Contacts of the helix formed by residues 239 - 252 (chain B) in PDB entry 1SMK
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 THR 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B PHE* 1.3 76.9 - - - +
240B GLN* 1.3 66.7 + - - +
241B GLU* 3.6 13.8 + - - +
242B GLU* 2.7 43.7 + - - +
243B ILE* 2.9 21.5 + - - +
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Residues in contact with GLN 240 (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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238B PHE 4.4 2.1 - - - +
239B THR* 1.3 73.6 - - - +
241B GLU* 1.3 59.7 + - + +
243B ILE* 3.2 27.2 + - - +
244B SER* 2.9 29.3 + - - -
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Residues in contact with GLU 241 (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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239B THR* 3.0 11.9 + - - +
240B GLN* 1.3 76.9 - - + +
242B GLU* 1.3 54.4 + - + +
244B SER* 3.0 7.8 + - - -
245B TYR* 2.7 36.8 + - - +
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Residues in contact with GLU 242 (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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204B VAL* 3.5 33.8 - - + +
237B SER 4.5 0.9 - - - +
238B PHE* 3.3 18.3 - - + +
239B THR* 2.7 47.5 + - - +
241B GLU* 1.3 74.2 - - + +
243B ILE* 1.3 58.1 + - - +
245B TYR* 4.2 9.2 - - + -
246B LEU* 2.7 42.7 + - + +
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Residues in contact with ILE 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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229B LEU* 3.9 22.2 - - + +
238B PHE* 3.5 28.9 - - + +
239B THR 2.9 13.7 + - - +
240B GLN* 3.2 34.5 - - - +
242B GLU* 1.3 75.0 - - - +
244B SER* 1.3 57.6 + - - +
247B THR* 2.8 36.2 + - - -
329B ASN* 6.0 4.3 - - - +
331B TYR* 3.4 39.9 - - + -
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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
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240B GLN 2.9 14.3 + - - -
241B GLU* 3.2 11.9 - - - -
243B ILE* 1.3 75.8 - - - +
245B TYR* 1.3 65.2 + - - +
247B THR* 3.9 1.2 - - - -
248B ASP* 3.0 27.3 + - - +
331B TYR* 4.2 11.6 + - - -
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Residues in contact with TYR 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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200B PHE* 4.8 3.8 + - - +
203B GLU* 4.3 6.6 + - - +
204B VAL* 3.8 15.9 - - + -
241B GLU 2.7 19.5 + - - +
242B GLU* 3.7 7.9 - - + +
244B SER* 1.3 71.4 + - - +
246B LEU* 1.3 85.7 + - + +
248B ASP* 3.2 8.1 + - - +
249B ARG* 2.7 86.6 + - + +
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Residues in contact with LEU 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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200B PHE* 3.6 29.6 - - + +
201B VAL* 4.0 14.4 - - + +
204B VAL* 3.6 31.0 - - + -
229B LEU* 4.2 20.2 - - + -
238B PHE* 4.0 28.5 - - + -
242B GLU* 2.7 25.5 + - + +
243B ILE 4.1 1.8 - - - +
245B TYR* 1.3 87.4 - - + +
247B THR* 1.3 61.8 + - - +
249B ARG* 4.0 2.0 - - - +
250B ILE* 2.9 35.3 + - + +
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Residues in contact with THR 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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226B LEU* 5.6 4.5 - - + -
227B PRO* 4.1 21.5 + - + +
229B LEU* 3.7 11.5 - - - +
243B ILE 2.8 22.7 + - - -
244B SER 3.9 1.3 - - - -
246B LEU* 1.3 75.7 - - - +
248B ASP* 1.3 58.5 + - - +
250B ILE* 4.0 0.7 - - - +
251B GLN* 2.7 60.0 + - + +
331B TYR* 3.5 33.3 - - + +
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Residues in contact with ASP 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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244B SER* 3.0 19.2 + - - +
245B TYR* 3.6 7.1 - - - +
247B THR* 1.3 77.9 - - - +
249B ARG* 1.3 66.9 + - - +
251B GLN* 3.2 10.1 + - - +
252B ASN* 3.0 49.6 + - - +
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Residues in contact with ARG 249 (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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89A SER* 5.0 4.6 + - - -
90A HIS* 4.4 2.6 + - - -
200B PHE* 3.3 43.3 - - + -
203B GLU* 3.7 17.0 + - - -
245B TYR* 2.7 61.2 + - + +
246B LEU* 4.0 3.1 - - - +
248B ASP* 1.3 78.7 - - - +
250B ILE* 1.3 57.5 + - - +
252B ASN* 3.4 2.9 - - - +
253B GLY* 2.9 28.1 + - - -
256B GLU* 2.8 41.5 + - - +
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Residues in contact with ILE 250 (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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193B ASP* 4.0 24.6 - - + +
196B ARG* 4.9 7.2 + - + -
197B ALA* 3.5 29.2 - - + +
200B PHE* 3.8 25.4 - - + -
201B VAL* 4.8 6.7 - - + -
216B VAL* 5.1 0.4 - - + -
225B ILE* 4.1 27.2 - - + +
227B PRO* 3.6 28.3 - - + -
229B LEU* 4.8 1.3 - - + -
246B LEU* 2.9 32.0 + - + +
247B THR 4.0 2.9 - - - +
249B ARG* 1.3 75.3 - - - +
251B GLN* 1.3 61.3 + - - +
252B ASN 3.4 0.3 + - - -
253B GLY* 3.5 8.8 + - - -
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Residues in contact with GLN 251 (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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222B GLY* 3.5 33.5 + - - +
223B VAL* 3.7 27.4 + - - +
225B ILE* 3.0 41.8 + - + +
226B LEU* 5.0 4.2 - - - +
227B PRO* 4.6 4.2 - - + +
247B THR* 2.7 47.7 + - + +
248B ASP* 3.7 7.8 - - - +
250B ILE* 1.3 77.8 - - - +
252B ASN* 1.3 66.9 + - - +
253B GLY 3.5 0.4 - - - -
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Residues in contact with ASN 252 (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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222B GLY* 5.2 4.6 - - - -
248B ASP* 3.0 44.2 + - - +
249B ARG* 3.4 5.4 - - - +
251B GLN* 1.3 86.7 + - - +
253B GLY* 1.3 66.0 + - - +
254B GLY 3.3 2.7 - - - -
255B THR* 3.2 21.3 + - + +
256B GLU* 3.1 20.9 + - - +
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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