Contacts of the strand formed by residues 255 - 265 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247F ASP* 6.3 2.2 - - + -
248F LEU 3.5 7.0 - - - +
249F THR* 3.2 24.2 + - + +
253F ASN* 3.3 46.2 + - - -
254F THR* 1.3 74.8 - - - +
256F ARG* 1.3 65.2 + - - +
257F TYR* 5.7 0.9 - - - -
283F ASP* 4.4 2.8 - - - +
379F MET* 5.2 5.7 - - - +
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Residues in contact with ARG 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F ASP* 3.8 2.6 - - - +
248F LEU* 3.2 30.3 + - - +
254F THR* 3.9 13.2 + - + +
255F HIS* 1.3 77.5 - - - +
257F TYR* 1.3 63.2 + - - +
283F ASP* 2.8 48.4 + - - +
284F ALA* 4.0 9.2 - - + -
369F THR 5.6 0.8 + - - -
370F TRP* 3.1 55.0 - - + +
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Residues in contact with TYR 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F ARG* 3.7 19.0 + - - -
246F ILE 3.2 13.0 - - - +
247F ASP* 3.5 14.8 - - - +
255F HIS 5.7 0.7 - - - -
256F ARG* 1.3 78.0 - - - +
258F ALA* 1.3 57.0 + - - +
259F ASP* 2.8 40.2 - - - -
281F ASP* 2.5 26.8 + - + -
282F GLY* 3.1 37.9 - - - -
283F ASP* 2.9 29.4 + - - -
284F ALA* 3.1 18.5 + - - -
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Residues in contact with ALA 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F LEU 3.8 0.3 - - - +
245F ARG* 3.4 0.5 - - - -
246F ILE* 2.9 36.7 + - + +
248F LEU* 5.3 0.2 - - + -
257F TYR* 1.3 76.3 - - - +
259F ASP* 1.3 69.8 + - - +
260F TYR* 4.0 10.3 - - + -
279F TYR* 4.1 10.1 - - + -
281F ASP 3.9 5.2 - - - -
282F GLY* 4.4 0.4 - - - -
284F ALA* 4.2 2.9 - - + -
367F TRP* 4.0 35.9 - - + +
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Residues in contact with ASP 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F ARG* 3.1 22.1 + - + +
244F LEU 3.3 7.9 - - - +
245F ARG* 3.0 32.6 + - - +
257F TYR* 2.8 30.0 - - - -
258F ALA* 1.3 91.6 - - - +
260F TYR* 1.3 73.9 + - - +
279F TYR* 3.4 5.2 - - - -
280F LEU* 3.0 35.3 + - + -
281F ASP* 3.1 16.7 + - - +
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Residues in contact with TYR 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F TYR 3.9 0.3 - - - +
243F ARG* 3.4 2.0 - - - -
244F LEU* 2.7 55.4 + - + +
246F ILE* 4.4 2.2 - - + -
258F ALA* 4.0 17.3 - - + -
259F ASP* 1.3 94.0 - - - +
261F GLY* 1.3 62.4 + - - +
263F PHE* 4.0 1.1 - - + +
276F TYR* 3.3 41.7 - + + -
278F MET 3.4 9.0 - - - -
279F TYR* 3.6 12.6 - + - -
280F LEU* 3.8 2.2 - - - -
286F ASN* 3.1 43.5 + - - -
287F ALA 3.5 1.2 + - - -
288F PHE* 3.2 52.8 + + + +
367F TRP* 3.9 4.1 - + - -
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Residues in contact with GLY 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F TYR* 1.3 70.0 - - - +
262F HIS* 1.3 59.1 + - - -
263F PHE 2.9 12.0 + - - -
276F TYR* 3.1 4.7 - - - +
277F SER* 2.8 30.7 + - - -
278F MET 3.2 2.6 + - - -
280F LEU* 2.9 27.0 - - - +
387F MET* 3.4 18.2 - - - -
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Residues in contact with HIS 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F ALA* 3.8 19.7 - - + +
242F TYR 3.0 15.8 + - - +
261F GLY* 1.3 70.7 - - - +
263F PHE* 1.3 68.0 + - - +
264F LYS* 3.5 5.9 + - - +
275F PHE* 3.6 24.4 - - + +
276F TYR* 4.0 0.7 - - - -
277F SER* 2.9 37.9 - - - +
387F MET* 3.2 28.7 - - + +
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Residues in contact with PHE 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ILE* 5.5 3.6 - - + -
233F ILE* 4.2 13.7 - - + -
237F THR* 3.6 30.5 - - + +
240F GLN 5.5 0.3 - - - +
242F TYR* 2.8 20.4 + - - +
244F LEU* 3.3 47.6 - - + +
260F TYR 4.0 3.4 - - - +
261F GLY 2.9 4.6 + - - -
262F HIS* 1.3 79.6 - - - +
264F LYS* 1.3 69.3 + - - +
265F LEU* 3.9 17.5 - - + -
274F LEU* 3.2 29.8 - - + -
275F PHE 3.2 9.2 - - - -
276F TYR* 4.1 7.2 - + + -
288F PHE* 5.4 0.9 - + - -
333F TRP* 4.6 9.9 - + - -
382F MET* 4.7 9.2 - - + -
384F LEU* 3.8 19.3 - - + -
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Residues in contact with LYS 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F THR* 3.4 27.6 - - - +
238F GLY* 4.9 12.0 - - - +
262F HIS 3.7 5.2 - - - +
263F PHE* 1.3 79.6 - - - +
265F LEU* 1.3 86.7 + - - +
266F THR* 4.9 9.8 - - + +
274F LEU* 4.2 0.7 - - - +
275F PHE* 2.8 60.1 + - + -
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Residues in contact with LEU 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F ASN* 4.4 15.7 - - - +
233F ILE* 3.5 34.1 - - + -
234F HIS* 2.6 38.6 + - + +
237F THR* 3.5 5.2 + - - -
238F GLY* 5.6 0.9 + - - -
263F PHE* 3.9 9.4 - - + -
264F LYS* 1.3 95.1 - - - +
266F THR* 1.3 62.3 + - - +
272F TYR* 4.3 17.3 - - + +
273F ARG 3.0 13.7 - - - +
274F LEU* 3.8 4.3 - - - -
333F TRP* 3.3 40.8 - - + +
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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