Contacts of the helix formed by residues 336 - 344 (chain A) in PDB entry 4JU5
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 ALA 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A THR* 1.3 73.5 - - - +
337A GLU* 1.3 58.9 - - - +
339A ILE* 3.6 1.0 + - - -
340A THR* 3.2 26.5 + - - -
274B ASN* 3.1 48.5 - - + +
277B THR* 4.2 19.3 - - + -
278B ALA* 3.6 6.5 - - - +
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Residues in contact with GLU 337 (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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335A THR* 3.3 4.8 - - - -
336A ALA* 1.3 75.8 - - - +
338A ARG* 1.3 65.1 + - - +
340A THR* 3.4 6.7 + - - -
341A GLU* 3.1 25.3 + - - +
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Residues in contact with ARG 338 (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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335A THR* 3.5 25.2 + - - +
336A ALA 3.4 0.4 - - - -
337A GLU* 1.3 78.0 - - - +
339A ILE* 1.3 56.4 + - + +
341A GLU* 3.9 4.7 - - - +
342A PHE* 3.0 30.7 + - - +
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Residues in contact with ILE 339 (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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335A THR 3.3 19.0 + - - +
336A ALA 3.7 5.8 - - - +
337A GLU 3.3 0.4 - - - -
338A ARG* 1.3 77.0 - - + +
340A THR* 1.3 51.5 + - - +
342A PHE* 3.2 7.5 + - + +
343A CYS* 2.7 49.6 + - - +
257B ILE* 4.2 11.0 - - + -
259B LEU* 5.8 3.1 - - + -
271B LYS 5.3 0.9 - - - +
274B ASN* 4.1 6.3 - - + +
275B PHE* 3.9 39.0 - - + +
278B ALA* 3.6 15.7 - - + -
288B PHE* 4.0 10.5 - - + -
315B VAL* 5.5 10.5 - - + -
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Residues in contact with THR 340 (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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336A ALA 3.2 16.9 + - - -
337A GLU* 3.8 7.7 - - - -
338A ARG 3.4 0.2 - - - -
339A ILE* 1.3 78.0 - - - +
341A GLU* 1.3 57.4 + - - +
343A CYS 3.4 0.3 + - - -
344A HIS* 3.1 55.3 + - + +
278B ALA* 3.4 19.9 + - - +
281B SER* 4.0 9.2 + - - +
282B PHE* 3.6 16.3 - - + -
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Residues in contact with GLU 341 (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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337A GLU 3.1 17.4 + - - +
338A ARG* 3.9 5.4 - - - +
340A THR* 1.3 73.5 - - - +
342A PHE* 1.3 64.0 + - - +
344A HIS* 3.5 20.8 + - - +
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Residues in contact with PHE 342 (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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322A GLU* 3.6 47.8 - - + -
338A ARG 3.0 19.4 + - - +
339A ILE* 3.5 10.3 - - + +
341A GLU* 1.3 75.3 - - - +
343A CYS* 1.3 65.7 + - - +
344A HIS 3.5 0.3 + - - -
345A ARG* 3.6 17.3 - - - +
257B ILE* 3.8 18.8 - - + -
315B VAL* 3.7 25.1 - - + -
317B LEU* 3.7 35.0 - - + +
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Residues in contact with CYS 343 (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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339A ILE* 2.7 27.6 + - - +
341A GLU 3.3 0.2 - - - -
342A PHE* 1.3 73.6 - - - +
344A HIS* 1.3 51.9 + - - +
345A ARG* 2.6 21.8 + - - +
346A PHE* 3.6 15.4 + - - -
257B ILE* 3.8 23.6 - - - -
282B PHE* 3.3 26.5 - - + -
286B ILE* 3.8 18.3 - - + +
288B PHE* 3.8 28.5 - - - -
317B LEU* 5.0 7.3 - - - +
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Residues in contact with HIS 344 (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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340A THR* 3.1 36.7 + - + +
341A GLU* 3.5 16.4 + - - +
342A PHE 3.3 0.8 - - - -
343A CYS* 1.3 71.5 - - - +
345A ARG* 1.3 55.6 + - - +
346A PHE* 3.3 18.7 + + - -
347A LEU* 4.9 5.4 + - - +
281B SER* 4.9 7.6 + - - -
282B PHE* 3.5 27.9 - + - -
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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