Contacts of the helix formed by residues 288 - 305 (chain c) in PDB entry 3J7Y
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 288 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270c TYR* 3.5 12.3 - - + -
286c GLY 3.9 1.9 - - - -
287c GLU* 1.3 100.5 + - - +
289c VAL* 1.3 61.9 + - - +
290c LEU* 3.4 6.4 - - - +
291c VAL* 3.1 29.4 + - - +
292c ALA* 3.0 27.9 + - - +
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Residues in contact with VAL 289 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257c LEU* 5.2 11.7 - - + -
270c TYR* 3.8 36.8 - - + -
272c VAL* 4.4 13.2 - - + -
288c THR* 1.3 72.3 - - - +
290c LEU* 1.3 66.2 + - + +
292c ALA* 3.2 8.0 + - - +
293c GLU* 2.9 41.2 + - + +
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Residues in contact with LEU 290 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288c THR* 5.3 4.0 - - - +
289c VAL* 1.3 83.2 - - + +
291c VAL* 1.3 60.4 + - + +
293c GLU* 3.2 19.8 + - - +
294c GLU* 2.9 39.3 + - + +
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Residues in contact with VAL 291 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K PRO* 6.1 2.7 - - + -
285c PRO 4.6 1.6 - - - +
286c GLY* 4.1 16.6 - - - -
287c GLU* 4.4 5.4 - - + +
288c THR* 3.1 30.4 + - - +
289c VAL 3.2 0.2 - - - -
290c LEU* 1.3 81.0 - - + +
292c ALA* 1.3 56.3 + - - +
294c GLU* 3.2 19.3 + - - +
295c GLU* 2.9 29.3 + - + +
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Residues in contact with ALA 292 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270c TYR* 3.5 22.4 - - + +
272c VAL* 3.4 26.9 - - + -
284c GLY 3.9 4.8 - - - +
285c PRO 3.4 15.3 - - - -
288c THR 3.0 14.1 + - - +
289c VAL 3.2 9.4 + - - +
291c VAL* 1.3 77.9 - - - +
293c GLU* 1.3 56.3 + - - +
295c GLU* 3.2 4.9 + - - +
296c ALA* 2.9 28.2 + - - +
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Residues in contact with GLU 293 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238c MET* 5.0 14.9 - - + +
255c SER* 3.3 32.8 + - - +
272c VAL* 3.6 23.7 - - + +
273c GLY 5.7 0.2 - - - -
274c LEU* 4.6 4.4 - - + +
289c VAL* 2.9 27.1 + - + +
290c LEU* 3.4 22.5 - - - +
292c ALA* 1.3 76.1 - - - +
294c GLU* 1.3 57.8 + - + +
296c ALA* 3.2 5.2 + - - +
297c ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 294 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237c PRO* 4.1 19.4 - - + +
238c MET* 5.6 6.1 - - + -
290c LEU* 2.9 21.8 + - - +
291c VAL* 3.3 21.4 - - - +
293c GLU* 1.3 75.2 - - + +
295c GLU* 1.3 58.2 + - - +
297c ALA* 3.2 8.5 + - - +
298c ARG* 2.9 43.3 + - + +
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Residues in contact with GLU 295 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K PHE* 3.7 7.2 - - - -
5K SER* 2.7 37.2 + - - +
8K PRO* 3.7 27.8 - - + -
284c GLY* 3.7 0.2 - - - -
285c PRO* 3.2 34.1 - - + +
291c VAL* 2.9 11.4 + - + +
292c ALA 3.2 9.2 + - - +
294c GLU* 1.3 76.1 - - - +
296c ALA* 1.3 57.4 + - - +
298c ARG* 3.2 9.5 + - - +
299c VAL* 2.9 53.3 + - - +
302c ARG* 3.7 6.4 + - - -
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Residues in contact with ALA 296 (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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272c VAL 3.5 25.1 - - - +
273c GLY 4.2 2.5 - - - +
274c LEU* 3.6 20.0 - - + -
282c ALA* 3.4 10.4 - - - +
283c GLU* 4.1 7.4 - - - -
284c GLY* 3.6 12.9 - - - +
292c ALA 2.9 8.8 + - - +
293c GLU* 3.3 10.8 - - - +
295c GLU* 1.3 76.5 - - - +
297c ALA* 1.3 57.0 + - - +
299c VAL* 3.2 2.5 + - - +
300c ALA* 2.9 24.8 + - - +
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Residues in contact with ALA 297 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237c PRO* 4.1 13.9 - - + -
238c MET* 4.1 11.7 - - + -
241c LEU* 3.0 37.9 - - + +
274c LEU* 3.4 12.7 - - + +
293c GLU 2.9 13.4 + - - +
294c GLU 3.3 10.5 - - - +
296c ALA* 1.3 77.3 - - - +
298c ARG* 1.3 56.6 + - - +
300c ALA* 3.2 1.9 + - - +
301c LEU* 2.9 24.8 + - - +
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Residues in contact with ARG 298 (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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5K SER* 5.1 9.2 + - - -
229c PHE* 3.8 53.0 + - + +
234c ILE* 3.9 22.7 + - - +
235c ILE* 5.5 1.2 - - - +
237c PRO* 4.2 21.9 - - + +
294c GLU* 2.9 25.6 + - - +
295c GLU* 3.2 20.6 + - - +
297c ALA* 1.3 75.5 - - - +
299c VAL* 1.3 58.3 + - - +
301c LEU* 3.2 5.5 + - - +
302c ARG* 2.9 41.7 + - - +
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Residues in contact with VAL 299 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K SER 5.0 1.3 - - - +
3K SER* 3.6 21.3 - - - +
4K PHE* 3.8 20.2 - - + +
282c ALA* 3.8 13.9 - - + -
283c GLU 4.1 19.5 - - - +
295c GLU* 2.9 39.6 + - - +
296c ALA* 3.4 8.1 - - - +
298c ARG* 1.3 74.9 - - - +
300c ALA* 1.3 57.7 + - - +
302c ARG* 3.2 12.1 + - - +
303c LYS* 2.9 39.6 + - - +
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Residues in contact with ALA 300 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241c LEU* 4.4 6.3 - - + -
274c LEU* 4.3 3.8 - - + -
281c ILE* 3.7 27.1 - - + +
282c ALA* 3.4 22.6 - - + +
296c ALA 2.9 8.3 + - - +
297c ALA* 3.3 13.0 - - - +
299c VAL* 1.3 76.9 - - - +
301c LEU* 1.3 57.2 + - - +
303c LYS* 3.2 8.1 + - - +
304c LEU* 2.9 36.4 + - + +
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Residues in contact with LEU 301 (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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229c PHE* 3.6 31.2 - - + -
232c TRP* 6.0 1.3 - - + -
234c ILE* 4.2 7.2 - - + -
237c PRO* 4.2 16.4 - - + +
240c LEU* 4.4 10.3 - - + -
241c LEU* 3.2 46.0 - - + +
244c GLU* 4.6 0.9 - - + -
297c ALA 2.9 6.9 + - - +
298c ARG 3.3 8.1 - - - +
300c ALA* 1.3 76.4 - - - +
302c ARG* 1.3 57.5 + - - +
304c LEU* 3.2 10.7 + - + +
305c TYR* 2.9 69.1 + - + +
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Residues in contact with ARG 302 (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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3K SER* 4.3 15.3 - - - -
4K PHE* 3.2 18.0 + - - +
5K SER* 3.1 41.8 + - - +
227c GLU* 3.3 29.0 - - - +
228c LEU* 3.0 30.0 + - + +
229c PHE* 3.3 27.8 - - + +
230c GLU* 5.6 0.2 + - - -
295c GLU* 3.7 5.3 + - - -
298c ARG* 2.9 23.9 + - - +
299c VAL* 3.3 11.1 - - - +
301c LEU* 1.3 77.3 - - - +
303c LYS* 1.3 63.0 + - - +
305c TYR* 3.2 9.1 + - - -
307c PHE* 3.1 34.8 + - + -
308c THR* 3.9 16.8 + - + +
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Residues in contact with LYS 303 (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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2K SER 5.7 0.9 - - - -
3K SER* 4.2 9.2 - - - +
280c LEU 5.8 0.2 + - - -
281c ILE 3.3 27.5 + - - +
282c ALA* 4.4 7.0 - - + +
283c GLU 5.4 0.6 - - - +
299c VAL* 2.9 30.9 + - + +
300c ALA* 3.2 9.6 + - - +
302c ARG* 1.3 78.5 - - - +
304c LEU* 1.3 65.4 + - + +
306c GLY* 3.6 8.7 + - - -
308c THR* 4.1 20.7 - - + +
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Residues in contact with LEU 304 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147c ASP* 3.2 24.8 - - - +
241c LEU* 5.0 6.3 - - + +
244c GLU* 3.9 30.3 - - + +
245c LEU* 5.3 12.3 - - + +
248c ARG* 4.7 25.0 + - + +
281c ILE* 5.7 5.8 - - + -
300c ALA* 2.9 21.3 + - + +
301c LEU* 3.2 19.7 + - + +
303c LYS* 1.3 79.8 - - + +
305c TYR* 1.3 67.5 + - + +
306c GLY 3.1 5.6 + - - -
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Residues in contact with TYR 305 (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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145c TYR* 4.0 4.9 - - - +
147c ASP* 3.8 20.2 - - - -
148c MET* 3.6 39.7 - - + +
149c PRO* 3.5 21.3 - - + +
228c LEU* 4.2 7.6 - - + -
232c TRP* 3.6 23.2 - + - -
240c LEU* 5.0 8.3 - - - +
244c GLU* 2.6 48.7 + - + +
248c ARG* 6.1 0.4 - - - -
301c LEU* 2.9 41.2 + - + +
302c ARG* 3.2 2.6 + - - +
304c LEU* 1.3 85.2 - - + +
306c GLY* 1.3 64.5 + - - +
307c PHE* 3.1 18.2 + - + -
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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