Contacts of the helix formed by residues 243 - 257 (chain C) in PDB entry 5G04
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 LEU 243 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LYS* 3.8 47.6 - - + +
238C TYR* 3.1 43.7 + - + +
241C LEU* 3.5 33.4 - - + +
242C GLN* 1.3 72.1 - - - +
244C ILE* 1.3 56.2 + - - +
245C GLU* 3.4 7.2 - - + -
246C GLU* 3.4 11.9 + - + +
247C ALA 3.1 19.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
238C TYR 4.8 0.2 - - - -
239C THR* 4.9 10.8 - - - +
242C GLN* 2.7 29.2 + - - +
243C LEU* 1.3 70.6 - - - +
245C GLU* 1.3 81.9 + - + +
247C ALA* 3.4 7.3 - - + +
248C LEU* 2.6 41.1 + - + +
272C ALA* 3.9 24.7 - - + +
275C ASN* 4.0 20.2 - - + +
276C ILE* 3.7 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C LEU* 4.7 3.8 - - + -
244C ILE* 1.3 94.1 - - + +
246C GLU* 1.3 80.8 + - + +
248C LEU* 3.5 11.4 + - - +
249C GLN* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 3.8 30.1 - - + +
243C LEU* 3.4 14.3 + - + +
244C ILE 3.2 0.4 - - - -
245C GLU* 1.3 92.2 - - + +
247C ALA* 1.3 58.2 + - - +
249C GLN* 3.4 19.9 + - - +
250C LYS* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ALA 3.8 10.5 - - - +
238C TYR* 3.3 34.0 - - + -
239C THR* 4.1 9.6 - - - +
243C LEU 3.1 8.3 + - - +
244C ILE* 3.1 14.5 + - + +
246C GLU* 1.3 71.8 - - - +
248C LEU* 1.3 58.0 + - + +
250C LYS* 2.9 5.2 + - - +
251C TYR* 2.7 44.7 + - + -
268C GLN* 5.8 0.2 - - - +
272C ALA* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 2.6 28.1 + - + +
245C GLU* 3.6 11.0 - - - +
247C ALA* 1.3 73.0 - - + +
249C GLN* 1.3 52.4 + - - +
251C TYR* 3.3 7.3 + - - +
252C GLN* 2.8 34.9 + - - +
269C ILE* 5.9 2.5 - - + -
272C ALA* 3.9 23.6 - - + -
273C TYR* 3.6 36.8 - - + +
276C ILE* 3.3 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLU 3.3 10.9 + - - +
246C GLU* 3.5 24.2 - - - +
247C ALA 3.2 0.2 - - - -
248C LEU* 1.3 74.4 - - - +
250C LYS* 1.3 67.3 + - - +
252C GLN* 3.1 23.9 + - - +
253C ASN* 3.2 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLU* 2.2 48.4 + - + +
234C LEU* 3.0 31.5 - - + +
235C ALA* 2.8 23.5 - - + +
238C TYR* 3.4 24.7 - - + -
246C GLU 2.9 12.3 + - - +
247C ALA* 2.9 9.2 + - - +
249C GLN* 1.3 77.6 - - - +
251C TYR* 1.3 60.8 - - - +
253C ASN* 3.5 21.8 + - + +
254C LEU* 3.2 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C PHE* 4.1 7.2 + + - -
235C ALA* 3.4 29.2 - - + -
236C HIS* 3.7 13.0 + - - +
247C ALA* 2.7 33.6 + - + +
248C LEU* 3.7 6.3 - - - +
250C LYS* 1.3 70.7 - - - +
252C GLN* 1.3 64.1 + - - +
254C LEU* 3.1 33.5 + - + +
255C ILE* 3.2 19.8 + - + +
264C TYR* 3.6 23.3 + + - -
265C ILE* 4.5 12.3 - - + -
268C GLN* 3.0 55.9 + - + +
269C ILE* 3.3 27.4 - - + -
272C ALA* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LEU 2.8 16.9 + - - +
249C GLN* 3.1 22.6 + - - +
251C TYR* 1.3 74.0 - - - +
253C ASN* 1.3 61.5 + - - +
255C ILE* 3.6 28.6 + - - +
256C ASP* 3.2 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.9 29.2 - - - -
231C GLU* 5.0 10.3 - - - +
249C GLN* 3.2 13.4 + - - +
250C LYS* 3.5 16.4 + - + +
252C GLN* 1.3 76.8 - - - +
254C LEU* 1.3 57.3 + - - +
256C ASP* 3.3 8.4 + - - +
257C VAL* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 4.6 8.7 - - + -
231C GLU* 4.4 12.1 - - + +
232C PHE* 3.6 49.4 - - + +
235C ALA* 4.5 8.3 - - + -
250C LYS* 3.2 22.7 - - + +
251C TYR* 3.1 39.4 + - + +
253C ASN* 1.3 75.4 - - + +
255C ILE* 1.3 64.5 + - - +
257C VAL* 3.3 14.2 - - + +
259C PHE* 3.2 28.6 + - + +
265C ILE* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LEU 5.7 0.2 - - - +
251C TYR 3.2 20.3 + - - +
252C GLN* 3.8 33.2 - - - +
253C ASN 3.5 0.2 - - - -
254C LEU* 1.3 74.9 - - - +
256C ASP* 1.3 60.0 + - - +
258C GLY* 3.4 8.3 + - - -
259C PHE 4.7 0.4 - - - -
260C SER* 2.3 49.3 + - - +
265C ILE* 4.1 17.9 - - + +
269C ILE* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLN* 3.2 22.1 + - - +
253C ASN* 3.5 9.0 - - - +
254C LEU 3.3 0.4 - - - -
255C ILE* 1.3 76.6 - - - +
257C VAL* 1.3 57.7 + - - +
258C GLY 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.5 51.6 - - + -
29C LEU* 3.2 33.3 - - + +
253C ASN* 3.0 11.8 + - - +
254C LEU* 3.3 24.7 - - + +
256C ASP* 1.3 76.3 - - - +
258C GLY* 1.3 57.0 + - - +
259C PHE* 3.7 20.7 - - + -
----------------------------------------------------------
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