Contacts of the helix formed by residues 242 - 253 (chain C) in PDB entry 3E8C
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 GLN 242 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 4.4 16.4 - - - +
241C ASP* 1.3 95.2 + - + +
243C PRO* 1.4 77.6 - - + +
244C ILE* 4.0 16.8 - - + -
245C GLN* 2.8 37.6 + - - +
246C ILE* 3.4 14.8 + - - +
15I ARG* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PRO* 4.4 9.6 - - + -
241C ASP 4.6 0.7 - - - +
242C GLN* 1.4 90.8 - - + +
244C ILE* 1.3 57.9 + - + +
246C ILE* 2.9 32.5 + - + +
247C TYR* 3.0 40.7 + - + +
15I ARG* 4.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 5.6 3.8 - - - +
24A GLU* 3.0 53.6 - - + +
28B LYS* 5.9 3.6 - - - +
242C GLN* 4.0 18.4 - - + -
243C PRO* 1.3 75.5 - - + +
245C GLN* 1.3 68.4 + - + +
247C TYR* 3.5 17.5 + - + +
248C GLU* 3.3 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 2.8 48.6 + - - +
25B ASP* 5.9 0.4 + - - -
28B LYS* 4.6 17.1 - - - +
240C ALA* 3.5 14.1 - - + -
241C ASP* 3.6 12.2 + - - +
242C GLN* 2.8 45.8 + - - +
244C ILE* 1.3 80.4 - - + +
246C ILE* 1.3 64.0 + - - +
248C GLU* 3.6 17.4 + - - +
249C LYS* 3.4 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PRO* 3.9 15.7 - - + +
203C GLU* 3.8 19.5 - - + +
238C PHE 3.7 20.0 - - - +
239C PHE 4.0 0.7 - - - -
240C ALA* 3.6 22.2 - - - +
242C GLN 3.6 9.0 - - - +
243C PRO* 2.9 21.4 + - + +
245C GLN* 1.3 77.6 - - - +
247C TYR* 1.3 56.6 + - + +
249C LYS* 3.3 10.3 + - - +
250C ILE* 3.0 43.6 + - + +
15I ARG* 3.8 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 5.7 10.5 - - - -
198C LEU* 6.2 2.9 - - + +
202C PRO* 3.8 30.7 - - + +
205C LEU* 3.9 16.8 - - + -
210C ILE* 3.7 40.6 - - + -
243C PRO* 3.0 37.0 + - + +
244C ILE* 3.7 14.4 - - + +
245C GLN 3.3 0.2 - - - -
246C ILE* 1.3 75.4 - - + +
248C GLU* 1.3 65.6 + - - +
250C ILE* 3.4 5.1 + - + +
251C VAL* 3.1 32.3 + - - +
22I ILE* 4.2 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 4.4 29.8 + - - +
24B GLU* 5.0 5.2 - - - +
244C ILE* 3.3 30.5 + - + +
245C GLN* 3.6 18.4 - - - +
246C ILE 3.3 0.4 - - - -
247C TYR* 1.3 78.9 - - + +
249C LYS* 1.3 61.8 + - + +
251C VAL* 4.1 3.4 - - - +
252C SER* 3.2 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.1 26.1 - - - +
24B GLU* 5.7 3.2 + - - -
237C PRO 5.7 0.7 - - - +
238C PHE* 3.8 27.3 - - + -
239C PHE 2.7 38.2 + - - +
240C ALA* 3.8 4.2 - - - +
245C GLN* 3.4 15.0 + - - +
246C ILE* 3.3 8.7 + - - +
247C TYR 3.3 0.4 - - - -
248C GLU* 1.3 76.7 - - + +
250C ILE* 1.3 63.5 + - - +
252C SER* 2.9 24.5 + - - -
253C GLY 4.1 1.0 + - - -
254C LYS 4.1 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PRO 3.2 27.4 - - - +
203C GLU 4.7 2.7 - - - +
205C LEU 3.5 22.2 - - - +
207C PRO* 3.8 12.3 - - + -
210C ILE* 3.6 25.4 - - + -
222C TRP* 3.7 18.1 - - + -
238C PHE* 3.7 31.5 - - + -
246C ILE* 3.0 30.4 + - + +
247C TYR* 3.4 6.0 + - + +
249C LYS* 1.3 76.9 - - - +
251C VAL* 1.3 61.4 + - - +
252C SER 3.5 0.2 + - - -
253C GLY* 3.9 1.9 + - - -
275C VAL* 3.5 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PRO* 4.5 16.2 - - + -
210C ILE* 4.1 29.8 - - + -
211C LEU* 4.3 28.9 - - + -
247C TYR 3.1 18.0 + - - +
248C GLU* 4.3 3.4 - - - +
250C ILE* 1.3 75.1 - - - +
252C SER* 1.3 63.8 + - - +
253C GLY 3.2 2.6 + - - -
275C VAL* 4.2 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLU 3.2 19.8 + - - -
249C LYS* 2.9 17.2 + - - -
250C ILE 3.3 1.0 - - - -
251C VAL* 1.3 75.9 - - - +
253C GLY* 1.3 60.0 + - - +
254C LYS* 3.0 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ILE 3.9 5.4 + - - -
251C VAL 3.2 4.6 - - - -
252C SER* 1.3 78.3 + - - +
254C LYS* 1.3 60.2 + - - +
255C VAL* 4.2 6.3 + - - +
273C LEU 6.0 1.1 - - - -
275C VAL* 3.8 21.8 - - - -
----------------------------------------------------------
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