Contacts of the strand formed by residues 239 - 246 (chain A) in PDB entry 3ONA
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 LYS 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A HIS* 2.9 28.8 - - - +
202A GLU* 2.9 45.7 + - + +
203A ASP* 2.9 20.5 + - - +
237A GLN* 2.8 42.8 + - - +
238A CYS* 1.3 76.1 - - - +
240A ILE* 1.3 61.5 + - - +
241A ASN* 4.1 8.3 + - - +
267A SER* 3.4 17.0 - - - +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 4.5 5.8 - - + -
168A VAL* 4.8 5.2 - - + -
199A LEU* 3.6 20.2 - - + -
200A THR 3.7 0.9 - - - -
201A HIS* 3.7 22.9 - - + -
204A CYS* 3.7 13.5 - - - -
208A PHE* 4.2 19.7 - - + -
238A CYS* 4.1 6.7 - - - -
239A LYS* 1.3 72.6 - - - +
241A ASN* 1.3 67.8 + - - +
242A LEU* 4.9 4.0 - - + +
267A SER 2.8 10.8 + - - +
268A GLU* 3.1 5.4 - - + +
269A THR 2.8 27.0 + - - +
284A ILE* 4.3 20.4 - - + -
286A TYR* 3.4 27.4 - - + +
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Residues in contact with ASN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR 3.7 0.3 - - - +
199A LEU* 3.4 5.9 - - - +
200A THR* 2.7 62.8 + - - +
201A HIS* 4.6 2.4 - - - +
202A GLU* 5.4 4.9 + - - +
239A LYS* 4.5 11.8 + - - +
240A ILE* 1.3 76.2 - - - +
242A LEU* 1.3 60.8 + - - +
269A THR* 3.5 22.5 + - + +
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 4.0 18.2 - - + -
170A ILE* 3.4 30.5 - - + -
197A ILE* 4.6 4.9 - - + -
198A THR 3.4 4.3 - - - +
199A LEU* 3.5 39.3 - - + -
224A PHE* 4.5 8.1 - - + -
240A ILE* 4.1 5.4 - - + -
241A ASN* 1.3 73.7 - - - +
243A GLU* 1.3 56.1 + - - +
244A ILE* 3.7 22.2 - - + -
269A THR* 2.8 13.5 + - - +
270A VAL* 3.2 11.4 - - + +
271A THR* 2.7 33.4 + - - +
282A VAL* 4.1 10.5 - - + -
284A ILE* 5.8 2.0 - - + -
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A THR* 3.7 2.4 - - - +
197A ILE* 3.4 5.4 - - - +
198A THR* 3.0 52.2 + - + +
241A ASN 4.2 0.2 - - - -
242A LEU* 1.3 75.4 - - - +
244A ILE* 1.3 67.3 + - - +
245A LYS* 3.7 23.7 - - - +
271A THR* 3.3 24.1 - - + +
273A VAL* 4.2 14.3 - - + +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ILE* 4.8 7.0 - - + -
172A MET* 4.8 10.3 - - - -
195A LEU* 4.2 18.8 - - + -
196A THR 3.7 2.0 - - - -
197A ILE* 4.0 21.3 - - + -
242A LEU* 3.7 22.4 - - + +
243A GLU* 1.3 82.1 - - - +
245A LYS* 1.3 55.2 + - - +
246A CYS* 5.5 1.7 - - - -
270A VAL* 3.7 30.7 - - + -
271A THR 2.8 11.8 + - - +
272A VAL* 3.4 14.3 - - + +
273A VAL 2.8 33.7 + - - +
277A LEU* 5.1 4.9 - - + -
280A LEU* 4.9 12.8 - - + -
282A VAL* 4.6 7.6 - - + -
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 3.3 9.3 - - - +
196A THR* 2.8 48.2 + - - +
243A GLU* 3.7 18.8 - - - +
244A ILE* 1.3 74.6 - - - +
246A CYS* 1.3 80.5 + - - +
247A ASN* 4.8 9.8 + - - +
249A GLY* 3.2 34.8 + - - +
250A ARG* 4.6 0.6 - - - +
273A VAL* 3.1 35.2 - - + +
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Residues in contact with CYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLU 3.9 5.8 - - - +
195A LEU* 4.4 3.6 - - - -
244A ILE* 5.5 1.8 - - - -
245A LYS* 1.3 99.4 + - - +
247A ASN* 1.3 63.3 + - - +
248A SER* 3.0 21.7 + - - +
249A GLY 3.6 0.2 + - - -
272A VAL* 6.2 1.8 - - - -
273A VAL 2.9 22.6 + - - +
274A GLY* 4.0 5.6 - - - -
275A ASP 4.2 0.2 - - - -
276A CYS* 2.0 56.8 - - + -
277A LEU* 5.6 0.7 - - - -
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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