Contacts of the helix formed by residues 234 - 246 (chain A) in PDB entry 1JQE
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ASP* 3.4 32.4 + - - +
231A ILE* 3.0 38.4 + - + +
232A ASP 3.1 2.0 + - - -
233A GLY* 1.3 75.5 - - - +
235A GLU* 1.3 59.8 + - - +
236A ASN* 3.0 18.2 + - - +
237A GLY 2.6 24.6 + - - -
238A ASP* 2.8 33.0 + - - +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 5.2 5.6 + - - +
233A GLY 3.1 7.2 + - - +
234A ASN* 1.3 73.9 + - - +
236A ASN* 1.3 63.5 + - - +
238A ASP* 3.2 6.5 + - - +
239A LEU* 3.0 45.4 + - + +
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Residues in contact with ASN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 2.9 40.4 + - - +
25A HIS* 3.1 39.5 + - - -
225A ASP 5.4 0.2 + - - -
228A ASP* 2.8 26.0 + - - +
234A ASN* 3.0 8.1 + - - +
235A GLU* 1.3 80.3 - - - +
237A GLY* 1.3 64.6 + - - +
239A LEU* 3.2 1.4 + - - +
240A LEU* 2.9 40.1 + - - +
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASP* 3.3 35.6 - - - +
229A CYS* 3.6 7.5 - - - -
231A ILE 5.3 0.2 - - - -
234A ASN* 2.6 16.9 + - - -
236A ASN* 1.3 73.5 - - - +
238A ASP* 1.3 56.7 + - - +
240A LEU* 3.4 1.4 + - - -
241A TRP* 3.0 36.6 + - - -
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ILE 5.3 1.6 - - - +
232A ASP* 5.5 1.4 - - - -
233A GLY* 3.7 20.0 + - - +
234A ASN 2.8 25.8 + - - +
235A GLU* 3.7 6.7 + - - +
237A GLY* 1.3 76.0 - - - +
239A LEU* 1.3 65.2 + - + +
241A TRP* 3.2 4.3 + - - +
242A ASP* 3.1 28.5 + - - +
251A ASN* 2.8 37.4 + - + +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 6.2 4.3 - - + +
18A SER* 4.7 4.0 + - - -
21A ARG* 3.1 52.7 - - - +
235A GLU* 3.0 33.0 + - + +
236A ASN 3.2 0.6 + - - +
238A ASP* 1.3 77.8 - - + +
240A LEU* 1.3 58.6 + - - +
242A ASP* 3.4 20.8 + - + +
243A PHE* 3.1 23.4 + - - +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER 5.7 0.2 - - - +
21A ARG* 3.8 35.9 - - + +
22A PHE* 4.5 3.4 - - - +
25A HIS* 4.3 7.2 - - + -
224A MET* 4.0 23.6 - - + -
225A ASP 3.7 23.1 - - - +
226A ILE* 4.5 2.5 - - - -
228A ASP* 5.2 1.8 - - + -
229A CYS* 3.7 22.4 - - - -
236A ASN* 2.9 40.6 + - - +
237A GLY* 5.0 0.7 - - - -
239A LEU* 1.3 74.2 - - - +
241A TRP* 1.3 60.7 + - - +
243A PHE* 3.2 7.5 + - + +
244A LEU* 2.8 34.9 + - - +
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Residues in contact with TRP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A CYS* 2.7 39.9 + - + +
230A PHE* 5.3 4.3 - + - -
237A GLY 3.0 27.6 + - - -
238A ASP* 3.3 9.2 - - - +
240A LEU* 1.3 75.5 - - - +
242A ASP* 1.3 59.4 + - - +
244A LEU* 3.3 7.4 + - + +
245A THR* 2.8 45.3 + - + +
250A PHE* 3.7 32.1 - + + -
251A ASN* 3.1 25.1 - - - +
259A ARG* 3.2 33.3 - - - +
262A LEU* 3.8 17.3 - - + -
263A GLY* 3.7 22.7 - - - -
266A LEU* 3.4 33.7 - - + -
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Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 5.4 2.0 - - - +
238A ASP 3.1 14.2 + - - +
239A LEU* 3.4 24.2 - - + +
241A TRP* 1.3 77.2 - - - +
243A PHE* 1.3 52.6 + - - +
245A THR* 3.9 0.7 - - - -
246A GLU* 2.6 36.6 + - - -
247A THR 3.1 22.1 + - - +
248A CYS* 3.8 4.2 - - - -
249A ASN* 2.9 19.7 + - - +
250A PHE* 2.8 25.5 + - - +
251A ASN 4.7 0.2 + - - -
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Residues in contact with PHE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 3.1 34.1 + - - +
19A PHE* 3.9 7.0 - + - -
22A PHE* 3.5 45.3 - + + -
179A TRP* 3.7 25.8 - + - -
224A MET* 3.7 18.2 - - + -
239A LEU 3.1 13.9 + - - +
240A LEU* 3.3 15.3 - - + +
242A ASP* 1.3 76.7 - - - +
244A LEU* 1.3 62.6 + - - +
246A GLU* 3.2 21.1 + - - +
500A QUN 3.2 51.0 - - + +
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TRP* 3.8 23.3 - - + -
182A LEU* 3.5 26.4 - - + +
183A TRP* 5.1 1.9 + - - -
190A PHE* 3.8 4.2 - - - -
224A MET* 3.6 29.8 - - + -
226A ILE* 4.1 19.7 - - + -
229A CYS* 4.1 13.2 - - - -
240A LEU 2.8 24.2 + - - +
241A TRP* 3.8 9.0 - - + +
243A PHE* 1.3 73.3 - - - +
245A THR* 1.3 64.5 + - + +
246A GLU* 4.9 2.6 - - - +
266A LEU* 4.1 25.4 - - + -
281A PHE* 4.4 18.2 - - + -
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Residues in contact with THR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU* 6.2 0.2 - - + -
190A PHE* 3.7 31.7 - - + -
191A PRO* 3.6 9.4 - - - +
241A TRP* 2.8 28.0 + - + +
242A ASP 3.7 0.3 + - - -
244A LEU* 1.3 78.5 - - + +
246A GLU* 1.3 70.3 + - - +
247A THR* 2.9 20.6 + - - -
250A PHE* 3.2 54.5 - - + +
262A LEU* 4.0 5.6 - - + -
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TRP* 5.4 0.9 - - - -
183A TRP* 4.4 4.5 + - - -
191A PRO* 3.1 20.6 - - + +
196A CYS* 3.1 29.5 - - - +
198A TYR* 3.0 35.2 + - - +
242A ASP 2.6 17.9 + - - -
243A PHE* 3.2 13.5 + - - +
244A LEU 4.9 3.1 - - - +
245A THR* 1.3 74.6 - - - +
247A THR* 1.3 54.1 + - - +
248A CYS* 4.3 0.8 - - - -
500A QUN 3.5 58.8 - - + +
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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