Contacts of the helix formed by residues 266 - 275 (chain A) in PDB entry 1TAQ
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 ARG 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PRO* 2.9 30.6 + - + +
265A ASP* 1.3 68.9 - - - +
267A GLU* 1.3 61.5 + - - +
269A LEU* 3.9 13.5 - - + +
270A ARG* 3.4 23.4 + - - +
282A LEU* 3.8 37.9 + - - +
283A HIS* 5.6 1.2 - - - +
285A PHE* 4.4 2.6 + - - +
286A GLY* 4.0 25.4 - - - +
289A GLU* 3.6 22.6 + - - -
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Residues in contact with GLU 267 (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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265A ASP* 2.9 26.7 + - - +
266A ARG* 1.3 75.4 - - - +
268A ARG* 1.3 85.5 + - + +
270A ARG* 3.1 28.9 + - - +
271A ALA* 3.2 14.4 + - - +
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Residues in contact with ARG 268 (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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101A GLU* 6.1 0.9 - - - -
105A LEU* 3.7 19.6 - - + +
265A ASP* 2.7 42.7 + - - +
267A GLU* 1.3 103.3 + - + +
269A LEU* 1.3 54.2 + - - +
270A ARG 3.1 1.1 - - - -
271A ALA* 3.6 11.7 - - + -
272A PHE* 2.7 34.7 + - - +
275A ARG* 4.5 6.1 + - - +
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Residues in contact with LEU 269 (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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102A LEU* 4.0 19.7 - - + -
105A LEU* 4.4 19.2 - - + +
106A LEU* 3.4 35.9 - - + -
264A PRO* 4.9 7.9 - - + -
265A ASP 2.7 19.8 + - - +
266A ARG* 4.2 15.9 - - - +
268A ARG* 1.3 72.3 - - - +
270A ARG* 1.3 54.5 + - - +
272A PHE* 3.4 6.0 - - + +
273A LEU* 2.8 47.2 + - + +
282A LEU* 3.8 26.2 - - + -
285A PHE* 4.2 10.8 - - + -
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Residues in contact with ARG 270 (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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266A ARG 3.4 14.0 + - - +
267A GLU* 3.1 32.3 + - - +
269A LEU* 1.3 78.9 - - - +
271A ALA* 1.3 76.4 + - - +
273A LEU* 3.8 0.6 - - - -
274A GLU* 2.9 60.5 + - - +
282A LEU* 3.4 29.6 - - + +
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Residues in contact with ALA 271 (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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267A GLU 3.2 14.2 + - - +
268A ARG* 3.9 13.5 - - + +
270A ARG* 1.3 89.7 - - - +
272A PHE* 1.3 62.3 + - - +
274A GLU* 3.5 4.9 + - - +
275A ARG* 3.1 37.6 + - - +
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Residues in contact with PHE 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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44A VAL* 4.4 5.6 - - + -
98A LEU* 3.3 34.3 - - + -
101A GLU* 3.0 39.0 - - + -
102A LEU* 3.6 31.6 - - + -
105A LEU* 3.9 12.1 - - + -
268A ARG 2.7 23.4 + - - +
269A LEU* 3.4 5.2 - - + +
271A ALA* 1.3 70.1 - - - +
273A LEU* 1.3 91.5 + - + +
275A ARG* 2.9 42.3 + - - +
276A LEU* 3.4 33.9 + - + +
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Residues in contact with LEU 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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102A LEU* 5.1 3.6 - - + -
269A LEU* 2.8 25.4 + - + +
270A ARG* 3.9 2.0 - - - +
272A PHE* 1.3 92.0 - - + +
274A GLU* 1.3 58.2 + - - +
276A LEU* 3.3 6.3 + - + +
277A GLU 3.1 3.1 + - - -
278A PHE* 2.7 59.5 + - + +
279A GLY* 3.3 13.5 - - - -
281A LEU* 5.1 2.2 - - + -
282A LEU* 3.8 37.2 - - + -
285A PHE* 3.8 26.7 - - + -
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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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37A ARG* 5.3 0.7 + - - -
270A ARG* 2.9 55.7 + - + +
271A ALA* 4.0 4.2 - - - +
273A LEU* 1.3 77.6 - - - +
275A ARG* 1.3 61.1 + - - +
277A GLU* 3.1 18.4 + - - +
279A GLY* 3.9 20.2 - - - +
282A LEU* 5.8 0.3 - - - +
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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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35A THR* 4.4 0.5 - - - +
37A ARG* 3.5 23.0 + - - +
39A GLU* 4.1 10.3 - - - +
98A LEU* 5.6 2.8 - - - +
101A GLU* 4.1 16.8 + - - -
105A LEU* 5.6 0.4 - - - +
268A ARG* 4.5 8.3 + - - +
271A ALA* 3.1 19.5 + - - +
272A PHE* 2.9 56.3 + - - +
274A GLU* 1.3 78.9 - - - +
276A LEU* 1.3 63.6 + - + +
277A GLU 3.2 0.7 - - - -
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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