Contacts of the helix formed by residues 294 - 303 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C ASN* 3.5 20.0 - - + +
281C ILE* 4.4 4.7 - - - -
292C ASP* 3.8 10.4 + - - +
293C LEU* 1.3 79.9 - - - +
295C LEU* 1.3 63.5 + - - +
296C GLN* 3.3 18.3 + - - +
297C ALA* 3.3 22.4 + - - +
298C ILE* 3.1 28.9 + - - +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ILE* 4.4 25.4 - - + -
277C ILE* 4.4 34.3 - - + -
278C ASN* 2.6 21.6 + - - +
281C ILE* 4.2 6.5 - - + +
294C THR* 1.3 69.1 - - - +
296C GLN* 1.3 66.7 + - - +
298C ILE* 4.4 13.0 - - + -
299C LEU* 3.1 51.3 + - + +
326C GLN* 6.2 1.1 - - + -
329C VAL* 5.7 1.6 - - + -
330C ILE* 5.2 9.0 - - + -
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Residues in contact with GLN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ILE* 3.3 28.0 - - - +
278C ASN* 3.0 23.7 + - - +
294C THR* 3.3 15.1 - - - +
295C LEU* 1.3 74.7 - - - +
297C ALA* 1.3 54.9 + - - +
299C LEU* 3.9 2.1 - - - +
300C GLY 2.9 13.2 + - - -
322C SER* 2.5 35.0 + - - +
326C GLN* 3.3 26.7 - - - +
338C GLU* 3.7 21.0 + - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ASP 5.5 1.8 - - - +
293C LEU* 4.2 16.6 - - + -
294C THR* 3.3 19.0 + - - +
296C GLN* 1.3 76.6 - - - +
298C ILE* 1.3 55.3 + - - +
300C GLY* 3.2 2.0 + - - -
301C TRP* 2.7 34.7 + - - +
322C SER* 4.3 3.1 - - - -
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Residues in contact with ILE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ILE* 4.0 23.8 - - + -
293C LEU* 3.9 28.9 - - + -
294C THR 3.1 18.0 + - - +
295C LEU* 3.8 13.2 - - + +
296C GLN 3.3 0.2 - - - -
297C ALA* 1.3 77.5 - - - +
299C LEU* 1.3 62.5 + - + +
301C TRP* 3.0 9.5 + - - +
302C LEU* 2.9 30.8 + - + +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C LEU* 3.1 44.2 + - + +
296C GLN* 3.9 3.1 - - - +
298C ILE* 1.3 80.0 - - + +
300C GLY* 1.3 57.8 + - - +
302C LEU* 4.4 8.5 - - + +
303C PHE* 2.9 54.6 + - + -
321C GLY 3.4 5.1 - - - +
322C SER* 4.5 3.8 - - - -
325C GLY* 3.8 19.7 - - - +
326C GLN* 3.9 13.9 - - + +
329C VAL* 3.7 37.9 - - + -
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Residues in contact with GLY 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C GLN 2.9 10.7 + - - -
297C ALA* 3.5 3.6 - - - -
299C LEU* 1.3 79.1 - - - +
301C TRP* 1.3 50.4 - - - +
304C SER* 2.2 38.3 + - - -
318C GLY* 3.5 12.5 - - - +
321C GLY* 4.2 0.5 - - - -
322C SER* 3.2 32.5 + - - -
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Residues in contact with TRP 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ALA 2.7 16.0 + - - +
298C ILE* 3.0 9.8 + - + +
300C GLY* 1.3 77.2 - - - +
302C LEU* 1.3 63.6 + - + +
304C SER* 3.7 16.4 + - - -
305C PRO* 4.2 3.3 - - - +
314C TRP* 5.6 12.6 - + - -
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C ILE* 2.9 18.5 + - + +
299C LEU* 3.9 11.9 - - + +
300C GLY 3.3 0.2 - - - -
301C TRP* 1.3 77.3 - - - +
303C PHE* 1.3 82.5 + - + +
304C SER 3.2 4.3 - - - -
305C PRO* 3.3 17.2 - - - +
306C LEU* 5.2 0.3 + - - +
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C LEU* 2.9 35.0 + - + +
302C LEU* 1.3 99.3 - - + +
304C SER* 1.3 58.5 + - - +
305C PRO* 3.4 1.6 - - - -
306C LEU* 3.5 29.6 + - + +
307C ALA* 3.0 29.8 + - - +
321C GLY* 3.4 22.9 - - - +
324C ILE* 4.6 10.9 - - + +
325C GLY* 3.6 27.4 - - - +
328C VAL* 4.6 25.4 - - + -
329C VAL* 5.5 4.0 - - + -
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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