Contacts of the helix formed by residues 272 - 283 (chain C) in PDB entry 3NO1
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 SER 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C TYR* 5.1 2.7 - - - -
270C GLU* 3.5 1.9 - - - +
271C PHE* 1.3 82.0 - - - +
273C ALA* 1.3 64.6 + - - +
274C SER* 3.4 11.0 + - - -
275C GLY* 3.2 23.8 + - - +
276C CYS* 3.2 9.7 + - - -
290C PHE* 3.5 20.0 - - - -
295C SER 5.5 0.7 - - - -
300C ALA* 6.3 0.7 - - - -
246F TRP* 3.9 19.8 - - - -
247F HIS* 3.9 16.0 + - - +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C SER* 1.3 73.0 - - - +
274C SER* 1.3 61.2 + - - +
276C CYS* 3.1 4.6 + - - +
277C ARG* 2.9 28.9 + - - +
290C PHE* 3.9 3.0 - - - -
300C ALA* 4.4 6.5 - - + +
303C ARG* 4.4 15.9 - - + -
304C THR* 3.4 35.8 - - - +
307C ILE* 5.3 4.8 - - + +
309D THR* 5.6 1.1 - - - +
310D SER* 4.2 14.1 - - - -
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Residues in contact with SER 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C SER* 3.4 5.7 + - - -
273C ALA* 1.3 78.7 - - - +
275C GLY* 1.3 56.3 + - - +
277C ARG* 3.1 28.5 + - - +
278C ASP* 3.0 26.3 + - - +
310D SER* 2.6 34.0 + - - -
247F HIS* 3.2 39.4 + - - +
248F ASN 4.4 0.2 - - - -
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Residues in contact with GLY 275 (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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250C LYS* 5.1 0.2 - - - +
270C GLU* 3.2 32.9 - - - +
271C PHE 5.6 0.2 - - - -
272C SER* 3.2 14.0 + - - -
273C ALA 3.2 0.4 - - - -
274C SER* 1.3 81.2 - - - +
276C CYS* 1.3 60.4 + - - +
278C ASP* 3.3 13.5 + - - +
279C LEU* 3.2 17.5 + - - +
247F HIS 5.0 0.4 + - - -
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Residues in contact with CYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLY* 4.2 2.9 - - - -
270C GLU* 4.0 11.7 - - - -
272C SER 3.2 7.3 + - - -
273C ALA 3.1 7.9 + - - +
275C GLY* 1.3 73.0 - - - +
277C ARG* 1.3 64.6 + - - +
279C LEU* 3.1 10.7 + - - +
280C MSE 3.0 34.5 + - + +
288C CYS* 3.7 15.9 - - - -
290C PHE* 3.3 40.4 - - - -
304C THR* 3.6 20.0 - - + -
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Residues in contact with ARG 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ALA 2.9 12.6 + - - +
274C SER* 3.2 26.4 + - - +
276C CYS* 1.3 76.7 - - - +
278C ASP* 1.3 79.1 + - - +
280C MSE 3.2 4.2 + - - +
281C GLU* 2.7 31.8 + - - -
307C ILE* 4.3 24.7 - - + +
311C TYR* 4.0 10.3 + - + +
281D GLU* 4.5 0.4 - - - -
310D SER* 3.1 27.2 + - - +
311D TYR* 3.4 53.4 - - + +
247F HIS 5.1 0.2 + - - -
248F ASN* 3.0 23.8 - - - +
251F ARG* 3.4 18.3 - - - +
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Residues in contact with ASP 278 (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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250C LYS* 3.8 25.3 + - + +
274C SER* 3.0 15.8 + - - +
275C GLY* 3.4 13.4 - - - +
277C ARG* 1.3 105.2 + - - +
279C LEU* 1.3 61.1 - - - +
281C GLU* 4.0 4.5 - - - +
282C THR* 2.8 32.3 + - - +
250F LYS* 5.5 10.0 - - - +
251F ARG* 2.9 24.1 + - - +
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Residues in contact with LEU 279 (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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249C ASP* 5.0 3.8 - - - +
250C LYS* 3.2 31.4 - - + +
253C MSE 3.1 32.3 - - + -
266C ALA* 3.9 4.9 - - + +
267C GLY* 3.7 35.9 - - - +
270C GLU* 3.8 26.9 - - + +
275C GLY 3.2 4.2 + - - +
276C CYS* 3.1 13.2 + - + +
278C ASP* 1.3 80.9 - - - +
280C MSE 1.3 61.7 + - - +
282C THR* 3.3 0.7 + - - -
283C GLY 3.2 3.1 + - - -
284C ALA* 3.1 27.3 + - + +
285C ILE* 4.0 12.6 - - + -
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Residues in contact with MSE 280 (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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251B ARG* 5.4 0.2 - - - -
254B ARG* 5.2 3.5 + - - -
276C CYS* 3.0 22.2 + - + +
277C ARG 3.7 4.7 - - - +
279C LEU* 1.3 74.0 - - - +
281C GLU* 1.3 65.7 + - - +
283C GLY* 3.0 15.7 + - - +
285C ILE* 4.0 13.2 - - + -
288C CYS* 4.0 15.5 - - + -
304C THR* 3.9 28.0 - - + +
307C ILE* 3.7 19.7 - - + -
308C ALA* 3.6 37.9 - - + +
311C TYR* 3.7 31.7 - - + -
313C VAL* 3.9 17.9 - - + +
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Residues in contact with GLU 281 (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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251B ARG* 3.1 34.9 + - - -
254B ARG* 4.3 11.8 + - - -
277C ARG* 2.7 23.0 + - - +
278C ASP* 4.0 6.1 - - - +
280C MSE 1.3 73.8 - - - +
282C THR* 1.3 62.2 + - - +
283C GLY 3.3 0.3 + - - -
311C TYR* 2.7 32.3 + - - +
281D GLU* 3.5 33.3 - - - +
251F ARG* 4.3 6.5 - - - +
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Residues in contact with THR 282 (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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254B ARG* 5.1 2.6 + - - -
250C LYS* 3.7 42.6 - - + +
251C ARG* 4.1 18.0 + - + +
254C ARG* 3.7 24.0 + - + +
258C TYR* 4.6 1.4 + - - -
278C ASP* 2.8 22.1 + - - +
279C LEU 3.6 5.4 - - - -
281C GLU* 1.3 78.0 - - - +
283C GLY* 1.3 59.4 + - - +
284C ALA* 4.2 0.9 - - - -
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Residues in contact with GLY 283 (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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254B ARG* 4.0 10.8 - - - -
254C ARG* 3.8 8.0 - - - +
257C ARG* 2.8 34.4 + - - -
258C TYR* 3.6 13.3 + - - -
279C LEU 3.2 0.4 + - - -
280C MSE 3.0 16.7 + - - -
281C GLU 3.1 0.4 - - - -
282C THR* 1.3 79.6 - - - +
284C ALA* 1.3 60.6 + - - +
285C ILE 3.4 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