Contacts of the strand formed by residues 250 - 254 (chain B) in PDB entry 3SN6
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 CYS 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B THR 3.0 9.0 - - - +
244B GLY* 4.0 0.2 - - - -
249B THR* 1.3 73.4 - - - +
251B ARG* 1.3 65.4 + - - +
263B THR* 3.5 0.5 - - - +
264B TYR* 2.8 54.2 + - + +
273B ILE* 3.7 16.3 - - - +
276B VAL* 3.6 18.4 - - - -
285B LEU* 4.3 11.2 - - + -
287B ALA* 3.5 32.1 - - - -
289B TYR* 4.5 4.5 + - - -
297B TRP* 4.9 2.7 - - - +
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLY* 3.2 28.0 + - - -
225B HIS* 3.4 30.9 + - + +
226B GLU* 4.7 13.9 + - - +
241B PHE 3.6 0.9 - - - +
242B ALA* 3.2 6.0 - - - -
243B THR* 2.9 33.6 + - - -
247B ASP* 4.7 4.8 + - - +
249B THR* 3.4 18.6 + - - +
250B CYS* 1.3 80.5 - - - +
252B LEU* 1.3 60.7 + - - +
253B PHE* 3.4 18.6 - - + -
260B GLU* 2.7 42.6 + - - +
262B MET 3.5 5.2 - - - +
263B THR* 3.1 23.6 + - - +
264B TYR* 4.5 3.8 - - - -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.8 28.5 - - + -
235B PHE* 5.2 4.5 - - + -
240B ALA* 3.9 17.0 - - + -
241B PHE 3.2 23.6 - - - +
242B ALA* 4.4 0.9 - - - +
251B ARG* 1.3 73.8 - - - +
253B PHE* 1.3 59.3 + - - +
260B GLU* 3.2 6.6 - - - +
261B LEU* 2.8 35.6 + - + -
262B MET* 2.9 18.3 + - + +
264B TYR* 3.6 28.9 - - + +
278B PHE* 4.1 19.1 - - + -
299B ALA* 3.9 7.6 - - + +
300B LEU* 6.1 0.4 - - + -
37G LEU* 4.2 11.2 - - + -
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Residues in contact with PHE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ALA* 5.6 1.1 - - + -
222B PHE* 3.5 31.4 - + + -
223B THR 4.3 1.3 - - - -
224B GLY 3.6 26.7 - - - -
225B HIS* 4.2 6.3 - + - -
229B ILE* 5.8 0.9 - - + -
240B ALA* 3.0 6.9 - - - +
241B PHE* 2.9 72.9 + + + -
243B THR* 3.1 25.8 - - + -
251B ARG* 3.4 30.1 - - + -
252B LEU* 1.3 76.7 - - - +
254B ASP* 1.3 60.4 + - - +
259B GLN 3.6 2.7 - - - -
260B GLU* 3.5 31.0 - - + -
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Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.5 4.6 - - - -
239B ASN* 3.4 18.6 - - - +
240B ALA* 4.0 1.3 - - - -
252B LEU 4.4 0.2 + - - -
253B PHE* 1.3 74.0 - - - +
255B LEU* 1.3 59.2 + - - +
256B ARG* 3.0 16.0 + - - +
257B ALA* 2.8 34.2 + - + -
258B ASP* 2.9 26.0 + - - -
259B GLN 3.1 10.6 + - - +
261B LEU* 3.7 22.0 - - + +
33G ALA* 3.4 25.4 - - - +
37G LEU* 4.1 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