Contacts of the helix formed by residues 294 - 303 (chain B) in PDB entry 5L26
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 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B ASN* 3.5 18.2 - - + +
281B ILE* 4.6 2.9 - - - -
292B ASP 3.7 10.7 + - - +
293B LEU* 1.3 80.8 - - - +
295B LEU* 1.3 64.5 + - - +
296B GLN* 3.4 17.0 + - - +
297B ALA* 3.3 22.7 + - - +
298B ILE* 3.1 29.6 + - - +
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Residues in contact with LEU 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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274B ILE* 4.5 23.8 - - + -
277B ILE* 4.5 24.7 - - + -
278B ASN* 2.6 21.4 + - - +
281B ILE* 4.2 19.5 - - + +
294B THR* 1.3 69.6 - - - +
296B GLN* 1.3 64.0 + - - +
298B ILE* 3.3 12.2 + - + -
299B LEU* 3.0 53.6 + - + +
326B GLN* 6.3 0.7 - - + -
329B VAL* 5.6 3.1 - - + -
330B ILE* 5.5 7.6 - - + -
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Residues in contact with GLN 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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274B ILE* 3.4 19.6 - - - +
278B ASN* 3.0 34.6 + - - +
294B THR* 3.4 12.8 - - - +
295B LEU* 1.3 75.3 - - - +
297B ALA* 1.3 55.4 + - - +
299B LEU* 3.9 5.0 - - - +
300B GLY 2.9 13.3 + - - -
322B SER* 2.7 34.0 + - - +
326B GLN* 3.2 28.8 - - - +
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Residues in contact with ALA 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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293B LEU* 4.1 14.8 - - + -
294B THR* 3.3 20.1 + - - +
296B GLN* 1.3 76.1 - - - +
298B ILE* 1.3 56.9 + - - +
300B GLY* 3.7 0.4 - - - -
301B TRP* 2.7 38.2 + - - +
322B SER* 4.7 2.0 - - - -
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Residues in contact with ILE 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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281B ILE* 4.0 25.1 - - + -
293B LEU* 3.8 31.2 - - + -
294B THR 3.1 16.4 + - - +
295B LEU* 3.3 15.5 + - + +
297B ALA* 1.3 76.3 - - - +
299B LEU* 1.3 58.8 + - + +
301B TRP* 3.3 5.6 + - - +
302B LEU* 2.8 39.1 + - + +
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Residues in contact with LEU 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 LEU* 3.0 41.0 + - + +
296B GLN 3.9 3.1 - - - +
298B ILE* 1.3 78.0 - - + +
300B GLY* 1.3 54.6 + - - +
302B LEU* 4.3 7.0 - - + -
303B PHE* 2.8 63.7 + - + +
321B GLY 3.9 2.2 - - - -
322B SER* 4.4 4.9 - - - -
325B GLY* 3.6 13.9 - - - +
326B GLN* 3.6 35.7 - - + +
329B VAL* 3.9 23.8 - - + -
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Residues in contact with GLY 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 GLN 2.9 10.3 + - - -
297B ALA* 3.7 2.5 - - - -
299B LEU* 1.3 77.3 - - - +
301B TRP* 1.3 49.5 - - - +
303B PHE 3.8 0.5 - - - -
304B SER* 2.2 39.9 + - - -
318B GLY* 3.3 12.6 - - - +
321B GLY* 4.0 0.5 - - - -
322B SER* 3.2 33.3 + - - -
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Residues in contact with TRP 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 ALA 2.7 21.3 + - - +
298B ILE* 3.8 5.6 - - - +
300B GLY* 1.3 72.9 - - - +
302B LEU* 1.3 61.9 + - - +
304B SER* 3.3 19.6 + - - -
305B PRO* 4.3 2.6 - - - +
314B TRP* 5.7 11.9 - + - -
318B GLY* 6.5 0.4 - - - -
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Residues in contact with LEU 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 ILE* 2.8 25.2 + - + +
299B LEU* 3.7 9.0 - - + +
301B TRP* 1.3 77.3 - - - +
303B PHE* 1.3 76.5 + - + +
304B SER 3.2 4.5 - - - -
305B PRO* 3.3 16.8 - - - +
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Residues in contact with PHE 303 (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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299B LEU* 2.8 53.4 + - + +
300B GLY 3.8 1.6 - - - -
302B LEU* 1.3 87.6 - - + +
304B SER* 1.3 63.9 + - - +
305B PRO* 3.4 2.5 - - - -
306B LEU* 3.3 30.9 + - + +
307B ALA* 3.2 21.3 + - - +
321B GLY* 3.4 19.5 - - - +
324B ILE* 4.4 12.9 - - + +
325B GLY* 3.7 20.0 - - - +
328B VAL* 5.1 15.0 - - + -
329B VAL* 5.4 4.9 - - + -
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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