Contacts of the helix formed by residues 270 - 281 (chain A) in PDB entry 2XHC
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 LYS 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A PRO 3.3 4.9 + - - +
269A VAL* 1.3 76.1 - - - +
271A ASP* 1.3 67.3 + - - +
272A ARG* 4.4 6.1 - - + +
273A GLU* 2.8 48.5 + - + +
274A MET* 3.0 10.0 + - - +
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Residues in contact with ASP 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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269A VAL 3.3 5.2 + - - +
270A LYS* 1.3 69.6 - - - +
272A ARG* 1.3 66.0 + - + +
274A MET* 3.2 7.2 + - - +
275A ARG* 3.1 24.9 + - - +
278A LEU* 5.6 0.5 - - - +
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Residues in contact with ARG 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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270A LYS* 3.2 5.7 - - + +
271A ASP* 1.3 80.7 - - + +
273A GLU* 1.3 63.3 + - + +
275A ARG* 3.1 32.2 - - - +
276A PRO* 3.6 2.4 - - - +
315A PHE* 3.9 12.3 - - + -
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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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269A VAL* 4.0 7.0 - - + +
270A LYS* 2.8 46.4 + - + +
272A ARG* 1.3 81.9 - - + +
274A MET* 1.3 56.4 + - - +
276A PRO* 3.3 15.2 - - - +
277A ILE* 4.0 2.6 - - - +
315A PHE* 4.7 6.9 - - + -
335A ILE* 3.9 15.0 - - + +
336A PHE* 2.9 66.3 + - + -
337A GLY 4.7 0.3 + - - -
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Residues in contact with MET 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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5A TRP* 3.6 38.1 - - + -
237A PHE* 3.7 29.8 - - - -
269A VAL* 3.1 31.4 - - + +
270A LYS 3.0 10.3 + - - +
271A ASP* 3.8 7.4 - - - +
273A GLU* 1.3 77.4 - - - +
275A ARG* 1.3 60.0 + - - +
276A PRO* 3.3 1.3 - - - -
277A ILE* 2.8 36.4 + - + +
278A LEU* 3.0 53.8 + - + +
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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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271A ASP 3.1 11.9 + - - +
272A ARG* 3.1 22.4 - - - +
274A MET* 1.3 76.5 - - - +
276A PRO* 1.3 85.9 - - + +
278A LEU* 3.3 14.0 + - + +
279A ARG* 2.8 68.5 + - - +
284A GLU* 5.0 10.5 + - - +
311A PRO 4.3 4.0 - - - +
313A GLU* 4.2 16.7 + - - +
314A ASP* 2.9 34.6 + - - +
315A PHE* 5.3 2.0 - - - -
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Residues in contact with PRO 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 ARG 3.6 2.2 - - - +
273A GLU 3.3 19.1 - - - +
274A MET 3.3 0.9 - - - -
275A ARG* 1.3 100.1 - - + +
277A ILE* 1.3 58.8 + - + +
279A ARG* 3.8 0.7 - - - +
280A LEU* 2.8 35.8 + - - +
311A PRO* 3.3 27.5 - - + +
312A PHE* 3.8 33.2 - - + -
315A PHE* 3.8 23.8 - - + -
335A ILE* 5.0 2.0 - - + -
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Residues in contact with ILE 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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39A VAL* 3.9 15.5 - - + +
41A PRO* 3.5 28.1 - - + +
232A PHE* 3.4 35.4 - - + -
237A PHE* 3.8 30.3 - - + -
273A GLU 4.0 12.3 - - - +
274A MET* 2.8 28.3 + - + +
276A PRO* 1.3 80.7 - - + +
278A LEU* 1.3 57.2 + - + +
280A LEU* 3.5 7.0 + - + +
281A ALA* 2.9 29.5 + - - +
312A PHE* 5.9 0.2 - - + -
335A ILE* 6.3 0.2 - - + -
336A PHE* 4.2 3.4 - - + -
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Residues in contact with LEU 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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5A TRP* 3.9 25.4 - - + +
37A ARG* 5.5 2.9 - - - +
39A VAL* 6.3 0.2 - - + -
271A ASP 5.6 0.7 - - - +
274A MET* 3.3 43.3 - - + +
275A ARG* 3.6 13.0 - - - +
277A ILE* 1.3 77.4 - - + +
279A ARG* 1.3 56.4 + - - +
281A ALA* 3.0 14.6 + - - +
283A LEU* 2.9 40.9 + - + -
284A GLU* 3.4 37.9 - - + +
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Residues in contact with ARG 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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275A ARG* 2.8 49.6 + - - +
276A PRO 3.9 0.2 - - - +
278A LEU* 1.3 70.8 - - - +
280A LEU* 1.3 68.3 + - - +
282A GLY* 3.0 13.2 + - - -
284A GLU* 4.0 28.9 + - + +
286A TYR* 3.3 61.2 + - + +
287A GLU* 5.2 5.1 + - - +
310A GLY 2.7 31.5 + - - +
311A PRO* 3.5 30.3 + - + -
313A GLU* 3.0 26.7 + - - +
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Residues in contact with LEU 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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41A PRO* 4.4 17.0 - - + -
42A GLU 3.8 24.7 - - - +
43A GLU* 4.8 11.2 - - + -
44A VAL 5.8 0.2 - - - +
231A LEU* 3.2 34.5 - - + -
276A PRO 2.8 20.6 + - - +
277A ILE* 3.6 6.3 - - + +
279A ARG* 1.3 77.8 - - - +
281A ALA* 1.3 59.8 + - - +
282A GLY* 3.3 1.0 + - - -
311A PRO* 4.1 22.3 - - + +
312A PHE* 4.2 9.2 - - + -
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Residues in contact with ALA 281 (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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39A VAL* 3.9 21.8 - - + -
277A ILE 2.9 17.9 + - - +
278A LEU* 3.0 8.0 + - - +
280A LEU* 1.3 76.6 - - - +
282A GLY* 1.3 63.5 + - - +
283A LEU* 3.2 32.8 - - + +
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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