Contacts of the helix formed by residues 290 - 302 (chain B) in PDB entry 1UES
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 LYS 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288B ALA 3.6 17.0 + - - +
289B PRO* 1.3 73.5 - - - +
291B GLY* 1.3 70.1 + - - +
292B LYS 3.7 0.2 + - - -
293B LEU 3.7 2.9 + - - -
294B GLY* 3.1 12.9 + - - -
384B TRP* 4.1 7.3 - - - +
385B ASP* 3.7 19.8 + - - +
388B GLU* 2.7 58.5 + - - +
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Residues in contact with GLY 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LYS* 1.3 81.5 - - - +
292B LYS* 1.3 63.8 + - - -
295B GLU* 3.0 36.7 + - - +
388B GLU* 5.7 0.2 - - - -
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLY* 1.3 70.3 - - - -
293B LEU* 1.3 57.0 + - - +
295B GLU* 3.5 10.9 + - - +
296B ALA* 2.8 29.3 + - + +
332B GLY* 5.2 7.5 - - - -
391B TYR* 3.6 47.0 + - + +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B PRO* 4.4 1.1 - - + -
290B LYS 3.7 0.6 + - - -
291B GLY 3.2 0.8 - - - -
292B LYS* 1.3 76.7 - - - +
294B GLY* 1.3 60.9 + - - +
296B ALA 3.0 1.0 + - - -
297B ILE* 2.8 46.8 + - + +
326B LEU* 4.7 2.9 - - + -
334B LEU* 4.1 19.1 - - + -
353B LEU* 4.7 4.0 - - + -
384B TRP* 4.1 13.2 - - + -
387B VAL* 3.6 32.3 - - + +
388B GLU* 3.8 33.4 - - + +
391B TYR* 3.4 35.5 - - + -
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PRO* 3.6 33.3 - - - +
290B LYS* 3.1 11.9 + - - -
291B GLY 3.7 2.7 - - - -
293B LEU* 1.3 79.7 - - - +
295B GLU* 1.3 61.8 + - - +
297B ILE* 3.5 3.0 + - - +
298B ASP* 3.2 29.8 + - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLY* 3.0 26.6 + - - +
292B LYS* 3.8 9.1 - - - +
294B GLY* 1.3 76.1 - - - +
296B ALA* 1.3 64.2 + - - +
298B ASP* 3.3 4.9 + - - -
299B LYS* 2.7 57.9 + - - +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LYS* 2.8 18.6 + - + +
293B LEU 3.0 4.2 + - - +
295B GLU* 1.3 76.2 - - - +
297B ILE* 1.3 58.0 + - - +
299B LYS* 4.5 2.9 - - - -
300B GLN* 2.8 49.1 + - - +
334B LEU* 3.9 7.0 - - + -
391B TYR* 3.3 30.7 - - + +
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B PRO* 3.9 24.7 - - + -
293B LEU* 2.8 32.6 + - + +
294B GLY* 3.9 4.3 - - - +
296B ALA* 1.3 77.8 - - - +
298B ASP* 1.3 58.8 + - - +
301B PHE* 2.7 37.4 + - + +
303B SER 4.1 1.1 + - - +
304B PHE* 4.0 21.5 - - + +
307B PHE* 3.7 42.4 - - + -
326B LEU* 4.5 10.8 - - + -
334B LEU* 3.8 20.0 - - + -
384B TRP* 4.5 3.6 - - + -
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Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B GLY 3.2 18.4 + - - +
295B GLU* 3.8 5.6 - - - +
297B ILE* 1.3 78.0 - - - +
299B LYS* 1.3 66.0 + - + +
302B GLY* 2.6 43.2 + - - +
303B SER* 3.5 4.5 - - - -
304B PHE* 3.4 25.1 + - - +
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B GLU* 2.7 56.4 + - - +
296B ALA* 3.9 4.7 - - - +
298B ASP* 1.3 84.2 - - + +
300B GLN* 1.3 64.8 + - + +
302B GLY* 4.4 1.4 + - - -
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Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ALA* 2.8 39.9 + - - +
299B LYS* 1.3 80.8 - - + +
301B PHE* 1.3 73.4 + - + +
332B GLY 3.3 19.6 - - - +
333B LYS* 3.2 28.7 - - - +
334B LEU* 2.8 37.9 + - - +
391B TYR* 4.1 0.5 + - - -
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ILE* 2.7 27.3 + - - +
300B GLN* 1.3 83.6 - - + +
302B GLY* 1.3 54.8 + - - +
303B SER 3.3 4.1 + - - +
306B LYS* 3.3 28.7 - - + +
307B PHE* 3.9 40.4 - + + +
310B GLU* 4.2 19.9 - - + +
326B LEU* 4.7 1.3 - - + -
334B LEU* 4.0 43.1 - - + -
335B SER* 4.8 1.3 - - - -
336B ILE* 3.6 37.0 - - + -
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ASP* 2.6 34.3 + - - +
299B LYS 4.4 1.6 + - - -
300B GLN 3.7 0.8 - - - -
301B PHE* 1.3 71.1 - - - +
303B SER* 1.3 61.3 + - - +
306B LYS* 5.0 1.8 - - - -
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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