Contacts of the helix formed by residues 270 - 274 (chain B) in PDB entry 3REO
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 ILE 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B VAL 3.5 18.4 - - - +
211B GLY* 3.5 26.0 - - - +
255B MET* 3.7 31.9 - - + -
267B ILE* 3.8 20.4 - - + -
268B LYS 3.2 17.0 - - - +
269B TRP* 1.3 83.9 - - - +
271B CYS* 1.3 68.8 + - - +
272B HIS 3.2 1.1 - - - -
273B ASP* 2.9 16.7 + - - +
274B TRP* 3.3 18.9 - - + +
282B LEU* 3.8 18.8 - - + -
300B GLU* 3.2 0.8 + - - -
370B SAH 3.6 22.4 - - + +
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Residues in contact with CYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.7 26.0 - - - +
270B ILE* 1.3 74.0 - - - +
272B HIS* 1.3 58.7 - - - +
273B ASP 3.2 1.2 + - - -
274B TRP* 3.2 13.1 + - - +
279B CYS* 3.3 26.2 - - - -
282B LEU* 5.2 5.2 - - - -
283B LEU* 5.0 9.9 - - - -
298B VAL* 4.5 9.4 - - - -
300B GLU* 2.7 24.5 + - - +
333B ARG* 2.9 18.7 + - - +
338B PHE* 4.0 18.6 - - + -
341B LEU* 5.1 4.9 - - + -
364B PHE* 5.8 1.3 - - - -
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Residues in contact with HIS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TRP* 3.6 49.8 + + + +
270B ILE 3.1 0.2 + - - -
271B CYS* 1.3 80.1 - - - +
273B ASP* 1.3 69.3 + - - +
274B TRP 3.3 0.4 - - - -
300B GLU* 3.2 16.0 + - - +
301B TYR* 5.2 3.8 - + - -
319B THR* 4.7 6.9 + - - -
323B MET* 3.3 17.5 - - + +
330B GLY* 3.1 3.1 - - - -
331B LYS 3.1 41.0 + - - +
332B GLU* 2.8 32.5 + - - +
333B ARG* 4.0 0.7 - - - +
338B PHE* 6.1 2.5 - - + -
369B EUG 3.2 22.6 + + - -
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 3.4 18.8 - - + -
269B TRP 3.5 3.9 - - - +
270B ILE* 2.9 15.5 + - - +
272B HIS* 1.3 86.1 - - - +
274B TRP* 1.3 72.8 + - + +
323B MET* 3.6 8.1 - - - +
327B ASN* 3.2 32.9 - - - +
328B PRO* 3.6 10.4 - - - +
330B GLY* 3.4 7.1 + - - -
369B EUG 2.6 28.8 + - - +
370B SAH 3.5 17.8 - - - +
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Residues in contact with TRP 274 (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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164B ASN* 5.4 7.0 - - - -
166B PHE* 3.9 21.7 - + - -
255B MET* 3.4 19.7 - - + +
256B PHE* 3.6 28.9 - + - -
270B ILE* 3.3 28.7 + - + +
271B CYS* 3.2 7.1 + - - +
272B HIS 3.3 0.8 - - - -
273B ASP* 1.3 92.8 + - + +
275B SER* 1.3 62.1 + - - +
278B HIS* 3.6 36.1 - + + -
279B CYS* 4.1 10.3 - - - +
282B LEU* 5.7 2.5 - - + -
328B PRO* 3.6 32.5 - - + -
329B GLY 3.6 9.2 - - - +
330B GLY* 3.8 1.6 - - - -
333B ARG* 2.8 22.2 + - - -
370B SAH 3.6 26.3 + - - -
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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
------------------------------------------------------------
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