Contacts of the helix formed by residues 256 - 265 (chain A) in PDB entry 2O7R
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A PRO* 3.2 38.9 - - + +
255A LEU* 1.3 77.5 - - - +
257A SER* 1.3 59.1 + - - +
259A ASP* 2.8 46.5 + - - +
260A LYS* 3.7 2.3 + - - +
292A LYS* 4.9 6.7 - - - +
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Residues in contact with SER 257 (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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180A LEU* 4.0 42.5 + - - +
183A ALA* 5.1 1.6 - - - +
255A LEU* 3.1 3.1 - - - +
256A TYR* 1.3 78.7 - - - +
258A PHE* 1.3 60.2 + - - +
259A ASP 3.1 0.2 - - - -
260A LYS* 3.1 11.9 + - - +
261A ILE* 3.0 28.9 + - - +
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Residues in contact with PHE 258 (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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176A TYR* 3.3 32.3 - + - -
180A LEU* 4.2 7.0 - - + -
255A LEU* 3.0 50.9 + - + +
257A SER* 1.3 80.9 - - - +
259A ASP* 1.3 61.0 + - - +
261A ILE* 3.3 12.2 + - + +
262A ARG* 2.9 32.1 + - - +
285A LEU* 3.9 11.7 - - + -
288A ARG* 3.8 16.8 - - + -
289A LEU* 3.8 46.2 - - + -
292A LYS* 3.7 17.7 - - + -
294A VAL* 3.7 5.4 - - + +
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Residues in contact with ASP 259 (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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255A LEU 4.0 0.2 + - - -
256A TYR* 2.8 30.7 + - - +
258A PHE* 1.3 78.7 - - - +
260A LYS* 1.3 55.5 + - - +
262A ARG* 3.1 37.3 + - - +
263A SER* 2.9 30.9 + - - -
292A LYS* 2.7 32.7 + - - +
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Residues in contact with LYS 260 (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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183A ALA* 2.9 44.4 + - + +
184A ALA* 4.0 15.2 + - - +
186A ALA* 4.9 3.9 - - - +
256A TYR 3.7 0.8 + - - +
257A SER* 3.1 15.4 + - - +
259A ASP* 1.3 75.5 - - - +
261A ILE* 1.3 60.8 - - - +
263A SER* 3.3 9.3 + - - +
264A LEU* 2.9 55.9 + - + +
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Residues in contact with ILE 261 (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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176A TYR* 5.6 1.1 - - + -
180A LEU* 3.8 29.6 - - + -
183A ALA* 4.4 7.6 - - + -
197A LEU* 4.6 16.2 - - + -
257A SER 3.0 17.1 + - - +
258A PHE* 3.7 21.1 - - + +
260A LYS* 1.3 75.9 - - - +
262A ARG* 1.3 61.6 + - - +
264A LEU* 3.4 2.5 + - - -
265A GLY 3.1 16.8 + - - -
266A TRP* 3.1 53.7 + - + +
268A VAL* 4.3 5.6 - - + -
289A LEU* 4.7 6.3 - - + -
294A VAL* 3.9 25.4 - - + -
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Residues in contact with ARG 262 (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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258A PHE 2.9 18.2 + - - +
259A ASP* 3.1 45.0 + - - +
261A ILE* 1.3 75.5 - - - +
263A SER* 1.3 61.1 + - - +
265A GLY* 2.9 21.8 + - - -
266A TRP 5.3 1.8 - - - +
292A LYS* 2.8 38.4 + - - +
293A GLY* 3.6 21.1 - - - +
294A VAL* 4.1 15.3 - - + +
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Residues in contact with SER 263 (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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259A ASP 2.9 18.8 + - - -
260A LYS* 3.7 13.3 - - - +
262A ARG* 1.3 82.7 - - - +
264A LEU* 1.3 61.6 + - - +
265A GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 264 (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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183A ALA* 3.9 17.3 - - + +
186A ALA* 3.8 30.5 - - + -
194A ILE 5.3 0.2 - - - +
260A LYS* 2.9 37.2 + - + +
261A ILE 3.9 1.6 - - - +
262A ARG 3.3 0.2 - - - -
263A SER* 1.3 77.9 - - - +
265A GLY* 1.3 60.0 - - - +
266A TRP* 3.3 42.2 + - + +
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Residues in contact with GLY 265 (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 LYS* 4.2 2.6 - - - +
261A ILE 3.1 0.4 + - - -
262A ARG 2.9 17.5 + - - -
263A SER 3.2 1.1 - - - -
264A LEU* 1.3 78.6 - - - +
266A TRP* 1.3 68.1 + - - +
267A ARG* 3.5 9.5 + - - +
295A ASP* 5.8 0.8 - - - +
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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