Contacts of the helix formed by residues 229 - 246 (chain Y) in PDB entry 3EXG
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 ASP 229 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y ILE* 4.1 1.2 - - - +
70Y ALA* 4.1 0.2 - - - -
226Y ASP* 3.4 21.5 + - - +
227Y GLY 3.3 1.2 - - - -
228Y MET* 1.3 78.3 - - - +
230Y ILE* 1.3 57.0 + - - +
231Y LEU* 2.5 42.6 + - - +
232Y CYS* 3.0 29.8 + - - -
233Y VAL* 3.2 14.1 + - - +
290Y LEU* 4.7 11.2 - - + -
294Y ARG* 2.8 43.2 + - - -
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Residues in contact with ILE 230 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Y TYR* 4.1 32.5 - - + -
39Y MET* 3.9 31.2 - - + -
70Y ALA* 3.6 17.4 - - - +
73Y VAL* 3.8 17.0 - - + +
74Y GLY* 3.4 30.1 - - - +
77Y ALA* 5.2 0.2 - - + -
228Y MET 3.6 3.6 + - - -
229Y ASP* 1.3 75.0 - - - +
231Y LEU* 1.3 64.6 + - + +
233Y VAL* 3.9 1.4 - - - +
234Y ARG* 3.0 22.9 + - - +
287Y PRO 4.8 3.1 - - - +
290Y LEU* 6.4 0.7 - - + -
291Y LEU* 4.0 24.5 - - + +
294Y ARG* 5.0 0.9 - - - +
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Residues in contact with LEU 231 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y PHE* 4.1 19.7 - - + -
9Y ILE* 3.8 10.7 - - + +
25Y THR* 3.7 22.0 - - + +
27Y LEU* 4.5 19.3 - - + -
35Y TYR* 4.8 3.6 - - + -
229Y ASP* 2.5 21.6 + - - +
230Y ILE* 1.3 86.0 - - + +
232Y CYS* 1.3 62.6 + - - +
233Y VAL 3.1 1.1 - - - -
234Y ARG* 3.6 31.6 + - - +
235Y GLU* 3.1 27.0 + - - +
291Y LEU* 5.2 5.4 - - + -
294Y ARG* 3.3 29.4 - - - +
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Residues in contact with CYS 232 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y ILE* 3.5 26.9 - - + -
10Y LYS* 4.1 17.5 - - - +
12Y CYS* 6.1 2.5 - - - -
225Y VAL* 3.8 18.6 - - + -
226Y ASP* 4.1 15.5 - - - +
229Y ASP* 3.0 23.3 + - - +
231Y LEU* 1.3 74.7 - - - +
233Y VAL* 1.3 61.3 + - - +
235Y GLU* 3.5 6.6 - - - +
236Y ALA* 2.8 32.4 + - - +
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Residues in contact with VAL 233 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Y ALA 3.6 26.5 - - - +
71Y CYS* 4.4 1.3 - - - +
74Y GLY* 3.8 5.6 - - - -
75Y LEU* 3.4 31.2 - - + -
225Y VAL* 4.4 7.2 - - + -
226Y ASP 3.5 17.3 - - - +
227Y GLY* 4.0 12.8 - - - -
229Y ASP 3.2 16.1 + - - +
230Y ILE 4.0 1.6 - - - +
231Y LEU 3.1 0.8 - - - -
232Y CYS* 1.3 75.1 - - - +
234Y ARG* 1.3 68.5 + - - +
236Y ALA* 4.0 1.4 - - - +
237Y THR* 3.0 28.4 + - - +
253Y MET* 5.3 0.2 - - + -
255Y LEU* 4.3 14.1 - - + -
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Residues in contact with ARG 234 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y THR* 2.9 26.1 + - - -
26Y VAL 2.9 23.6 + - - -
27Y LEU* 4.2 9.1 - - - +
28Y THR* 5.5 0.4 - - - +
31Y ASP* 5.1 6.1 + - - -
35Y TYR* 3.1 39.5 + - + -
74Y GLY 3.3 12.4 + - - +
77Y ALA* 3.5 25.8 - - + +
230Y ILE 3.0 18.5 + - - +
231Y LEU* 3.8 22.9 + - + +
233Y VAL* 1.3 78.8 - - - +
235Y GLU* 1.3 66.5 + - - +
237Y THR* 3.2 1.7 + - - -
238Y ARG* 2.8 63.2 + - + +
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Residues in contact with GLU 235 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y ILE* 3.4 31.6 - - + -
21Y PRO* 4.3 11.7 - - + -
22Y PRO* 3.3 28.1 - - + +
24Y THR 5.0 0.2 - - - -
25Y THR* 2.9 26.9 + - - -
231Y LEU 3.1 11.1 + - - +
232Y CYS* 3.0 8.5 + - - +
234Y ARG* 1.3 86.5 + - - +
236Y ALA* 1.3 69.7 + - - +
237Y THR 3.0 0.5 + - - -
238Y ARG* 3.0 20.3 + - - +
239Y PHE* 2.9 21.7 + - - +
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Residues in contact with ALA 236 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y CYS* 5.1 0.9 - - - -
21Y PRO* 4.1 16.0 - - + +
223Y LEU* 4.2 8.3 - - + -
225Y VAL* 3.8 22.0 - - + -
232Y CYS 2.8 18.1 + - - +
233Y VAL* 4.0 3.1 - - - +
235Y GLU* 1.3 74.8 - - - +
237Y THR* 1.3 57.6 + - - +
239Y PHE* 3.2 2.8 + - - +
240Y ALA* 2.9 31.9 + - - +
253Y MET* 3.8 19.7 - - + -
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Residues in contact with THR 237 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Y GLY 4.2 2.2 - - - -
75Y LEU* 3.7 34.2 - - - +
78Y GLY* 3.7 7.0 - - - +
79Y ILE* 3.4 31.0 - - + -
162Y LEU* 4.6 11.2 - - + -
190Y ILE* 5.1 1.5 - - + +
233Y VAL 3.0 18.2 + - - -
234Y ARG 3.8 2.7 - - - -
235Y GLU 3.0 1.2 - - - -
236Y ALA* 1.3 76.9 - - - +
238Y ARG* 1.3 58.7 + - - +
240Y ALA* 4.0 2.0 - - - +
241Y ALA* 2.9 34.5 + - - +
253Y MET* 3.8 13.6 - - + +
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Residues in contact with ARG 238 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Y VAL 5.6 0.8 + - - -
35Y TYR* 4.8 2.0 + - - -
77Y ALA 2.9 23.6 + - - -
78Y GLY* 3.7 19.5 - - - -
234Y ARG* 2.8 55.5 + - - +
235Y GLU* 3.3 21.2 + - - +
237Y THR* 1.3 76.7 - - - +
239Y PHE* 1.3 59.3 + - - +
241Y ALA* 4.0 1.8 - - - +
242Y ALA* 3.2 24.3 + - - +
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Residues in contact with PHE 239 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Y LEU* 4.3 13.7 - - + -
19Y GLU* 3.3 28.3 - - + -
20Y GLY* 3.6 13.0 - - - -
21Y PRO* 3.7 26.9 - - + -
22Y PRO* 5.3 3.1 - - + -
223Y LEU* 4.0 22.4 - - + -
235Y GLU 2.9 11.4 + - - +
236Y ALA 3.4 6.5 - - - +
238Y ARG* 1.3 76.9 - - - +
240Y ALA* 1.3 63.1 + - + +
242Y ALA* 3.2 6.1 + - - +
243Y TYR* 3.0 37.1 + + + +
251Y ILE* 4.1 21.3 - - + -
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Residues in contact with ALA 240 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Y ILE* 3.9 20.9 - - + -
223Y LEU* 5.3 1.3 - - + -
236Y ALA 2.9 16.7 + - - +
237Y THR* 4.0 2.2 - - - +
239Y PHE* 1.3 85.8 - - + +
241Y ALA* 1.3 60.5 + - - +
243Y TYR* 3.4 8.3 - - - +
244Y CYS* 3.0 31.5 + - - +
251Y ILE* 4.1 18.5 - - + +
253Y MET* 4.3 12.1 - - + -
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Residues in contact with ALA 241 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Y GLY 4.3 9.2 - - - +
79Y ILE* 4.6 5.6 - - + -
160Y VAL* 4.7 4.7 - - + -
190Y ILE* 3.8 13.6 - - + +
237Y THR 2.9 19.3 + - - +
238Y ARG* 4.0 3.4 - - - +
240Y ALA* 1.3 75.9 - - - +
242Y ALA* 1.3 53.8 + - - +
244Y CYS* 2.9 5.7 + - - +
245Y ARG* 2.8 64.5 + - - +
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Residues in contact with ALA 242 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238Y ARG 3.2 16.6 + - - +
239Y PHE* 3.2 7.2 + - - +
241Y ALA* 1.3 74.0 - - - +
243Y TYR* 1.3 67.6 + - - +
244Y CYS 3.0 0.3 + - - -
245Y ARG* 3.0 11.2 + - - +
246Y SER* 2.8 27.6 + - - -
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Residues in contact with TYR 243 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Y LEU* 4.1 21.3 - - + -
221Y PRO* 3.2 26.2 - - + +
239Y PHE* 3.0 20.2 + + + +
240Y ALA* 3.4 13.7 - - - +
242Y ALA* 1.3 78.9 - - - +
244Y CYS* 1.3 62.6 + - - +
246Y SER* 3.0 21.2 + - - -
248Y LYS* 3.5 56.9 + - + +
249Y GLY 3.1 24.0 - - - -
250Y PRO 3.6 10.0 + - - -
251Y ILE* 4.1 20.6 - - + -
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Residues in contact with CYS 244 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160Y VAL* 3.8 15.9 - - + -
188Y PRO* 4.0 15.7 - - + +
189Y CYS 3.9 21.5 - - - -
190Y ILE* 3.8 21.1 - - - -
240Y ALA 3.0 14.9 + - - +
241Y ALA* 2.9 11.0 + - - +
243Y TYR* 1.3 77.9 - - - +
245Y ARG* 1.3 66.6 + - - +
246Y SER 3.0 1.3 - - - -
247Y GLY* 2.9 15.9 + - - -
248Y LYS 4.1 1.2 + - - -
249Y GLY 3.4 24.4 + - - -
251Y ILE* 4.4 3.4 - - - -
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Residues in contact with ARG 245 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Y GLY 5.0 0.8 + - - -
79Y ILE* 4.6 4.8 - - - +
80Y ASN* 3.6 18.9 + - - +
83Y ASP* 2.9 39.4 + - - -
158Y ASP* 2.9 59.6 + - - +
159Y GLU* 3.9 0.4 - - - +
160Y VAL* 3.6 15.6 - - + +
188Y PRO* 5.5 1.6 - - - -
241Y ALA* 2.8 43.1 + - - +
242Y ALA* 3.0 8.1 + - - +
244Y CYS* 1.3 73.7 - - - +
246Y SER* 1.3 58.1 + - - +
247Y GLY* 3.0 6.2 + - - -
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Residues in contact with SER 246 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242Y ALA 2.8 15.1 + - - -
243Y TYR* 3.0 14.6 + - - -
244Y CYS 3.0 1.0 - - - -
245Y ARG* 1.3 75.4 - - - +
247Y GLY* 1.3 58.2 + - - +
248Y LYS* 3.2 28.7 + - - +
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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