Contacts of the helix formed by residues 273 - 291 (chain A) in PDB entry 2ADU
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 TYR 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ASP* 2.6 34.2 + - - +
246A ASP 4.3 5.8 - - - -
247A ILE* 4.0 21.8 - - + -
268A THR* 3.6 28.9 - - + -
270A ASN* 3.4 22.8 + - + +
271A PRO 3.0 1.2 - - - -
272A LYS* 1.3 104.3 + - + +
274A ASP* 1.3 67.6 + - - +
275A THR 3.1 2.9 - - - -
276A LEU* 2.7 24.8 + - + +
277A LEU* 2.9 13.9 + - + +
315A ILE* 4.0 16.8 - - + -
454A TYR* 3.1 47.8 - + + -
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 4.8 7.3 + - - -
270A ASN 4.7 0.9 - - - +
271A PRO* 3.0 43.0 + - - +
272A LYS 3.4 0.2 - - - -
273A TYR* 1.3 76.3 - - - +
275A THR* 1.3 60.1 + - - +
277A LEU* 3.3 11.0 + - - +
278A LYS* 2.9 29.9 + - - +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS 4.8 4.5 + - - -
273A TYR 3.1 0.8 - - - -
274A ASP* 1.3 76.0 - - - +
276A LEU* 1.3 61.1 + - - +
278A LYS* 3.8 6.7 - - + +
279A ALA* 2.9 29.3 + - - +
311A TYR* 4.1 14.5 - - + -
312A GLU 3.6 11.7 - - - +
313A VAL* 3.4 26.7 - - + -
314A GLU 5.8 0.2 + - - -
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Residues in contact with LEU 276 (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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247A ILE* 3.9 23.8 - - + -
272A LYS 5.3 0.2 + - - -
273A TYR* 2.7 25.6 + - + +
275A THR* 1.3 74.7 - - - +
277A LEU* 1.3 62.7 + - + +
279A ALA* 3.3 3.6 + - - +
280A VAL* 3.1 35.8 + - + +
313A VAL* 3.7 13.1 - - + +
315A ILE* 4.6 10.5 - - + -
322A VAL* 4.1 27.4 - - + -
367A GLY 4.3 11.9 - - - +
368A SER* 4.6 2.7 - - - +
369A THR* 4.7 7.4 - - + -
454A TYR* 4.1 27.4 - - + +
456A ALA* 3.9 11.0 - - + -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.6 30.5 - - + -
266A THR* 3.7 33.7 - - + +
268A THR* 3.7 28.7 - - + +
273A TYR 2.9 15.0 + - - +
274A ASP* 3.6 12.6 - - - +
276A LEU* 1.3 74.7 - - + +
278A LYS* 1.3 55.3 + - - +
280A VAL* 3.3 1.4 + - - -
281A LYS* 2.8 38.3 + - - +
456A ALA* 4.0 9.0 - - + -
458A PHE* 3.5 17.3 - - + -
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Residues in contact with LYS 278 (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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274A ASP 2.9 17.6 + - - +
275A THR* 3.8 7.6 - - + +
277A LEU* 1.3 75.6 - - - +
279A ALA* 1.3 57.9 + - - +
281A LYS* 3.7 9.7 - - + +
282A ASP* 2.8 39.5 + - + +
311A TYR* 3.0 38.0 + - + -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR 2.9 16.9 + - - +
276A LEU 3.4 6.1 - - - +
277A LEU 3.2 0.2 - - - -
278A LYS* 1.3 76.9 - - - +
280A VAL* 1.3 57.9 + - - +
282A ASP* 3.7 2.1 - - - +
283A ALA* 3.0 28.0 + - - +
308A MET* 4.4 4.5 - - - +
311A TYR* 3.3 47.0 - - + -
322A VAL* 3.9 19.5 - - + -
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Residues in contact with VAL 280 (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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276A LEU* 3.1 20.3 + - + +
277A LEU 3.8 3.1 - - - +
279A ALA* 1.3 73.0 - - + +
281A LYS* 1.3 58.8 + - - +
283A ALA* 3.2 5.1 + - - -
284A THR* 2.8 29.1 + - - -
308A MET* 4.2 5.8 - - + -
365A THR* 3.4 31.6 + - - +
366A PHE 4.5 0.2 - - - -
367A GLY* 3.7 30.1 - - - +
456A ALA* 3.6 24.2 - - + +
457A GLN* 4.0 8.5 - - - -
458A PHE* 4.1 9.6 - - + +
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 2.8 22.4 + - - +
278A LYS* 3.7 9.6 - - + +
280A VAL* 1.3 73.7 - - - +
282A ASP* 1.3 58.2 + - - +
284A THR* 3.3 2.3 + - - -
285A ASN* 3.0 49.0 + - - +
458A PHE* 3.5 45.5 - - + -
477A ASP 4.7 5.3 + - - -
478A TYR* 4.5 21.2 - - + +
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Residues in contact with ASP 282 (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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278A LYS* 2.8 23.0 + - + +
279A ALA 3.7 3.4 - - - +
281A LYS* 1.3 79.3 - - - +
283A ALA* 1.3 52.1 + - - +
285A ASN* 3.6 6.9 + - - +
286A THR* 2.6 44.1 + - - -
307A VAL* 3.4 11.5 - - - +
311A TYR* 2.5 33.7 + - - +
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Residues in contact with ALA 283 (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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279A ALA 3.0 17.0 + - - +
280A VAL 3.2 5.4 + - - +
282A ASP* 1.3 77.5 - - - +
284A THR* 1.3 56.9 + - - +
286A THR* 3.2 5.8 + - - -
287A GLY* 2.9 24.1 + - - -
304A ILE* 3.8 29.4 - - + +
307A VAL* 4.1 8.9 - - - +
308A MET* 3.9 28.5 - - + +
365A THR* 3.9 4.3 - - - +
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL 2.8 14.7 + - - -
281A LYS 3.7 4.3 - - - -
283A ALA* 1.3 76.8 - - - +
285A ASN* 1.3 59.0 + - - +
287A GLY* 3.0 2.8 + - - -
288A ILE* 2.9 41.2 + - + +
363A ILE* 3.8 18.8 - - + +
365A THR* 2.7 29.8 + - + +
458A PHE* 3.0 40.2 + - + +
459A GLU* 4.5 2.5 - - - +
460A HIS* 4.9 3.6 - - + +
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Residues in contact with ASN 285 (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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281A LYS* 3.0 38.2 + - - +
282A ASP* 4.1 7.4 - - - +
284A THR* 1.3 77.2 - - - +
286A THR* 1.3 56.7 + - - +
288A ILE* 3.6 13.0 - - - +
289A LYS* 3.0 27.9 + - - +
460A HIS* 4.5 2.1 - - - -
474A ARG* 2.8 36.6 + - - +
478A TYR* 4.6 2.9 + - - +
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Residues in contact with THR 286 (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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282A ASP* 2.6 28.3 + - - -
283A ALA* 3.3 7.9 - - - +
284A THR 3.0 0.2 - - - -
285A ASN* 1.3 75.1 - - - +
287A GLY* 1.3 61.0 + - - +
289A LYS* 3.5 5.7 + - + +
290A CYS* 3.1 33.6 + - - -
303A ALA* 4.2 23.6 - - + +
307A VAL* 3.5 32.3 - - + +
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Residues in contact with GLY 287 (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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283A ALA 2.9 10.1 + - - -
284A THR 3.0 4.0 + - - -
286A THR* 1.3 77.1 - - - +
288A ILE* 1.3 62.3 + - - +
290A CYS* 3.5 1.0 + - - -
291A ALA* 3.1 23.4 + - - +
300A VAL* 3.8 12.6 - - - +
304A ILE* 3.5 30.3 - - - +
363A ILE* 3.9 9.4 - - - +
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Residues in contact with ILE 288 (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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135A CYS* 6.3 1.3 - - - -
284A THR* 2.9 22.4 + - + +
285A ASN* 3.6 20.6 - - - +
287A GLY* 1.3 76.7 - - - +
289A LYS* 1.3 60.1 + - - +
291A ALA* 3.3 13.9 + - - +
363A ILE* 3.8 22.9 - - + -
460A HIS* 3.7 40.2 - - + -
462A ILE* 4.4 8.0 - - + +
469A LYS* 2.9 23.2 + - - +
471A VAL* 3.6 28.0 - - + -
474A ARG* 3.8 10.5 - - - +
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Residues in contact with LYS 289 (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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135A CYS* 6.2 4.9 - - - -
138A PRO* 4.0 13.9 - - + +
285A ASN 3.0 18.6 + - - +
286A THR* 3.9 6.3 - - - +
288A ILE* 1.3 80.0 - - - +
290A CYS* 1.3 62.7 + - - +
291A ALA 3.8 1.2 - - - +
469A LYS* 3.0 20.0 + - - +
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Residues in contact with CYS 290 (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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138A PRO* 4.3 8.3 - - - +
286A THR* 3.1 26.4 + - - +
287A GLY* 3.9 3.6 - - - +
288A ILE 3.4 0.2 - - - -
289A LYS* 1.3 77.9 - - - +
291A ALA* 1.3 60.6 + - - +
295A VAL* 2.9 30.4 - - + +
299A ASP 5.0 2.0 - - - +
300A VAL* 4.3 13.7 - - + -
303A ALA* 3.7 28.0 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 3.7 5.7 - - - +
287A GLY 3.1 17.0 + - - +
288A ILE* 3.5 8.3 - - - +
289A LYS 3.2 1.6 - - - -
290A CYS* 1.3 79.8 - - - +
292A GLY* 1.3 58.5 + - - +
295A VAL* 3.9 0.7 - - - -
300A VAL* 4.4 3.8 - - + -
355A MET* 3.7 21.3 - - + -
363A ILE* 4.5 2.5 - - + -
462A ILE* 3.7 27.6 - - + -
469A LYS* 3.0 27.2 + - - +
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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