Contacts of the helix formed by residues 271 - 282 (chain A) in PDB entry 1UBE
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 SER 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ASP* 3.1 18.1 + - - -
265A LEU* 3.5 26.3 - - - +
269A GLY 3.1 6.9 + - - -
270A ILE* 1.3 67.8 - - - +
272A ARG* 1.3 70.4 + - - +
273A GLU* 3.9 7.7 + - - +
274A GLY* 3.3 21.3 + - - -
275A SER* 3.0 17.8 + - - -
308A ARG* 5.3 3.6 - - - +
312A LEU* 5.0 4.7 - - - +
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Residues in contact with ARG 272 (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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45A GLY 4.9 7.4 - - - +
270A ILE 2.9 9.7 + - - +
271A SER* 1.3 69.0 - - - +
273A GLU* 1.3 78.6 + - - +
275A SER* 2.6 30.9 + - - -
276A LEU* 2.8 26.9 - - + +
315A THR* 4.6 9.7 + - - +
318A ALA* 4.6 9.1 - - - +
319A ASN* 2.5 39.1 - - - +
322A GLU* 3.5 32.2 + - - +
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Residues in contact with GLU 273 (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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271A SER* 3.9 4.5 + - - +
272A ARG* 1.3 97.5 + - + +
274A GLY* 1.3 54.9 + - - +
276A LEU* 2.4 43.5 + - - +
277A ILE 3.0 5.2 + - - -
308A ARG* 4.1 6.5 - - - +
311A LEU* 3.6 27.6 - - + +
312A LEU* 3.2 57.4 - - + +
318A ALA* 5.7 3.4 - - + -
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Residues in contact with GLY 274 (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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263A ASP* 4.7 9.9 - - - -
271A SER* 3.3 20.0 + - - -
272A ARG 3.2 0.2 + - - -
273A GLU* 1.3 77.7 - - - +
275A SER* 1.3 55.9 + - - +
276A LEU 3.3 0.2 + - - -
277A ILE* 3.4 16.5 + - - +
278A ASP* 2.7 35.4 + - - +
304A LYS* 5.3 4.4 - - - +
308A ARG* 4.9 6.0 - - - +
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 5.4 0.2 - - - -
46A SER* 4.0 7.4 + - - -
47A ILE* 3.2 28.7 + - - +
48A SER* 3.7 16.5 + - - -
261A GLU 6.0 0.4 - - - -
262A PHE* 4.9 12.0 - - - +
263A ASP 6.1 0.6 - - - +
270A ILE* 5.2 1.8 - - - -
271A SER 3.0 12.3 + - - -
272A ARG* 2.6 22.4 + - - -
274A GLY* 1.3 73.2 - - - -
276A LEU* 1.3 56.6 + - - -
278A ASP* 4.0 5.6 + - - +
279A MET* 3.0 35.4 + - - +
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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
----------------------------------------------------------
47A ILE* 4.7 14.4 - - + -
272A ARG* 2.8 53.4 - - + +
273A GLU* 2.4 28.0 + - - +
275A SER* 1.3 70.9 - - - +
277A ILE* 1.3 54.5 + - - +
279A MET* 4.5 2.0 - - + -
280A GLY* 2.3 38.9 + - - +
286A ILE* 3.7 2.8 - - - +
311A LEU* 4.4 9.0 - - + -
318A ALA* 5.0 7.2 - - + +
321A ILE* 4.0 15.3 - - + +
322A GLU* 3.6 44.2 - - + +
325A ILE* 4.9 6.1 - - + -
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Residues in contact with ILE 277 (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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273A GLU 3.0 9.3 + - - +
274A GLY* 3.8 9.6 - - - +
276A LEU* 1.3 77.5 - - - +
278A ASP* 1.3 70.9 + - - +
280A GLY* 2.7 6.9 + - - -
281A VAL* 2.9 27.2 + - + +
286A ILE* 3.7 13.4 - - + +
293A PHE* 4.3 24.5 - - + -
304A LYS* 3.1 49.4 - - + +
307A ALA* 4.0 9.2 - - + -
308A ARG* 3.6 21.1 - - + +
311A LEU* 3.6 19.0 - - + +
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Residues in contact with ASP 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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243A ARG* 3.2 30.4 + - - +
261A GLU 6.0 1.1 - - - +
263A ASP* 4.2 2.3 - - - +
274A GLY 2.7 21.6 + - - +
275A SER* 4.0 5.7 - - - +
277A ILE* 1.3 83.0 - - - +
279A MET* 1.3 67.7 + - + +
281A VAL* 2.9 18.0 + - - +
282A GLU* 3.0 20.9 + - - +
304A LYS* 2.8 33.3 + - - -
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Residues in contact with MET 279 (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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47A ILE* 3.7 25.6 - - + +
48A SER* 3.6 27.1 - - - -
51A VAL* 3.3 37.9 - - + -
275A SER 3.0 22.6 + - - +
276A LEU* 4.0 3.1 - - + +
278A ASP* 1.3 79.7 - - + +
280A GLY* 1.3 60.9 + - - +
281A VAL 3.3 0.9 + - - -
282A GLU* 4.7 11.2 - - - +
283A HIS* 3.3 40.0 + - + +
325A ILE* 5.2 15.0 - - + +
329A LEU* 4.6 9.4 - - + -
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Residues in contact with GLY 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 2.3 29.2 + - - -
277A ILE 2.7 6.1 + - - -
279A MET* 1.3 68.4 - - - +
281A VAL* 1.3 53.8 + - - -
283A HIS* 4.8 0.9 - - - -
284A GLY 4.3 0.7 - - - -
285A PHE* 2.8 16.4 + - - -
286A ILE* 2.7 39.7 + - - +
321A ILE* 4.4 11.0 - - - +
325A ILE* 5.6 2.0 - - - -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 2.9 24.0 + - + +
278A ASP* 3.3 14.1 - - - +
280A GLY* 1.3 76.3 - - - +
282A GLU* 1.3 65.5 + - + +
283A HIS 2.8 6.0 + - - -
284A GLY* 3.0 15.8 + - - +
286A ILE* 3.2 43.8 - - + +
287A ARG* 5.5 0.4 - - - -
288A LYS* 5.8 2.9 - - + +
293A PHE* 4.6 11.0 - - + -
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Residues in contact with GLU 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 ASP* 3.0 20.0 + - - +
279A MET* 3.7 10.1 + - - +
281A VAL* 1.3 80.2 - - + +
283A HIS* 1.3 78.2 + - + +
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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
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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