Contacts of the strand formed by residues 247 - 252 (chain m) in PDB entry 5K0Y
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 TRP 247 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2m THR* 4.1 16.8 + - - -
3m GLU* 4.0 27.6 - - + -
4m GLN* 4.8 0.7 - - - -
5m MET* 4.2 18.8 - - + -
240m CYS 4.0 0.7 - - - +
241m PHE* 3.5 5.8 - - - -
242m SER* 3.0 33.2 + - - -
245m ARG* 3.4 53.7 - - + +
246m TYR* 1.3 74.9 - - - +
248m LEU* 1.3 61.1 + - - +
249m CYS* 5.3 2.0 - - - -
258m ILE* 4.4 5.2 - - + -
259m TRP 3.3 11.9 - - - +
260m ASP* 3.2 34.7 + - - +
267m VAL* 3.6 37.5 - - + -
291m TRP* 3.9 15.9 + + + -
312m VAL* 4.5 3.1 - - + -
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Residues in contact with LEU 248 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199m THR* 4.2 1.1 - - + -
208m ALA* 3.8 33.2 - - + -
216m ALA* 4.1 14.8 - - + -
218m LEU* 4.6 9.2 - - + -
230m LEU* 4.6 7.2 - - + -
239m LEU* 4.0 20.6 - - + -
240m CYS 3.8 30.1 - - - +
241m PHE* 4.0 17.0 - - + +
247m TRP* 1.3 72.9 - - - +
249m CYS* 1.3 60.9 + - - +
258m ILE* 3.9 0.3 - - - -
259m TRP* 3.0 39.2 + - + +
261m LEU* 3.5 24.1 - - + +
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Residues in contact with CYS 249 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5m MET* 4.8 1.3 - - - -
239m LEU* 3.5 4.5 - - - +
240m CYS 3.2 32.6 + - - +
247m TRP* 5.2 2.2 - - - -
248m LEU* 1.3 76.9 - - - +
250m ALA* 1.4 60.0 + - - +
257m LYS 3.9 4.3 - - - -
258m ILE* 3.5 26.9 - - + -
289m LEU* 3.4 25.3 - - + +
291m TRP* 3.4 39.0 - - - +
298m LEU* 4.0 11.4 - - + -
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Residues in contact with ALA 250 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236m ILE* 3.9 16.6 - - + -
238m ALA 3.5 5.4 - - - -
239m LEU* 3.7 16.2 - - + -
249m CYS* 1.4 74.1 - - - +
251m ALA* 1.4 60.2 + - - +
252m THR* 3.4 4.2 + - + +
256m ILE* 3.5 2.3 - - - +
257m LYS 3.0 31.8 + - - -
259m TRP* 3.5 30.9 - - + -
289m LEU* 3.8 3.1 - - - +
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Residues in contact with ALA 251 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236m ILE* 3.7 0.7 - - - -
237m ASN* 3.0 29.5 + - + +
238m ALA 3.0 18.3 + - - +
250m ALA* 1.4 68.2 - - - +
252m THR* 1.4 62.4 + - - +
256m ILE* 4.4 6.3 - - - +
286m CYS* 3.5 39.5 - - + +
288m SER 4.6 3.6 - - - +
289m LEU* 3.6 17.3 - - + +
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Residues in contact with THR 252 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232m GLY* 5.7 2.0 - - - -
234m ASP* 3.6 21.5 - - - +
235m ILE 3.2 11.0 - - - +
236m ILE* 4.0 13.0 - - + -
237m ASN* 4.0 3.8 - - - -
250m ALA* 3.4 14.1 + - + +
251m ALA* 1.4 77.8 - - - +
253m GLY* 1.4 66.2 + - - +
254m PRO* 3.8 8.7 - - - +
255m SER 2.7 33.0 + - - +
257m LYS* 3.7 33.0 - - + +
259m TRP* 5.1 2.0 - - + -
272m GLN* 3.9 6.2 - - - +
286m CYS 4.0 8.3 + - - -
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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