Contacts of the helix formed by residues 247 - 259 (chain F) in PDB entry 3EBL
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 THR 247 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28F LYS* 5.1 11.4 - - - +
35F ARG* 5.5 0.7 + - - -
241F ASP* 3.2 8.5 - - - +
242F GLY* 4.1 14.8 - - - -
245F PHE 5.1 3.8 - - - +
246F VAL* 1.3 79.5 - - - +
248F LEU* 1.3 59.2 + - - +
249F GLN* 3.6 11.2 + - - +
250F ASP* 2.6 38.7 + - - +
251F ARG* 2.9 31.4 + - - +
297F LEU* 4.2 1.6 - - - -
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Residues in contact with LEU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F ARG* 3.8 47.3 - - + +
237F GLU* 3.8 46.9 - - + +
238F ARG* 4.6 5.2 - - + +
241F ASP* 2.8 29.7 + - + +
247F THR* 1.3 68.7 - - - +
249F GLN* 1.3 60.7 + - - +
251F ARG* 4.0 9.2 - - + -
252F ASP* 2.9 38.0 + - - +
297F LEU* 3.9 13.9 - - + +
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Residues in contact with GLN 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F ASP* 4.8 0.2 + - - -
247F THR* 3.2 10.1 - - - +
248F LEU* 1.3 79.6 - - - +
250F ASP* 1.3 56.7 + - - +
252F ASP* 3.5 6.9 + - - +
253F TRP* 3.1 25.8 + - - +
601F NO3 4.0 16.1 + - - +
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Residues in contact with ASP 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 3.6 32.9 + - - +
245F PHE 4.5 2.6 - - - +
246F VAL* 3.7 6.0 - - - +
247F THR* 2.6 46.9 + - - +
249F GLN* 1.3 73.0 - - - +
251F ARG* 1.3 107.8 + - - +
253F TRP* 3.0 7.8 + - - +
254F TYR* 2.9 30.2 + - + -
401F GA4 3.9 9.8 - - - +
601F NO3 4.2 3.1 + - - -
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Residues in contact with ARG 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F SER* 2.8 30.3 + - - -
227F MET* 3.8 25.2 - - - +
237F GLU* 6.0 1.1 - - - +
246F VAL* 3.2 20.6 - - + +
247F THR 2.9 22.1 + - - +
248F LEU* 3.7 14.1 - - + +
249F GLN 3.4 0.2 - - - -
250F ASP* 1.3 103.1 + - - +
252F ASP* 1.3 65.0 + - - +
254F TYR* 3.2 19.7 + - - +
255F TRP* 3.2 34.3 + - + +
297F LEU* 4.2 15.3 - - + -
298F THR* 4.6 13.7 - - + -
401F GA4 3.5 26.9 + - - +
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Residues in contact with ASP 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ARG* 2.8 43.3 + - - -
248F LEU 2.9 23.6 + - - +
249F GLN* 3.7 5.6 - - - +
251F ARG* 1.3 75.2 - - - +
253F TRP* 1.3 64.2 + - - +
255F TRP* 3.5 2.1 + - - +
256F LYS* 3.0 24.5 + - - +
265F ARG* 3.3 33.3 + - - +
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Residues in contact with TRP 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 3.6 31.7 - - + +
36F ARG 2.8 22.7 + - - -
37F ALA* 5.2 4.0 - - - -
39F GLY* 3.8 23.8 - - - -
40F THR 3.2 26.2 - - - -
41F PHE* 4.0 22.0 - + + -
125F VAL* 4.1 6.7 - - + -
158F PRO* 4.7 2.2 - - + -
249F GLN 3.1 13.5 + - - +
250F ASP* 3.0 10.4 + - - +
252F ASP* 1.3 77.4 - - - +
254F TYR* 1.3 82.7 + + - +
256F LYS* 3.3 10.5 + - + +
257F ALA* 3.0 37.8 + - + -
601F NO3 3.9 22.7 - - - +
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Residues in contact with TYR 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ARG* 2.9 36.7 + - + +
123F SER* 3.5 26.8 - - - +
125F VAL* 3.5 25.9 - - + +
126F HIS* 2.6 42.4 + + - -
227F MET* 4.1 9.6 - - + -
250F ASP* 2.9 32.3 + - + +
251F ARG* 3.2 30.7 + - - +
253F TRP* 1.3 86.7 - + - +
255F TRP* 1.3 66.6 + - - +
257F ALA* 3.2 4.6 + - - +
258F TYR* 3.0 24.4 + - - +
401F GA4 3.5 13.7 - - + +
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Residues in contact with TRP 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F PHE* 3.8 20.4 - + - -
202F ASN* 3.7 8.7 - - - -
227F MET* 3.4 51.3 - - + +
228F PHE 3.5 20.9 + - - -
229F GLY* 3.7 13.3 - - - -
251F ARG* 3.2 31.7 + - + +
252F ASP 3.9 5.6 - - - +
254F TYR* 1.3 77.2 - - - +
256F LYS* 1.3 56.2 + - - +
258F TYR* 4.6 5.4 - + - +
259F LEU* 2.9 54.4 + - + +
265F ARG* 3.9 35.0 - - + -
269F ALA 4.4 1.6 - - - -
270F CYS* 3.5 36.3 - - + -
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Residues in contact with LYS 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY* 6.0 7.0 - - - -
161F ARG* 2.7 30.4 + - - +
252F ASP 3.0 17.0 + - - +
253F TRP* 3.3 10.1 + - + +
255F TRP* 1.3 77.0 - - - +
257F ALA* 1.3 51.5 + - - +
259F LEU* 3.5 6.9 - - - +
260F PRO 5.1 0.7 - - - +
261F GLU* 5.7 0.5 - - - -
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Residues in contact with ALA 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY* 4.9 3.8 - - - +
125F VAL* 4.0 14.1 - - + -
157F ALA* 3.4 11.5 - - - +
158F PRO* 3.5 14.8 - - + +
161F ARG* 3.1 32.0 + - - +
253F TRP* 3.0 36.9 + - + +
254F TYR 3.4 8.7 - - - +
255F TRP 3.2 0.2 - - - -
256F LYS* 1.3 79.0 - - - +
258F TYR* 1.3 56.2 + - - +
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Residues in contact with TYR 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F PHE* 3.7 55.4 - + + -
155F ARG 5.7 0.4 - - - -
157F ALA* 3.8 9.6 - - + +
160F HIS 4.3 3.8 - - - -
161F ARG* 3.3 10.8 - - - +
162F TYR* 2.8 61.5 + + + -
163F PRO* 3.9 1.0 - - - +
165F ALA* 3.9 17.1 - - + +
166F TYR* 3.4 54.2 + + - -
254F TYR 3.0 15.0 + - - +
255F TRP* 4.2 6.3 - + + +
257F ALA* 1.3 75.5 - - - +
259F LEU* 1.3 80.1 + - + +
269F ALA* 4.6 1.6 - - + -
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Residues in contact with LEU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F ARG* 3.0 22.0 + - - -
162F TYR* 4.5 0.4 - - + -
255F TRP* 2.9 48.0 + - + +
256F LYS* 3.5 4.0 - - - +
258F TYR* 1.3 79.6 - - + +
260F PRO* 1.3 81.4 - - + +
263F ALA* 4.2 5.6 - - + -
264F ASP 3.4 30.7 - - - +
265F ARG* 4.1 9.6 - - + -
267F HIS* 4.1 12.8 - - + +
269F ALA* 3.8 28.9 - - + -
270F CYS* 4.1 11.0 - - + +
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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