Contacts of the helix formed by residues 258 - 263 (chain E) in PDB entry 2OJW
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 THR 258 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127E GLN* 3.6 20.9 - - + +
128E HIS 4.2 0.7 - - - -
129E PRO* 4.8 2.2 - - + -
256E PHE* 4.3 4.9 - - + -
257E SER* 1.3 76.5 - - - +
259E LYS* 1.3 65.9 + - - +
260E ALA* 3.8 9.1 + - - +
261E MET* 2.9 45.7 + - + +
262E ARG* 3.1 20.9 + - - +
269E TYR* 5.3 0.5 - - - +
360E LEU* 3.7 42.0 - - + -
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Residues in contact with LYS 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ASN 4.3 7.9 + - - +
127E GLN* 2.9 24.3 + - - +
128E HIS* 4.1 20.0 - - + -
258E THR* 1.3 69.4 - - - +
260E ALA* 1.3 55.9 + - - +
262E ARG* 3.3 25.5 + - - +
263E GLU* 3.1 49.2 + - + +
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Residues in contact with ALA 260 (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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258E THR* 3.2 9.2 + - - +
259E LYS* 1.3 75.6 - - - +
261E MET* 1.3 63.4 + - - +
262E ARG 3.3 0.5 + - - -
263E GLU* 3.3 26.2 + - - +
264E GLU 5.1 0.2 - - - +
266E GLY* 3.3 13.9 - - - -
269E TYR* 3.7 34.3 - - + -
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Residues in contact with MET 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E PHE* 4.2 10.3 - - + +
257E SER* 3.8 10.1 - - - -
258E THR* 2.9 44.9 + - + +
260E ALA* 1.3 77.2 - - - +
262E ARG* 1.3 53.3 + - - +
266E GLY* 3.4 22.6 - - - -
269E TYR* 4.0 13.2 - - + +
270E ILE* 3.9 32.0 - - + +
273E ALA* 3.9 25.4 - - + -
334E LYS* 3.4 1.9 - - - -
335E GLY 2.8 38.1 + - - +
337E PHE* 4.2 11.9 - - + -
360E LEU* 4.9 6.3 - - + -
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Residues in contact with ARG 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E HIS* 3.1 29.3 + - - +
130E TRP* 3.5 52.9 - - - +
257E SER* 3.0 50.2 + - - +
258E THR 3.1 10.3 + - - +
259E LYS* 3.3 28.0 - - - +
260E ALA 3.2 0.2 - - - -
261E MET* 1.3 75.3 - - - +
263E GLU* 1.3 65.1 + - - +
334E LYS* 3.5 18.1 + - - +
335E GLY* 3.9 11.7 - - - +
501E ADP 3.7 6.5 - - - +
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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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259E LYS* 3.1 51.9 + - + +
260E ALA* 3.3 18.8 + - - +
262E ARG* 1.3 82.0 - - - +
264E GLU* 1.3 70.6 + - - +
266E GLY* 3.1 7.3 + - - -
269E TYR* 6.0 0.7 - - - -
334E LYS* 3.1 16.6 - - - +
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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