Contacts of the helix formed by residues 238 - 250 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LEU 4.2 0.4 + - - -
237A GLU* 1.3 75.7 - - + +
239A THR* 1.3 54.8 + - - +
240A VAL 3.2 2.9 + - - -
241A HIS* 3.3 33.8 + - - +
242A ALA* 2.8 34.4 + - + +
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLU* 3.5 39.9 + - + +
230A GLY* 3.7 23.6 - - - -
231A GLU* 4.2 1.3 - - + +
235A LEU* 3.2 16.0 + - - +
236A LEU 3.1 21.3 + - - -
237A GLU 3.8 4.0 - - - -
238A ASP* 1.3 75.0 - - - +
240A VAL* 1.3 57.8 + - - +
242A ALA* 3.7 2.8 - - - +
243A THR* 2.8 35.3 + - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU* 4.0 28.3 - - + +
226A ALA* 4.1 22.1 - - + +
227A GLU* 3.7 27.4 - - - +
238A ASP 3.2 0.8 + - - -
239A THR* 1.3 71.8 - - - +
241A HIS* 1.3 68.2 + - + +
243A THR* 3.4 3.5 + - - -
244A ALA* 3.1 21.7 + - - +
264A ILE* 4.1 13.6 - - + +
266A ARG* 4.7 8.7 - - - +
272A LEU* 3.8 21.7 - - + +
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Residues in contact with HIS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASP* 3.3 31.7 + - - +
240A VAL* 1.3 77.1 - - + +
242A ALA* 1.3 66.0 + - - +
244A ALA* 3.2 3.4 + - - -
245A ARG* 3.0 19.5 + - - +
266A ARG* 6.3 0.8 - - - -
272A LEU* 3.7 36.5 - - + +
281A ILE* 3.1 43.5 - - + +
283A GLN* 5.5 5.1 - - + -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU* 3.8 22.3 - - + +
237A GLU 4.0 12.8 - - - +
238A ASP* 2.8 24.6 + - + +
239A THR 3.7 3.4 - - - +
241A HIS* 1.3 73.2 - - - +
243A THR* 1.3 56.6 + - - +
245A ARG* 3.4 7.7 + - - +
246A TYR* 2.8 30.7 + - - +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 5.4 0.2 - - + -
226A ALA* 3.0 39.1 + - + +
229A TYR* 3.5 24.0 - - + -
230A GLY* 3.3 15.8 - - - -
235A LEU* 3.8 8.2 - - - +
239A THR 2.8 25.9 + - - -
240A VAL 3.6 5.2 - - - -
241A HIS 3.2 0.2 - - - -
242A ALA* 1.3 70.8 - - - +
244A ALA* 1.3 60.5 + - - +
246A TYR* 3.3 1.0 + - - +
247A ILE* 2.9 44.6 + - + +
264A ILE* 5.5 2.0 - - + -
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL 3.1 13.8 + - - +
241A HIS* 3.2 8.9 + - - +
243A THR* 1.3 76.8 - - - +
245A ARG* 1.3 62.7 + - - +
247A ILE* 4.1 0.2 - - - +
248A ALA* 3.1 25.6 + - - +
262A VAL* 4.1 16.4 - - + +
264A ILE* 4.3 17.9 - - + +
272A LEU* 5.4 6.3 - - + -
273A TYR 6.1 0.7 - - - -
274A THR* 3.8 14.1 - - + +
281A ILE* 4.1 15.9 - - + -
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Residues in contact with ARG 245 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A HIS 3.0 11.6 + - - +
242A ALA* 3.6 11.2 - - - +
244A ALA* 1.3 75.5 - - - +
246A TYR* 1.3 66.3 + - - +
248A ALA* 3.4 9.3 + - - +
249A ASP* 3.0 69.9 + - - +
274A THR* 2.8 21.1 + - - -
275A ASP 3.6 10.3 + - - -
276A SER* 4.6 1.2 + - - +
278A ASP 2.8 29.7 + - - -
279A SER* 3.5 18.7 + - - -
280A GLU 3.6 6.9 + - - -
281A ILE* 4.0 11.9 - - + +
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASP* 5.1 1.8 + - - -
229A TYR* 3.4 34.8 - + - -
233A HIS* 3.7 27.1 - + + +
235A LEU* 3.9 27.6 - - + -
242A ALA 2.8 18.8 + - - +
243A THR* 3.3 3.8 + - - +
245A ARG* 1.3 78.1 - - - +
247A ILE* 1.3 61.2 + - - +
249A ASP* 3.2 5.2 + - - +
250A LEU* 3.2 45.8 + - + +
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.1 23.3 - - + -
213A ILE* 3.8 32.2 - - + +
219A VAL* 4.0 15.5 - - + -
229A TYR* 3.7 26.2 - - + +
243A THR* 2.9 39.4 + - + +
244A ALA 4.1 2.5 - - - +
246A TYR* 1.3 73.5 - - - +
248A ALA* 1.3 59.0 + - - +
249A ASP 3.3 0.2 + - - -
250A LEU* 3.5 7.8 + - - +
260A ARG* 2.9 30.8 + - - -
262A VAL* 3.7 23.3 - - + -
264A ILE* 5.4 1.6 - - + -
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ALA 3.1 19.8 + - - +
245A ARG* 3.7 6.7 - - - +
247A ILE* 1.3 75.8 - - - +
249A ASP* 1.3 66.4 + - - +
250A LEU 4.3 0.3 - - - +
252A PHE* 5.7 0.2 - - - -
260A ARG* 3.5 16.7 + - - +
262A VAL* 3.6 18.5 - - + +
274A THR* 3.9 15.9 - - + -
275A ASP 4.1 1.3 - - - -
276A SER* 3.1 35.1 - - - +
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Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ARG* 3.0 54.7 + - - +
246A TYR* 3.2 4.5 + - - +
247A ILE 3.2 0.2 - - - -
248A ALA* 1.3 77.3 - - - +
250A LEU* 1.3 68.7 + - - +
251A PRO* 3.3 6.8 - - - +
276A SER* 3.8 15.6 - - - +
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASP* 4.1 18.4 - - + +
213A ILE* 3.8 23.8 - - + -
214A SER* 5.6 1.6 - - - +
229A TYR* 3.5 24.7 - - - +
246A TYR* 3.2 41.7 + - + +
247A ILE* 3.8 2.7 - - - +
248A ALA 4.3 0.3 - - - +
249A ASP* 1.3 78.1 - - - +
251A PRO* 1.3 82.0 - - + +
252A PHE* 3.6 3.1 + - - -
260A ARG* 2.2 36.8 + - - +
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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