Contacts of the helix formed by residues 347 - 352 (chain A) in PDB entry 2HHQ
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 ARG 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A LEU* 3.5 16.4 - - - +
304A ALA 3.5 22.6 + - - +
305A ASP* 3.5 23.2 + - - +
345A PHE* 4.3 8.3 - - + -
346A LEU* 1.3 73.2 - - - +
348A PRO* 1.3 69.6 - - + +
349A GLU* 3.2 28.3 - - - +
350A THR* 2.9 36.0 + - + +
351A ALA* 3.0 7.6 + - - +
440A GLU* 2.7 41.3 + - - +
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Residues in contact with PRO 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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332A ILE* 3.2 43.7 - - + +
333A VAL* 3.8 20.4 - - - +
334A GLY* 3.9 8.1 - - - +
335A ILE* 4.3 12.8 - - + -
345A PHE* 5.4 0.7 - - + -
346A LEU 3.5 0.8 - - - -
347A ARG* 1.3 84.4 - - + +
349A GLU* 1.3 72.5 + - - +
352A LEU* 2.8 42.2 + - + +
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Residues in contact with GLU 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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347A ARG* 3.2 32.9 - - - +
348A PRO* 1.3 91.5 - - - +
350A THR* 1.3 71.0 + - + +
352A LEU* 4.5 0.8 - - - -
353A ALA* 3.2 22.3 + - - +
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Residues in contact with THR 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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304A ALA 5.3 0.7 + - - +
305A ASP 4.3 21.5 + - - +
306A ARG* 5.3 2.8 - - - -
307A VAL* 5.1 2.3 - - - +
346A LEU* 4.6 8.5 - - - +
347A ARG* 2.9 31.3 + - + +
348A PRO 3.2 0.2 - - - -
349A GLU* 1.3 90.1 - - + +
351A ALA* 1.3 75.9 + - - +
353A ALA* 3.2 4.9 + - - +
354A ASP* 3.2 22.6 + - - +
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Residues in contact with ALA 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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307A VAL* 4.2 11.2 - - - -
335A ILE* 3.8 23.6 - - + -
346A LEU* 3.9 21.1 - - + -
347A ARG 3.0 13.2 + - - +
350A THR* 1.3 81.7 + - - +
352A LEU* 1.3 62.6 + - - +
354A ASP 3.1 12.6 + - - +
357A PHE* 3.4 33.1 - - + +
358A VAL* 4.3 0.3 - - - +
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Residues in contact with LEU 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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320A VAL* 5.8 0.4 - - + -
332A ILE* 3.8 33.0 - - + -
335A ILE* 4.0 20.4 - - + -
348A PRO* 2.8 27.6 + - + +
349A GLU* 4.5 1.1 - - - +
351A ALA* 1.3 72.6 - - - +
353A ALA* 1.3 57.2 + - - +
354A ASP 3.4 0.2 - - - -
357A PHE* 4.3 0.7 - - + -
358A VAL* 3.5 17.5 - - - +
361A LEU* 4.1 16.6 - - + -
380A LEU* 4.0 13.0 - - + -
383A LYS* 3.9 20.6 - - + +
385A ILE* 4.0 24.7 - - + +
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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