Contacts of the helix formed by residues 238 - 253 (chain B) in PDB entry 2YNU
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 SER 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B ALA* 4.9 12.0 - - - +
195B GLY 3.5 18.8 + - - +
196B HIS 5.1 3.2 + - - -
197B THR 6.0 1.2 - - - -
239B ILE* 1.3 69.0 + - - +
240B SER* 2.8 15.0 + - - -
241B SER* 3.1 13.5 + - - -
242B TRP* 3.0 23.1 + - - +
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Residues in contact with ILE 239 (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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231B LEU* 4.0 23.3 - - + -
238B SER* 1.3 71.8 - - - +
240B SER* 1.3 64.2 + - - +
242B TRP* 3.4 24.6 - - + +
243B ALA* 3.8 2.9 + - - +
290B ALA 3.6 26.0 - - - +
292B SER 5.3 7.2 - - - +
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Residues in contact with SER 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 SER* 2.8 11.7 + - - -
239B ILE* 1.3 80.8 - - - +
241B SER* 1.3 69.8 + - - -
243B ALA* 3.3 17.2 + - - +
244B ASP* 3.5 7.2 - - - +
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Residues in contact with SER 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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194B ALA* 3.6 23.8 - - - -
238B SER* 3.1 10.7 + - - -
240B SER* 1.3 77.2 + - - +
242B TRP* 1.3 67.4 - - - +
243B ALA 2.7 4.7 + - - -
244B ASP* 2.8 21.3 + - - +
245B SER* 3.1 13.2 + - - -
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Residues in contact with TRP 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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194B ALA 3.5 12.2 + - - -
195B GLY* 3.5 23.1 - - - -
196B HIS* 3.7 38.8 - - + -
221B CYS 4.0 7.4 - - - -
222B LEU* 3.2 25.8 + - + +
224B ARG* 4.7 8.1 - - + -
231B LEU* 3.6 62.6 - - + -
238B SER 3.0 10.8 + - - +
239B ILE* 3.4 22.9 - - + +
240B SER 3.2 0.2 - - - -
241B SER* 1.3 77.0 - - - +
243B ALA* 1.3 60.6 + - - +
245B SER* 3.6 1.4 + - - -
246B ILE* 3.3 27.4 + - + +
286B THR* 3.9 8.1 - - + +
290B ALA* 4.3 10.3 - - + -
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Residues in contact with ALA 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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239B ILE 3.8 4.2 + - - +
240B SER 3.3 13.5 + - - +
241B SER 2.7 4.2 + - - -
242B TRP* 1.3 78.3 - - - +
244B ASP* 1.3 65.8 + - - +
245B SER 3.4 0.7 + - - -
246B ILE* 3.5 6.1 + - - +
247B LYS* 3.2 30.8 + - + +
287B ILE* 5.6 4.5 - - + +
290B ALA* 4.5 16.6 - - + +
291B GLU* 4.8 17.3 - - + -
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Residues in contact with ASP 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 SER 3.5 15.2 - - - +
241B SER* 2.8 12.6 + - - +
243B ALA* 1.3 74.8 - - - +
245B SER* 1.3 63.4 + - - +
247B LYS* 3.5 15.2 + - - +
248B ASN* 3.2 30.1 + - - +
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Residues in contact with SER 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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192B PRO* 3.5 28.3 - - - +
193B GLY* 3.0 22.7 - - - -
194B ALA 2.5 31.1 + - - -
222B LEU* 4.7 6.7 - - - -
241B SER* 3.1 6.0 + - - -
242B TRP* 3.7 7.2 - - - -
243B ALA 3.2 0.2 - - - -
244B ASP* 1.3 74.8 - - - +
246B ILE* 1.3 65.7 + - - +
247B LYS 3.1 1.3 - - - -
248B ASN* 3.0 19.1 + - - +
249B ILE* 3.3 4.8 + - - +
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Residues in contact with ILE 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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222B LEU* 3.2 39.0 - - + +
223B VAL* 4.6 6.7 - - + -
242B TRP* 3.3 24.7 - - + +
243B ALA* 3.5 8.4 + - - +
245B SER* 1.3 76.8 - - - +
247B LYS* 1.3 58.4 + - - +
249B ILE* 3.1 26.3 + - + +
250B VAL* 3.1 14.5 + - + +
283B LEU* 4.1 21.8 - - + +
286B THR* 3.4 17.9 - - + -
287B ILE* 3.5 35.4 - - + +
290B ALA* 5.8 0.4 - - + -
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Residues in contact with LYS 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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243B ALA* 3.2 20.6 + - + +
244B ASP* 3.7 16.4 - - + +
245B SER 3.1 0.8 - - - -
246B ILE* 1.3 77.5 - - + +
248B ASN* 1.3 54.2 + - - +
250B VAL* 3.3 10.8 + - + +
251B SER* 2.7 37.1 + - - -
287B ILE* 4.1 21.1 - - + +
291B GLU* 3.5 26.1 + - - -
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Residues in contact with ASN 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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190B TYR* 3.5 21.5 + - - +
192B PRO* 2.8 25.6 + - + +
244B ASP* 3.2 17.6 + - - +
245B SER* 3.0 8.6 + - - +
247B LYS* 1.3 76.1 - - - +
249B ILE* 1.3 64.0 + - - +
251B SER* 3.2 14.5 + - - -
252B LYS* 3.1 26.0 + - - +
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Residues in contact with ILE 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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190B TYR* 4.6 2.0 - - + -
192B PRO* 3.8 12.8 - - + -
202B VAL* 3.7 31.9 - - + -
217B LEU* 4.0 26.5 - - + -
222B LEU* 3.8 20.0 - - + -
223B VAL* 5.6 1.8 - - + -
245B SER 3.7 9.6 - - - +
246B ILE* 3.1 19.1 + - + +
248B ASN* 1.3 76.7 - - - +
250B VAL* 1.3 56.9 + - + +
252B LYS* 2.7 36.3 + - - +
253B LYS 3.4 2.9 + - - -
254B TYR* 4.4 17.0 - - + -
256B ILE* 5.5 0.9 - - + -
283B LEU* 4.4 18.6 - - + -
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Residues in contact with VAL 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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246B ILE* 3.1 21.3 + - + +
247B LYS* 3.5 10.5 - - - +
249B ILE* 1.3 76.7 - - - +
251B SER* 1.3 57.5 + - - +
253B LYS* 2.9 37.0 + - + +
283B LEU* 4.8 17.3 - - + -
287B ILE* 4.8 12.6 - - + -
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Residues in contact with SER 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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247B LYS* 2.7 25.2 + - - +
248B ASN* 3.2 23.8 + - - -
249B ILE 3.2 0.2 - - - -
250B VAL* 1.3 73.1 - - - +
252B LYS* 1.3 59.5 + - - +
253B LYS* 3.3 17.4 - - - +
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Residues in contact with LYS 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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179B GLU* 2.7 35.4 + - - -
190B TYR* 3.5 43.3 - - + +
248B ASN 3.1 12.5 + - - +
249B ILE* 2.7 20.3 + - - +
251B SER* 1.3 72.7 - - - +
253B LYS* 1.3 70.1 + - - +
254B TYR* 3.4 42.0 + - + +
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Residues in contact with LYS 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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249B ILE 3.4 2.8 + - - -
250B VAL* 2.9 24.8 + - + +
251B SER* 3.7 18.1 - - - +
252B LYS* 1.3 81.7 - - - +
254B TYR* 1.3 64.7 + - - +
255B PRO* 3.6 6.2 - - - +
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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