Contacts of the helix formed by residues 247 - 259 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E LYS* 5.0 8.7 - - - +
35E ARG* 5.5 0.2 + - - -
241E ASP* 3.1 9.0 - - - +
242E GLY* 4.2 14.4 - - - -
245E PHE 4.9 4.5 - - - +
246E VAL* 1.3 78.8 - - - +
248E LEU* 1.3 62.9 + - - +
249E GLN* 3.7 13.6 + - - +
250E ASP* 2.7 42.4 + - - +
251E ARG* 3.0 24.0 + - - +
297E LEU* 4.4 2.5 - - - -
601E NO3 5.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ARG* 3.8 47.1 - - + +
237E GLU* 3.5 43.3 - - + +
238E ARG* 4.5 4.3 - - - +
241E ASP* 2.5 26.2 + - + +
247E THR* 1.3 69.2 - - - +
249E GLN* 1.3 59.9 + - + +
251E ARG* 3.2 10.1 + - + +
252E ASP* 2.9 38.8 + - - +
297E LEU* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E ASP* 5.9 0.2 - - - +
247E THR* 3.3 11.9 - - - +
248E LEU* 1.3 75.7 - - + +
250E ASP* 1.3 59.6 + - - +
252E ASP* 3.6 7.3 + - - +
253E TRP* 3.0 26.9 + - - +
601E NO3 3.7 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 250 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ARG* 3.7 33.9 + - - +
245E PHE 4.5 2.3 - - - +
246E VAL* 3.7 5.6 - - - +
247E THR* 2.7 47.2 + - - +
249E GLN* 1.3 75.2 - - - +
251E ARG* 1.3 103.3 + - - +
253E TRP* 3.1 7.2 + - - +
254E TYR* 2.9 30.0 + - + -
401E GA4 3.7 11.2 - - - +
601E NO3 4.2 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E SER* 2.9 28.3 + - - -
227E MET* 3.7 28.0 - - - +
237E GLU* 5.6 2.0 - - - +
246E VAL* 3.3 20.1 - - + +
247E THR 3.0 14.9 + - - +
248E LEU* 3.2 19.3 + - + +
250E ASP* 1.3 104.2 + - - +
252E ASP* 1.3 65.6 + - - +
254E TYR* 3.2 15.4 + - - +
255E TRP* 3.1 36.8 + - + +
297E LEU* 4.3 13.9 - - + -
298E THR* 4.5 13.9 - - + -
401E GA4 3.4 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ARG* 2.6 44.2 + - - -
248E LEU 2.9 22.3 + - - +
249E GLN* 3.8 6.7 + - - +
251E ARG* 1.3 74.0 - - - +
253E TRP* 1.3 64.3 + - - +
255E TRP* 3.3 5.6 + - - +
256E LYS* 2.9 27.7 + - - +
265E ARG* 3.4 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 253 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ARG* 3.6 28.8 - - + +
36E ARG 2.9 26.6 + - - -
37E ALA* 5.4 3.1 - - - -
39E GLY* 3.7 26.2 - - - -
40E THR 3.2 28.0 - - - -
41E PHE* 3.9 22.9 - + + -
125E VAL* 4.2 5.6 - - + -
158E PRO* 4.4 3.6 - - + -
249E GLN 3.0 14.9 + - - +
250E ASP* 3.1 13.2 + - - +
252E ASP* 1.3 77.1 - - - +
254E TYR* 1.3 78.4 + + - +
256E LYS* 3.5 6.6 + - - +
257E ALA* 2.9 37.4 + - + +
601E NO3 3.3 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ARG* 2.8 36.1 + - + -
123E SER* 3.5 27.9 - - - +
124E PHE* 5.2 0.2 - - - -
125E VAL* 3.4 26.1 - - + +
126E HIS* 2.5 43.0 + + - -
227E MET* 4.1 8.1 - - + -
250E ASP* 2.9 29.5 + - - +
251E ARG* 3.2 20.1 + - - +
253E TRP* 1.3 86.1 - + - +
255E TRP* 1.3 66.6 + - - +
257E ALA* 3.2 4.0 + - - +
258E TYR* 3.0 24.6 + - - +
401E GA4 3.6 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 255 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PHE* 3.7 26.7 - + - -
202E ASN* 3.9 7.0 - - - -
227E MET* 3.6 40.1 - - + +
228E PHE* 3.6 26.4 + - - -
229E GLY* 3.6 11.6 - - - -
251E ARG* 3.1 34.0 + - + +
252E ASP* 3.8 3.6 - - - +
254E TYR* 1.3 74.1 - - - +
256E LYS* 1.3 59.3 + - - +
258E TYR* 3.1 11.8 + + - -
259E LEU* 2.9 48.1 + - + +
265E ARG* 3.6 36.6 - - + -
269E ALA 4.5 0.9 - - - -
270E CYS* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLY* 6.4 1.8 - - - -
161E ARG* 2.5 35.2 + - - +
252E ASP* 2.9 18.4 + - + +
253E TRP* 3.6 7.0 - - - +
255E TRP* 1.3 75.8 - - - +
257E ALA* 1.3 50.3 + - - +
259E LEU* 3.8 3.8 - - - +
260E PRO 5.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLY 4.8 3.4 - - - +
125E VAL* 4.2 8.7 - - + -
157E ALA* 3.3 11.2 - - - +
158E PRO* 3.5 22.4 - - + +
161E ARG* 3.3 24.5 + - - +
253E TRP* 2.9 41.0 + - + +
254E TYR* 3.5 7.2 - - - +
255E TRP 3.1 0.4 - - - -
256E LYS* 1.3 78.0 - - - +
258E TYR* 1.3 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 258 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PHE* 3.7 61.0 - + + -
155E ARG 5.9 0.4 - - - -
157E ALA* 3.7 10.8 - - + -
160E HIS 4.5 3.1 - - - -
161E ARG* 3.3 8.2 - - - +
162E TYR* 2.7 64.7 + - + +
163E PRO* 4.2 1.4 - - - +
165E ALA* 4.0 16.2 - - + +
166E TYR* 3.2 46.7 - + - -
254E TYR 3.0 15.2 + - - +
255E TRP* 3.1 8.3 + + - +
257E ALA* 1.3 74.7 - - - +
259E LEU* 1.3 76.5 + - + +
269E ALA* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ARG* 2.6 33.5 + - - -
162E TYR* 4.5 0.7 - - + -
255E TRP* 2.9 33.3 + - + +
256E LYS* 3.8 2.6 - - - +
258E TYR* 1.3 89.8 - - + +
260E PRO* 1.4 74.2 - - + +
263E ALA* 4.1 5.8 - - + -
264E ASP* 3.4 28.7 - - - +
265E ARG* 4.3 3.8 - - + -
267E HIS* 3.9 25.6 - - + +
269E ALA* 4.1 12.3 - - + -
270E CYS* 3.9 27.1 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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