Contacts of the helix formed by residues 247 - 261 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C ASP* 3.0 35.9 + - - +
246C LEU* 1.3 107.3 - - + +
248C ALA* 1.3 56.9 + - - +
249C ASN 3.4 1.8 - - - -
250C LYS* 3.3 11.7 + - + +
251C ASN* 2.9 42.1 + - - +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C VAL* 3.6 5.3 - - + +
238C VAL* 3.9 9.7 - - - +
239C ALA* 3.6 29.4 - - + +
244C ASP 3.4 17.0 + - - +
245C TYR 3.2 11.3 + - - +
246C LEU 3.5 0.2 - - - -
247C HIS* 1.3 77.4 - - - +
249C ASN* 1.3 58.4 + - - +
251C ASN* 3.8 1.6 - - - +
252C ALA* 2.9 33.6 + - - +
273C PHE* 4.0 13.0 - - + -
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Residues in contact with ASN 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C VAL* 3.6 22.6 - - - +
245C TYR 4.7 1.6 + - - -
246C LEU 5.2 0.8 + - - -
247C HIS 3.4 0.6 - - - -
248C ALA* 1.3 77.7 - - - +
250C LYS* 1.3 63.2 + - - +
252C ALA* 3.5 2.6 + - - +
253C MSE 3.1 30.4 + - - +
269C LEU 4.7 3.8 - - - +
270C THR 5.1 1.6 + - - +
272C THR* 5.2 2.8 - - - +
273C PHE* 4.4 16.1 - - - +
274C GLY 4.8 1.4 + - - -
277C ASP* 2.9 28.8 + - - +
278C PHE* 3.5 45.8 - - + +
281C SER* 4.4 9.2 - - - +
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C HIS* 3.3 12.2 + - + +
248C ALA 3.3 0.2 - - - -
249C ASN* 1.3 76.2 - - - +
251C ASN* 1.3 70.1 + - - +
253C MSE 3.2 11.2 + - + +
254C ASP* 3.0 36.3 + - - +
281C SER* 4.2 22.4 + - - +
283C ARG* 6.0 3.1 - - - +
286C TYR* 3.1 46.9 + - + +
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Residues in contact with ASN 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C VAL* 4.0 15.0 - - + +
244C ASP* 3.9 11.9 + - - +
247C HIS* 2.9 40.6 + - - +
248C ALA* 3.9 4.1 - - - +
250C LYS* 1.3 79.8 + - - +
252C ALA* 1.3 56.3 + - - +
254C ASP* 3.4 11.2 + - - +
255C CYS* 2.9 37.4 + - - -
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C TRP* 3.0 33.3 + - + +
235C VAL* 3.6 23.6 - - + -
238C VAL* 4.1 11.8 - - + +
248C ALA 2.9 18.7 + - - +
249C ASN* 3.6 5.2 - - - +
251C ASN* 1.3 77.8 - - - +
253C MSE 1.3 58.1 + - + +
255C CYS* 3.5 0.6 + - - -
256C TRP* 3.0 24.4 + - - +
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Residues in contact with MSE 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ASN 3.1 18.7 + - - +
250C LYS* 3.2 10.3 + - - +
252C ALA* 1.3 75.7 - - + +
254C ASP* 1.3 65.6 + - - +
256C TRP* 3.3 1.3 + - - +
257C ILE* 2.9 32.3 + - - +
278C PHE* 3.9 30.3 - - + -
281C SER* 3.7 40.4 - - - +
282C PHE* 4.2 2.2 - - - +
286C TYR* 3.8 38.8 - - + -
290C TYR* 3.5 33.2 - - + +
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Residues in contact with ASP 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LYS* 3.0 36.5 + - - +
251C ASN* 3.6 14.5 - - - +
253C MSE 1.3 75.2 - - - +
255C CYS* 1.3 59.9 + - - +
257C ILE* 3.8 3.1 - - - +
258C ASN* 2.9 43.9 + - - +
286C TYR* 2.6 29.6 + - - -
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Residues in contact with CYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASN* 3.9 19.5 + - - +
27C PHE* 4.4 19.3 - - - -
234C TRP* 3.7 22.2 - - + -
238C VAL* 5.5 1.3 - - - -
251C ASN* 2.9 25.2 + - - +
252C ALA* 5.3 0.4 - - - -
254C ASP* 1.3 79.9 - - - +
256C TRP* 1.3 55.8 + - - +
258C ASN* 3.4 10.4 + - - +
259C THR* 2.8 33.1 + - - -
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Residues in contact with TRP 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 3.8 29.8 - - + -
19C MSE 4.1 14.8 - - + -
22C ALA* 3.7 23.8 - - + -
229C THR 4.9 0.7 - - - -
230C VAL* 3.8 43.6 - - + +
234C TRP* 3.7 26.1 - + + +
252C ALA 3.0 17.7 + - - +
253C MSE 3.7 3.8 - - - +
255C CYS* 1.3 75.1 - - - +
257C ILE* 1.3 64.5 + - - +
259C THR* 3.2 4.1 + - - -
260C PHE* 3.1 53.1 + + + +
264C ASN 4.3 2.8 + - - -
265C ALA* 3.4 36.8 + - + +
290C TYR* 4.0 17.0 - + - +
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Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C MSE 2.9 20.7 + - - +
254C ASP* 4.0 3.1 - - - +
256C TRP* 1.3 79.6 - - + +
258C ASN* 1.4 61.7 + - - +
261C GLY* 2.8 33.3 + - - +
262C ALA* 3.8 25.8 - - + +
265C ALA* 4.2 19.1 - - + -
285C PRO* 5.9 2.2 - - + -
286C TYR* 3.9 27.6 - - + -
289C ALA* 4.3 15.5 - - + -
290C TYR* 4.1 17.9 - - + +
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Residues in contact with ASN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASN* 5.4 4.2 + - - +
254C ASP* 2.9 35.3 + - - +
255C CYS* 3.6 10.5 - - - +
257C ILE* 1.4 79.8 - - - +
259C THR* 1.3 62.3 + - - +
261C GLY 4.7 0.9 + - - -
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Residues in contact with THR 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA 4.3 0.2 - - - +
22C ALA* 4.1 8.6 - - - -
25C THR* 3.9 19.5 - - - +
26C ASN* 2.8 21.8 + - - -
79C TYR 4.2 2.9 - - - +
81C PRO* 3.9 28.4 - - + +
255C CYS 2.8 21.4 + - - -
256C TRP* 3.6 5.6 - - - -
257C ILE 3.1 0.2 - - - -
258C ASN* 1.3 81.3 - - - +
260C PHE* 1.3 90.6 + - + +
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Residues in contact with PHE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 3.3 29.6 - - - -
21C ALA* 4.0 8.1 - - + -
22C ALA* 4.1 3.1 - - + -
79C TYR* 3.5 45.9 - + + +
80C LEU* 4.2 10.5 - - + -
81C PRO* 4.0 12.6 - - + -
256C TRP* 3.1 66.2 + + + +
259C THR* 1.3 98.9 - - + +
261C GLY* 1.3 62.0 + - - +
264C ASN* 2.8 36.6 + - + +
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Residues in contact with GLY 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ILE* 2.8 24.0 + - - +
258C ASN 4.6 0.8 + - - -
259C THR 3.7 0.8 - - - -
260C PHE* 1.3 75.9 - - - +
262C ALA* 1.4 68.5 + - - -
263C LYS 3.3 2.9 - - - -
264C ASN* 2.9 18.7 + - - -
265C ALA* 3.6 5.2 + - - -
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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