Contacts of the helix formed by residues 342 - 346 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C PRO 2.9 6.7 + - - +
341C TYR* 1.3 78.3 - - - +
343C GLN* 1.3 64.8 + - - +
344C TYR* 3.0 20.6 + - - +
345C LEU* 2.8 64.8 + - + +
383C PRO* 3.6 13.7 - - - +
384C GLY 3.6 3.8 + - - -
407C LEU 5.3 0.4 - - - +
409C PRO* 3.5 27.7 - - + +
413C GLN* 6.1 0.7 - - - +
482C LEU* 4.0 7.6 - - - +
186D ASN* 4.8 0.2 - - - -
188D ASP* 3.4 9.0 - - - +
190D THR* 5.5 1.0 + - - -
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Residues in contact with GLN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C ASP* 1.3 70.2 - - - +
344C TYR* 1.3 66.5 + - + +
346C HIS* 3.0 47.1 + - + +
383C PRO* 4.3 3.8 - - - +
386C ASN* 3.1 20.6 + - - +
186D ASN* 3.0 28.7 + - + +
188D ASP* 2.8 21.7 + - + +
190D THR* 4.2 14.6 - - + -
191D HIS* 4.1 36.2 + - + +
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Residues in contact with TYR 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C MET 4.7 0.7 - - - +
169C GLU* 3.3 20.3 - - - +
170C ALA* 3.3 39.1 + - + +
172C LYS* 3.7 17.5 - - + -
173C PRO* 3.4 23.0 - - + +
342C ASP* 3.0 17.6 + - - +
343C GLN* 1.3 78.7 - - - +
345C LEU* 1.3 55.4 + - - +
346C HIS* 3.1 10.8 + - - -
347C ARG 4.7 0.5 + - - -
413C GLN* 4.0 12.3 - - + -
414C HIS* 2.6 27.4 + + - -
482C LEU* 4.9 1.8 - - + -
190D THR* 3.5 31.6 - - + +
194D LYS* 2.3 41.1 + - + +
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Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C MET* 4.9 2.7 - - - -
170C ALA* 3.9 14.1 - - + -
340C PRO* 3.7 33.4 - - + +
342C ASP* 2.8 33.4 + - + +
344C TYR* 1.3 73.7 - - - +
346C HIS* 1.3 63.4 + - - +
347C ARG 3.0 5.4 + - - -
348C PHE* 3.1 44.2 + - + +
349C ALA 4.7 0.3 + - - -
383C PRO* 4.8 0.2 - - - +
407C LEU* 5.4 3.8 - - + +
479C PHE* 4.5 19.1 - - + -
482C LEU* 3.5 28.0 - - + -
487C LEU* 4.2 8.7 - - + -
490C LEU* 5.6 2.2 - - + -
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Residues in contact with HIS 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 5.7 0.4 - - + -
169C GLU* 2.8 36.4 + - + +
343C GLN* 3.0 43.8 + - - +
344C TYR* 3.1 12.6 - + - -
345C LEU* 1.3 77.8 - - - +
347C ARG* 1.3 97.5 + - + +
348C PHE 3.5 0.4 + - - -
349C ALA* 5.1 3.0 + - - +
350C ALA 5.4 0.5 + - - -
382C GLU* 4.6 4.3 - - - +
383C PRO* 3.9 30.1 - - + +
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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