Contacts of the helix formed by residues 271 - 278 (chain A) in PDB entry 2MWI
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 GLU 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PRO* 4.3 23.4 - - - +
207A LEU* 4.0 15.1 - - + +
211A THR* 4.5 2.3 + - - -
212A THR* 2.6 42.2 + - - +
214A VAL* 4.4 1.8 - - + -
269A LEU 3.2 4.1 + - - -
270A ILE* 1.3 70.9 - - - +
272A GLU* 1.3 58.6 + - - +
274A ILE* 2.8 37.3 + - - +
275A ARG* 3.6 3.3 + - - +
291A LEU 4.0 4.3 - - - +
294A LEU* 3.4 21.1 - - + +
296A SER* 2.7 33.9 + - - +
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Residues in contact with GLU 272 (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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207A LEU* 2.6 36.7 - - + +
208A ASN* 2.8 31.3 - - - +
209A GLU* 3.2 15.4 + - - +
211A THR* 3.4 9.8 - - + +
270A ILE* 3.0 9.5 + - + +
271A GLU* 1.3 78.8 - - - +
273A ASP* 1.3 63.2 + - - +
275A ARG* 3.0 57.5 + - - +
276A ASP* 4.1 1.0 + - - +
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Residues in contact with ASP 273 (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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236A HIS* 4.0 10.2 + - - -
238A HIS 5.2 2.0 - - - +
239A LEU* 3.3 40.2 - - + +
240A PHE* 4.3 18.1 + - - +
270A ILE* 2.8 24.9 + - + +
272A GLU* 1.3 79.1 + - - +
274A ILE* 1.3 63.7 + - + +
276A ASP* 3.4 14.2 + - - +
277A LEU* 3.3 16.5 + - - +
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Residues in contact with ILE 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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214A VAL* 3.6 23.3 - - + -
223A LEU* 4.2 13.5 - - + -
232A ILE* 5.7 0.2 - - + -
239A LEU* 5.5 0.7 - - + -
269A LEU* 4.6 12.1 - - + -
270A ILE 3.6 4.0 - - - +
271A GLU* 2.8 31.0 + - - +
273A ASP* 1.3 75.0 - - + +
275A ARG* 1.3 54.2 + - - +
276A ASP 2.9 1.9 + - - -
277A LEU* 3.0 24.2 + - + +
278A ALA* 2.7 32.7 + - - +
291A LEU* 3.5 11.7 - - + -
294A LEU* 3.2 39.0 - - + -
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Residues in contact with ARG 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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198A GLU 5.6 0.4 - - - +
204A PRO* 2.9 53.6 + - + -
205A ALA* 3.8 24.3 + - - +
207A LEU* 4.8 0.9 - - + -
271A GLU 3.6 4.3 + - - +
272A GLU* 3.0 45.2 + - - +
274A ILE* 1.3 77.9 - - - +
276A ASP* 1.3 71.0 + - - +
278A ALA* 3.6 10.9 - - - +
279A ALA* 3.9 6.9 + - - +
291A LEU* 3.5 18.4 - - + +
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Residues in contact with ASP 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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236A HIS* 3.4 21.5 + - + -
272A GLU 4.7 0.9 - - - +
273A ASP* 3.4 18.6 + - - +
274A ILE 3.0 0.6 - - - -
275A ARG* 1.3 88.7 - - + +
277A LEU* 1.3 65.3 + - - +
278A ALA 3.1 1.1 - - - -
279A ALA* 3.0 22.8 + - - +
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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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223A LEU* 3.4 20.4 - - + -
231A ARG 5.1 1.1 - - - +
232A ILE* 3.6 28.7 - - + -
236A HIS* 3.3 29.6 + - + +
239A LEU* 4.6 4.3 - - + -
273A ASP 3.3 4.1 + - - +
274A ILE* 3.0 41.9 + - + +
276A ASP* 1.3 73.8 - - - +
278A ALA* 1.3 58.7 + - - +
279A ALA 2.9 5.8 - - - -
280A SER* 2.9 30.6 + - - +
283A TYR* 3.2 35.6 - - + -
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Residues in contact with ALA 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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223A LEU* 4.4 4.5 - - + -
274A ILE 2.7 16.6 + - - +
275A ARG* 3.6 9.6 - - - +
276A ASP 3.1 0.2 - - - -
277A LEU* 1.3 80.0 - - - +
279A ALA* 1.3 55.9 + - - +
280A SER 3.1 1.3 - - - -
283A TYR* 3.1 38.8 - - - +
284A ARG* 3.6 1.7 - - - -
285A GLY 4.5 0.3 + - - -
289A LEU* 3.8 6.2 - - + +
291A LEU* 3.6 33.2 - - + -
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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