Contacts of the helix formed by residues 247 - 261 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASN* 4.7 16.4 - - - +
74B PHE* 5.5 1.3 - - + -
196B LYS* 4.6 1.7 + - - -
221B TYR* 3.8 25.2 - - + +
245B VAL* 3.1 9.9 - - - +
246B GLY* 1.3 80.7 + - - +
248B ASP* 1.3 65.1 + - + +
249B GLU* 3.4 22.0 - - + +
250B MET* 3.4 15.6 + - - +
251B ALA* 3.0 23.9 + - - +
274B PHE 3.9 9.0 - - - -
275B ASP* 3.7 15.2 + - - +
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B THR* 1.3 75.3 - - + +
249B GLU* 1.3 65.4 + - - +
251B ALA* 3.7 5.4 - - - -
252B LEU* 3.0 29.7 + - - +
274B PHE 2.9 29.9 + - - +
275B ASP* 5.3 0.4 - - + -
276B ASN 3.4 2.3 + - - -
277B THR* 2.8 33.3 + - + -
279B LEU* 4.5 11.4 - - + -
280B SER* 2.4 28.2 + - - +
287B LEU* 3.0 19.3 - - + +
289B SER* 3.1 3.1 + - - -
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER 5.4 0.4 - - - -
72B ASN* 3.3 19.3 - - - +
73B ILE* 3.1 25.4 + - - +
221B TYR 3.7 22.7 - - - +
222B THR* 4.7 0.4 - - - -
223B TYR* 3.6 31.1 - - + +
247B THR* 3.1 12.0 - - + +
248B ASP* 1.3 82.9 - - - +
250B MET* 1.3 62.1 + - - +
251B ALA 3.1 1.0 + - - -
252B LEU* 3.3 7.1 + - - +
253B GLY 3.4 7.3 + - - -
279B LEU* 3.3 11.5 - - - +
278I ARG* 2.9 30.0 + - - +
282I MET* 3.1 14.6 - - - +
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Residues in contact with MET 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 3.9 14.4 - - + +
184B SER 3.6 34.8 - - - +
185B GLY* 3.7 6.5 - - - +
219B GLY* 4.0 2.9 - - - -
220B ASP 4.0 2.5 - - - -
221B TYR* 3.0 42.8 - - + -
222B THR 3.6 16.8 - - - +
225B SER* 3.8 8.3 - - - +
226B GLY* 3.5 12.5 - - - -
245B VAL* 3.5 9.2 - - + -
246B GLY* 4.1 2.0 - - - +
247B THR* 3.4 28.8 + - - +
249B GLU* 1.3 74.8 - - - +
251B ALA* 1.3 57.7 + - - +
253B GLY 3.8 1.1 - - - -
254B VAL* 3.1 30.5 + - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 3.8 21.8 - - + -
247B THR 3.0 17.6 + - - +
248B ASP* 3.4 12.1 - - - +
249B GLU 3.0 0.6 - - - -
250B MET* 1.3 77.0 - - - +
252B LEU* 1.3 65.2 + - - +
253B GLY 3.1 1.1 - - - -
254B VAL* 3.6 1.0 - - - +
255B ILE* 2.9 31.5 + - - +
271B ILE* 4.6 1.3 - - + -
273B GLY* 4.2 2.0 - - - -
287B LEU* 3.9 24.9 - - + -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B TYR* 3.5 15.0 - - + -
248B ASP 3.0 18.5 + - - +
249B GLU 3.3 3.6 + - - +
251B ALA* 1.3 77.4 - - - +
253B GLY* 1.3 57.4 + - - +
255B ILE* 3.3 3.6 + - + +
256B HIS* 2.8 35.4 + - - +
279B LEU* 3.8 45.3 - - + +
282B MET* 5.1 4.5 - - + +
283B VAL* 3.0 46.4 - - + -
287B LEU* 4.5 8.5 - - + -
282I MET* 4.1 24.2 - - + +
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 3.3 38.3 - - - -
226B GLY 3.6 6.5 - - - -
227B ILE* 3.5 9.6 - - - +
249B GLU 3.4 3.6 + - - -
250B MET 3.6 2.9 + - - -
251B ALA 3.1 0.6 - - - -
252B LEU* 1.3 78.3 - - - +
254B VAL* 1.3 54.9 + - - +
257B GLY* 2.5 35.2 + - - -
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 3.7 17.9 - - + -
226B GLY 3.6 10.3 + - - +
230B VAL* 3.1 35.8 - - + +
243B ILE* 3.8 9.0 - - + -
245B VAL* 3.7 17.7 - - + -
250B MET 3.1 21.6 + - - +
251B ALA 3.2 4.7 + - - +
253B GLY* 1.3 74.1 - - - +
255B ILE* 1.3 59.5 + - - +
257B GLY* 3.0 0.7 + - - -
258B ALA* 2.8 29.3 + - - +
269B LEU* 5.2 0.9 - - + -
271B ILE* 3.5 31.0 - - + -
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ALA 2.9 22.5 + - - +
252B LEU* 3.6 7.9 - - - +
254B VAL* 1.3 75.6 - - - +
256B HIS* 1.3 61.3 + - + +
258B ALA* 3.7 2.3 - - - +
259B GLN* 3.0 51.8 + - - +
265B VAL* 4.3 11.0 - - + +
271B ILE* 3.7 31.2 - - + -
283B VAL* 4.8 9.2 - - + -
284B ARG 4.4 8.5 - - - +
285B PRO* 4.6 11.0 - - + +
287B LEU* 4.1 33.2 - - + -
330B SER* 4.6 10.1 - - - -
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Residues in contact with HIS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B TYR* 2.7 28.4 + + + +
227B ILE* 5.2 1.1 - - + -
252B LEU 2.8 17.7 + - - +
253B GLY 4.1 2.0 - - - +
255B ILE* 1.3 75.1 - - + +
257B GLY* 1.3 66.6 + - - +
259B GLN* 3.0 31.2 + - - -
260B ASP* 2.9 31.7 + - - +
283B VAL* 4.0 20.4 - - + +
284B ARG 5.1 5.0 + - - -
256I HIS* 6.0 1.2 + - - -
282I MET 3.3 25.6 - - - -
283I VAL* 3.6 14.8 - - - -
284I ARG* 3.5 37.4 + - + +
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ILE* 4.1 17.7 - - - +
230B VAL* 3.4 18.6 - - - -
231B GLU* 3.7 3.3 - - - +
234B LEU* 5.2 0.4 - - - -
253B GLY 2.5 25.0 + - - -
254B VAL 3.0 0.2 + - - -
256B HIS* 1.3 75.4 - - - +
258B ALA* 1.3 64.8 + - - +
260B ASP* 3.5 6.6 + - - +
261B ARG* 3.3 18.2 + - - +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B VAL* 3.9 4.0 - - + +
234B LEU* 4.3 7.6 - - + -
254B VAL 2.8 14.9 + - - +
255B ILE* 3.7 4.5 - - - +
257B GLY* 1.3 73.8 - - - +
259B GLN* 1.3 65.0 + - - +
261B ARG* 2.7 21.8 + - - +
262B GLY 3.2 4.2 + - - -
263B LEU* 3.4 20.0 + - + -
265B VAL* 4.7 5.2 - - + -
269B LEU* 3.5 37.2 - - + -
271B ILE* 5.4 0.2 - - + -
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Residues in contact with GLN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ILE* 3.0 28.1 + - - +
256B HIS* 3.0 35.6 - - + +
258B ALA* 1.3 78.3 - - - +
260B ASP* 1.3 65.8 + - - +
262B GLY* 2.7 16.8 + - - -
263B LEU 3.5 17.1 + - - +
264B ASN* 5.6 0.2 - - - -
265B VAL* 4.5 11.7 - - + +
284B ARG 3.1 21.2 + - - +
285B PRO* 4.6 4.9 - - - +
284I ARG* 5.3 10.0 - - + +
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Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ILE* 4.8 10.0 - - - +
231B GLU* 4.8 4.5 - - - +
256B HIS 2.9 28.4 + - - +
257B GLY* 3.6 9.0 - - - +
259B GLN* 1.3 72.8 - - - +
261B ARG* 1.3 60.6 - - + +
262B GLY* 3.0 6.4 + - - -
284I ARG* 2.6 40.3 + - - +
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLU* 2.8 55.7 + - - +
234B LEU* 3.2 56.9 + - + +
235B GLU* 4.2 14.3 + - - +
257B GLY 3.3 17.0 - - - +
258B ALA 2.7 11.7 + - - +
260B ASP* 1.3 70.9 - - - +
262B GLY* 1.3 57.1 + - - +
263B LEU* 3.5 6.1 + - + +
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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