Contacts of the strand formed by residues 246 - 250 (chain C) in PDB entry 4J2X
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 PHE 246 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LYS* 3.1 4.6 - - - -
213C VAL* 2.7 57.1 + - + +
214C ALA* 4.8 2.7 - - - -
215C LEU* 5.1 6.7 - - + -
229C LEU* 3.3 56.1 - - + -
230C HIS* 4.0 9.0 - - - -
231C VAL* 4.0 3.6 - - + -
236C PHE* 3.5 25.8 - + - -
244C GLY* 3.6 15.5 - - - -
245C ALA* 1.3 73.4 - - - +
247C TYR* 1.3 69.3 + - - +
248C ILE 3.5 0.9 + - - -
276C LEU* 4.5 12.8 - - + -
277C VAL 3.5 7.6 - - - +
278C CYS* 3.8 32.8 - - + -
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Residues in contact with TYR 247 (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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210C GLY 3.3 26.7 - - - +
211C THR 3.3 3.4 - - - -
212C LYS* 3.8 25.6 - - + +
246C PHE* 1.3 73.0 - - - +
248C ILE* 1.3 61.1 + - - +
249C HIS* 3.3 30.5 - + + +
275C LYS 3.3 1.2 - - - +
276C LEU* 3.2 6.6 - - - -
277C VAL* 2.8 54.9 + - + +
278C CYS 4.7 0.4 - - - -
279C SER* 3.6 28.4 + - - -
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ILE* 3.6 26.2 - - + -
208C ALA 4.3 3.1 - - - +
209C SER* 3.4 5.5 - - - -
210C GLY 2.9 21.9 + - - -
211C THR 2.9 20.9 + - - +
213C VAL* 4.0 11.0 - - + -
247C TYR* 1.3 72.2 - - - +
249C HIS* 1.3 60.6 + - - +
268C ILE* 4.0 27.3 - - + +
274C VAL* 3.9 21.5 - - + -
275C LYS 3.5 2.0 - - - -
276C LEU* 3.9 24.0 - - + -
290C ILE* 4.1 17.9 - - + -
314C PHE* 4.9 0.4 - - + -
356C ILE* 4.1 14.6 - - + -
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Residues in contact with HIS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C SER* 3.7 2.2 + - - -
210C GLY* 3.8 20.8 + - - -
247C TYR* 3.3 33.0 - + + +
248C ILE* 1.3 71.9 - - - +
250C LEU* 1.3 60.5 + - - +
251C LEU* 3.7 0.8 + - + -
261C PHE* 4.4 1.3 - + - -
263C VAL* 3.6 33.3 - - + +
274C VAL* 3.1 8.9 - - - -
275C LYS* 2.8 43.5 + - + +
277C VAL* 3.7 29.0 - - + +
186D VAL* 4.2 28.4 - - + +
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Residues in contact with LEU 250 (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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209C SER* 2.8 24.1 + - - +
248C ILE 4.0 0.2 + - - -
249C HIS* 1.3 71.5 - - - +
251C LEU* 1.3 74.0 + - - +
263C VAL* 3.4 4.2 - - - -
264C ARG* 2.8 44.1 + - + +
265C ASP 3.9 22.7 - - - +
266C GLY* 4.8 9.4 - - - +
267C TYR 4.9 1.8 - - - +
268C ILE* 3.8 9.9 - - + -
272C GLN* 3.4 47.6 - - + +
273C THR 3.7 9.9 - - - +
274C VAL* 4.4 0.2 - - - -
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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