Contacts of the helix formed by residues 278 - 288 (chain C) in PDB entry 2Y0N
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 GLU 278 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ILE* 3.4 29.0 - - + +
197C LEU* 3.8 25.2 - - + +
198C VAL* 5.0 2.4 + - - +
274C LEU* 3.8 16.5 - - + +
275C TYR* 2.8 38.6 + - + +
277C TYR* 1.3 70.2 - - - +
279C GLN* 1.3 62.1 + - - +
280C ALA 3.5 0.7 - - - -
281C GLN* 3.5 15.2 + - - +
282C TYR* 3.3 19.8 + - - +
451C TYR* 5.2 0.5 + - - -
455C HIS* 3.0 17.1 + - - -
458C ARG* 2.5 35.2 + - - -
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Residues in contact with GLN 279 (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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270C PRO 5.0 6.8 + - - +
274C LEU* 3.5 37.0 + - - +
275C TYR 3.8 4.8 + - - -
276C PRO* 3.2 23.8 - - + +
277C TYR 3.1 1.6 - - - -
278C GLU* 1.3 76.4 - - - +
280C ALA* 1.3 67.0 + - - +
282C TYR* 3.2 8.8 + - - +
283C LYS* 3.2 26.3 + - + +
588G ASN* 4.2 13.9 + - - -
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Residues in contact with ALA 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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277C TYR 4.1 7.2 + - - +
278C GLU 3.5 0.2 - - - -
279C GLN* 1.3 78.2 - - - +
281C GLN* 1.3 62.1 + - - +
283C LYS* 3.6 10.7 + - - +
284C LYS* 3.1 39.1 + - + +
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Residues in contact with GLN 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 3.9 40.6 - - + +
198C VAL* 3.0 27.6 + - - +
199C LYS* 4.9 0.6 - - - +
200C LEU* 3.5 35.4 - - + +
277C TYR 4.9 0.8 + - - -
278C GLU* 3.5 20.9 + - - +
279C GLN 3.2 0.2 - - - -
280C ALA* 1.3 78.3 - - - +
282C TYR* 1.3 57.7 + - - +
284C LYS* 3.2 7.4 + - - +
285C VAL* 2.8 36.4 + - + +
451C TYR* 4.9 4.1 + - - +
455C HIS* 5.7 1.2 + - - -
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Residues in contact with TYR 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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269C LEU* 3.8 18.4 - - + -
270C PRO* 3.3 38.6 - - + +
274C LEU* 3.7 21.8 - - + -
278C GLU 3.3 2.2 + - - +
279C GLN* 3.2 12.8 + - - +
281C GLN* 1.3 75.5 - - - +
283C LYS* 1.3 73.4 + - + +
285C VAL* 3.2 3.4 + - + +
286C THR* 3.1 58.2 + - + +
447C PRO* 4.5 12.5 - - + +
451C TYR* 3.7 24.8 + + - +
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Residues in contact with LYS 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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279C GLN* 3.2 12.8 + - + +
280C ALA* 3.7 12.6 - - - +
282C TYR* 1.3 85.8 - - + +
284C LYS* 1.3 63.8 + - + +
286C THR* 3.6 5.4 + - - -
287C SER* 3.3 23.4 + - - -
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Residues in contact with LYS 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 ALA* 3.1 26.9 + - - +
281C GLN* 3.7 6.5 - - - +
283C LYS* 1.3 81.2 - - + +
285C VAL* 1.3 65.2 + - + +
287C SER* 3.6 10.9 + - - -
288C SER* 3.6 13.9 + - - -
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Residues in contact with VAL 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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200C LEU* 4.1 34.5 - - + +
201C PRO* 6.1 0.9 - - + -
281C GLN* 2.8 23.6 + - + +
282C TYR* 3.2 3.6 + - - +
284C LYS* 1.3 78.9 - - + +
286C THR* 1.3 67.6 + - + +
287C SER 3.4 0.7 + - - -
288C SER* 3.5 19.3 + - - +
445C PRO* 5.1 1.4 - - - +
450C ILE* 3.5 41.7 - - + +
451C TYR* 5.0 4.9 - - + +
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Residues in contact with THR 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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282C TYR* 3.1 55.6 + - + +
283C LYS* 3.6 5.0 + - - -
285C VAL* 1.3 81.1 - - + +
287C SER* 1.3 64.6 + - - +
288C SER 3.3 7.2 + - - +
444C PRO* 3.9 30.5 - - + +
445C PRO* 4.5 16.6 - - - +
447C PRO* 5.7 2.9 - - + -
450C ILE* 4.8 4.9 - - + -
451C TYR* 6.2 0.4 - - + -
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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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283C LYS 3.3 20.3 + - - -
284C LYS* 3.8 8.1 - - - -
285C VAL 3.3 0.2 - - - -
286C THR* 1.3 78.8 + - - +
288C SER* 1.3 60.8 + - - +
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Residues in contact with SER 288 (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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284C LYS 3.6 10.7 + - - -
285C VAL* 3.5 13.5 + - - +
286C THR 3.3 8.7 - - - +
287C SER* 1.3 81.4 + - - +
443C GLN 5.0 1.2 - - - +
445C PRO* 3.9 20.9 - - - +
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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