Contacts of the helix formed by residues 236 - 245 (chain C) in PDB entry 5XVO
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 ALA 236 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASP* 4.0 6.7 - - - +
235C GLU* 1.3 79.2 + - - +
237C PHE* 1.3 67.2 + - - +
238C PRO* 3.9 12.1 - - + -
239C ILE* 3.2 20.0 + - + +
240C MET* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASP* 3.6 27.5 + - - +
174C ALA* 3.6 44.2 - - + -
175C GLY* 3.7 13.2 - - - -
178C TYR* 4.3 13.5 - + + -
236C ALA* 1.3 71.7 - - - +
238C PRO* 1.3 76.9 - - + +
240C MET* 2.9 12.8 + - + +
241C LYS* 2.9 57.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ALA* 3.7 11.2 - - + -
237C PHE* 1.3 100.7 - - + +
239C ILE* 1.3 68.1 + - + +
241C LYS* 3.5 15.2 - - + +
242C ARG* 3.4 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ASN* 4.4 0.4 - - - +
235C GLU* 3.8 36.3 - - + +
236C ALA* 3.2 23.2 + - + +
237C PHE 3.1 0.6 - - - -
238C PRO* 1.3 83.6 - - + +
240C MET* 1.3 66.9 + - - +
242C ARG* 3.1 7.3 + - - +
243C LYS* 2.9 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASP* 3.1 41.7 - - + +
172C ILE* 3.9 10.8 - - + +
175C GLY* 4.1 12.3 - - - -
228C ILE* 4.9 0.6 - - - +
229C ILE* 3.9 22.4 - - + +
232C ASN* 3.7 28.7 - - + +
233C ARG* 4.1 11.2 - - - +
235C GLU* 3.6 21.1 - - + +
236C ALA 3.1 10.1 + - - +
237C PHE* 2.9 20.1 + - + +
239C ILE* 1.3 78.8 - - - +
241C LYS* 1.3 64.1 - - - +
243C LYS* 3.3 7.5 + - - +
244C LEU* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.5 40.6 + - + +
237C PHE* 2.9 47.0 + - + +
238C PRO* 3.5 17.9 - - - +
240C MET* 1.3 77.8 - - - +
242C ARG* 1.3 65.8 + - + +
244C LEU* 3.2 24.0 + - - +
245C PHE* 3.4 19.1 - - + -
24G G 3.5 36.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C PRO* 3.4 14.4 + - - +
239C ILE* 3.1 9.6 + - - +
241C LYS* 1.3 79.3 - - + +
243C LYS* 1.3 64.4 + - + +
245C PHE* 3.2 36.1 + - + +
246C ALA 4.4 0.9 + - - -
249C MET* 5.8 1.6 - - - +
23G C 5.7 1.2 + - - -
24G G 3.7 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ILE* 3.8 12.5 - - + +
232C ASN* 3.3 41.9 + - - +
235C GLU* 5.9 0.7 - - - -
239C ILE* 2.9 32.9 + - + +
240C MET* 3.6 5.6 - - - +
242C ARG* 1.3 75.9 - - + +
244C LEU* 1.3 62.3 + - - +
246C ALA* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C GLY* 3.4 25.6 - - - +
178C TYR* 3.8 14.4 - - + -
179C GLY* 3.6 18.2 - - - +
182C LEU* 4.4 11.4 - - + +
225C VAL* 4.0 23.6 - - + -
228C ILE* 3.9 22.0 - - + -
229C ILE* 4.0 11.0 - - + -
237C PHE* 6.3 0.2 - - + -
240C MET 3.1 19.9 + - - +
241C LYS* 3.4 10.1 - - - +
242C ARG 3.1 0.4 - - - -
243C LYS* 1.3 72.9 - - - +
245C PHE* 1.3 62.4 + - - +
246C ALA 3.0 6.4 + - - -
247C LEU* 3.1 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.3 26.7 - + - -
182C LEU* 4.5 13.2 - - + -
241C LYS* 3.4 28.9 - - + -
242C ARG* 3.2 28.9 + - + +
243C LYS 3.1 1.8 - - - -
244C LEU* 1.3 74.7 - - - +
246C ALA* 1.3 60.7 + - - +
247C LEU 3.0 6.3 - - - -
248C PHE* 3.1 43.6 + + + +
249C MET* 3.5 18.3 + - + +
----------------------------------------------------------
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