Contacts of the helix formed by residues 337 - 345 (chain D) in PDB entry 2ONL
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 337 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257D LEU 4.9 2.0 + - - -
258D CYS 4.2 1.6 - - - +
291D TRP* 3.1 37.5 + + + -
292D SER* 3.3 25.3 + - - -
335D PRO 4.7 7.6 - - - -
336D LEU* 1.3 79.2 - - - +
338D THR* 1.3 58.6 + - - +
339D SER 3.2 2.7 - - - -
340D ARG* 2.9 53.6 + - - +
341D VAL* 2.8 36.3 + - - +
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Residues in contact with THR 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PHE* 5.7 1.8 - - + -
150D ILE* 4.9 4.0 - - + -
158D PHE* 2.9 34.3 - - + -
255D ILE* 3.2 18.8 - - + +
256D LEU* 2.8 27.6 + - + +
257D LEU 3.9 1.3 + - - +
258D CYS 4.2 4.5 + - - -
259D GLY* 3.8 9.6 - - - +
336D LEU* 3.3 13.5 - - - +
337D HIS* 1.3 74.0 - - - +
339D SER* 1.3 60.4 + - - +
340D ARG 3.6 0.2 + - - -
342D LEU* 2.8 44.0 + - + +
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Residues in contact with SER 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 3.5 26.3 + - - +
151D GLN* 4.1 7.8 + - - +
153D ARG* 3.6 30.3 + - - +
155D ASP* 5.5 0.6 + - - -
156D GLN 4.8 2.2 - - - -
157D ALA* 5.0 5.2 - - - -
158D PHE* 4.8 13.2 - - - +
336D LEU 4.7 2.8 + - - -
337D HIS* 3.2 1.0 - - - +
338D THR* 1.3 78.7 - - - +
340D ARG* 1.3 58.8 + - - +
342D LEU* 4.7 0.5 - - - +
343D LYS* 3.1 27.2 + - - +
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Residues in contact with ARG 340 (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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291D TRP* 3.2 30.1 - - - +
337D HIS* 2.9 51.8 + - - +
339D SER* 1.3 78.4 - - - +
341D VAL* 1.3 55.4 + - - +
343D LYS* 3.3 4.4 + - - +
344D GLU* 2.6 48.4 + - + +
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Residues in contact with VAL 341 (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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258D CYS 3.7 18.4 - - - +
259D GLY* 3.0 26.7 - - - +
260D TYR* 3.5 23.1 - - + -
291D TRP* 3.7 20.6 - - + -
337D HIS* 2.8 18.3 + - + +
340D ARG* 1.3 74.2 - - + +
342D LEU* 1.3 61.2 + - + +
344D GLU* 2.7 38.8 + - - +
345D ASP 3.3 3.1 + - - -
348D ARG* 3.5 21.9 + - - +
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Residues in contact with LEU 342 (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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147D PHE* 3.9 36.6 - - + +
150D ILE* 4.6 5.8 - - + -
151D GLN* 3.4 41.1 - - + +
255D ILE* 5.2 3.8 - - + +
259D GLY* 3.9 28.9 - - - +
338D THR* 2.8 33.4 + - + +
340D ARG 3.5 0.2 - - - -
341D VAL* 1.3 72.9 - - - +
343D LYS* 1.3 63.1 + - - +
344D GLU 3.3 0.2 + - - -
345D ASP 3.4 20.0 + - - +
346D LYS* 3.8 1.0 + - - -
348D ARG* 5.8 1.3 - - - +
349D TRP* 4.8 23.6 - - + +
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Residues in contact with LYS 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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151D GLN* 2.6 47.2 + - - +
152D ASP* 4.3 9.5 - - - +
153D ARG 4.6 7.3 + - - +
339D SER 3.1 19.3 + - - +
340D ARG* 3.3 5.3 + - - +
341D VAL 3.2 0.4 - - - -
342D LEU* 1.3 76.9 - - - +
344D GLU* 1.3 69.0 + - - +
345D ASP* 3.1 1.4 + - - -
346D LYS* 4.2 10.2 + - - +
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Residues in contact with GLU 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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260D TYR* 5.1 2.6 + - - -
340D ARG* 2.6 25.9 + - + +
341D VAL* 2.7 24.5 + - - +
343D LYS* 1.3 74.5 - - - +
345D ASP* 1.3 57.6 + - + +
346D LYS 4.3 0.2 + - - -
348D ARG* 3.3 20.0 + - - +
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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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341D VAL 3.3 3.6 + - - -
342D LEU* 3.6 7.5 - - - +
343D LYS 3.1 0.6 + - - -
344D GLU* 1.3 82.7 - - + +
346D LYS* 1.3 58.0 + - - +
347D GLU* 2.7 29.0 + - - +
348D ARG* 2.3 79.9 + - + +
349D TRP* 3.4 5.9 + - - +
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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