Contacts of the helix formed by residues 345 - 352 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A THR* 3.8 5.5 + - - +
231A LYS* 3.7 7.6 - - - +
265A PRO* 3.2 14.9 - - + +
269A LEU* 3.6 20.0 - - + +
344A ASP* 1.3 84.1 + - - +
346A ALA* 1.3 65.9 + - - +
347A ASP* 3.2 11.7 - - - +
348A ARG* 3.0 43.7 + - + -
349A MET* 3.0 19.8 + - - +
374A PHE 2.9 11.0 + - - -
375A SER* 4.9 1.1 - - - +
376A ALA 5.7 0.4 - - - +
502A MG 2.4 30.5 - - - -
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 4.4 7.2 - - + +
344A ASP 3.3 0.4 - - - -
345A GLU* 1.3 70.3 - - - +
347A ASP* 1.3 61.7 + - - +
349A MET* 3.1 19.2 + - + +
350A ILE* 2.8 37.5 + - + +
373A LEU* 3.7 35.4 - - + -
374A PHE 2.8 17.3 + - - +
375A SER* 4.6 0.9 - - - -
382A ILE* 4.7 4.0 - - + -
385A PHE* 5.5 3.8 - - + -
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Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A GLU* 3.3 16.1 - - - +
346A ALA* 1.3 72.9 + - - +
348A ARG* 1.3 77.0 + - - +
350A ILE* 3.0 5.0 + - - +
351A ASP* 2.9 35.7 + - - +
375A SER* 3.2 20.6 + - - +
376A ALA* 3.4 21.2 + - - +
377A THR* 3.2 31.3 + - - +
379A PRO* 5.9 0.2 - - + -
382A ILE* 3.7 19.1 - - + +
348B ARG* 6.4 0.2 - - - +
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A PRO* 4.3 10.5 - - + +
266A SER* 4.9 11.3 + - - -
269A LEU* 6.2 0.2 - - - +
345A GLU* 3.0 42.5 + - + +
347A ASP* 1.3 93.0 + - - +
349A MET* 1.3 62.7 + - - +
351A ASP* 3.2 10.5 + - - +
352A MET* 2.9 53.3 + - - +
351B ASP* 2.8 39.5 + - - +
377B THR* 6.3 3.4 - - - -
379B PRO* 5.8 6.8 - - - +
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Residues in contact with MET 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ILE* 3.6 34.1 - - + +
264A CYS 3.8 2.0 - - - -
265A PRO* 3.6 35.4 - - + -
321A PRO* 4.0 6.1 - - - -
343A LEU* 4.1 16.2 - - + -
344A ASP 3.8 13.2 - - - +
345A GLU 3.0 14.7 + - - +
346A ALA* 3.1 17.9 + - + +
348A ARG* 1.3 75.7 - - - +
350A ILE* 1.3 62.5 + - + +
352A MET 3.3 4.9 + - - -
354A PHE* 3.1 37.4 + - + +
358A ILE* 3.5 30.5 - - + -
385A PHE* 6.4 0.2 - - + -
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ALA* 2.8 19.8 + - + +
347A ASP 3.5 6.1 - - - +
349A MET* 1.3 74.6 - - - +
351A ASP* 1.3 70.0 + - - +
353A GLY* 3.0 14.8 + - - +
354A PHE 4.9 1.3 - - - +
355A GLU* 4.0 32.7 + - + +
358A ILE* 5.3 4.7 - - + -
381A LYS* 3.6 45.0 + - + +
382A ILE* 3.7 20.2 - - + -
385A PHE* 4.3 35.4 - - + -
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Residues in contact with ASP 351 (chain A).
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* 2.9 19.9 + - - +
348A ARG* 3.2 13.4 + - - +
350A ILE* 1.3 79.5 - - - +
352A MET* 1.3 59.9 + - - +
353A GLY 3.6 0.5 + - - -
381A LYS* 6.1 0.2 - - - +
382A ILE* 5.9 1.4 - - - +
348B ARG* 2.9 54.5 + - - +
351B ASP* 3.6 19.7 - - + +
352B MET* 3.9 29.0 - - + +
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A PRO* 3.9 19.5 - - + +
266A SER* 5.6 3.6 - - - -
348A ARG* 2.9 52.9 + - - +
349A MET 3.3 1.3 + - - +
350A ILE 3.0 0.8 - - - -
351A ASP* 1.3 77.5 - - - +
353A GLY* 1.3 59.8 + - - +
354A PHE* 3.4 40.6 + - + -
351B ASP* 3.7 31.4 - - + +
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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