Contacts of the helix formed by residues 247 - 262 (chain C) in PDB entry 1RZR
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 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C LYS* 5.1 1.6 - - - +
221C TYR* 3.9 24.0 + - + +
245C VAL* 3.2 4.0 + - - +
246C GLY* 1.3 90.0 - - - +
248C ASP* 1.3 63.9 + - - +
249C GLU* 3.8 3.2 + - - +
250C MSE 3.5 38.1 + - + +
251C ALA* 3.5 17.5 + - - +
274C PHE* 3.4 23.4 + - - -
275C ASP* 4.8 11.7 - - - +
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Residues in contact with ASP 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C THR* 1.3 74.1 - - - +
249C GLU* 1.3 69.8 + - - +
250C MSE 3.0 2.5 + - - -
251C ALA* 3.1 6.6 + - - +
252C LEU* 2.9 27.7 + - + +
274C PHE 2.3 23.1 - - - +
275C ASP* 2.8 19.1 - - - +
276C ASN* 3.0 24.8 + - - -
277C THR* 3.5 12.2 + - - -
279C LEU* 3.2 23.1 - - + -
280C SER* 3.7 4.2 + - - -
287C LEU* 3.9 5.7 - - + +
289C SER* 3.2 15.1 + - - -
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN* 5.4 5.2 + - - -
221C TYR* 3.6 18.6 - - - +
222C THR* 3.3 21.8 - - - -
223C TYR* 3.3 22.0 + - - +
247C THR* 3.8 3.0 + - - +
248C ASP* 1.3 79.4 - - - +
250C MSE 1.3 60.6 + - - +
252C LEU* 3.6 15.2 - - - +
279C LEU* 4.0 16.3 - - + +
278G ARG* 3.8 25.6 + - - +
282G MSE 3.6 30.0 - - + +
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Residues in contact with MSE 250 (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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183C VAL* 4.2 9.4 - - + -
184C SER* 3.7 29.4 - - - +
185C GLY 3.9 0.9 - - - +
219C GLY 4.1 0.9 - - - +
221C TYR* 3.4 52.9 - - + +
222C THR 3.8 11.0 - - - +
225C SER* 3.6 20.9 - - - +
226C GLY* 3.8 4.8 - - - -
245C VAL* 3.4 15.7 - - + -
246C GLY* 3.9 10.1 - - - +
247C THR* 3.5 33.5 + - + +
248C ASP 3.0 0.4 - - - -
249C GLU* 1.3 75.0 - - - +
251C ALA* 1.3 66.8 + - - +
252C LEU 2.9 1.8 - - - -
253C GLY* 2.7 16.3 + - - -
254C VAL* 2.8 12.6 + - + +
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 3.4 17.7 - - + +
247C THR 3.5 11.6 + - - +
248C ASP 3.1 4.8 + - - +
250C MSE 1.3 77.9 - - - +
252C LEU* 1.3 56.8 + - - +
254C VAL* 3.1 15.6 - - - +
255C ILE* 2.8 33.3 + - - +
271C ILE* 5.1 0.7 - - + -
273C GLY* 4.5 1.1 - - - -
287C LEU* 3.3 39.3 - - + -
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C TYR* 4.0 8.1 - - + -
248C ASP* 2.9 32.3 + - - +
249C GLU* 3.6 9.6 - - - +
250C MSE 2.8 1.2 + - - -
251C ALA* 1.3 73.6 - - - +
253C GLY* 1.3 58.5 + - - +
255C ILE* 2.6 28.9 + - + +
256C HIS* 2.9 19.9 + - + -
279C LEU* 4.1 19.3 - - + +
282C MSE 4.3 5.2 - - + +
283C VAL* 2.9 35.2 - - + -
287C LEU* 4.7 10.1 - - + -
282G MSE 3.3 46.0 - - + +
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Residues in contact with GLY 253 (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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223C TYR* 3.8 15.7 - - - -
226C GLY* 3.5 20.8 - - - -
227C ILE* 3.1 18.8 + - - +
249C GLU 3.7 3.2 + - - -
250C MSE 2.7 13.2 + - - -
252C LEU* 1.3 75.0 - - - +
254C VAL* 1.3 61.0 + - - -
255C ILE 3.0 0.2 + - - -
257C GLY* 2.9 23.4 + - - -
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Residues in contact with VAL 254 (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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183C VAL* 4.4 13.5 - - + -
226C GLY* 3.7 7.4 - - - +
229C ALA* 5.3 0.2 - - + -
230C VAL* 3.2 19.3 - - + +
243C ILE* 3.4 37.0 - - + -
245C VAL* 3.5 30.3 - - + -
250C MSE 2.8 18.8 + - + +
251C ALA* 3.1 11.0 - - - +
253C GLY* 1.3 73.6 - - - +
255C ILE* 1.3 56.7 + - - +
258C ALA* 3.1 22.2 - - + +
271C ILE* 3.9 17.9 - - + -
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Residues in contact with ILE 255 (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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251C ALA 2.8 18.6 + - - +
252C LEU* 2.6 18.8 + - - +
254C VAL* 1.3 71.4 - - - +
256C HIS* 1.3 62.8 + - + +
258C ALA* 3.4 2.9 + - - +
259C GLN 3.2 10.0 + - - -
265C VAL* 3.2 16.6 - - + +
271C ILE* 3.4 41.7 - - + -
283C VAL* 5.0 8.3 - - + -
284C ARG* 2.6 49.6 + - + +
285C PRO* 3.8 24.5 - - + +
287C LEU* 4.5 14.1 - - + -
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Residues in contact with HIS 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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223C TYR* 3.1 41.8 + + - +
227C ILE* 3.6 8.1 - - + -
252C LEU* 2.9 39.3 + - + -
255C ILE* 1.3 75.3 - - + +
257C GLY* 1.3 55.1 + - - +
258C ALA 3.0 1.8 - - - -
259C GLN* 2.9 10.0 + - - +
260C ASP* 2.5 45.3 + - - +
283C VAL* 4.8 8.5 - - + -
284C ARG* 4.0 29.7 + - + +
282G MSE 3.8 14.5 + - - -
283G VAL* 4.8 0.4 - - - -
284G ARG* 4.2 21.6 + - - +
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Residues in contact with GLY 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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227C ILE* 3.1 23.8 - - - +
230C VAL* 3.5 12.1 - - - +
253C GLY 2.9 13.0 + - - -
256C HIS* 1.3 77.4 - - - +
258C ALA* 1.3 58.2 + - - +
260C ASP* 3.2 10.5 - - - -
261C ARG* 3.0 36.3 + - - +
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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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230C VAL* 3.7 7.8 - - + +
234C LEU* 4.6 4.5 - - - -
254C VAL 3.1 22.4 + - - +
255C ILE* 3.5 7.2 - - - +
256C HIS 3.0 0.6 - - - -
257C GLY* 1.3 78.6 - - - +
259C GLN* 1.3 61.1 + - - +
262C GLY 3.5 2.3 + - - -
263C LEU* 2.8 33.3 + - - +
265C VAL* 4.5 1.3 - - + -
269C LEU* 3.3 39.9 - - + -
271C ILE* 5.8 0.4 - - + -
284C ARG* 5.1 0.2 - - - -
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Residues in contact with GLN 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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255C ILE 3.2 2.6 + - - -
256C HIS* 2.9 12.3 + - - +
258C ALA* 1.3 75.4 - - - +
260C ASP* 1.3 68.1 + - - +
261C ARG 3.5 0.2 - - - -
262C GLY* 3.5 11.2 + - - -
263C LEU 3.7 12.6 - - - +
265C VAL* 5.6 0.2 - - - -
284C ARG* 2.7 66.9 + - - +
284G ARG* 5.5 1.0 - - - +
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Residues in contact with ASP 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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227C ILE* 4.1 7.6 - - - +
256C HIS* 2.5 37.3 + - - +
257C GLY* 3.2 5.4 + - - +
258C ALA 3.3 0.2 - - - -
259C GLN* 1.3 80.8 - - - +
261C ARG* 1.3 86.7 + - - +
262C GLY* 3.1 1.8 + - - -
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Residues in contact with ARG 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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227C ILE* 3.2 25.9 + - - +
231C GLU* 2.8 44.7 + - - +
234C LEU* 3.4 26.5 - - + -
235C GLU* 3.2 29.5 + - - +
257C GLY* 3.0 31.8 + - - +
258C ALA 4.5 0.2 - - - +
260C ASP* 1.3 97.0 - - - +
262C GLY* 1.3 57.3 + - - +
263C LEU* 3.9 9.9 - - + -
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Residues in contact with GLY 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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258C ALA 3.5 0.6 + - - -
259C GLN 3.5 10.6 + - - -
260C ASP 3.1 3.7 - - - -
261C ARG* 1.3 81.5 - - - +
263C LEU* 1.3 71.7 + - - +
264C ASN* 5.4 0.2 - - - +
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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