Contacts of the helix formed by residues 242 - 248 (chain B) in PDB entry 1SXQ
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 MET 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ILE* 3.6 13.2 - - + +
239B PRO* 2.9 28.1 + - + +
241B ASN* 1.3 95.0 - - - +
243B VAL* 1.3 65.5 + - - +
244B SER 3.5 2.0 - - - -
245B GLU* 3.4 34.4 + - + +
246B LYS* 3.2 15.6 + - - +
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Residues in contact with VAL 243 (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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166B LYS* 5.8 0.9 - - - +
213B PHE* 4.2 13.7 - - + -
238B ILE* 4.0 10.1 - - + -
239B PRO 3.7 6.1 - - - +
240B MET* 3.3 18.5 + - - +
241B ASN 3.6 0.6 - - - -
242B MET* 1.3 75.9 - - - +
244B SER* 1.3 61.5 + - - +
246B LYS* 3.1 3.6 + - - +
247B ASN* 2.9 39.6 + - - +
272B GLU* 3.6 29.2 - - + +
400B UDP 3.6 41.3 - - + +
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Residues in contact with SER 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS* 3.6 25.9 + - - +
173B GLN 6.1 1.1 - - - -
175B SER* 3.7 15.9 - - - -
242B MET 3.5 0.6 - - - -
243B VAL* 1.3 78.0 - - - +
245B GLU* 1.3 66.7 + - - +
247B ASN* 3.4 1.5 + - - +
248B SER* 2.8 30.9 + - - -
272B GLU* 3.1 30.6 + - - +
275B ALA* 4.6 5.6 - - - +
276B SER* 3.7 3.7 - - - -
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Residues in contact with GLU 245 (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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175B SER* 5.0 3.4 - - - +
178B THR* 5.3 1.4 - - - +
241B ASN 3.9 6.6 - - - +
242B MET* 3.6 44.2 - - + +
243B VAL 3.2 0.2 - - - -
244B SER* 1.3 81.6 + - - +
246B LYS* 1.3 62.5 + - - +
248B SER* 3.4 18.7 + - - -
249B GLN* 3.7 12.6 + - - +
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Residues in contact with LYS 246 (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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185B ILE* 3.5 10.8 - - + +
211B GLU* 2.8 33.9 + - - -
213B PHE* 3.6 32.5 - - + -
235B THR* 4.5 2.9 + - - +
238B ILE* 3.5 33.4 - - + -
242B MET 3.2 2.2 + - - +
243B VAL 3.1 9.3 + - - +
245B GLU* 1.3 76.9 - - - +
247B ASN* 1.3 65.9 + - - +
249B GLN* 3.1 54.4 + - - +
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Residues in contact with ASN 247 (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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185B ILE* 3.8 14.8 - - + +
186B TYR* 5.4 0.3 - - - -
187B GLY 4.9 2.8 + - - -
213B PHE* 3.7 22.0 - - - -
243B VAL* 2.9 27.1 + - - +
244B SER 3.7 6.1 - - - +
246B LYS* 1.3 75.7 - - - +
248B SER* 1.3 58.3 + - - +
249B GLN 3.0 5.7 + - - -
250B ALA* 3.0 17.2 + - - +
253B ALA* 4.6 8.3 - - + +
269B ARG* 6.2 0.4 - - - +
272B GLU* 3.4 29.3 + - - +
273B THR* 3.8 13.3 + - - -
276B SER* 3.7 13.9 - - - +
278B ALA* 3.3 14.6 - - - +
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Residues in contact with SER 248 (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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175B SER* 3.2 12.8 - - - -
178B THR* 3.4 30.8 - - - -
180B LYS* 2.8 23.5 + - - +
244B SER 2.8 17.6 + - - -
245B GLU* 3.4 14.8 - - - -
246B LYS 3.1 0.4 - - - -
247B ASN* 1.3 76.0 - - - +
249B GLN* 1.3 54.4 + - - +
250B ALA 3.1 2.0 - - - -
277B ASP* 3.0 30.8 + - - +
278B ALA 4.3 1.8 - - - +
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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