Contacts of the helix formed by residues 251 - 255 (chain B) in PDB entry 3PU3
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 ASP 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B OGA 3.1 14.7 - - - +
249B HIS* 3.3 10.8 + - - -
250B ILE* 1.3 81.2 - - - +
252B SER* 1.3 67.8 + - - +
253B GLY 3.4 0.3 + - - -
254B GLY* 3.1 16.5 + - - -
255B ALA* 3.6 23.6 - - + +
257B ALA* 3.8 9.4 - - - +
315B ILE* 5.4 1.9 - - - +
319B TRP 4.7 1.0 + - - -
321B TYR* 2.7 38.7 + - - -
335B HIS* 3.3 28.0 + - + +
348B ALA* 4.7 0.5 - - - +
352B GLU* 4.6 0.9 - - - +
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Residues in contact with SER 252 (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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250B ILE 3.5 2.3 + - - -
251B ASP* 1.3 72.0 - - - +
253B GLY* 1.3 61.8 + - - +
255B ALA* 3.2 20.6 + - - +
352B GLU* 2.6 28.4 + - - -
361B THR 3.8 7.9 - - - -
362B GLN* 3.3 12.7 + - - +
363B PHE* 2.6 42.5 + - - +
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Residues in contact with GLY 253 (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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252B SER* 1.3 70.1 + - - +
254B GLY* 1.3 65.1 + - - +
255B ALA 3.0 2.9 + - - -
337B LEU* 3.5 6.9 - - - +
345B GLN* 3.6 13.5 - - - +
349B TYR* 4.5 7.0 - - - -
352B GLU* 2.6 21.5 + - - -
363B PHE* 4.5 3.4 - - - -
366B PHE* 3.4 38.7 - - - -
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Residues in contact with GLY 254 (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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250B ILE* 4.5 1.3 - - - -
251B ASP 3.1 11.3 + - - -
253B GLY* 1.3 77.7 - - - +
255B ALA* 1.3 64.5 + - - +
317B SER* 2.7 32.3 + - - -
318B GLY 4.4 7.2 - - - -
345B GLN* 3.5 8.4 - - - +
348B ALA* 3.4 27.5 - - - +
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Residues in contact with ALA 255 (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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251B ASP* 3.6 21.6 + - + +
252B SER 3.2 17.3 + - - +
253B GLY 3.0 2.0 - - - -
254B GLY* 1.3 79.9 - - - +
256B SER* 1.3 67.3 + - - +
315B ILE 4.7 0.3 - - - +
316B PRO 4.7 1.7 - - - +
317B SER* 4.3 5.1 - - - -
318B GLY 4.9 1.0 + - - -
335B HIS* 3.9 20.9 - - + +
336B PHE 3.5 14.6 - - - +
337B LEU* 3.9 8.1 - - + -
363B PHE* 4.0 12.1 - - + -
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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