Contacts of the helix formed by residues 279 - 287 (chain C) in PDB entry 5X1V
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 279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C ARG 3.4 20.9 - - - +
247C LYS* 4.0 17.3 - - - +
275C GLU* 2.9 38.6 + - + +
276C GLY 3.7 3.6 - - - -
278C ARG* 1.3 108.8 - - + +
280C PHE* 1.3 61.6 + - - +
281C ASP 3.5 2.5 - - - -
282C GLU* 3.3 39.9 + - + +
283C ILE* 3.4 8.1 - - + +
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Residues in contact with PHE 280 (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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271C ILE* 4.2 19.7 - - + -
276C GLY 3.2 10.3 + - - +
277C VAL* 3.3 20.6 + - + +
278C ARG 3.4 2.4 + - - -
279C ARG* 1.3 75.3 - - - +
281C ASP* 1.3 69.4 + - - +
283C ILE* 3.2 3.4 + - - +
284C LEU* 3.0 51.6 + - + +
290C ILE* 3.7 46.2 - - + -
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Residues in contact with ASP 281 (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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279C ARG 3.5 1.0 - - - -
280C PHE* 1.3 87.2 - - - +
282C GLU* 1.3 61.0 + - - +
284C LEU* 4.0 8.2 - - - +
285C GLU* 3.3 24.4 + - - +
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Residues in contact with GLU 282 (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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247C LYS* 3.5 12.1 - - - +
248C ALA* 3.0 44.8 + - + +
249C SER 4.8 0.5 + - - -
279C ARG* 3.3 34.2 + - + +
281C ASP* 1.3 75.7 - - - +
283C ILE* 1.3 63.6 + - - +
285C GLU* 3.8 7.8 + - - +
286C ALA* 3.4 15.1 + - - +
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Residues in contact with ILE 283 (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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245C ILE* 3.8 20.9 - - + +
246C ARG 3.6 26.5 - - - +
247C LYS* 3.7 22.4 - - - +
248C ALA* 4.6 4.9 - - - +
251C VAL* 4.2 0.8 - - + +
269C SER* 3.8 12.8 - - - -
271C ILE* 3.8 18.6 - - + -
276C GLY* 3.5 25.8 - - - +
279C ARG 3.4 16.8 - - - +
280C PHE* 3.2 6.9 + - - +
282C GLU* 1.3 78.3 - - - +
284C LEU* 1.3 55.0 + - - +
286C ALA* 3.2 5.2 + - - +
287C SER* 2.6 35.2 + - - +
290C ILE* 4.1 4.7 - - + -
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Residues in contact with LEU 284 (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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280C PHE* 3.0 42.2 + - + +
281C ASP* 4.0 9.4 - - - +
283C ILE* 1.3 75.0 - - - +
285C GLU* 1.3 65.0 + - - +
287C SER* 3.1 22.2 - - - +
288C ASP 6.1 0.4 - - - -
289C GLY* 5.3 8.1 - - - -
290C ILE* 4.0 23.7 - - + +
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Residues in contact with GLU 285 (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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281C ASP 3.3 16.3 + - - +
282C GLU* 3.9 7.9 - - - +
283C ILE 3.4 0.2 - - - -
284C LEU* 1.3 79.6 - - - +
286C ALA* 1.3 60.5 + - + +
287C SER 3.7 3.1 + - - +
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Residues in contact with ALA 286 (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 ALA* 4.1 2.9 - - + -
251C VAL* 3.8 21.8 - - + +
252C HIS* 3.7 31.5 + - + -
255C ARG* 2.7 30.1 + - - -
282C GLU 3.4 14.5 + - - +
283C ILE 3.2 5.3 + - - +
285C GLU* 1.3 82.2 - - + +
287C SER* 1.3 50.9 + - - +
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Residues in contact with SER 287 (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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251C VAL* 3.5 8.8 - - - +
255C ARG* 4.1 2.9 - - - +
267C ILE 3.6 7.4 - - - -
269C SER* 2.8 23.8 + - - -
283C ILE 2.6 24.9 + - - -
284C LEU* 3.1 18.6 + - - +
285C GLU 4.2 3.1 - - - +
286C ALA* 1.3 78.7 - - - +
288C ASP* 1.3 66.1 + - - +
289C GLY* 3.5 22.0 - - - -
290C ILE* 4.8 0.2 - - - -
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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