Contacts of the helix formed by residues 303 - 314 (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 GLY 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A SER* 3.0 18.6 + - - -
293A PHE* 3.7 4.2 - - - -
301A GLY 4.0 1.4 + - - -
302A GLN* 1.3 72.1 - - - +
304A LYS* 1.3 57.1 + - - -
305A GLU* 3.1 3.1 - - - -
306A ASN* 2.5 30.4 + - - +
307A ALA 3.1 7.8 + - - -
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Residues in contact with LYS 304 (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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233A LEU* 6.3 2.9 - - + -
243A ARG* 4.5 12.1 - - - +
263A ASP* 4.8 9.4 + - - +
274A GLY* 5.3 3.8 - - - +
277A ILE* 3.1 28.5 - - + +
278A ASP* 2.8 35.6 + - - +
293A PHE* 3.1 29.8 - - + -
303A GLY* 1.3 69.6 - - - -
305A GLU* 1.3 57.9 + - - +
307A ALA 3.5 0.2 + - - -
308A ARG* 2.9 25.9 + - + +
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Residues in contact with GLU 305 (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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233A LEU* 5.4 4.0 - - - +
234A LYS 5.6 0.5 - - - +
235A ASP* 5.3 12.3 - - + +
240A VAL* 4.2 25.4 - - + +
265A LEU* 4.9 11.5 - - - +
303A GLY 2.8 3.0 + - - -
304A LYS* 1.3 79.3 - - - +
306A ASN* 1.3 57.0 + - - +
308A ARG* 3.2 15.8 - - - +
309A LYS* 2.8 46.2 + - - +
312A LEU* 5.1 5.0 - - - +
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Residues in contact with ASN 306 (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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300A LEU 4.4 1.6 + - - -
301A GLY* 3.0 14.5 - - - -
302A GLN* 3.0 37.4 + - - +
303A GLY* 2.5 17.4 + - - +
305A GLU* 1.3 69.5 - - - +
307A ALA* 1.3 58.8 + - - +
308A ARG 3.1 1.1 - - - -
309A LYS* 2.9 30.1 + - + +
310A PHE* 2.8 24.1 + - - +
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Residues in contact with ALA 307 (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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277A ILE* 4.0 11.0 - - + -
293A PHE* 3.8 32.5 - - + -
300A LEU* 3.9 21.5 - - + -
301A GLY* 4.2 6.7 - - - +
303A GLY 3.1 2.2 + - - -
304A LYS 3.9 3.4 - - - +
306A ASN* 1.3 75.7 - - - +
308A ARG* 1.3 68.3 + - - +
310A PHE* 3.0 10.3 + - - +
311A LEU* 2.8 27.5 + - + +
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Residues in contact with ARG 308 (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* 5.3 3.4 - - - +
273A GLU* 4.5 4.5 - - + -
274A GLY* 4.9 11.0 - - - +
277A ILE* 3.6 12.7 - - + +
304A LYS* 2.9 19.9 + - + +
305A GLU* 3.2 24.5 - - - +
307A ALA* 1.3 74.7 - - - +
309A LYS* 1.3 53.5 + - - +
311A LEU* 2.8 10.6 + - - +
312A LEU* 2.6 44.1 + - + +
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Residues in contact with LYS 309 (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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305A GLU* 2.8 37.5 - - - +
306A ASN* 2.9 33.2 + - - +
308A ARG* 1.3 78.4 - - - +
310A PHE* 1.3 62.0 - - - +
312A LEU* 2.9 36.0 + - + +
313A GLU* 3.1 20.5 + - - +
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Residues in contact with PHE 310 (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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298A GLU* 4.7 5.6 - - - -
299A GLN 4.3 9.6 - - - -
300A LEU* 3.2 62.1 - - + +
306A ASN 2.8 9.4 + - - +
307A ALA* 3.0 7.6 + - - +
309A LYS* 1.3 77.6 - - - +
311A LEU* 1.3 65.8 + - + +
313A GLU* 3.3 6.6 + - + +
314A ASN* 2.4 65.9 + - - +
317A VAL* 4.1 15.5 - - + -
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Residues in contact with LEU 311 (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* 3.6 32.4 - - + +
276A LEU* 4.4 8.5 - - + -
277A ILE* 3.6 35.0 - - + +
286A ILE* 5.4 6.3 - - + -
300A LEU* 4.3 23.3 - - + -
307A ALA* 2.8 17.9 + - + +
308A ARG 3.3 6.1 - - - +
310A PHE* 1.3 75.0 - - + +
312A LEU* 1.3 64.1 - - - +
314A ASN* 3.0 19.8 - - - +
315A THR* 4.2 0.5 + - - -
317A VAL* 4.3 8.7 - - + -
318A ALA* 4.0 27.2 - - + +
321A ILE* 4.6 11.2 - - + -
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Residues in contact with LEU 312 (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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268A GLN* 6.1 0.7 - - - +
271A SER* 5.0 5.2 - - - +
273A GLU* 3.2 41.5 - - + +
305A GLU* 5.1 5.2 - - - +
308A ARG* 2.6 29.2 + - + +
309A LYS* 2.9 29.2 + - + +
311A LEU* 1.3 75.2 - - - +
313A GLU* 1.3 57.9 + - + +
314A ASN 3.4 1.9 + - - -
315A THR* 4.4 8.8 + - - -
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Residues in contact with GLU 313 (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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309A LYS* 3.3 24.1 - - - +
310A PHE* 3.6 9.4 + - - +
312A LEU* 1.3 74.7 - - + +
314A ASN* 1.3 68.9 + - - +
315A THR* 3.9 2.8 + - - -
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Residues in contact with ASN 314 (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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310A PHE* 2.4 72.1 + - - +
311A LEU 3.0 6.5 - - - +
312A LEU 3.3 1.0 - - - -
313A GLU* 1.3 88.2 - - - +
315A THR* 1.3 62.8 + - - +
316A ASP* 3.4 10.2 - - - +
317A VAL* 3.2 19.9 - - + +
318A ALA* 3.0 23.2 + - - +
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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