Contacts of the helix formed by residues 345 - 352 (chain B) in PDB entry 5H1Y
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 GLU 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B THR* 3.9 6.6 + - - +
231B LYS* 3.7 8.5 - - - +
265B PRO* 3.1 25.3 - - + +
269B LEU* 3.4 21.1 - - + +
344B ASP* 1.3 82.9 + - - +
346B ALA* 1.3 64.0 + - - +
347B ASP* 3.2 11.2 - - - +
348B ARG* 3.1 34.4 + - + +
349B MET* 3.0 19.4 + - - +
374B PHE 3.1 10.6 + - - -
375B SER* 4.8 1.1 - - - +
376B ALA 5.8 0.4 - - - +
502B MG 2.6 30.0 - - - -
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Residues in contact with ALA 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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343B LEU* 4.5 5.6 - - + +
344B ASP 3.3 0.2 - - - -
345B GLU* 1.3 69.7 - - - +
347B ASP* 1.3 61.5 + - - +
349B MET* 3.2 20.6 + - + +
350B ILE* 2.9 38.2 + - + +
358B ILE* 6.3 0.9 - - + -
373B LEU* 3.8 33.2 - - + -
374B PHE 2.8 18.4 + - - +
375B SER* 4.5 0.2 - - - -
382B ILE* 4.6 3.6 - - + -
385B PHE* 5.3 4.9 - - + -
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Residues in contact with ASP 347 (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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345B GLU* 3.4 16.1 - - - +
346B ALA* 1.3 79.9 + - - +
348B ARG* 1.3 85.2 + - - +
350B ILE* 3.4 2.3 + - - +
351B ASP* 3.0 32.3 + - - +
375B SER* 3.0 24.8 + - - +
376B ALA* 3.1 21.6 + - - +
377B THR* 3.1 28.0 + - - +
379B PRO* 5.9 0.2 - - + -
382B ILE* 3.7 19.4 - - + +
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Residues in contact with ARG 348 (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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347A ASP* 6.4 0.4 - - - +
351A ASP* 2.9 39.1 + - - +
377A THR* 5.7 10.3 + - + -
379A PRO* 5.5 11.3 - - - +
265B PRO* 4.1 14.0 - - + +
266B SER* 4.5 14.6 + - - -
345B GLU* 3.1 40.8 + - + +
347B ASP* 1.3 92.0 + - - +
349B MET* 1.3 58.0 + - - +
351B ASP* 3.3 10.5 + - - +
352B MET* 2.9 51.1 + - - +
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Residues in contact with MET 349 (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 ILE* 3.4 29.2 - - + +
264B CYS 3.7 19.3 - - - -
265B PRO* 3.7 19.5 - - + -
321B PRO* 4.0 10.3 - - - -
343B LEU* 3.8 22.9 - - + -
344B ASP 3.1 19.5 - - - +
345B GLU 3.0 11.9 + - - +
346B ALA* 3.2 14.1 + - + +
348B ARG* 1.3 77.4 - - - +
350B ILE* 1.3 62.6 + - + +
352B MET* 3.2 6.7 + - - -
353B GLY 3.3 0.3 + - - -
354B PHE* 3.0 38.1 + - + +
358B ILE* 4.1 20.0 - - + -
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Residues in contact with ILE 350 (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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346B ALA* 2.9 24.5 + - + +
347B ASP 3.8 0.7 - - - +
349B MET* 1.3 71.2 - - - +
351B ASP* 1.3 62.0 + - - +
353B GLY* 2.9 21.1 + - - -
354B PHE 4.7 1.6 - - - +
355B GLU* 3.9 36.9 + - + +
358B ILE* 5.2 4.5 - - + -
381B LYS* 3.9 37.8 + - + +
382B ILE* 3.5 26.7 - - + -
385B PHE* 4.3 31.0 - - + -
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Residues in contact with ASP 351 (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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348A ARG* 2.8 54.2 + - - +
351A ASP* 3.6 20.8 - - + +
352A MET* 3.7 30.8 - - + +
347B ASP* 3.0 21.8 + - - +
348B ARG* 3.3 13.4 + - - +
350B ILE* 1.3 79.7 - - - +
352B MET* 1.3 59.6 - - - +
353B GLY* 3.2 1.3 + - - -
382B ILE* 5.9 0.9 - - - +
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Residues in contact with MET 352 (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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351A ASP* 3.9 29.4 - - + +
265B PRO* 3.8 39.0 - - + +
266B SER* 5.7 2.2 - - - -
348B ARG* 2.9 41.7 + - - +
349B MET 3.8 1.3 - - - +
350B ILE 3.2 0.8 - - - -
351B ASP* 1.3 74.6 - - - +
353B GLY* 1.3 61.4 + - - +
354B PHE* 3.5 38.9 + - + -
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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