Contacts of the helix formed by residues 247 - 261 (chain F) in PDB entry 1SXG
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221F TYR* 3.5 27.7 - - + +
245F VAL* 3.2 5.5 + - - +
246F GLY* 1.3 82.0 + - - +
248F ASP* 1.3 59.6 + - - +
249F GLU* 3.0 29.4 - - + +
250F MET* 3.2 30.0 - - + +
251F ALA* 2.9 27.8 + - - +
274F PHE 3.7 9.2 - - - -
275F ASP* 4.3 9.5 + - - +
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Residues in contact with ASP 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F THR* 1.3 71.5 - - - +
249F GLU* 1.3 67.7 + - - +
251F ALA* 2.9 6.9 + - - +
252F LEU* 2.8 29.7 + - - +
273F GLY* 3.6 2.6 - - - -
274F PHE 3.1 23.3 + - - +
275F ASP* 4.0 3.3 + - + +
276F ASN 2.9 4.6 + - - -
277F THR* 2.8 31.4 + - + +
279F LEU* 4.4 8.5 - - + -
280F SER* 2.5 28.1 + - - +
287F LEU* 3.7 7.9 - - + +
289F SER* 2.6 26.1 + - - -
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Residues in contact with GLU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ASN* 5.3 0.5 + - - -
73F ILE* 3.8 14.5 - - + +
221F TYR 3.6 12.9 - - - +
222F THR* 4.3 2.1 - - - -
223F TYR* 3.5 33.2 + - - +
247F THR* 3.0 13.3 - - + +
248F ASP* 1.3 80.6 - - - +
250F MET* 1.3 61.4 + - - +
252F LEU* 3.3 15.3 + - - +
253F GLY 3.7 0.3 + - - -
279F LEU* 3.6 26.1 - - + +
278P ARG* 3.3 31.6 + - - -
282P MET* 3.7 17.4 - - + +
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Residues in contact with MET 250 (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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183F VAL* 3.6 19.3 - - + +
184F SER 4.3 11.9 - - - +
185F GLY* 4.4 6.5 - - - -
219F GLY* 3.3 32.8 - - - +
220F ASP 3.6 0.4 - - - +
221F TYR* 3.2 38.1 - - - -
222F THR 3.8 9.6 - - - +
223F TYR* 4.5 0.2 - - - +
225F SER* 3.4 14.4 - - - +
226F GLY* 3.7 11.8 - - - -
245F VAL* 3.6 14.8 - - + -
247F THR* 3.2 18.7 - - + +
249F GLU* 1.3 75.9 - - - +
251F ALA* 1.3 62.6 + - - +
252F LEU 3.2 0.3 + - - -
253F GLY 3.3 2.6 + - - -
254F VAL* 3.0 26.2 + - - +
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Residues in contact with ALA 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F VAL* 3.4 25.0 - - + +
247F THR 2.9 15.1 + - - +
248F ASP* 2.9 12.8 + - - +
250F MET* 1.3 78.6 - - - +
252F LEU* 1.3 55.7 + - - +
254F VAL* 3.5 2.4 + - - +
255F ILE* 2.9 34.0 + - - +
271F ILE* 4.2 2.1 - - + +
273F GLY* 4.0 7.2 - - - -
287F LEU* 3.3 25.6 - - + -
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Residues in contact with LEU 252 (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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223F TYR* 3.7 10.5 - - + -
248F ASP 2.8 30.3 + - - +
249F GLU 3.5 9.4 - - - +
250F MET 3.1 0.4 - - - -
251F ALA* 1.3 74.5 - - - +
253F GLY* 1.3 55.5 + - - +
255F ILE* 3.0 9.3 + - - +
256F HIS* 2.8 36.9 + - - -
279F LEU* 4.0 25.4 - - + +
282F MET 4.2 8.3 - - - +
283F VAL* 3.2 32.5 - - + -
287F LEU* 3.8 18.6 - - + -
282P MET* 4.0 34.1 - - + +
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Residues in contact with GLY 253 (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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223F TYR* 3.3 41.2 - - - -
227F ILE* 3.4 18.9 - - - +
249F GLU 3.7 0.8 + - - -
250F MET 3.3 4.0 + - - -
252F LEU* 1.3 75.9 - - - +
254F VAL* 1.3 55.0 + - - +
256F HIS* 4.3 0.9 - - - -
257F GLY* 2.6 33.1 + - - -
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Residues in contact with VAL 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F VAL* 4.5 12.8 - - + -
226F GLY* 2.9 23.6 - - - +
230F VAL* 3.1 28.2 - - + +
243F ILE* 3.9 19.7 - - + -
245F VAL* 4.4 20.9 - - + -
250F MET 3.0 20.9 + - - +
251F ALA* 3.7 8.7 - - - +
253F GLY* 1.3 73.2 - - - +
255F ILE* 1.3 65.3 + - - +
258F ALA* 3.3 21.5 + - - +
269F LEU* 5.2 1.1 - - + +
271F ILE* 4.9 7.9 - - + -
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Residues in contact with ILE 255 (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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251F ALA 2.9 23.2 + - - +
252F LEU* 3.0 11.9 + - - +
254F VAL* 1.3 80.0 - - - +
256F HIS* 1.3 72.5 + - + +
258F ALA* 3.3 2.9 + - - +
259F GLN* 3.1 43.3 + - + +
265F VAL* 3.4 36.4 - - + +
271F ILE* 3.4 29.8 - - + -
283F VAL* 4.5 8.7 - - + -
284F ARG 4.0 13.5 - - - +
285F PRO* 4.7 5.6 - - + +
287F LEU* 5.1 5.2 - - + -
330F SER* 3.9 8.1 - - - -
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Residues in contact with HIS 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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223F TYR* 2.9 41.3 - + - +
227F ILE* 5.7 1.1 - - + -
252F LEU 2.8 14.2 + - - +
253F GLY* 4.0 2.7 - - - +
255F ILE* 1.3 71.5 - - + +
257F GLY* 1.3 54.8 + - - +
258F ALA 3.0 4.5 - - - -
259F GLN* 2.7 43.7 + - - +
260F ASP* 2.9 15.0 + - - +
283F VAL* 3.8 25.0 - - + +
284F ARG 4.9 5.6 - - - -
256P HIS* 6.2 1.8 - - - -
282P MET 3.3 21.8 + - - -
283P VAL* 4.1 4.2 - - - -
284P ARG* 3.4 43.8 + - + +
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Residues in contact with GLY 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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227F ILE* 4.0 21.4 - - - +
230F VAL* 4.4 11.1 - - - +
231F GLU* 5.0 4.4 - - - +
234F LEU* 4.8 0.9 - - - +
253F GLY 2.6 23.6 + - - -
254F VAL 4.2 1.3 - - - -
256F HIS* 1.3 71.6 - - - +
258F ALA* 1.3 56.0 + - - +
260F ASP* 4.0 8.3 + - - +
261F ARG* 3.1 28.6 + - - +
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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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230F VAL* 4.1 6.5 - - + +
234F LEU* 4.5 9.4 - - - -
254F VAL 3.3 18.4 + - - +
255F ILE 3.7 4.7 - - - +
256F HIS 3.0 1.2 - - - -
257F GLY* 1.3 76.7 - - - +
259F GLN* 1.3 56.5 + - - +
261F ARG* 3.5 3.8 + - - +
262F GLY 3.4 3.3 + - - -
263F LEU* 2.8 45.3 + - + +
265F VAL* 4.7 6.1 - - + -
269F LEU* 3.9 26.2 - - + -
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Residues in contact with GLN 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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255F ILE* 3.1 17.1 - - + +
256F HIS* 2.7 39.4 + - - +
258F ALA* 1.3 76.2 - - - +
260F ASP* 1.3 58.9 + - - +
262F GLY* 2.6 27.4 + - - -
263F LEU 3.4 16.1 - - - +
265F VAL* 4.6 10.8 - - + +
284F ARG 3.0 23.9 + - - +
285F PRO* 3.9 12.3 - - - +
284P ARG* 5.0 4.1 + - - +
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Residues in contact with ASP 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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227F ILE* 5.4 4.0 - - - +
256F HIS* 2.9 8.9 + - - +
257F GLY* 4.3 8.2 - - - +
259F GLN* 1.3 75.7 - - - +
261F ARG* 1.3 58.9 - - + +
262F GLY* 2.7 10.7 + - - -
284P ARG* 2.5 49.1 + - - -
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Residues in contact with ARG 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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231F GLU* 3.6 49.2 + - + +
234F LEU* 4.0 31.5 + - + +
235F GLU* 4.5 11.9 + - - +
257F GLY 3.1 19.3 - - - +
258F ALA 3.5 7.8 + - - +
259F GLN 3.1 0.6 - - - -
260F ASP* 1.3 75.9 - - - +
262F GLY* 1.3 60.5 + - - +
263F LEU* 3.3 10.4 + - + +
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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
------------------------------------------------------------
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