Contacts of the helix formed by residues 243 - 259 (chain X) in PDB entry 3G90
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 ASN 243 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X GLU* 4.1 1.0 - - - +
241X LYS* 3.5 30.2 - - - +
242X GLU* 1.3 74.9 - - - +
244X VAL* 1.3 63.7 + - - +
245X ASP 3.1 1.8 - - - -
246X ILE* 3.3 25.0 + - + +
247X TRP 3.6 0.2 + - - -
344X PRO* 2.6 42.4 + - - +
347X ARG* 3.0 37.0 + - - +
348X ILE 3.6 17.9 - - - +
349X SER* 4.4 9.1 - - - +
350X VAL* 5.2 0.9 - - - -
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Residues in contact with VAL 244 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186X ILE* 3.3 25.4 - - + -
188X ARG* 3.7 18.1 - - + -
231X ALA* 3.7 13.2 - - + +
233X GLU* 3.5 21.7 + - + +
234X VAL* 3.7 31.2 - - + -
240X TYR* 4.0 8.7 - - + -
241X LYS 3.0 23.3 + - - +
242X GLU 3.0 1.2 + - - +
243X ASN* 1.3 78.9 + - - +
245X ASP* 1.3 64.2 + - - +
247X TRP* 3.7 15.8 - - - +
248X SER* 4.0 6.8 + - - -
347X ARG* 3.8 1.8 - - - +
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Residues in contact with ASP 245 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177X ILE* 4.1 13.4 - - + +
181X HIS* 3.0 23.0 + - - +
186X ILE* 3.8 1.9 - - - +
187X HIS* 3.0 23.4 + - - +
188X ARG* 2.8 31.2 + - - -
190X LEU* 3.2 24.6 - - + +
242X GLU 3.3 6.6 + - - +
243X ASN 3.1 0.8 - - - -
244X VAL* 1.3 78.6 - - - +
246X ILE* 1.3 63.4 + - + +
247X TRP 3.2 1.6 - - - -
248X SER* 3.1 9.4 + - - -
249X VAL* 3.1 26.3 + - - +
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Residues in contact with ILE 246 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X LEU* 3.7 30.7 - - + -
177X ILE* 6.2 0.7 - - + -
243X ASN* 3.3 17.4 + - - +
245X ASP* 1.3 74.8 - - - +
247X TRP* 1.3 65.2 + - - +
249X VAL* 3.3 7.0 + - + +
250X GLY* 3.0 19.2 + - - -
339X MET* 3.7 32.7 - - + +
347X ARG* 3.8 12.3 - - + -
348X ILE* 3.5 28.5 - - + +
349X SER 3.9 4.3 - - - +
350X VAL* 3.8 32.1 - - + +
353X ALA* 4.3 0.2 - - + -
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Residues in contact with TRP 247 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228X TYR 5.0 0.6 + - - -
229X TYR 3.4 16.3 + - - -
230X ARG 3.3 13.3 + - - -
231X ALA* 3.4 25.1 - - + -
232X PRO* 3.5 22.7 - - + -
235X ILE* 6.3 0.2 - - + -
243X ASN 3.6 4.0 + - - -
244X VAL 3.7 11.4 - - - +
245X ASP 3.2 0.2 - - - -
246X ILE* 1.3 76.9 - - - +
248X SER* 1.3 61.8 + - - +
250X GLY* 3.1 5.0 + - - -
251X CYS* 3.0 34.0 + - - -
263X PHE* 3.6 25.7 - + - -
275X VAL* 3.9 22.0 - - + -
279X LEU* 3.6 27.4 - - + -
339X MET 4.0 14.1 - - - -
340X LEU* 4.0 6.2 - - + +
341X VAL 3.6 38.8 - - - -
342X ILE 4.0 0.7 - - - -
347X ARG* 3.8 9.6 - - - +
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Residues in contact with SER 248 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188X ARG 4.9 6.4 + - - -
189X ASP 5.1 0.2 - - - -
190X LEU* 3.8 34.6 + - - +
229X TYR* 2.7 28.4 + - - -
230X ARG* 4.7 1.4 - - - -
231X ALA 5.0 0.3 + - - -
244X VAL 4.0 9.2 + - - -
245X ASP* 3.1 15.4 + - - -
247X TRP* 1.3 78.2 - - - +
249X VAL* 1.3 57.9 + - - +
251X CYS* 3.2 5.9 + - - +
252X ILE* 3.1 34.0 + - - +
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Residues in contact with VAL 249 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170X LEU* 4.5 20.8 - - + +
173X MET* 4.6 12.8 - - + -
174X LEU* 4.9 14.4 - - + -
177X ILE* 3.6 26.7 - - + -
190X LEU* 3.9 8.3 - - + -
245X ASP 3.1 15.3 + - - +
246X ILE* 3.6 10.5 - - - +
247X TRP 3.3 0.2 - - - -
248X SER* 1.3 75.0 - - - +
250X GLY* 1.3 58.9 + - - +
252X ILE* 3.5 8.6 + - - +
253X MET* 3.0 27.5 + - - +
339X MET* 4.0 22.9 - - + -
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Residues in contact with GLY 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246X ILE 3.0 14.3 + - - -
247X TRP 3.1 5.5 + - - -
249X VAL* 1.3 74.9 - - - +
251X CYS* 1.3 57.3 - - - +
253X MET* 4.6 2.7 - - - -
254X GLY* 3.0 24.4 + - - -
336X LEU* 3.6 11.8 - - - +
339X MET* 3.9 21.3 - - - -
340X LEU* 3.8 16.5 - - - +
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Residues in contact with CYS 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228X TYR 4.0 9.0 - - - +
229X TYR* 3.7 22.6 - - + -
247X TRP* 3.0 45.2 + - - -
248X SER 3.2 8.7 + - - +
250X GLY* 1.3 74.1 - - - +
252X ILE* 1.3 59.6 + - - +
255X GLU* 3.0 29.6 + - - +
262X LEU* 3.8 14.9 + - + +
263X PHE* 3.7 27.6 - - + -
340X LEU* 4.1 2.0 - - - -
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Residues in contact with ILE 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153X LEU* 3.5 27.4 - - + -
157X ILE* 4.7 6.0 - - + +
173X MET* 4.3 10.5 - - + -
190X LEU* 4.4 20.4 - - + +
191X LYS* 4.4 5.6 - - - -
192X PRO* 4.2 9.9 - - + -
195X ILE* 4.0 24.2 - - + -
229X TYR* 4.1 15.5 - - + -
248X SER 3.1 21.5 + - - +
249X VAL* 3.8 9.2 - - - +
251X CYS* 1.3 73.0 - - - +
253X MET* 1.3 54.4 + - - +
255X GLU* 2.9 10.4 + - - +
256X MET* 2.7 45.4 + - + +
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Residues in contact with MET 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166X MET* 4.9 6.3 - - - -
170X LEU* 3.8 36.1 - - + +
249X VAL* 3.0 19.9 + - + +
250X GLY* 4.0 2.9 - - - +
252X ILE* 1.3 75.7 - - - +
254X GLY* 1.3 61.3 + - - +
256X MET* 3.3 14.6 + - - +
257X VAL* 3.2 26.7 + - + +
332X ALA* 3.1 45.8 - - + +
335X LEU* 4.3 15.5 - - + -
336X LEU* 3.8 26.0 - - + -
339X MET* 4.8 7.2 - - - +
358X TYR* 4.1 8.5 - - + -
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Residues in contact with GLY 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X GLY 3.0 17.6 + - - -
251X CYS 3.9 1.1 - - - -
252X ILE 3.2 0.2 - - - -
253X MET* 1.3 77.3 - - - +
255X GLU* 1.3 57.6 + - - +
257X VAL* 3.5 0.8 + - - +
258X ARG* 2.9 31.7 + - - +
262X LEU* 3.7 11.8 - - - +
313X PHE* 3.6 24.8 - - - -
336X LEU* 3.8 8.5 - - - +
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Residues in contact with GLU 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X ILE* 3.5 36.7 - - + +
192X PRO* 4.3 1.2 - - - +
229X TYR* 2.6 38.7 + - - -
251X CYS 3.0 11.5 + - - +
252X ILE* 2.9 10.2 + - - +
254X GLY* 1.3 74.2 - - - +
256X MET* 1.3 57.2 + - - +
257X VAL 3.2 0.2 - - - -
259X HIS* 2.7 33.8 + - - +
260X LYS* 3.3 25.1 - - - +
261X ILE* 3.7 24.0 + - - +
262X LEU* 4.1 2.1 + - - +
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Residues in contact with MET 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LEU* 4.8 7.2 - - + -
157X ILE* 3.8 27.4 - - + +
159X MET 4.5 2.4 - - - +
160X GLU* 5.7 0.2 - - - -
161X LEU* 3.8 15.3 + - + +
166X MET* 3.5 47.6 - - + +
169X LEU* 3.7 28.9 - - + -
170X LEU* 4.2 15.3 - - + -
173X MET* 4.5 6.1 - - - -
252X ILE* 2.7 33.3 + - + +
253X MET* 3.3 10.7 + - - +
255X GLU* 1.3 72.3 - - - +
257X VAL* 1.3 56.8 + - - +
259X HIS* 3.2 25.3 + - - -
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Residues in contact with VAL 257 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166X MET* 4.0 23.1 - - + -
253X MET* 3.2 19.2 + - + +
254X GLY 3.8 4.5 - - - +
255X GLU 3.2 0.2 - - - -
256X MET* 1.3 77.1 - - - +
258X ARG* 1.3 63.3 + - - +
259X HIS* 3.3 15.5 + - - -
313X PHE* 4.0 9.6 - - + -
317X LEU* 3.6 47.6 - - + +
318X PHE* 3.7 37.0 - - + -
336X LEU* 4.7 7.4 - - + -
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Residues in contact with ARG 258 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254X GLY 2.9 18.5 + - - +
257X VAL* 1.3 75.6 - - - +
259X HIS* 1.3 69.6 + - - +
260X LYS* 3.1 39.8 + - + +
261X ILE 5.3 1.4 + - - -
262X LEU* 3.7 27.6 + - - +
278X GLN* 2.7 33.1 + - - +
312X LEU* 3.0 46.4 + - - +
313X PHE* 4.0 11.2 - - + -
317X LEU* 4.3 22.1 - - + +
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Residues in contact with HIS 259 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157X ILE* 2.7 32.5 + - - +
158X GLN* 4.3 6.3 - - - -
159X MET* 3.2 31.6 + - - -
160X GLU* 4.0 15.5 + - - +
255X GLU 2.7 22.3 + - - -
256X MET 3.2 19.1 + - - -
257X VAL 3.4 20.3 + - - -
258X ARG* 1.3 73.9 - - - +
260X LYS* 1.3 61.6 + - - +
317X LEU* 5.3 6.3 + - + -
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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
------------------------------------------------------------
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