Contacts of the helix formed by residues 266 - 274 (chain C) in PDB entry 1IXR
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 GLY 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265C VAL* 1.3 81.2 - - - +
267C LEU* 1.3 56.4 + - - -
268C ALA* 2.4 23.0 + - - -
269C THR 3.0 13.9 + - - -
270C LEU* 3.5 9.2 + - - -
300C ARG 4.9 0.2 - - - -
301C GLY* 3.7 13.9 - - - -
302C ARG* 3.4 11.9 - - - +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C GLY* 1.3 68.7 - - - -
268C ALA* 1.3 68.4 + - - +
270C LEU* 4.8 2.7 - - - -
271C ALA* 2.8 27.7 + - - +
278C PRO* 2.9 38.6 - - + +
281C LEU* 3.5 13.7 - - + -
282C GLU* 3.2 36.8 - - + +
286C GLU* 3.6 7.0 - - - +
302C ARG* 2.8 41.5 - - - +
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL 5.4 1.1 - - - +
266C GLY* 2.4 13.9 + - - +
267C LEU* 1.3 80.3 - - - +
269C THR* 1.3 67.7 + - - +
271C ALA* 3.7 2.6 + - - +
272C THR* 3.7 12.3 + - - -
278C PRO* 5.4 2.5 - - - +
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Residues in contact with THR 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ARG* 5.1 5.8 - - - +
260C PHE* 3.7 26.0 - - + -
265C VAL* 3.8 14.6 + - - +
266C GLY 3.0 4.0 + - - -
268C ALA* 1.3 79.2 - - - +
270C LEU* 1.3 55.0 + - - +
272C THR* 2.5 38.3 + - + -
273C ALA* 3.1 13.0 + - + +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C ILE* 4.8 6.5 - - + +
255C VAL* 5.3 4.3 - - + -
256C LEU* 3.7 33.7 - - + +
260C PHE* 4.2 11.4 - - + -
265C VAL* 3.6 17.6 - - + +
266C GLY 3.5 9.4 + - - +
267C LEU* 4.4 0.9 - - - +
269C THR* 1.3 78.8 - - - +
271C ALA* 1.3 55.0 + - - +
272C THR 2.9 0.2 + - - -
273C ALA* 3.0 8.0 + - - -
274C LEU* 2.7 67.4 + - + +
281C LEU* 3.8 13.9 - - + -
286C GLU* 5.1 0.4 - - - +
295C LEU* 6.0 2.2 - - + -
302C ARG* 4.2 22.0 - - + -
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Residues in contact with ALA 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C LEU* 2.8 24.7 + - + +
268C ALA 4.0 1.8 - - - +
269C THR 2.9 0.2 + - - -
270C LEU* 1.3 74.1 - - - +
272C THR* 1.3 50.9 + - - +
274C LEU* 4.4 1.3 - - - -
275C SER 3.3 2.3 + - - -
276C GLU* 2.5 43.3 + - - +
277C ASP 4.5 0.2 - - - -
278C PRO* 3.3 40.6 - - + -
281C LEU* 3.8 18.6 - - + -
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Residues in contact with THR 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C ALA 3.7 8.5 + - - -
269C THR* 2.5 19.3 + - + -
271C ALA* 1.3 70.2 - - - +
273C ALA* 1.3 55.7 + - - +
274C LEU 2.9 4.9 - - - -
275C SER* 2.5 29.1 + - - +
276C GLU 4.4 3.1 + - - +
278C PRO* 6.1 0.9 - - - +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C VAL* 4.2 13.1 - - + +
259C ARG* 3.2 33.2 + - - +
260C PHE* 3.4 29.2 - - + -
269C THR* 3.1 10.9 + - + +
270C LEU 3.0 5.5 + - - +
272C THR* 1.3 77.1 - - - +
274C LEU* 1.3 57.4 + - - +
275C SER* 3.2 1.9 - - - -
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ARG* 2.4 59.7 + - - +
251C GLU* 4.6 1.1 - - + -
252C ILE* 3.5 51.1 - - + +
255C VAL* 4.1 15.5 - - + -
270C LEU* 2.7 38.7 + - + +
271C ALA 3.8 5.6 - - - +
273C ALA* 1.3 76.9 - - - +
275C SER* 1.3 67.0 + - - +
276C GLU* 4.2 3.6 - - + -
281C LEU* 3.7 16.8 - - + -
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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
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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