Contacts of the helix formed by residues 253 - 258 (chain C) in PDB entry 2O5J
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 ALA 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C PHE* 5.1 0.2 - - - -
250C ARG* 3.4 44.2 + - + +
252C LYS* 1.3 72.5 - - - +
254C VAL* 1.3 66.7 + - + +
256C TYR* 3.2 31.3 - - - +
257C VAL* 3.8 7.0 + - - +
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C PHE* 3.9 28.6 - - + -
242C LEU* 5.1 13.0 - - + -
250C ARG* 4.1 22.7 - - - +
253C ALA* 1.3 70.3 - - + +
255C ALA* 1.3 60.8 + - - +
256C TYR 3.0 6.3 + - - -
257C VAL* 3.3 20.9 + - + +
258C TYR* 3.7 40.7 + - + +
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C VAL* 6.3 1.1 - - + -
235C LEU* 5.8 2.2 - - + -
239C PHE* 4.4 14.3 - - + -
252C LYS* 4.1 5.3 - - - +
253C ALA 3.2 1.2 - - - -
254C VAL* 1.3 77.5 - - - +
256C TYR* 1.3 61.0 + - - +
258C TYR* 3.9 5.8 - - - -
259C GLY* 3.5 17.0 + - - -
298C PHE* 3.2 49.0 - - + -
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Residues in contact with TYR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LYS* 2.9 59.8 + - + +
253C ALA* 3.2 15.4 + - - +
254C VAL 3.0 0.2 - - - -
255C ALA* 1.3 77.3 - - - +
257C VAL* 1.3 58.9 + - + +
258C TYR 3.2 0.2 - - - -
259C GLY* 2.7 21.0 + - - -
260C LEU* 3.0 17.3 + - + +
261C ILE* 4.4 16.1 + - + +
292C ARG 4.3 2.5 - - - -
293C PHE* 3.4 48.3 + + + +
296C GLY* 5.5 1.7 - - - -
298C PHE* 4.1 10.3 - + - -
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ALA 3.9 10.5 - - - +
254C VAL* 3.3 20.4 + - + +
256C TYR* 1.3 75.3 - - + +
258C TYR* 1.3 72.8 + - + +
259C GLY 3.4 0.5 + - - -
261C ILE* 6.1 1.1 - - - -
262C ALA* 4.8 14.7 + - + +
263C ASP* 3.2 29.7 + - - +
264C PRO* 3.1 23.0 - - - +
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLY* 4.4 0.4 - - - -
170C PRO* 3.3 40.4 - - + +
186C VAL* 6.5 0.4 - - + -
242C LEU* 5.8 8.3 - - + -
254C VAL* 3.7 34.4 + - + +
255C ALA* 3.9 6.1 - - - +
256C TYR 3.2 0.6 - - - -
257C VAL* 1.3 95.4 - - + +
259C GLY* 1.3 56.9 + - - +
263C ASP* 2.8 27.6 - - + -
264C PRO* 4.2 11.1 - - - +
290C LEU* 3.7 25.5 - - - +
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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