Contacts of the helix formed by residues 272 - 278 (chain A) in PDB entry 4RQE
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A THR* 4.3 5.8 - - - -
269A ILE* 4.6 0.2 - - - -
271A THR* 1.3 75.1 - - - +
273A GLU* 1.3 65.9 + - - +
274A GLN 3.2 0.2 - - - -
275A PRO* 3.1 13.9 - - - +
276A ILE* 3.1 38.1 + - - +
296A GLY 3.3 17.2 + - - -
298A SER* 2.3 36.8 + - - -
300A CYS* 4.2 0.4 - - - -
323A LYS* 3.6 7.6 + - - -
325A GLU* 3.8 13.8 - - - +
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Residues in contact with GLU 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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271A THR* 3.1 10.4 + - + +
272A SER* 1.3 77.9 - - - +
274A GLN* 1.3 66.6 + - + +
277A ALA* 2.9 32.7 + - + +
325A GLU* 4.2 5.6 - - - +
327A PHE* 3.5 29.2 - - + -
398A CYS* 4.3 4.3 - - - -
402A GLN* 3.5 26.7 + - - +
427A ASN* 2.6 32.7 + - - +
601A SER 3.2 25.2 + - - +
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Residues in contact with GLN 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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229A MET* 3.6 16.9 - - + +
234A MET* 3.8 19.5 - - - +
237A VAL* 3.7 28.5 + - + +
238A ALA* 4.3 1.2 - - - +
242A GLN* 3.5 25.9 - - - +
246A GLU* 4.8 0.8 + - - -
247A LEU* 4.3 8.3 - - - +
269A ILE* 3.8 11.4 - - - +
270A ALA* 3.5 24.8 + - - +
271A THR* 3.7 8.3 + - - +
273A GLU* 1.3 85.1 - - + +
275A PRO* 1.4 71.5 - - + +
277A ALA* 3.8 4.6 - - - +
278A ALA* 3.0 24.9 + - - +
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Residues in contact with PRO 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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225A THR* 3.7 25.1 - - - +
226A PRO* 3.5 23.3 - - + +
229A MET* 3.5 20.9 - - + -
269A ILE* 3.8 7.6 - - + -
271A THR 3.3 13.2 - - - +
272A SER 3.1 13.9 - - - +
274A GLN* 1.4 89.0 - - + +
276A ILE* 1.3 56.2 + - - +
278A ALA* 3.2 4.3 + - + +
279A LEU* 2.9 28.2 + - - +
188C VAL* 4.9 2.0 - - + +
195C PHE* 3.7 18.4 - - + -
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Residues in contact with ILE 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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223A ILE* 4.4 7.2 - - + -
225A THR* 3.7 15.9 - - + -
272A SER* 3.1 27.0 + - - +
273A GLU 4.1 0.7 - - - +
275A PRO* 1.3 75.2 - - - +
277A ALA* 1.3 53.7 + - - +
279A LEU* 3.2 20.0 - - + +
294A TYR* 4.0 25.6 - - + -
296A GLY* 3.6 33.7 - - - +
325A GLU* 4.7 2.7 - - + -
327A PHE* 3.5 39.7 - - + -
329A TYR* 2.5 24.5 + - - -
195C PHE* 4.9 2.2 - - + -
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Residues in contact with ALA 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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237A VAL* 4.6 3.8 - - + -
273A GLU* 2.9 21.0 + - + +
274A GLN* 3.8 6.7 - - - +
276A ILE* 1.3 77.6 - - - +
278A ALA* 1.3 56.8 + - - +
279A LEU 3.1 2.6 + - - -
280A HIS 3.7 5.4 + - - -
281A ARG 4.3 2.8 + - - -
327A PHE* 3.5 17.9 - - + -
329A TYR* 3.1 19.2 + - - -
402A GLN* 4.2 13.2 - - - +
406A LEU* 3.4 25.8 - - + +
408A ILE* 5.4 0.9 - - - +
425A MET* 4.5 4.7 - - + +
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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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229A MET* 4.2 15.5 - - + -
233A VAL* 5.0 10.8 - - + -
237A VAL* 5.2 2.7 - - + -
274A GLN 3.0 18.4 + - - +
275A PRO 3.2 4.7 + - - +
277A ALA* 1.3 74.6 - - - +
279A LEU* 1.3 62.5 + - - +
280A HIS 3.3 0.8 + - - -
281A ARG* 3.7 21.1 + - + +
406A LEU* 4.2 15.9 - - + -
184C LYS* 5.7 1.2 - - - +
187C VAL* 5.5 4.2 - - - +
188C VAL* 4.1 19.1 - - + +
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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