Contacts of the helix formed by residues 341 - 346 (chain B) in PDB entry 2PO5
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 HIS 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B ILE* 5.1 1.6 - - - -
130B SER* 4.6 2.5 - - - +
131B PRO* 4.6 8.1 - - - -
132B ILE* 3.8 18.5 - - + +
337B PHE* 2.4 76.0 - + + +
339B SER 4.3 2.4 + - - -
340B ASP* 1.3 78.1 - - - +
342B ILE* 1.3 67.8 + - - +
343B GLU* 3.1 25.9 + - + +
344B THR* 3.1 13.4 + - + +
345B LEU* 3.0 26.5 + - - +
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Residues in contact with ILE 342 (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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122B GLN* 3.8 37.0 - - + +
123B TYR* 3.7 41.3 + - + +
126B ILE* 3.8 24.0 - - + +
130B SER* 5.2 1.0 + - - -
341B HIS* 1.3 75.4 - - + +
343B GLU* 1.3 88.7 + - - +
346B TYR* 3.0 55.9 + - + +
347B GLU* 3.2 2.8 + - - +
501B CHD 5.7 6.1 - - + +
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Residues in contact with GLU 343 (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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263B CYS* 3.9 17.0 - - - -
302B GLN* 3.1 20.3 + - - +
303B SER* 3.6 25.1 + - - +
337B PHE* 3.5 4.7 - - + -
341B HIS* 3.1 32.2 + - - +
342B ILE* 1.3 100.7 - - - +
344B THR* 1.3 57.0 + - - +
347B GLU* 3.1 28.2 - - - +
348B LEU* 3.1 5.7 + - - +
501B CHD 4.5 21.2 + - - +
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Residues in contact with THR 344 (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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334B PRO* 3.7 31.6 - - + -
337B PHE* 3.8 5.8 - - + -
339B SER 4.8 1.8 - - - +
340B ASP* 2.9 23.8 + - - -
341B HIS* 3.1 32.7 + - + +
343B GLU* 1.3 79.1 - - - +
345B LEU* 1.3 67.4 + - - +
346B TYR 3.3 0.4 - - - -
348B LEU* 3.5 9.6 - - + +
349B ASP* 3.0 36.7 + - - +
367B ARG* 4.0 10.5 - - - -
370B SER* 4.4 5.4 - - - +
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Residues in contact with LEU 345 (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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126B ILE* 3.6 43.3 - - + +
131B PRO* 4.2 17.5 - - + -
340B ASP* 3.8 36.6 - - + +
341B HIS 3.0 12.1 + - - +
344B THR* 1.3 80.4 + - - +
346B TYR* 1.3 58.7 + - - +
349B ASP* 3.4 29.6 - - - +
350B ILE* 3.6 11.8 - - - +
367B ARG* 4.0 3.6 - - - +
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Residues in contact with TYR 346 (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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122B GLN* 3.5 54.1 + - + +
125B ARG* 4.0 32.8 + - + +
126B ILE* 3.7 10.8 - - + -
342B ILE* 3.0 25.6 + - + +
345B LEU* 1.3 79.6 - - - +
347B GLU* 1.3 66.9 + - + +
348B LEU 3.5 0.2 - - - -
350B ILE* 2.9 27.0 + - + +
351B GLU* 2.8 53.9 + - + +
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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