Contacts of the helix formed by residues 342 - 346 (chain D) in PDB entry 1JIQ
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 ASP 342 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ASN* 4.7 0.2 - - - -
188C ASP* 3.5 9.0 - - - +
190C THR* 5.4 0.9 + - - -
340D PRO 2.9 5.1 + - - +
341D TYR* 1.3 81.2 - - - +
343D GLN* 1.3 67.0 + - - +
344D TYR* 3.2 20.5 + - - +
345D LEU* 2.9 69.2 + - + +
383D PRO* 3.6 9.7 - - - +
384D GLY 3.6 3.2 + - - -
407D LEU 5.4 0.2 - - - +
408D ILE* 5.6 0.2 - - - -
409D PRO* 3.6 25.5 - - + +
413D GLN* 6.0 1.4 - - - +
482D LEU* 3.8 8.7 - - - +
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Residues in contact with GLN 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ASN* 3.0 21.9 + - + +
188C ASP* 2.9 20.3 + - + +
190C THR* 4.2 8.7 - - + -
191C HIS* 4.0 37.1 + - + +
194C LYS* 4.3 16.4 - - - +
342D ASP* 1.3 69.4 - - - +
344D TYR* 1.3 66.4 + - - +
346D HIS* 2.9 48.5 + - + +
383D PRO* 4.3 2.7 - - - +
386D ASN* 2.9 30.0 + - - +
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Residues in contact with TYR 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C THR* 3.4 37.9 - - + +
194C LYS* 4.0 22.6 - - + +
166D MET 4.6 0.5 - - - +
169D GLU* 3.3 19.9 - - - +
170D ALA* 3.2 40.7 + - - +
172D LYS* 3.6 20.9 - - + +
173D PRO* 3.4 31.4 - - + +
342D ASP* 3.2 16.6 + - - +
343D GLN* 1.3 78.5 - - - +
345D LEU* 1.3 56.4 + - - +
346D HIS* 3.2 10.0 + - - -
347D ARG 4.7 0.5 + - - -
413D GLN* 4.0 11.7 - - + -
414D HIS* 2.5 29.7 + + - -
482D LEU* 4.9 2.5 - - + -
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET* 4.8 2.7 - - - -
170D ALA* 3.9 15.0 - - + -
340D PRO* 3.6 32.5 - - + +
342D ASP* 2.9 33.1 + - + +
344D TYR* 1.3 74.6 - - - +
346D HIS* 1.3 63.3 + - - +
347D ARG 3.0 4.8 + - - +
348D PHE* 3.0 46.9 + - + +
349D ALA 4.7 0.2 + - - -
383D PRO* 5.1 0.2 - - - +
407D LEU* 5.6 2.9 - - + +
409D PRO* 5.7 0.2 - - + -
479D PHE* 4.5 15.5 - - + -
482D LEU* 3.6 30.7 - - + -
487D LEU* 3.9 10.3 - - + -
490D LEU* 5.6 1.8 - - + -
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Residues in contact with HIS 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C LYS* 6.1 2.1 + - - -
165D LEU* 5.8 0.2 - - + -
169D GLU* 2.7 37.7 + - + +
343D GLN* 2.9 41.7 + - + +
344D TYR* 3.1 12.6 - + - -
345D LEU* 1.3 77.7 - - - +
347D ARG* 1.3 93.7 + - + +
348D PHE 3.5 0.4 + - - -
349D ALA* 5.1 2.6 + - - +
350D ALA* 5.4 0.7 + - - +
382D GLU* 4.6 4.3 - - - +
383D PRO* 3.6 34.4 - - + +
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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