Contacts of the helix formed by residues 341 - 345 (chain C) in PDB entry 1JLH
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 341 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C PRO 2.9 7.1 + - - -
340C TYR* 1.3 77.4 - - - +
342C GLN* 1.3 66.6 + - - +
343C TYR* 3.2 21.4 - - - +
344C LEU* 3.0 59.9 + - + +
382C PRO* 3.5 16.4 - - - +
383C GLY* 4.1 2.8 + - - +
406C LEU 5.6 0.2 - - - +
407C ILE* 5.7 0.2 - - - -
408C PRO* 3.6 26.7 - - + +
412C GLN* 6.0 1.4 - - - +
424C LEU* 6.0 0.2 - - - +
481C LEU* 5.0 7.7 - - - +
185D ASN* 4.7 0.4 - - - -
187D ASP* 3.5 9.8 - - - +
189D THR* 5.3 2.4 - - - +
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Residues in contact with GLN 342 (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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341C ASP* 1.3 71.6 - - - +
343C TYR* 1.3 55.6 + - - +
345C HIS* 2.9 54.3 + - + +
382C PRO* 4.5 2.1 - - - +
385C ASN* 3.0 20.7 + - - +
185D ASN* 2.9 30.4 + - - +
187D ASP* 2.9 13.2 + - + +
189D THR* 3.2 23.1 - - - +
190D HIS* 4.0 37.1 + - + +
193D LYS* 4.2 14.4 - - - +
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Residues in contact with TYR 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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165C MET 4.6 0.9 - - - +
168C GLU* 3.3 19.5 - - - +
169C ALA* 3.1 40.7 + - - +
171C LYS* 3.6 20.6 - - + +
172C PRO* 3.2 31.6 - - + +
341C ASP* 3.2 16.2 + - - +
342C GLN* 1.3 78.8 - - - +
344C LEU* 1.3 56.5 + - + +
345C HIS* 3.1 11.0 + + - -
346C ARG 4.8 0.7 + - - -
412C GLN* 4.0 11.2 - - + -
413C HIS* 2.7 39.9 + + - -
481C LEU* 5.7 0.4 - - + -
189D THR* 3.9 15.7 + - + -
193D LYS* 3.8 36.8 - - + +
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Residues in contact with LEU 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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165C MET* 5.3 2.2 - - - -
169C ALA* 3.3 29.4 - - + -
339C PRO* 3.6 27.4 - - + +
341C ASP* 3.0 39.5 + - + +
343C TYR* 1.3 74.4 - - - +
345C HIS* 1.3 63.3 + - - +
346C ARG 3.1 4.6 + - - -
347C PHE* 3.1 38.2 + - + +
348C ALA 4.7 0.2 + - - -
382C PRO* 4.2 0.2 - - - +
406C LEU* 5.7 2.7 - - + -
408C PRO* 5.7 0.2 - - + -
478C PHE* 4.5 17.5 - - + -
481C LEU* 4.1 22.7 - - + -
486C LEU* 4.2 11.0 - - + -
489C LEU* 5.6 1.8 - - + -
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Residues in contact with HIS 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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168C GLU* 2.7 36.9 + - + +
342C GLN* 2.9 41.5 + - - +
343C TYR* 3.1 13.0 - - - -
344C LEU* 1.3 77.6 - - - +
346C ARG* 1.3 94.5 + - + +
347C PHE 3.5 0.4 - - - -
348C ALA* 5.1 2.8 + - - +
349C ALA* 5.4 0.7 + - - +
381C GLU* 4.4 4.4 - - - +
382C PRO* 3.6 35.7 - - + +
193D LYS* 6.5 0.9 - - - -
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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