Contacts of the helix formed by residues 273 - 284 (chain A) in PDB entry 2C11
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLN* 5.3 2.0 - - - -
261A ILE* 5.6 5.6 - - - -
264A VAL* 3.9 12.5 - - - +
271A TYR* 3.6 0.9 - - - +
272A ASP* 1.3 80.3 - - - +
274A LEU* 1.3 65.7 + - - +
275A ALA* 3.4 10.7 + - - +
276A GLN* 2.9 34.8 + - - +
277A LEU* 3.2 12.5 + - - +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.0 61.9 + - + +
188A LEU* 3.5 12.8 - - + +
190A GLN* 3.8 16.3 + - + +
191A ALA* 4.2 16.2 - - + +
245A LEU* 4.7 11.2 - - + -
247A LEU* 4.2 15.3 - - + -
261A ILE* 5.6 5.2 - - + +
264A VAL* 4.2 23.5 - - + +
273A SER* 1.3 73.4 - - - +
275A ALA* 1.3 62.9 + - - +
277A LEU* 3.2 11.2 + - + +
278A GLU* 2.9 24.4 + - - +
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLN* 3.8 27.0 + - + +
273A SER* 3.6 8.7 - - - +
274A LEU* 1.3 79.7 - - - +
276A GLN* 1.3 53.3 + - - +
277A LEU 3.1 0.2 + - - -
278A GLU* 3.3 2.5 + - - +
279A ALA* 2.8 37.5 + - - +
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A TYR 4.8 0.7 - - - +
271A TYR* 3.7 14.1 - - + +
272A ASP* 3.0 53.6 + - - +
273A SER* 2.9 21.8 + - - +
275A ALA* 1.3 76.2 - - - +
277A LEU* 1.3 61.0 + - - +
279A ALA* 3.7 7.3 - - - +
280A GLN* 3.2 35.7 + - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ALA* 5.4 2.0 - - + -
194A LEU* 3.4 27.1 - - + -
245A LEU* 4.5 5.2 - - + -
264A VAL* 4.2 16.2 - - + -
266A TYR* 3.4 37.7 - - + -
271A TYR* 3.8 39.9 - - + -
273A SER 3.2 9.4 + - - +
274A LEU* 3.2 16.7 + - + +
275A ALA 3.1 0.2 - - - -
276A GLN* 1.3 74.0 - - - +
278A GLU* 1.3 54.3 + - - +
279A ALA 3.0 1.1 - - - -
280A GLN* 3.0 4.2 + - - +
281A PHE* 2.7 34.9 + - - +
286A VAL* 4.1 9.6 - - + -
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLN 3.1 27.4 - - - +
191A ALA* 2.8 24.7 - - - +
192A SER 4.7 0.2 - - - +
193A GLY* 3.3 11.9 - - - +
194A LEU* 2.5 37.6 + - - +
274A LEU 2.9 10.0 + - - +
275A ALA* 3.7 3.4 - - - +
277A LEU* 1.3 75.0 - - - +
279A ALA* 1.3 50.3 + - - +
281A PHE* 3.2 10.0 + - - +
282A GLU* 2.6 85.0 + - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ALA 2.8 17.8 + - - +
276A GLN* 3.7 9.9 - - - +
278A GLU* 1.3 78.2 - - - +
280A GLN* 1.3 52.0 + - - +
282A GLU* 3.3 6.8 + - - +
283A ALA* 2.7 36.1 + - - +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A ARG* 6.0 1.8 - - - +
271A TYR* 4.3 16.9 + - + -
276A GLN* 3.2 29.3 + - - +
277A LEU 3.0 3.6 + - - +
279A ALA* 1.3 77.0 - - - +
281A PHE* 1.3 60.9 + - - +
283A ALA* 3.8 7.2 - - + -
284A GLY 2.9 7.6 + - - -
285A LEU* 2.8 70.0 + - + +
286A VAL* 3.6 15.0 - - + -
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Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY* 3.4 7.6 - - - -
194A LEU* 3.3 47.3 - - + -
197A HIS* 3.8 37.5 - + + -
277A LEU 2.7 13.4 + - - +
278A GLU* 3.3 28.7 - - - +
280A GLN* 1.3 78.1 - - - +
282A GLU* 1.3 65.5 + - + +
284A GLY* 3.2 13.5 + - - -
286A VAL* 3.6 27.6 + - + +
288A VAL* 4.3 7.0 - - + -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY* 4.8 2.6 + - - -
278A GLU* 2.6 65.6 + - - +
279A ALA* 3.8 5.4 - - - +
281A PHE* 1.3 79.8 - - + +
283A ALA* 1.3 62.5 + - - +
284A GLY* 3.5 0.5 + - - -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ALA 2.7 18.3 + - - +
280A GLN* 3.5 14.4 - - + +
282A GLU* 1.3 79.5 - - - +
284A GLY* 1.3 56.7 + - - +
285A LEU* 4.6 3.8 - - + +
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLN 2.9 3.0 + - - -
281A PHE 3.2 11.1 + - - -
282A GLU 4.5 0.4 - - - -
283A ALA* 1.3 79.8 - - - +
285A LEU* 1.3 63.9 + - - +
286A VAL 3.4 6.2 + - - -
287A ASN 5.3 0.3 + - - -
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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