Contacts of the helix formed by residues 272 - 279 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B THR* 1.3 72.0 - - - +
273B ALA* 1.3 68.0 + - + +
275B ALA* 3.4 2.2 + - - +
276B GLU* 3.0 69.4 + - + +
282B ASP* 4.1 13.2 - - + -
430B VAL* 3.8 11.4 - - + +
431B ILE 2.6 14.4 + - - +
432B ASP 3.4 19.0 + - - +
433B PHE* 3.7 31.4 - + + -
434B PRO* 3.4 31.0 - - + -
447B MET* 5.3 2.7 - - + -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 2.8 10.5 + - - +
272B PHE* 1.3 88.5 - - + +
274B GLU* 1.3 61.3 + - + +
276B GLU* 3.6 3.8 + - - +
277B ARG* 3.3 26.4 + - - +
432B ASP 5.0 1.0 + - - -
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL 4.9 1.6 - - - +
270B MET* 3.8 12.9 - - + +
271B THR* 2.7 47.3 + - - +
273B ALA* 1.3 71.2 - - + +
275B ALA* 1.3 58.4 + - - +
277B ARG* 3.7 16.8 - - - +
278B ARG* 2.8 82.3 + - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B MET* 4.0 16.5 - - + +
271B THR 2.8 13.2 + - - +
272B PHE* 3.7 6.1 - - - +
274B GLU* 1.3 78.1 - - - +
276B GLU* 1.3 56.8 + - - +
279B TYR* 2.7 31.2 + - - +
280B GLY 3.0 4.5 + - - -
281B SER 3.3 19.4 - - - +
282B ASP* 4.5 1.1 - - - -
284B PRO* 3.9 14.6 - - + -
430B VAL* 4.3 16.2 - - + -
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.0 56.2 + - + +
273B ALA* 4.1 4.5 - - - +
275B ALA* 1.3 77.2 - - - +
277B ARG* 1.3 58.3 + - - +
280B GLY* 2.8 32.3 + - - +
281B SER* 3.9 7.6 - - - +
282B ASP* 3.5 17.8 + - - +
317B ARG* 3.1 15.0 + - - +
403B ALA* 4.5 16.2 - - + +
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA 3.3 16.0 + - - +
274B GLU* 3.6 18.4 - - - +
275B ALA 3.2 0.2 - - - -
276B GLU* 1.3 81.7 - - - +
278B ARG* 1.3 109.5 + - - +
292B LEU* 3.5 15.0 + - - +
294B ASP* 3.2 31.1 - - + +
317B ARG* 3.0 25.7 + - - +
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B MET* 4.2 8.7 - - - +
274B GLU* 2.8 64.4 + - - +
277B ARG* 1.3 112.7 - - - +
279B TYR* 1.3 87.6 + - + +
291B GLU* 3.6 29.4 - - - +
292B LEU* 2.8 36.9 + - - +
410B ARG* 4.8 0.2 - - - -
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B MET* 3.3 29.3 - - - +
275B ALA 2.7 16.0 + - - +
278B ARG* 1.3 94.5 - - + +
280B GLY* 1.3 61.9 + - - +
281B SER* 3.2 7.3 + - - +
284B PRO* 3.5 35.4 - - + -
286B LEU* 3.5 24.3 - - + +
288B ASN 5.2 0.4 - - - -
289B PRO 6.1 0.2 - - - -
290B MET 3.9 9.4 - - - -
291B GLU* 4.4 13.7 + - + -
292B LEU* 4.1 6.1 - - - -
407B GLY* 3.5 18.0 - - - +
410B ARG* 3.4 47.8 + - - +
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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
------------------------------------------------------------
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