Contacts of the helix formed by residues 342 - 347 (chain B) in PDB entry 1OJ7
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 HIS 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ILE* 4.0 5.8 - - - +
331B ARG* 3.3 34.6 + - - -
335B GLU* 4.2 4.4 + - - -
340B PRO 3.7 0.4 - - - -
341B THR* 1.3 89.6 + - - +
343B LEU* 1.3 66.5 + - - +
344B SER* 3.8 9.6 - - - +
345B ASP* 3.0 36.2 + - - +
346B TYR* 3.3 13.9 - - - -
385B ALA 5.3 2.4 + - - -
386B ALA* 3.5 6.9 + - - -
387B ARG* 3.7 25.0 + - + +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.0 30.7 - - + -
277B HIS* 5.8 0.2 - - + -
279B LEU* 5.1 0.2 - - + -
287B ILE* 4.0 22.7 - - + +
342B HIS* 1.3 70.4 - - - +
344B SER* 1.3 58.1 + - - +
346B TYR* 3.0 23.7 + - - +
348B LEU* 3.1 47.2 + - + +
350B GLY* 4.6 11.2 - - - +
352B SER* 6.1 0.7 - - - +
353B ILE* 4.7 7.6 - - + -
356B LEU* 5.9 1.1 - - + -
383B TYR* 3.8 26.7 - - + +
386B ALA* 2.9 19.7 + - + +
387B ARG* 3.9 16.6 - - + -
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B HIS* 3.8 8.7 - - - +
343B LEU* 1.3 74.8 - - - +
345B ASP* 1.3 65.5 + - - +
346B TYR 3.1 0.2 - - - -
347B GLY* 3.1 12.6 + - - -
348B LEU 3.3 13.9 + - - +
349B ASP* 5.8 1.6 - - - -
387B ARG* 2.9 20.0 + - - +
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLU* 4.1 2.1 - - - +
340B PRO* 3.5 31.9 - - + +
341B THR 3.5 0.9 + - - -
342B HIS* 3.0 50.3 + - - +
344B SER* 1.3 78.7 + - - +
346B TYR* 1.3 63.1 + - + +
347B GLY 3.5 0.6 + - - -
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Residues in contact with TYR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B LEU* 3.9 30.7 - - + +
283B GLN* 3.5 46.7 - - + +
287B ILE* 3.4 26.9 - - + -
339B VAL* 4.0 1.0 - - - +
340B PRO* 2.8 53.4 + - + +
342B HIS 3.3 16.8 - - - -
343B LEU 3.0 7.8 + - - +
345B ASP* 1.3 80.5 - - - +
347B GLY* 1.3 60.8 + - - +
348B LEU* 3.3 11.9 + - + +
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Residues in contact with GLY 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B SER* 3.1 14.7 + - - -
345B ASP 3.5 1.0 + - - -
346B TYR* 1.3 78.0 - - - +
348B LEU* 1.3 63.5 + - - +
349B ASP* 3.9 2.4 + - - +
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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