Contacts of the helix formed by residues 247 - 261 (chain B) in PDB entry 1VLP
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 HIS 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B ASP* 2.9 38.0 + - - +
245B TYR 3.2 0.2 - - - -
246B LEU* 1.3 101.7 - - + +
248B ALA* 1.3 63.4 + - - +
249B ASN 3.4 2.2 + - - -
250B LYS* 3.5 9.2 + - + +
251B ASN* 3.0 35.4 + - - +
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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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235B VAL* 3.9 5.2 - - + -
238B VAL* 4.0 4.1 - - + +
239B ALA* 3.6 28.9 - - + +
244B ASP 3.4 19.7 + - - +
245B TYR 3.0 12.4 + - - +
246B LEU 3.5 0.2 - - - -
247B HIS* 1.3 78.1 - - - +
249B ASN* 1.3 59.1 + - - +
251B ASN* 3.8 5.2 - - - +
252B ALA* 2.8 33.3 + - - +
273B PHE* 3.9 12.6 - - + -
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Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 3.7 22.5 - - - +
245B TYR 4.6 0.8 + - - -
246B LEU 5.3 0.6 + - - -
247B HIS 3.4 0.6 - - - -
248B ALA* 1.3 80.1 - - - +
250B LYS* 1.3 64.4 + - - +
252B ALA* 3.4 2.3 + - - +
253B MSE 3.1 30.6 + - - +
269B LEU 4.8 4.0 - - - +
270B THR 5.2 1.8 + - - +
272B THR* 5.3 2.6 + - - -
273B PHE* 4.2 19.2 - - - +
274B GLY 4.9 1.2 + - - -
277B ASP* 2.8 29.1 + - - +
278B PHE* 3.5 41.9 - - + +
281B SER* 4.3 8.5 - - - +
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B HIS* 3.5 11.5 + - + +
248B ALA 3.3 0.4 - - - -
249B ASN* 1.3 79.1 - - - +
251B ASN* 1.3 60.4 + - - +
253B MSE 3.3 12.7 + - - +
254B ASP* 2.9 36.3 + - - +
281B SER* 4.0 21.0 + - - +
286B TYR* 3.9 27.4 - - + +
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Residues in contact with ASN 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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238B VAL* 4.0 16.5 - - + +
244B ASP* 4.1 12.1 + - - +
247B HIS* 3.0 39.4 + - - +
248B ALA* 3.8 4.5 - - - +
250B LYS* 1.3 77.8 - - - +
252B ALA* 1.3 57.5 + - - +
254B ASP* 3.3 12.7 + - - +
255B CYS* 3.0 34.4 + - - -
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Residues in contact with ALA 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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234B TRP* 3.0 33.8 + - + +
235B VAL* 3.7 24.7 - - + -
238B VAL* 4.0 10.4 - - + +
248B ALA 2.8 21.5 + - - +
249B ASN* 3.6 5.2 - - - +
251B ASN* 1.3 69.3 - - - +
253B MSE 1.3 60.1 + - + +
255B CYS 3.5 0.9 + - - -
256B TRP* 3.0 26.0 + - - +
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Residues in contact with MSE 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 ASN 3.1 15.3 + - - +
250B LYS* 3.7 17.0 - - - +
252B ALA* 1.3 74.4 - - + +
254B ASP* 1.3 59.8 + - - +
256B TRP* 3.7 0.7 - - - +
257B ILE* 2.9 37.4 + - - +
268B ALA* 5.9 0.2 - - + -
278B PHE* 3.9 30.5 - - + -
281B SER* 3.5 34.1 - - - +
282B PHE* 4.2 3.1 - - - -
286B TYR* 3.6 46.9 - - + -
290B TYR* 3.6 31.6 - - + +
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Residues in contact with ASP 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 LYS* 2.9 22.1 + - - +
251B ASN* 3.5 15.9 - - - +
252B ALA 3.2 0.2 - - - -
253B MSE 1.3 77.2 - - - +
255B CYS* 1.3 58.9 + - - +
257B ILE* 3.8 3.3 - - - +
258B ASN* 2.8 46.1 + - - +
286B TYR* 2.6 35.2 + - - -
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Residues in contact with CYS 255 (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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26B ASN* 3.9 18.6 - - - +
27B PHE* 4.2 21.3 - - - -
234B TRP* 3.5 21.5 - - + -
238B VAL* 5.2 2.0 - - - -
251B ASN* 3.0 21.4 + - - +
252B ALA* 3.9 0.9 - - - +
254B ASP* 1.3 74.1 - - - +
256B TRP* 1.3 61.3 + - - +
258B ASN* 3.9 5.6 - - - +
259B THR* 2.6 34.6 + - - -
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Residues in contact with TRP 256 (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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18B THR* 4.0 24.0 - - + -
19B MSE 4.1 17.7 - - + -
22B ALA* 3.7 19.1 - - + -
229B THR 4.9 0.4 - - - -
230B VAL* 3.6 51.0 - - + +
234B TRP* 3.8 18.2 - + + +
252B ALA 3.0 17.9 + - - +
253B MSE 3.7 3.8 - - - +
255B CYS* 1.3 75.7 - - - +
257B ILE* 1.3 62.9 + - - +
259B THR* 3.1 4.4 + - - -
260B PHE* 3.0 59.0 + + + +
264B ASN 4.5 2.0 + - - -
265B ALA* 3.3 34.4 + - - +
290B TYR* 3.9 17.5 - + - +
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Residues in contact with ILE 257 (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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253B MSE 2.9 24.5 + - - +
254B ASP* 3.8 4.0 - - - +
256B TRP* 1.3 75.8 - - - +
258B ASN* 1.3 68.0 + - - +
261B GLY* 2.8 34.9 + - - +
262B ALA* 3.9 31.9 - - + +
265B ALA* 4.5 13.5 - - + -
285B PRO 6.1 0.2 - - - -
286B TYR* 3.7 31.9 - - + -
289B ALA* 4.7 10.3 - - + -
290B TYR* 4.2 13.5 - - + +
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Residues in contact with ASN 258 (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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26B ASN* 5.6 2.0 - - - +
254B ASP* 2.8 37.5 + - - +
255B CYS* 4.0 6.2 - - - +
257B ILE* 1.3 82.4 - - - +
259B THR* 1.3 60.3 + - - +
261B GLY 4.7 0.6 + - - -
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Residues in contact with THR 259 (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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21B ALA 4.4 0.2 - - - +
22B ALA* 4.0 7.9 - - - -
25B THR* 3.9 32.6 - - - +
26B ASN* 2.7 22.9 + - - -
79B TYR 4.4 2.1 - - - +
81B PRO* 3.8 18.6 - - + +
255B CYS 2.6 21.0 + - - -
256B TRP* 3.1 4.9 + - - -
258B ASN* 1.3 80.7 - - - +
260B PHE* 1.3 87.2 + - + +
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Residues in contact with PHE 260 (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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18B THR* 3.3 28.7 - - - -
21B ALA* 4.0 15.0 - - + -
22B ALA* 4.0 7.9 - - + -
79B TYR* 3.7 45.8 - + + +
80B LEU* 4.4 8.7 - - + -
81B PRO* 4.0 5.8 - - + -
256B TRP* 3.0 68.5 + + + +
259B THR* 1.3 95.5 - - + +
261B GLY* 1.3 62.9 + - - +
264B ASN* 2.8 34.9 + - + +
265B ALA* 5.9 0.2 - - - -
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Residues in contact with GLY 261 (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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257B ILE* 2.8 24.5 + - - +
258B ASN 4.7 0.6 + - - -
259B THR 3.8 1.0 - - - -
260B PHE* 1.3 75.8 - - - +
262B ALA* 1.3 59.2 + - - -
263B LYS 3.2 3.4 - - - -
264B ASN* 2.9 24.8 + - - +
265B ALA* 3.5 5.7 + - - -
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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