Contacts of the helix formed by residues 286 - 292 (chain C) in PDB entry 5E9W
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 VAL 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C LEU* 3.5 15.7 - - + +
205C GLY* 3.5 18.6 - - - +
283C CYS* 3.5 19.3 + - - -
284C GLN 3.2 20.6 - - - +
285C PHE* 1.3 77.3 - - - +
287C CYS* 1.3 69.5 + - - +
288C HIS* 3.0 7.4 + - - -
289C TYR* 3.0 23.5 + - - +
290C SER 4.3 0.9 + - - -
300C MET* 4.0 20.4 - - + +
317C THR 4.1 1.4 + - - -
501C SAH 3.4 34.8 - - + +
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Residues in contact with CYS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C CYS* 3.5 23.1 - - - -
286C VAL* 1.3 76.8 - - - +
288C HIS* 1.3 57.9 + - - +
290C SER* 2.8 31.2 + - - +
291C PHE* 3.5 13.9 - - + -
300C MET* 4.1 13.0 - - - -
301C LEU* 6.3 0.2 - - - -
314C PHE* 4.0 12.8 - - - -
317C THR 5.0 1.0 + - - -
318C THR* 4.1 15.7 - - + +
373C VAL* 5.3 1.3 - - + -
378C LEU* 5.2 9.9 - - + -
470C PHE* 3.6 28.9 - - + -
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Residues in contact with HIS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C PHE* 3.3 36.7 + - + -
286C VAL 3.6 2.7 + - - -
287C CYS* 1.3 76.1 - - - +
289C TYR* 1.3 83.2 + + - +
290C SER 3.3 0.7 + - - -
291C PHE* 3.4 3.2 + - - +
318C THR* 3.0 17.0 + - - +
319C PRO* 3.3 19.6 - - + +
370C GLU* 3.5 42.5 + - + -
371C PHE* 3.3 43.2 + - - +
373C VAL* 3.4 20.4 - - + -
467C TYR* 5.2 2.9 - + - -
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Residues in contact with TYR 289 (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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263C SER* 5.5 0.2 + - - -
285C PHE 3.6 12.7 + - - -
286C VAL* 3.0 25.1 + - - +
288C HIS* 1.3 102.0 + + - +
290C SER* 1.3 60.2 + - - +
291C PHE 3.4 0.5 + - - -
292C GLU* 4.0 6.9 + - - +
296C GLN* 4.9 2.3 + - - -
300C MET* 5.7 0.2 - - + -
368C VAL* 3.8 22.8 + - + +
369C PRO 3.5 26.0 - - - -
370C GLU* 4.1 16.1 + - + +
371C PHE* 3.6 21.3 - + + -
501C SAH 3.5 55.9 + + + +
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Residues in contact with SER 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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263C SER* 4.1 9.6 - - - -
286C VAL 4.3 0.4 + - - -
287C CYS* 2.8 18.6 + - - +
289C TYR* 1.3 75.1 - - - +
291C PHE* 1.3 68.3 + - - +
292C GLU 3.1 8.1 + - - -
293C SER 3.5 0.2 - - - +
296C GLN* 3.2 27.6 - - - +
297C ALA* 3.0 26.5 + - - -
300C MET* 3.7 32.5 - - - +
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Residues in contact with PHE 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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287C CYS* 3.5 14.6 - - + -
288C HIS 3.4 8.7 + - - +
289C TYR 3.3 2.4 - - - -
290C SER* 1.3 91.0 - - - +
292C GLU* 1.3 59.9 + - - +
293C SER 3.1 4.1 + - - +
297C ALA* 4.1 14.8 - - + -
301C LEU* 5.8 1.1 - - + -
353C LEU 4.1 8.3 - - - +
354C PHE* 3.4 28.5 - + - -
355C GLY 2.9 20.6 + - - -
371C PHE* 3.9 7.2 - - + +
372C LEU 3.7 19.2 - - - +
373C VAL* 3.8 33.0 - - + -
374C TYR 5.0 1.6 - - - -
377C LEU* 4.0 23.3 - - + -
378C LEU* 4.0 30.3 - - + -
381C MET* 4.5 5.4 - - - -
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Residues in contact with GLU 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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264C LYS* 5.6 0.8 - - - -
289C TYR 4.2 4.4 - - - +
290C SER 3.1 1.0 - - - -
291C PHE* 1.3 77.7 - - - +
293C SER* 1.3 60.9 + - - +
296C GLN* 3.0 34.4 + - - +
354C PHE* 4.0 0.9 - - - +
355C GLY* 3.2 17.8 + - - -
371C PHE* 3.5 46.4 - - + -
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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