Contacts of the helix formed by residues 242 - 254 (chain B) in PDB entry 3DVA
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 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A PHE* 6.1 0.7 - - - -
193B GLY 3.3 20.2 - - - +
194B LYS* 3.3 15.5 + - - +
195B ALA* 2.8 37.9 + - + +
235B LEU* 5.2 3.1 + - - +
237B THR 5.0 2.4 + - - -
240B PRO 3.9 1.4 + - - -
241B LEU* 1.3 68.7 - - - +
243B ILE* 1.3 62.1 + - - +
244B GLU* 3.5 9.9 + - - +
245B THR* 2.8 35.0 + - - -
246B ILE* 3.0 28.5 + - + +
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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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353A PHE* 3.6 36.9 - - + -
241B LEU* 3.1 22.4 + - + +
242B ASP* 1.3 71.8 + - - +
244B GLU* 1.3 65.7 + - - +
246B ILE* 3.1 8.2 + - + -
247B ILE* 2.8 34.9 + - + +
275B GLU* 4.1 26.2 - - + +
279B ARG* 3.4 47.3 - - - +
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Residues in contact with GLU 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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353A PHE* 5.0 12.2 - - + -
194B LYS* 5.6 6.1 - - - +
242B ASP* 3.7 7.0 - - - +
243B ILE* 1.3 79.4 - - - +
245B THR* 1.3 61.0 + - - +
247B ILE* 4.2 1.8 - - - +
248B GLY* 3.0 27.2 + - - -
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Residues in contact with THR 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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194B LYS* 4.2 12.3 + - - -
195B ALA* 4.2 24.4 + - + +
196B ASP* 5.1 0.7 - - - -
197B ILE* 4.2 24.2 - - + +
233B VAL* 4.3 6.8 - - + +
242B ASP* 2.8 33.2 + - - -
244B GLU* 1.3 75.7 - - - +
246B ILE* 1.3 65.4 - - - +
248B GLY* 4.1 1.0 - - - -
249B SER* 3.3 22.0 + - - -
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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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195B ALA* 5.5 0.7 - - + -
205B THR* 5.0 0.9 - - - +
207B ILE* 3.7 26.9 - - + -
233B VAL* 5.1 9.9 - - + -
235B LEU* 3.6 31.9 - - + -
241B LEU* 3.9 25.1 - - + -
242B ASP* 3.0 24.1 + - + +
243B ILE* 3.7 8.7 - - + +
245B THR* 1.3 78.0 - - - +
247B ILE* 1.3 65.0 + - + +
249B SER* 3.5 4.5 + - - -
250B VAL* 3.3 21.8 + - - +
272B VAL* 4.5 7.0 - - + -
275B GLU* 6.4 1.1 - - + -
276B ILE* 3.9 22.0 - - + -
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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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243B ILE* 2.8 42.1 + - + +
244B GLU* 4.3 1.6 - - - +
246B ILE* 1.3 72.8 - - + +
248B GLY* 1.3 60.5 + - - +
250B VAL* 3.2 3.4 + - + +
251B GLU* 2.8 52.2 + - + +
275B GLU* 4.2 2.7 - - + +
276B ILE* 3.9 37.9 - - + +
279B ARG* 4.0 23.8 - - + +
280B ALA* 4.0 15.7 - - + -
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Residues in contact with GLY 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 GLU 3.0 19.8 + - - -
245B THR* 4.1 0.9 - - - -
246B ILE 3.4 0.2 - - - -
247B ILE* 1.3 75.7 - - - +
249B SER* 1.3 60.7 + - - +
251B GLU* 3.4 16.2 + - - +
252B LYS* 3.4 19.6 + - - +
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Residues in contact with SER 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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197B ILE* 5.1 2.7 - - - -
205B THR* 2.9 33.3 + - - +
231B GLU* 2.6 33.4 + - - +
233B VAL* 4.4 7.6 - - - -
245B THR 3.3 17.1 + - - -
246B ILE 3.8 4.3 - - - -
247B ILE 3.2 0.4 - - - -
248B GLY* 1.3 77.5 - - - +
250B VAL* 1.3 56.6 + - - +
252B LYS* 3.2 6.2 + - - +
253B THR* 3.0 30.8 + - - +
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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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205B THR* 4.3 8.5 - - + +
246B ILE* 3.3 17.9 + - + +
247B ILE* 3.2 7.5 + - - +
249B SER* 1.3 73.4 - - - +
251B GLU* 1.3 61.1 + - - +
252B LYS 3.1 0.7 - - - -
253B THR* 3.6 6.1 - - - +
254B GLY* 2.8 31.6 + - - +
256B ALA* 3.9 24.9 - - + -
276B ILE* 3.9 36.8 - - + -
280B ALA* 4.4 11.9 - - + +
283B SER 4.0 2.8 - - - +
284B LEU* 3.9 20.2 - - + -
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Residues in contact with GLU 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 ILE* 2.8 42.8 + - + +
248B GLY* 3.6 13.8 - - - +
249B SER 3.3 0.2 - - - -
250B VAL* 1.3 76.0 - - - +
252B LYS* 1.3 59.8 + - - +
254B GLY* 4.6 1.3 + - - -
279B ARG 5.2 2.1 - - - +
280B ALA* 4.5 6.0 - - + +
283B SER* 4.0 27.4 - - - +
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B GLU* 4.1 12.5 + - - +
201B GLY 2.8 21.0 + - - -
202B LYS* 3.8 42.5 + - + +
231B GLU* 2.6 39.1 + - - -
248B GLY 3.4 9.1 + - - +
249B SER* 3.2 6.4 + - - +
250B VAL 3.1 0.6 - - - -
251B GLU* 1.3 81.0 - - - +
253B THR* 1.3 68.4 + - - +
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Residues in contact with THR 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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201B GLY 4.4 2.2 - - - +
202B LYS* 3.8 28.1 - - - +
203B ASP* 3.9 8.1 - - - +
204B ILE* 3.8 24.5 - - - +
205B THR* 2.7 29.5 + - - +
231B GLU* 4.7 1.6 - - + -
249B SER* 3.0 10.6 + - - +
250B VAL* 3.6 3.1 - - - -
252B LYS* 1.3 86.7 - - - +
254B GLY* 1.3 64.7 + - - +
255B ARG* 3.0 22.2 + - - +
285B GLU* 4.5 6.8 - - - +
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Residues in contact with GLY 254 (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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250B VAL 2.8 19.1 + - - -
251B GLU 4.6 0.9 - - - -
252B LYS 3.7 0.6 - - - -
253B THR* 1.3 71.3 + - - +
255B ARG* 1.3 66.0 + - - +
283B SER* 2.9 24.5 - - - +
284B LEU* 3.5 8.0 - - - +
285B GLU* 2.9 36.8 + - - +
286B ALA 3.9 0.9 + - - -
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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