Contacts of the helix formed by residues 272 - 280 (chain A) in PDB entry 1EQR
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 PHE 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A THR* 1.3 72.2 - - - +
273A ALA* 1.3 66.3 + - + +
275A ALA* 3.3 2.4 + - - +
276A GLU* 3.0 54.5 + - + +
282A ASP* 3.7 26.0 - - + -
430A VAL* 3.9 9.6 - - - +
431A ILE 2.7 9.0 + - - +
432A ASP 3.4 18.1 + - - +
433A PHE* 3.2 41.1 - + + -
434A PRO* 3.8 26.5 - - + -
447A MET* 4.7 8.3 - - + -
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 3.1 8.8 + - - +
272A PHE* 1.3 85.2 - - + +
274A GLU* 1.3 63.0 + - + +
276A GLU* 3.1 5.8 + - - +
277A ARG* 2.8 26.7 + - - +
432A ASP 4.9 0.8 + - - -
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Residues in contact with GLU 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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269A VAL 4.4 3.5 - - - +
270A MET* 3.6 22.3 - - + -
271A THR* 3.1 37.9 + - - +
273A ALA* 1.3 76.1 - - + +
275A ALA* 1.3 65.4 + - - +
277A ARG* 4.3 20.0 + - - +
278A ARG* 2.9 57.0 + - - +
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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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270A MET* 3.7 20.8 - - - -
271A THR 2.9 16.4 + - - +
272A PHE* 3.4 9.6 - - - +
274A GLU* 1.3 77.0 - - - +
276A GLU* 1.3 54.9 + - - +
279A TYR* 2.9 30.0 + - - +
281A SER 3.3 23.3 - - - +
282A ASP* 4.6 2.0 - - - -
284A PRO* 4.3 12.1 - - + -
430A VAL* 4.4 11.2 - - + -
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Residues in contact with GLU 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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272A PHE* 3.0 54.5 + - + +
273A ALA* 3.7 4.3 - - - +
275A ALA* 1.3 72.9 - - + +
277A ARG* 1.3 70.5 + - - +
278A ARG 3.1 1.3 - - - -
280A GLY* 3.2 24.4 + - - +
281A SER* 3.3 28.0 + - - +
282A ASP* 4.5 3.6 + - - +
317A ARG* 3.3 16.0 + - - +
403A ALA* 4.1 9.8 - - + +
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Residues in contact with ARG 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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273A ALA 2.8 22.4 + - - +
274A GLU* 3.6 20.7 + - - +
276A GLU* 1.3 71.5 - - - +
278A ARG* 1.3 96.6 + - - +
291A GLU* 4.9 3.0 + - - -
292A LEU* 3.8 13.2 - - - +
293A THR* 5.3 0.7 - - - -
294A ASP* 4.3 17.2 - - + +
317A ARG* 2.8 26.6 + - - +
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Residues in contact with ARG 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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270A MET* 4.8 14.6 - - - +
274A GLU* 2.9 49.1 + - - +
277A ARG* 1.3 112.3 - - - +
279A TYR* 1.3 90.1 + - + +
291A GLU* 3.1 39.8 + - + +
292A LEU* 3.0 31.5 + - - +
410A ARG* 4.5 0.2 + - - -
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Residues in contact with TYR 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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270A MET* 3.6 32.6 - - + +
275A ALA* 2.9 24.3 + - - +
278A ARG* 1.3 105.8 + - + +
280A GLY* 1.3 64.8 + - - +
281A SER* 3.4 5.8 + - - +
284A PRO* 3.4 31.4 - - + -
286A LEU* 3.1 27.0 - - + +
288A ASN 4.8 1.3 - - - -
289A PRO 5.7 0.4 - - - -
290A MET 3.7 15.7 - - - -
291A GLU* 4.0 14.8 + - + -
292A LEU* 4.0 7.0 - - - -
407A GLY* 3.3 20.1 - - - +
410A ARG* 3.5 37.5 + - - +
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Residues in contact with GLY 280 (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 3.6 0.6 + - - -
276A GLU* 3.2 24.3 + - - +
279A TYR* 1.3 78.4 - - - +
281A SER* 1.3 59.6 + - - +
292A LEU* 3.9 6.7 - - - +
403A ALA* 3.1 47.5 - - - +
404A ASP* 4.1 3.5 + - - +
407A GLY* 4.7 1.4 - - - -
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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