Contacts of the helix formed by residues 247 - 261 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244D ASP* 2.8 33.6 + - - +
245D TYR 3.2 0.4 - - - -
246D LEU* 1.3 94.8 - - + +
248D ALA* 1.3 58.8 + - - +
249D ASN 3.4 2.0 - - - -
250D LYS* 3.4 11.7 + - + +
251D ASN* 2.8 49.2 + - - +
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Residues in contact with ALA 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D VAL* 4.5 3.8 - - + +
238D VAL* 4.0 4.0 - - - +
239D ALA* 3.6 31.2 - - + +
244D ASP 3.3 17.7 + - - +
245D TYR* 3.1 13.0 + - - +
247D HIS* 1.3 77.8 - - - +
249D ASN* 1.3 58.7 + - - +
251D ASN* 3.7 6.6 - - - +
252D ALA* 2.8 33.5 + - - +
273D PHE* 4.2 10.5 - - + -
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Residues in contact with ASN 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D VAL* 3.6 24.6 - - - +
245D TYR 4.7 1.2 + - - -
246D LEU 5.4 0.2 + - - -
247D HIS 3.4 0.4 - - - -
248D ALA* 1.3 78.3 - - - +
250D LYS* 1.3 63.3 + - - +
252D ALA* 3.4 4.3 + - - +
253D MSE 3.0 30.9 + - - +
269D LEU 4.8 2.3 - - - +
270D THR 5.1 1.6 + - - +
272D THR* 5.1 3.1 - - - -
273D PHE* 4.3 16.6 - - - +
274D GLY 4.9 1.2 + - - -
277D ASP* 3.0 29.2 + - - +
278D PHE* 3.6 44.3 - - + +
281D SER* 4.3 9.0 - - - +
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Residues in contact with LYS 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D HIS* 3.4 14.2 + - + +
248D ALA 3.3 0.2 - - - -
249D ASN* 1.3 76.5 - - - +
251D ASN* 1.3 66.5 + - - +
253D MSE 3.2 10.9 + - - +
254D ASP* 2.9 34.3 + - - +
281D SER* 4.1 24.0 + - - -
286D TYR* 3.2 38.1 + - + +
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Residues in contact with ASN 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 3.9 16.6 - - + +
244D ASP* 3.9 12.9 + - - +
247D HIS* 2.8 49.5 + - - +
248D ALA* 3.7 5.4 - - - +
250D LYS* 1.3 72.2 - - - +
252D ALA* 1.3 56.7 - - - +
254D ASP* 3.4 10.6 + - - +
255D CYS* 3.0 36.4 + - - -
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D TRP* 3.0 35.4 + - + +
235D VAL* 3.8 31.0 - - + -
238D VAL* 4.0 12.5 - - + +
248D ALA 2.8 18.2 + - - +
249D ASN 3.7 4.3 - - - +
251D ASN* 1.3 77.6 - - - +
253D MSE 1.3 58.2 + - + +
255D CYS* 4.7 0.4 - - - -
256D TRP* 3.0 18.7 + - - +
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Residues in contact with MSE 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ASN 3.0 17.8 + - - +
250D LYS* 3.2 9.6 + - - +
252D ALA* 1.3 75.3 - - + +
254D ASP* 1.3 66.4 + - - +
256D TRP* 3.7 0.5 - - - +
257D ILE* 2.9 31.1 + - - +
278D PHE* 4.0 30.5 - - + -
281D SER* 3.7 33.2 - - - +
282D PHE* 4.1 3.4 - - + -
286D TYR* 3.7 45.8 - - + -
290D TYR* 3.5 33.4 - - + +
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Residues in contact with ASP 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D LYS* 2.9 32.1 + - - +
251D ASN* 3.5 11.4 - - - +
253D MSE 1.3 75.7 - - - +
255D CYS* 1.3 60.9 + - - +
257D ILE* 3.9 2.9 - - - +
258D ASN* 2.9 44.2 + - - +
286D TYR* 2.5 36.5 + - - -
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Residues in contact with CYS 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASN* 3.9 16.7 + - - +
27D PHE* 4.4 19.7 - - - -
234D TRP* 3.7 21.1 - - + -
238D VAL* 5.5 2.2 - - - -
251D ASN* 3.0 23.6 + - - +
252D ALA* 4.0 0.9 - - - +
253D MSE 3.3 0.2 - - - -
254D ASP* 1.3 76.2 - - - +
256D TRP* 1.3 63.1 + - - +
258D ASN* 3.5 9.9 + - - +
259D THR* 2.8 30.8 + - - -
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Residues in contact with TRP 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D THR* 4.0 28.3 - - - -
19D MSE 4.1 14.6 - - + -
22D ALA* 3.6 21.1 - - + -
229D THR 4.9 1.1 - - - -
230D VAL* 3.9 40.6 - - + +
234D TRP* 3.7 27.2 - + + +
252D ALA 3.0 17.2 + - - +
253D MSE 3.7 3.6 - - - +
255D CYS* 1.3 74.7 - - - +
257D ILE* 1.3 64.7 + - - +
259D THR* 3.0 7.1 + - - -
260D PHE* 3.0 55.3 + + + +
264D ASN 4.4 2.6 + - - -
265D ALA* 3.4 36.3 + - - +
290D TYR* 4.1 17.7 - + - +
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Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D MSE 2.9 20.4 + - - +
254D ASP* 4.0 3.1 - - - +
256D TRP* 1.3 79.0 - - - +
258D ASN* 1.3 63.5 + - - +
261D GLY* 2.8 32.5 + - - +
262D ALA* 3.7 26.2 - - + +
265D ALA* 4.2 18.4 - - + -
285D PRO* 5.8 1.3 - - + -
286D TYR* 4.0 24.7 - - + -
289D ALA* 4.0 23.6 - - + -
290D TYR* 4.1 14.1 - - + +
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Residues in contact with ASN 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASN* 5.5 2.9 - - - +
254D ASP* 2.9 36.3 + - - +
255D CYS* 3.8 10.8 - - - +
256D TRP 3.3 0.2 - - - -
257D ILE* 1.3 79.3 - - - +
259D THR* 1.3 62.2 + - - +
261D GLY 4.8 0.3 + - - -
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Residues in contact with THR 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ALA 4.5 0.2 - - - +
22D ALA* 4.2 7.2 - - - -
25D THR* 4.0 22.1 - - + +
26D ASN* 2.7 29.6 + - - -
79D TYR 4.3 2.4 - - - +
81D PRO* 3.9 27.0 - - + +
255D CYS 2.8 10.5 + - - -
256D TRP* 3.0 9.5 + - - -
258D ASN* 1.3 80.9 - - - +
260D PHE* 1.3 88.7 + - + +
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Residues in contact with PHE 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D THR* 3.3 30.1 - - - -
21D ALA* 4.1 6.7 - - + -
22D ALA* 4.0 4.9 - - + -
79D TYR* 3.5 47.5 - + + +
80D LEU* 4.2 9.6 - - + -
81D PRO* 4.0 12.8 - - + -
256D TRP* 3.0 68.0 + + + +
257D ILE* 5.5 0.2 - - - -
259D THR* 1.3 99.1 - - + +
261D GLY* 1.3 61.1 + - - +
264D ASN* 3.1 29.9 - - + +
265D ALA* 5.9 0.2 - - - -
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Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ILE* 2.8 24.3 + - - -
258D ASN 4.7 1.0 + - - -
259D THR 3.8 0.6 - - - -
260D PHE* 1.3 75.7 - - - +
262D ALA* 1.3 60.2 + - - +
263D LYS* 3.2 3.1 - - - -
264D ASN* 2.9 24.0 + - - -
265D ALA* 3.5 5.5 + - - -
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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