
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Residues in contact with GLY 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C TYR* 1.3 70.3 - - - +
262C HIS* 1.3 58.2 + - - -
263C PHE 2.9 13.5 + - - -
276C TYR* 3.1 4.3 - - - +
277C SER* 2.8 31.0 + - - -
278C MET 3.2 2.6 + - - -
280C LEU* 2.9 27.9 - - - +
387C MET* 3.5 17.7 - - - -
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Residues in contact with HIS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ALA* 3.8 19.5 - - + +
242C TYR 3.0 15.8 + - - +
261C GLY* 1.3 70.3 - - - +
263C PHE* 1.3 67.9 + - - +
264C LYS* 3.5 6.1 + - - +
275C PHE* 3.6 23.8 - - + -
276C TYR* 4.0 0.4 - - - -
277C SER* 2.9 38.6 - - - +
280C LEU* 5.9 0.4 - - + -
387C MET* 3.2 28.3 - - + +
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Residues in contact with PHE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ILE* 5.6 3.4 - - + -
233C ILE* 4.2 13.7 - - + -
237C THR* 3.6 31.2 - - + +
240C GLN 5.5 0.2 - - - +
242C TYR* 2.8 20.6 + - - +
244C LEU* 3.3 48.5 - - + +
260C TYR 4.0 2.9 - - - +
261C GLY 2.9 4.8 + - - -
262C HIS* 1.3 80.0 - - - +
264C LYS* 1.3 69.4 + - - +
265C LEU* 3.9 17.7 - - + -
274C LEU* 3.2 29.2 - - + -
275C PHE 3.2 9.2 - - - -
276C TYR* 4.1 7.4 - + + -
288C PHE* 5.4 0.7 - + - -
333C TRP* 4.6 10.1 - + - -
382C MET* 4.7 9.0 - - + -
384C LEU* 3.8 19.3 - - + -
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Residues in contact with LYS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C THR* 3.4 26.5 - - - +
238C GLY* 4.9 12.0 - - - +
262C HIS 3.7 4.5 - - - +
263C PHE* 1.3 81.0 - - - +
265C LEU* 1.3 82.4 + - - +
266C THR* 4.9 10.0 - - + +
274C LEU* 4.2 0.7 - - - +
275C PHE* 2.9 64.6 + - + -
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ASN* 4.3 15.9 - - - +
233C ILE* 3.5 33.9 - - + -
234C HIS* 2.5 38.7 + - + +
237C THR* 3.5 5.2 + - - -
238C GLY* 5.7 0.9 + - - -
263C PHE* 3.9 9.2 - - + -
264C LYS* 1.3 94.7 - - - +
266C THR* 1.3 62.3 + - - +
272C TYR* 4.3 16.6 - - + +
273C ARG 3.1 13.9 - - - +
274C LEU* 3.9 4.5 - - - -
333C TRP* 3.3 40.6 - - + +
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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