Contacts of the helix formed by residues 284 - 292 (chain C) in PDB entry 2AYN
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 TYR 284 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C VAL* 3.3 21.7 - - - +
283C LYS* 1.3 95.4 - - + +
285C LEU* 1.3 66.5 + - - +
286C PHE* 3.3 9.6 - - + +
287C THR* 3.7 13.6 + - - +
288C GLY 3.7 2.9 + - - -
346C VAL* 3.4 5.5 - - - +
347C LYS* 3.6 27.8 - - + +
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Residues in contact with LEU 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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276C CYS* 4.0 7.1 - - + -
284C TYR* 1.3 72.8 - - - +
286C PHE* 1.3 66.2 + - - +
288C GLY* 3.0 12.8 + - - -
289C LEU* 3.0 37.6 + - + -
325C ILE* 4.4 7.4 - - + -
327C MET* 3.8 27.1 - - + -
346C VAL* 4.0 6.5 - - + -
347C LYS 2.8 18.6 + - - +
348C PHE* 4.0 13.0 - - + -
349C PRO* 4.2 4.5 - - + +
352C LEU* 3.7 29.2 - - + -
477C LEU* 4.4 2.2 - - + -
479C TYR* 3.9 25.6 - - + +
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Residues in contact with PHE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C TYR* 4.2 7.1 - - + +
285C LEU* 1.3 78.2 - - - +
287C THR* 1.3 68.0 + - - +
289C LEU* 2.8 14.2 + - + +
290C LYS* 2.8 45.3 + - + +
352C LEU* 5.3 8.7 - - + -
353C ASP 3.6 22.9 - - - -
354C MET* 5.0 3.1 - - - -
356C GLU* 4.0 25.4 - - + -
357C LEU* 3.7 39.5 - - + -
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Residues in contact with THR 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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281C GLU* 3.6 26.0 - - + +
282C VAL* 3.9 15.3 - - + -
283C LYS* 4.5 2.1 + - - +
284C TYR* 3.7 23.7 + - - +
285C LEU 3.4 0.4 - - - -
286C PHE* 1.3 78.3 - - - +
288C GLY* 1.3 56.5 + - - +
290C LYS* 3.5 10.4 - - - +
291C LEU* 3.0 37.4 + - + +
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Residues in contact with GLY 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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276C CYS* 3.6 6.3 - - - -
277C PHE 3.3 39.0 + - - -
282C VAL* 3.9 6.0 - - - +
284C TYR 3.7 3.2 + - - -
285C LEU 3.0 8.3 + - - -
286C PHE 2.9 1.8 + - - -
287C THR* 1.3 77.8 - - - +
289C LEU* 1.3 66.4 + - - +
291C LEU* 3.5 6.4 + - - +
292C ARG* 3.3 12.8 + - - +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 4.3 13.9 - - + -
275C SER 3.9 13.0 - - - +
276C CYS* 3.8 12.3 - - + -
285C LEU* 3.0 45.6 + - + +
286C PHE* 2.8 16.9 + - + +
288C GLY* 1.3 69.9 - - - +
290C LYS* 1.3 67.3 - - - +
292C ARG* 2.9 18.4 + - - +
293C LEU* 3.4 13.4 - - + +
325C ILE* 3.9 18.8 - - + -
352C LEU* 5.2 1.1 - - + -
354C MET* 4.0 31.6 - - + -
357C LEU* 4.1 14.4 - - + -
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Residues in contact with LYS 290 (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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286C PHE* 2.8 34.1 + - + +
287C THR* 3.5 9.4 - - - +
289C LEU* 1.3 76.0 - - - +
291C LEU* 1.3 53.6 + - + +
293C LEU* 2.6 42.0 + - - +
294C GLN* 3.3 19.1 + - + +
356C GLU 6.0 1.1 - - - -
357C LEU* 4.5 16.5 - - + +
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Residues in contact with LEU 291 (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 PHE* 4.2 31.4 - - + -
281C GLU* 6.0 7.4 - - + +
282C VAL* 5.5 4.5 - - + -
287C THR* 3.0 23.0 + - + +
288C GLY* 3.6 7.4 - - - +
290C LYS* 1.3 79.6 - - + +
292C ARG* 1.3 57.2 + - - +
293C LEU 3.0 4.7 + - - -
294C GLN* 3.6 20.1 + - + +
295C GLU* 4.4 4.7 + - - +
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Residues in contact with ARG 292 (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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274C LEU* 6.6 0.2 - - + -
275C SER* 3.7 37.9 + - - +
277C PHE* 2.9 52.0 - - - +
288C GLY 3.3 6.9 + - - +
289C LEU 2.9 12.8 + - - +
291C LEU* 1.3 75.7 - - - +
293C LEU* 1.3 68.9 + - + +
295C GLU* 4.3 20.1 - - - +
328C VAL* 3.7 26.9 - - - +
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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