Contacts of the helix formed by residues 286 - 292 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LEU* 3.4 22.9 - - + +
205B GLY* 3.5 8.5 - - - +
283B CYS* 3.4 17.8 - - - -
284B GLN 3.3 18.4 - - - +
285B PHE* 1.3 75.9 - - - +
287B CYS* 1.3 69.1 + - - +
288B HIS* 3.1 4.4 - - - -
289B TYR* 2.8 29.3 + - - +
290B SER 4.2 0.9 + - - -
300B MET* 4.0 16.3 - - + +
317B THR 4.2 1.2 + - - -
501B SAH 3.3 44.9 - - + +
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Residues in contact with CYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B CYS* 3.4 23.1 - - - -
286B VAL* 1.3 78.6 - - - +
288B HIS* 1.3 58.3 + - - +
290B SER* 2.8 31.7 + - - +
291B PHE* 3.7 11.6 - - + -
300B MET* 3.9 15.3 - - - -
301B LEU* 6.1 0.4 - - - -
314B PHE* 3.8 25.4 - - - -
317B THR 5.2 0.8 + - - -
318B THR* 4.2 15.5 + - + +
373B VAL* 5.2 3.4 - - + -
378B LEU* 5.6 8.3 - - + -
470B PHE* 3.9 15.7 - - + -
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Residues in contact with HIS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 3.3 38.0 + - + +
286B VAL 3.6 2.3 + - - -
287B CYS* 1.3 74.7 - - - +
289B TYR* 1.3 82.9 + + - +
290B SER 3.3 0.3 + - - -
291B PHE* 3.5 2.6 + - - +
318B THR* 3.0 21.6 + - - +
319B PRO* 3.3 20.9 - - + +
370B GLU* 3.4 41.5 + - + -
371B PHE* 3.3 44.1 + - - +
373B VAL* 3.6 15.0 - - + -
467B TYR* 4.9 4.0 + + - -
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Residues in contact with TYR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER* 5.5 0.3 - - - -
285B PHE 3.6 13.3 + - - -
286B VAL* 2.8 24.7 + - - +
288B HIS* 1.3 98.5 + + - +
290B SER* 1.3 60.0 + - - +
291B PHE 3.3 0.7 + - - -
292B GLU* 4.1 6.1 + - - +
296B GLN* 5.0 2.6 + - - -
300B MET* 5.5 0.4 - - + -
368B VAL* 3.6 25.3 - - + +
369B PRO 3.3 27.1 - - - -
370B GLU* 3.8 19.5 + - + -
371B PHE* 3.6 19.1 - + - -
501B SAH 3.4 56.2 + + + +
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER* 4.1 9.6 - - - -
286B VAL 4.2 0.2 + - - -
287B CYS* 2.8 20.4 + - - +
289B TYR* 1.3 75.8 - - - +
291B PHE* 1.3 67.9 + - - +
292B GLU 3.2 7.3 + - - -
293B SER 3.5 0.3 - - - +
296B GLN* 3.1 18.6 - - - +
297B ALA* 2.9 30.1 + - - -
300B MET* 3.7 39.9 - - - +
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B CYS* 3.7 12.8 - - + -
288B HIS 3.5 3.3 + - - +
289B TYR 3.3 2.2 - - - -
290B SER* 1.3 90.2 - - - +
292B GLU* 1.3 59.1 + - - +
293B SER 3.2 3.6 - - - +
297B ALA* 3.9 16.2 - - + -
301B LEU* 5.7 0.7 - - + -
353B LEU 4.0 5.2 - - - -
354B PHE* 3.4 29.9 - + - -
355B GLY 2.8 21.3 + - - -
371B PHE* 3.7 14.2 - - + +
372B LEU 3.7 22.6 - - - +
373B VAL* 3.7 27.1 - - + -
374B TYR 5.2 0.9 - - - -
377B LEU* 3.8 24.0 - - + -
378B LEU* 4.1 31.4 - - + -
381B MET* 4.3 8.5 - - + -
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B LYS* 5.4 2.4 + - - -
289B TYR 4.3 4.0 - - - +
290B SER 3.2 0.6 - - - -
291B PHE* 1.3 77.6 - - - +
293B SER* 1.3 59.6 + - - +
296B GLN* 3.0 33.8 + - - +
354B PHE 3.9 0.9 - - - -
355B GLY* 3.3 16.7 + - - -
371B PHE* 3.4 45.8 - - + -
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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