Contacts of the helix formed by residues 229 - 246 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C GLU 5.2 0.2 - - - +
9C ILE* 4.4 4.6 - - - +
10C LYS 5.7 0.6 + - - -
70C ALA* 4.3 0.2 - - - -
226C ASP* 3.1 16.5 + - - +
227C GLY 3.2 0.2 - - - -
228C MET* 1.3 77.6 - - - +
230C ILE* 1.3 59.5 + - - +
231C LEU* 3.0 31.0 + - - +
232C CYS* 3.6 21.1 + - - -
233C VAL* 2.6 33.0 + - - +
290C LEU* 5.0 12.7 - - + +
294C ARG* 3.0 37.3 + - - -
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.9 39.9 - - + -
39C MET* 4.7 13.5 - - + -
70C ALA* 3.9 14.7 - - + +
73C VAL* 4.0 13.5 - - + +
74C GLY* 3.7 25.4 - - - +
77C ALA* 5.2 0.4 - - + -
228C MET 3.7 4.8 + - - -
229C ASP* 1.3 74.0 + - - +
231C LEU* 1.3 76.7 + - + +
233C VAL* 3.9 7.2 - - - -
234C ARG* 3.1 20.6 + - + +
287C PRO 5.2 1.8 - - - +
291C LEU* 4.6 26.9 - - + +
294C ARG* 5.4 2.7 - - - +
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.9 25.8 - - + -
9C ILE* 3.7 11.9 - - + -
25C THR* 4.0 12.4 - - + +
27C LEU* 4.1 28.3 - - + -
35C TYR* 5.1 2.2 - - + -
229C ASP* 3.0 11.0 + - - +
230C ILE* 1.3 94.1 - - + +
232C CYS* 1.3 58.6 + - - +
234C ARG* 3.4 26.0 + - - +
235C GLU* 3.1 25.5 + - - +
291C LEU* 5.8 3.6 - - + -
294C ARG* 3.2 30.5 - - + +
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Residues in contact with CYS 232 (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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9C ILE* 3.6 28.9 - - + -
10C LYS* 4.5 11.2 - - - +
12C CYS* 5.9 4.3 - - - -
21C PRO* 5.9 0.8 - - + +
225C VAL* 4.4 9.8 - - + +
226C ASP* 3.7 18.6 - - - -
229C ASP* 3.6 28.5 - - - -
231C LEU* 1.3 76.0 - - - +
233C VAL* 1.3 63.9 + - - +
234C ARG 3.1 0.7 - - - -
235C GLU* 3.3 10.5 - - + -
236C ALA* 2.7 31.7 + - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 3.8 22.0 - - - +
71C CYS* 4.1 12.8 - - - +
74C GLY* 4.0 11.9 - - - -
75C LEU* 4.2 10.8 - - + -
225C VAL* 4.2 8.5 - - + -
226C ASP 3.8 13.7 - - - +
227C GLY* 3.9 13.2 - - - -
229C ASP 2.6 32.5 + - - +
230C ILE 3.8 4.0 - - - +
232C CYS* 1.3 78.6 - - - +
234C ARG* 1.3 57.3 + - - +
236C ALA* 3.3 2.5 + - - +
237C THR* 2.5 33.5 + - - +
255C LEU* 4.4 14.6 - - + -
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Residues in contact with ARG 234 (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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25C THR* 3.0 31.9 + - - +
26C VAL 3.3 19.4 + - - -
27C LEU* 4.0 14.5 - - - +
28C THR* 5.2 1.8 - - - +
31C ASP* 4.9 4.9 + - - +
35C TYR* 3.3 42.6 + - - -
74C GLY 3.4 15.6 + - - +
77C ALA* 3.6 19.5 - - + +
78C GLY* 4.1 0.4 - - - +
230C ILE* 3.1 16.2 + - + +
231C LEU* 3.4 12.4 + - - +
233C VAL* 1.3 80.8 - - - +
235C GLU* 1.3 66.5 + - - +
237C THR* 3.2 2.7 + - - -
238C ARG* 2.3 62.8 + - - +
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Residues in contact with GLU 235 (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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9C ILE* 3.6 24.5 - - + -
21C PRO* 4.3 8.6 - - + +
22C PRO* 3.2 31.6 - - - +
25C THR* 3.2 28.0 + - - -
231C LEU 3.1 16.7 + - - +
232C CYS* 3.0 13.3 + - + +
234C ARG* 1.3 83.7 + - - +
236C ALA* 1.3 63.8 + - - +
238C ARG* 3.1 20.3 + - - +
239C PHE* 2.9 22.3 + - - +
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Residues in contact with ALA 236 (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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12C CYS* 5.1 0.2 - - - -
21C PRO* 4.4 10.4 - - + +
223C LEU* 4.5 5.4 - - + -
225C VAL* 3.5 29.4 - - + -
232C CYS 2.7 20.6 + - - +
233C VAL 3.5 4.7 - - - +
235C GLU* 1.3 74.4 - - - +
237C THR* 1.3 58.8 + - - +
239C PHE* 2.9 10.3 + - - +
240C ALA* 2.7 31.2 + - - +
253C MET* 3.8 14.9 - - + +
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Residues in contact with THR 237 (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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74C GLY 4.1 1.6 + - - -
75C LEU* 3.0 45.1 - - + +
78C GLY* 3.8 17.9 - - - +
79C ILE* 3.9 11.9 - - + -
162C LEU* 4.2 7.2 - - + -
190C ILE* 5.6 3.1 - - + -
192C ILE* 5.9 0.4 - - + -
233C VAL 2.5 23.8 + - - -
234C ARG* 3.6 4.7 - - - -
235C GLU 3.2 0.2 - - - -
236C ALA* 1.3 78.1 - - - +
238C ARG* 1.3 57.8 + - - +
240C ALA* 4.4 1.6 - - - +
241C ALA* 2.9 29.0 + - + +
253C MET* 4.3 10.0 - - - +
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Residues in contact with ARG 238 (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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31C ASP* 5.9 0.6 + - - -
35C TYR* 4.7 1.8 + - - -
77C ALA 2.8 26.9 + - - -
78C GLY* 3.6 18.8 - - - +
234C ARG* 2.3 68.9 + - - +
235C GLU* 3.5 20.6 + - - +
236C ALA 3.1 0.2 - - - -
237C THR* 1.3 76.5 - - - +
239C PHE* 1.3 57.1 + - - +
241C ALA* 3.9 2.0 - - - +
242C ALA* 2.9 31.9 + - - +
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Residues in contact with PHE 239 (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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17C LEU* 4.1 20.4 - - + -
19C GLU* 3.3 24.0 - - + -
20C GLY* 3.5 21.5 - - - -
21C PRO* 3.7 23.6 - - + -
22C PRO* 5.3 3.6 - - + -
223C LEU* 3.7 31.0 - - + -
235C GLU 2.9 12.8 + - - +
236C ALA 2.9 8.7 + - - +
238C ARG* 1.3 77.4 - - - +
240C ALA* 1.3 61.2 + - - +
242C ALA* 4.2 3.4 - - - +
243C TYR* 3.3 29.4 + + + +
251C ILE* 4.7 5.6 - - + -
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Residues in contact with ALA 240 (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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190C ILE* 3.9 29.8 - - + -
223C LEU* 5.3 1.1 - - + -
236C ALA 2.7 16.5 + - - +
237C THR* 4.1 2.5 - - - +
239C PHE* 1.3 73.6 - - + +
241C ALA* 1.3 67.9 + - - +
242C ALA 3.0 1.3 - - - -
243C TYR* 2.9 18.7 + - - +
244C CYS* 3.0 16.1 + - - -
251C ILE* 4.1 16.6 - - + -
253C MET* 4.3 13.7 - - + -
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Residues in contact with ALA 241 (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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78C GLY 3.8 15.3 - - - +
79C ILE* 4.5 4.3 - - + -
160C VAL* 3.7 10.7 - - + +
190C ILE* 3.7 11.5 - - + +
237C THR 2.9 20.3 + - - +
238C ARG* 3.9 3.4 - - - +
240C ALA* 1.3 77.9 - - - +
242C ALA* 1.3 63.7 + - - +
244C CYS* 3.3 3.1 + - - +
245C ARG* 3.0 48.3 + - - +
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Residues in contact with ALA 242 (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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238C ARG 2.9 19.8 + - - +
239C PHE* 4.2 4.5 - - - +
241C ALA* 1.3 73.8 - - - +
243C TYR* 1.3 70.0 + - - +
245C ARG* 3.3 18.8 + - - +
246C SER* 3.4 13.9 + - - -
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Residues in contact with TYR 243 (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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17C LEU* 4.1 23.8 - - + -
221C PRO* 3.3 24.3 - - + +
239C PHE* 3.3 22.7 + + + +
240C ALA* 3.3 10.8 - - - +
242C ALA* 1.3 76.7 - - - +
244C CYS* 1.3 62.7 + - - +
246C SER* 2.8 25.6 + - - -
248C LYS* 3.4 63.5 + - + +
249C GLY 3.5 19.7 - - - -
250C PRO 3.6 11.6 + - - -
251C ILE* 4.1 23.1 - - + -
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Residues in contact with CYS 244 (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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160C VAL* 3.6 15.3 - - + -
188C PRO* 3.9 28.4 - - + +
189C CYS 4.2 1.8 - - - -
190C ILE* 3.6 30.7 - - - -
240C ALA 3.0 8.8 + - - -
241C ALA 3.6 7.0 - - - +
243C TYR* 1.3 75.5 - - - +
245C ARG* 1.3 65.8 + - - +
247C GLY* 3.2 14.0 + - - -
248C LYS 4.3 0.3 + - - -
249C GLY* 3.4 26.8 + - - +
251C ILE* 3.8 9.6 - - - -
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Residues in contact with ARG 245 (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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78C GLY 4.8 0.4 + - - -
79C ILE* 4.6 3.2 - - - +
80C ASN* 3.5 17.8 + - - +
83C ASP* 2.9 38.0 + - - -
158C ASP* 2.6 71.5 + - - +
160C VAL* 3.8 13.0 - - + +
188C PRO* 5.8 0.9 - - - -
241C ALA* 3.0 38.5 + - - +
242C ALA* 3.3 10.3 + - - +
244C CYS* 1.3 75.5 - - - +
246C SER* 1.3 56.5 + - - +
247C GLY* 3.1 5.8 + - - -
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Residues in contact with SER 246 (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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242C ALA 3.4 8.2 + - - -
243C TYR* 2.8 18.8 + - - -
244C CYS 3.2 0.2 - - - -
245C ARG* 1.3 74.8 - - - +
247C GLY* 1.3 55.3 + - - +
248C LYS* 3.3 18.1 + - - +
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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
------------------------------------------------------------
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