Contacts of the helix formed by residues 261 - 266 (chain E) in PDB entry 2ONK
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 TYR 261 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252E VAL* 3.5 28.3 - - + +
253E GLU* 3.6 27.9 + - + -
258E SER* 2.9 14.3 + - - -
259E PRO 2.7 6.5 + - - -
260E ASP* 1.3 98.2 - - + +
262E ALA* 1.3 52.0 - - - +
263E GLU* 2.7 20.1 + - - +
264E LEU* 2.8 39.4 + - + -
265E TYR* 3.2 32.3 + - + -
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E SER 3.4 2.8 + - - -
259E PRO* 3.0 15.9 + - + +
261E TYR* 1.3 75.8 - - - +
263E GLU* 1.3 56.4 + - - +
265E TYR* 3.7 14.8 - - - +
266E SER* 2.8 32.6 + - - -
280E GLY 4.3 1.0 - - - +
281E LYS* 5.5 0.7 - - - -
282E PRO* 4.2 19.3 - - + -
324J VAL 4.7 2.2 - - - +
325J PRO* 4.2 13.9 - - + +
327J ARG* 6.2 2.5 - - - +
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Residues in contact with GLU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E ASP 5.7 1.1 - - - +
261E TYR* 2.7 8.4 + - - +
262E ALA* 1.3 73.7 - - - +
264E LEU* 1.3 74.0 + - + +
266E SER* 2.5 26.7 + - - +
267E LYS* 3.6 7.3 + - - +
316J ARG* 5.1 6.6 + - - -
324J VAL* 3.2 59.4 + - + +
325J PRO* 4.1 1.3 - - - -
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Residues in contact with LEU 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LEU* 3.3 11.2 - - + +
168E LEU* 5.6 0.2 - - - +
253E GLU* 3.6 37.5 - - + +
261E TYR* 2.8 44.6 + - + +
263E GLU* 1.3 83.3 - - + +
265E TYR* 1.3 57.0 + - - +
267E LYS* 2.8 36.0 + - + +
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Residues in contact with TYR 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E LEU* 4.0 11.2 - - + -
252E VAL* 2.4 39.5 + - - +
253E GLU 3.6 18.2 - - - -
256E LEU* 3.3 42.0 - - + -
257E SER 3.1 12.6 + - - -
258E SER 3.2 31.7 + - - -
261E TYR* 3.2 15.8 + - + +
262E ALA* 3.7 15.7 - - - +
264E LEU* 1.3 75.3 - - - +
266E SER* 1.3 61.6 + - - +
267E LYS 3.0 1.3 + - - -
268E VAL* 3.3 11.4 - - - +
280E GLY* 2.9 36.3 + - - +
281E LYS 3.8 13.2 - - - -
282E PRO* 4.0 2.2 - - + -
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Residues in contact with SER 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E SER* 5.0 2.4 + - - -
262E ALA 2.8 15.3 + - - -
263E GLU* 2.5 20.8 + - - +
265E TYR* 1.3 75.3 - - - +
267E LYS* 1.3 64.9 + - - +
268E VAL 3.3 1.5 + - - +
269E LYS* 5.6 0.5 - - - +
279E THR* 3.7 20.4 - - - +
280E GLY 3.5 9.4 - - - -
325J PRO* 4.3 22.5 - - - +
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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