Contacts of the helix formed by residues 297 - 306 (chain C) in PDB entry 4KEU
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 ASN 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292C LYS* 5.2 1.1 - - - -
295C GLY 3.6 5.1 + - - +
296C VAL* 1.4 76.1 - - - +
298C GLU* 1.3 63.2 + - - +
299C GLU* 3.2 22.3 + - - +
300C VAL* 3.0 42.2 + - - +
301C ILE* 3.3 13.0 + - - +
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Residues in contact with GLU 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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292C LYS* 3.3 36.1 + - - +
297C ASN* 1.3 76.6 - - - +
299C GLU* 1.3 65.1 + - - +
301C ILE* 3.2 32.5 - - + +
302C ALA* 3.1 27.4 + - - +
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Residues in contact with GLU 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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297C ASN* 3.1 20.6 - - - +
298C GLU* 1.3 87.4 + - - +
300C VAL* 1.3 59.7 + - + +
302C ALA* 3.6 6.0 + - - +
303C THR* 2.8 30.6 + - - -
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Residues in contact with VAL 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ILE* 4.1 11.2 - - + -
248C SER* 3.3 29.8 - - - +
296C VAL* 3.6 23.8 - - + -
297C ASN* 3.0 31.5 + - - +
299C GLU* 1.3 77.0 - - + +
301C ILE* 1.3 65.3 + - - +
303C THR* 3.1 7.4 + - - -
304C ILE* 3.1 31.3 + - + +
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Residues in contact with ILE 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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18C PHE* 4.0 26.0 - - + -
288C ILE* 5.0 11.7 - - + -
291C LEU* 5.8 4.3 - - + -
292C LYS* 4.2 21.5 - - + +
296C VAL* 4.2 12.8 - - + -
297C ASN 3.3 16.6 - - - +
298C GLU* 3.2 36.3 - - + +
300C VAL* 1.3 74.9 - - - +
302C ALA* 1.3 67.4 + - + +
304C ILE* 3.3 5.0 + - - -
305C PHE* 3.1 46.3 + - + +
306C LYS* 6.2 1.3 - - - -
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Residues in contact with ALA 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 GLU* 3.1 15.2 + - + +
299C GLU* 3.8 7.4 - - - +
301C ILE* 1.3 86.6 - - + +
303C THR* 1.3 60.3 + - - +
306C LYS* 3.0 47.4 + - + +
307C GLU* 3.0 9.4 + - - +
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Residues in contact with THR 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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248C SER* 4.1 18.4 - - - +
249C ASP* 4.1 11.9 - - + +
299C GLU 2.8 19.9 + - - -
300C VAL* 3.1 12.4 + - - -
302C ALA* 1.3 78.2 - - - +
304C ILE* 1.3 58.3 + - - +
307C GLU* 3.6 17.5 - - + +
308C ASN* 2.8 49.3 + - - +
311C LYS* 4.9 1.6 - - - +
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Residues in contact with ILE 304 (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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243C ILE* 3.9 29.6 - - + -
248C SER* 3.8 18.8 - - - +
251C ILE* 3.6 27.4 - - + +
252C MET* 4.2 4.2 - - - +
253C ILE* 3.9 35.8 + - + +
291C LEU* 5.3 2.7 - - + -
300C VAL* 3.1 22.9 + - + +
301C ILE* 3.8 6.7 - - - +
302C ALA 3.3 0.2 - - - -
303C THR* 1.3 78.5 - - - +
305C PHE* 1.3 73.6 + - + +
306C LYS 3.6 0.2 - - - -
308C ASN* 3.6 9.6 - - - +
309C PRO* 3.3 18.4 - - - +
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Residues in contact with PHE 305 (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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17C GLY 3.4 1.9 - - - +
18C PHE* 3.2 43.6 - + + -
19C THR 2.8 41.8 + - - +
20C LEU* 4.7 0.4 - - + -
253C ILE* 3.7 46.7 - - + -
283C ILE* 3.5 30.5 - - + -
288C ILE* 4.1 21.3 - - + -
291C LEU* 5.9 2.5 - - + -
301C ILE* 3.1 33.6 + - + +
304C ILE* 1.3 89.2 - - + +
306C LYS* 1.3 60.9 + - + +
309C PRO* 3.6 10.5 - - - +
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Residues in contact with LYS 306 (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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16C ILE* 4.2 4.6 - - + +
17C GLY* 3.8 12.1 - - - +
18C PHE* 3.8 39.9 - - + +
301C ILE* 6.2 1.1 - - - -
302C ALA* 3.0 28.7 + - + +
304C ILE 3.6 0.2 - - - -
305C PHE* 1.3 83.9 - - - +
307C GLU* 1.3 68.4 + - - +
308C ASN 3.5 0.7 - - - -
309C PRO* 3.4 3.3 - - - +
310C LYS* 3.1 24.3 + - - +
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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