Contacts of the helix formed by residues 238 - 250 (chain B) in PDB entry 3VAS
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 ASP 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B LEU 3.9 1.4 + - - -
237B GLU* 1.3 74.2 - - - +
239B THR* 1.3 54.2 + - - +
240B VAL 3.2 3.2 + - - -
241B HIS* 3.3 24.5 + - + -
242B ALA* 2.8 30.4 + - + +
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Residues in contact with THR 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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227B GLU* 3.8 26.0 - - + +
230B GLY* 3.6 24.7 - - - -
231B GLU* 4.1 2.0 - - + +
235B LEU 2.8 28.4 + - - +
236B LEU* 3.4 14.7 + - - +
237B GLU 4.0 0.4 - - - -
238B ASP* 1.3 72.9 - - - +
240B VAL* 1.3 55.9 + - - +
242B ALA* 3.4 2.7 + - - +
243B THR* 2.7 40.2 + - - +
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Residues in contact with VAL 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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223B GLU* 4.2 8.5 - - + +
226B ALA* 4.1 18.2 - - + +
227B GLU* 3.8 29.4 - - + +
238B ASP 3.3 0.8 - - - -
239B THR* 1.3 74.8 - - - +
241B HIS* 1.3 65.2 + - + +
243B THR* 3.2 6.9 + - - -
244B ALA* 3.0 22.5 + - - +
264B ILE* 4.1 12.7 - - + +
266B ARG* 3.6 34.1 - - - +
272B LEU* 3.8 20.4 - - + -
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Residues in contact with HIS 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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238B ASP* 3.3 25.9 + - + +
240B VAL* 1.3 77.0 - - + +
242B ALA* 1.3 63.3 + - - +
244B ALA* 3.2 1.9 + - - -
245B ARG* 3.0 19.2 + - - +
266B ARG* 4.0 15.3 + - - -
272B LEU* 3.7 38.0 - - + +
281B ILE* 3.2 41.2 - - + +
283B GLN* 5.4 6.5 - - + -
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Residues in contact with ALA 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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235B LEU* 3.6 23.5 - - + +
237B GLU 3.7 13.7 - - - +
238B ASP* 2.8 22.2 + - + +
239B THR 3.6 4.3 - - - +
241B HIS* 1.3 73.2 - - - +
243B THR* 1.3 56.8 + - - +
245B ARG* 3.6 7.1 - - - +
246B TYR* 2.9 29.3 + - - +
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Residues in contact with THR 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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196B LEU* 5.6 0.4 - - + -
226B ALA* 3.1 35.1 + - + +
229B TYR* 3.5 25.6 - - + -
230B GLY* 3.2 17.7 - - - -
235B LEU* 3.7 7.5 - - - +
239B THR 2.7 24.5 + - - -
240B VAL* 3.5 5.8 - - - -
241B HIS 3.2 0.4 - - - -
242B ALA* 1.3 71.8 - - - +
244B ALA* 1.3 66.9 + - - +
246B TYR* 3.2 1.8 + - - +
247B ILE* 2.9 37.4 + - + +
264B ILE* 5.6 1.6 - - + -
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Residues in contact with ALA 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 VAL 3.0 12.3 + - - +
241B HIS* 3.7 9.2 - - - +
243B THR* 1.3 77.9 - - - +
245B ARG* 1.3 61.6 + - - +
247B ILE* 3.7 0.4 + - - -
248B ALA* 3.1 24.8 + - - +
262B VAL* 4.1 18.3 - - + +
264B ILE* 4.2 19.9 - - + +
272B LEU* 5.3 6.3 - - + -
274B THR* 3.8 16.0 - - + +
281B ILE* 4.5 11.9 - - + -
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Residues in contact with ARG 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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241B HIS 3.0 15.7 + - - +
242B ALA* 3.6 8.3 - - - +
244B ALA* 1.3 77.9 - - - +
246B TYR* 1.3 62.8 + - - +
248B ALA* 3.3 11.6 + - - +
249B ASP* 2.9 62.6 + - + +
274B THR* 2.9 20.8 + - - +
275B ASP 3.6 9.9 + - - -
276B SER* 4.5 1.2 + - - +
278B ASP 2.5 31.8 + - - -
279B SER* 3.8 12.9 + - - -
280B GLU 3.6 8.7 + - - -
281B ILE* 4.1 12.6 - - + +
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Residues in contact with TYR 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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210B ASP* 4.8 2.4 + - - -
229B TYR* 3.3 34.3 - + - -
233B HIS* 3.7 27.8 - + + -
235B LEU* 3.9 25.6 - - + -
242B ALA 2.9 19.0 + - - +
243B THR 3.2 4.2 + - - +
245B ARG* 1.3 78.1 - - - +
247B ILE* 1.3 61.7 + - - +
249B ASP* 3.3 4.4 + - - +
250B LEU* 3.2 47.2 + - + +
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Residues in contact with ILE 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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196B LEU* 4.2 21.5 - - + -
213B ILE* 3.9 25.3 - - + +
219B VAL* 4.1 17.0 - - + -
229B TYR* 3.7 32.5 - - + +
243B THR* 2.9 38.3 + - + +
244B ALA* 4.1 1.3 - - - +
246B TYR* 1.3 76.0 - - - +
248B ALA* 1.3 63.2 + - - +
249B ASP 3.3 0.2 + - - -
250B LEU* 3.5 6.4 + - - +
260B ARG* 2.9 27.5 + - - -
262B VAL* 3.7 24.9 - - + -
264B ILE* 5.4 2.2 - - + -
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Residues in contact with ALA 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 ALA 3.1 19.9 + - - +
245B ARG* 3.6 22.0 - - - +
247B ILE* 1.3 79.1 - - - +
249B ASP* 1.3 60.6 + - - +
250B LEU 4.3 0.3 - - - +
252B PHE* 5.7 0.2 - - - -
260B ARG* 3.6 16.6 + - - +
262B VAL* 3.6 17.2 - - + +
274B THR* 4.0 5.2 - - + -
275B ASP 4.0 4.5 - - - -
276B SER* 3.1 32.9 - - - +
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Residues in contact with ASP 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG* 2.9 52.9 + - - +
246B TYR* 3.8 3.8 - - - +
247B ILE 3.2 0.2 - - - -
248B ALA* 1.3 77.4 - - - +
250B LEU* 1.3 66.9 + - - +
251B PRO* 3.4 6.9 - - - +
276B SER* 3.5 18.9 - - - +
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Residues in contact with LEU 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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210B ASP* 4.0 17.3 - - + +
213B ILE* 3.6 23.8 - - + -
214B SER* 5.4 2.2 - - - +
229B TYR* 3.6 24.2 - - - +
246B TYR* 3.2 41.7 + - + +
247B ILE* 3.9 3.1 - - - +
248B ALA 4.3 0.3 - - - +
249B ASP* 1.3 76.8 - - - +
251B PRO* 1.3 81.1 - - + +
252B PHE* 3.5 3.1 + - - -
260B ARG* 2.1 37.9 + - - +
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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