Contacts of the helix formed by residues 347 - 351 (chain A) in PDB entry 3JXI
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 ASN 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A LEU* 3.7 8.9 - - - +
345A ASP 4.4 0.4 + - - -
346A THR* 1.3 71.4 - - - +
348A LEU* 1.3 68.4 + - - +
349A GLU* 3.2 31.7 + - - +
350A ALA* 3.1 35.7 + - + +
351A LEU* 3.7 10.9 + - - +
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Residues in contact with LEU 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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300A LEU* 3.6 26.7 - - + +
301A ARG* 4.1 6.5 - - + -
309A THR* 4.3 13.1 + - - +
310A VAL* 4.2 8.1 - - + -
311A LEU* 3.2 44.0 - - + +
335A LEU* 4.5 13.0 - - + +
336A LEU* 3.9 12.7 - - + +
339A CYS* 3.8 26.2 - - + +
346A THR* 3.7 4.8 + - - -
347A ASN* 1.3 75.1 - - - +
349A GLU* 1.3 58.9 + - - +
350A ALA 3.1 3.7 + - - -
351A LEU* 3.4 35.7 + - + +
359A PRO* 4.9 0.7 - - - +
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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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311A LEU* 3.8 7.8 - - + +
332A TYR* 3.0 39.8 + - - +
336A LEU* 3.7 21.9 - - + +
347A ASN* 3.2 23.6 + - - +
348A LEU* 1.3 76.7 - - - +
350A ALA* 1.3 58.4 + - - +
358A SER* 3.5 11.6 + - - -
359A PRO* 3.4 22.6 - - + +
360A LEU* 5.2 2.0 + - + +
375A ILE* 4.1 12.1 - - - +
378A ARG* 5.6 3.2 + - - +
379A GLU* 3.8 23.2 - - - +
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Residues in contact with ALA 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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347A ASN* 3.1 34.3 + - + +
349A GLU* 1.3 78.9 - - - +
351A LEU* 1.3 65.1 + - + +
352A LEU* 3.5 19.6 + - - +
358A SER* 4.0 4.4 + - - -
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Residues in contact with LEU 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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301A ARG* 3.9 30.5 - - + +
303A GLN* 5.0 9.4 - - - +
309A THR* 4.1 11.2 - - + -
312A HIS* 3.0 22.2 + - - -
346A THR* 5.2 9.6 - - - +
347A ASN 3.8 13.7 - - - +
348A LEU* 3.4 35.6 + - + +
350A ALA* 1.3 82.6 - - + +
352A LEU* 1.3 60.1 + - - +
358A SER* 4.1 0.9 - - - -
359A PRO* 3.9 8.5 - - - +
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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