Contacts of the helix formed by residues 343 - 348 (chain D) in PDB entry 1OL1
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 343 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D ASN 6.1 0.2 - - - -
211D ARG* 5.1 0.4 + - - -
212D ALA* 5.0 3.2 - - - +
339D LEU 4.1 10.2 - - - +
340D SER 3.3 6.3 + - - +
341D LEU 4.9 1.1 - - - -
342D ILE* 1.3 81.7 - - - +
344D ALA* 1.3 57.6 + - - +
345D ASP* 2.9 27.3 - - - +
346D PRO* 3.9 1.6 - - + -
347D TYR* 3.0 44.0 - - + +
348D LEU* 5.6 0.2 - - - +
397D THR* 4.2 14.6 + - - +
404D HIS* 3.2 34.3 + - - -
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Residues in contact with ALA 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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197D VAL 5.7 0.2 - - - +
200D MET* 5.3 0.2 - - + -
208D ASN* 3.4 26.0 + - - +
211D ARG* 3.3 32.7 - - + +
342D ILE 3.8 3.8 + - - -
343D ASP* 1.3 72.2 - - - +
345D ASP* 1.3 63.3 + - - +
346D PRO 3.6 1.1 - - - -
347D TYR 3.6 2.9 - - - -
348D LEU* 3.4 46.0 + - + +
349D LYS* 5.1 0.3 + - - +
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Residues in contact with ASP 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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208D ASN* 3.5 38.1 - - - +
343D ASP* 2.9 24.0 - - - +
344D ALA* 1.3 82.1 + - - +
346D PRO* 1.3 78.1 - - + +
349D LYS* 5.1 6.1 + - - +
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Residues in contact with PRO 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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343D ASP* 3.9 4.5 - - + +
344D ALA 4.1 0.2 - - - -
345D ASP* 1.3 107.3 - - + +
347D TYR* 1.3 85.3 + - + +
348D LEU 3.6 1.6 - - - -
349D LYS* 2.8 44.1 - - + +
350D TYR* 3.8 4.0 - - - -
393D ASP* 4.1 26.5 - - + +
397D THR* 5.6 0.4 - - - +
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Residues in contact with TYR 347 (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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340D SER* 3.8 28.9 - - - +
343D ASP* 3.0 35.0 - - + +
344D ALA* 3.5 3.2 + - - -
346D PRO* 1.3 93.5 - - + +
348D LEU* 1.3 64.6 + - + +
349D LYS 3.0 5.1 + - - -
350D TYR* 3.5 29.8 + + - +
355D ILE* 3.8 29.2 - - + +
390D CYS* 4.8 3.6 - - - -
393D ASP* 2.9 29.7 + - + -
394D LEU* 3.0 29.3 - - + +
397D THR* 2.6 32.4 + - + -
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Residues in contact with LEU 348 (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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194D LYS* 4.7 10.0 - - - +
195D PRO* 4.4 21.6 - - + +
196D LYS 4.4 4.9 - - - +
197D VAL* 3.8 30.1 - - - +
199D TYR* 3.6 37.0 - - + -
211D ARG* 4.7 3.4 - - - +
240D ASP* 4.1 19.3 - - - +
344D ALA* 3.4 35.8 + - + +
347D TYR* 1.3 78.7 - - + +
349D LYS* 1.3 62.7 + - - +
350D TYR 3.2 3.4 + - - +
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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