Contacts of the strand formed by residues 257 - 267 (chain C) in PDB entry 1RE3
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 THR 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C GLU* 5.4 8.1 - - - +
250C LEU 3.1 14.6 - - - +
251C GLU* 3.7 26.7 - - + +
255C GLY 3.9 6.2 + - - +
256C ARG* 1.3 79.5 - - - +
258C SER* 1.3 63.9 + - - +
259C THR* 6.1 1.3 - - - +
285C ASP* 3.9 8.5 - - - +
372C TRP* 4.2 4.4 - - - -
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Residues in contact with SER 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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249C GLU* 3.5 0.5 - - - +
250C LEU* 3.0 30.8 + - - +
257C THR* 1.3 75.5 - - - +
259C THR* 1.3 71.4 + - - +
285C ASP* 3.2 20.0 - - - -
286C ALA* 3.3 19.6 - - - +
372C TRP* 3.2 41.4 - - - -
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Residues in contact with THR 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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247C ARG* 4.3 20.8 + - - +
248C VAL 3.0 13.0 - - - +
249C GLU* 3.9 20.2 - - + +
257C THR* 6.1 1.1 - - - +
258C SER* 1.3 82.6 - - - +
260C ALA* 1.3 62.4 + - - +
261C ASP* 4.6 2.9 + - - -
284C GLY* 3.0 20.1 - - - -
285C ASP* 3.1 9.1 + - - -
286C ALA* 3.0 23.6 + - - -
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Residues in contact with ALA 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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246C LEU 3.5 1.6 - - - +
247C ARG* 3.5 1.0 - - - -
248C VAL* 2.8 40.4 + - + +
259C THR* 1.3 75.9 - - - +
261C ASP* 1.3 63.8 + - - +
262C TYR* 4.0 11.4 - - + -
281C PHE* 4.0 5.4 - - + -
283C GLY 3.7 5.2 - - - -
286C ALA* 4.2 4.3 - - + -
287C GLY 3.8 22.2 - - - +
369C TRP* 3.9 20.0 - - + -
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Residues in contact with ASP 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ALA* 6.2 0.7 - - + -
246C LEU 3.3 5.6 - - - +
247C ARG* 2.7 53.1 + - - +
259C THR* 4.6 3.2 - - - -
260C ALA* 1.3 83.1 + - - +
262C TYR* 1.3 58.1 + - - +
281C PHE* 3.5 10.3 - - - -
282C ALA* 2.6 45.4 + - + +
283C GLY 2.9 16.2 + - - +
284C GLY* 5.8 0.4 - - - -
392C LEU* 4.3 14.6 - - + +
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Residues in contact with TYR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ALA* 3.3 6.9 - - - +
246C LEU* 2.9 54.8 + - + +
248C VAL* 4.6 2.0 - - + -
260C ALA* 4.0 24.9 - - + -
261C ASP* 1.3 77.6 - - - +
263C ALA* 1.3 60.4 + - - +
265C PHE* 4.2 3.0 - - + +
278C TYR* 3.6 41.3 - + + -
280C TYR 3.7 2.2 - - - -
281C PHE* 3.7 16.1 - + + -
282C ALA* 4.7 1.1 - - - -
288C ASP* 2.8 39.7 + - - -
289C ALA 3.5 2.1 + - - -
290C PHE* 3.4 43.1 + + + -
369C TRP* 3.6 10.2 - + - -
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Residues in contact with ALA 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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244C TYR 4.2 1.1 - - - -
261C ASP 4.3 0.4 - - - -
262C TYR* 1.3 69.2 - - - +
264C MET* 1.3 77.8 + - + +
265C PHE 3.3 2.1 + - - -
278C TYR* 3.5 3.8 - - - +
279C ALA 3.0 16.5 + - - -
280C TYR* 3.0 43.6 + - + +
282C ALA* 4.4 3.4 - - + +
389C PHE* 3.4 32.5 - - + -
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Residues in contact with MET 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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243C PRO* 3.4 29.6 - - + -
244C TYR 2.9 15.2 + - - +
263C ALA* 1.3 96.1 - - + +
265C PHE* 1.3 65.4 + - - +
266C LYS* 3.6 13.5 + - - +
277C THR* 3.6 1.7 + - - +
278C TYR* 3.2 14.8 - - - -
279C ALA* 3.6 18.8 - - + +
280C TYR* 3.8 18.6 - - + +
389C PHE* 3.8 21.9 - - + -
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Residues in contact with PHE 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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194C PHE* 3.9 22.7 - + - -
233C ILE* 4.1 7.0 - - + -
237C SER* 3.9 14.7 - - - +
244C TYR* 2.8 26.0 + - + +
245C ALA 4.1 0.9 - - - -
246C LEU* 3.7 45.3 - - + +
262C TYR* 4.2 2.9 - - + +
263C ALA 3.3 1.2 - - - -
264C MET* 1.3 77.4 - - - +
266C LYS* 1.3 73.6 + - - +
267C VAL* 3.5 28.9 - - + -
276C LEU* 3.3 31.4 - - + -
277C THR 3.5 4.5 - - - -
278C TYR* 4.2 8.7 - + + -
335C TRP* 5.1 2.2 - + - -
384C MET* 6.2 0.2 - - + -
386C ILE* 3.5 31.0 - - + -
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Residues in contact with LYS 266 (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 SER* 3.3 21.3 - - - +
238C THR* 3.5 23.3 - - + -
244C TYR 6.0 0.9 - - - +
264C MET* 4.3 10.3 - - - +
265C PHE* 1.3 83.8 - - - +
267C VAL* 1.3 64.4 + - - +
268C GLY 4.1 0.2 - - - -
275C ARG 3.5 1.0 - - - +
276C LEU* 3.7 1.7 - - - +
277C THR* 2.8 56.7 + - - +
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Residues in contact with VAL 267 (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* 4.1 9.6 - - + +
233C ILE* 3.6 20.4 - - + -
234C HIS* 2.7 44.4 + - + +
237C SER* 3.3 6.0 + - - +
238C THR* 3.8 6.5 - - - +
265C PHE* 3.5 29.6 - - + -
266C LYS* 1.3 73.9 - - - +
268C GLY* 1.3 63.9 + - - +
274C TYR* 3.7 24.0 - - + +
275C ARG 3.3 4.5 - - - +
276C LEU* 4.9 1.3 - - + -
335C TRP* 4.0 19.1 - - + -
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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