Contacts of the helix formed by residues 237 - 250 (chain C) in PDB entry 4U2M
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 MET 237 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C CYS 3.7 24.0 - - - +
177C SER* 4.4 0.4 - - - -
209C LEU* 3.7 34.1 - - + -
212C PHE* 5.1 6.5 - - + -
213C MET* 3.8 20.0 - - + -
232C ALA* 2.8 12.8 + - + +
235C LEU* 2.8 51.8 - - + +
236C GLN* 1.3 73.4 - - - +
238C GLU* 1.3 64.2 + - - +
239C HIS 3.2 2.7 - - - -
240C VAL* 3.2 19.6 + - + +
241C VAL* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C GLN 3.7 5.3 + - - +
237C MET* 1.3 74.1 - - - +
239C HIS* 1.3 64.7 + - - +
241C VAL* 3.1 11.0 + - - +
242C ASP* 3.0 31.0 + - - +
162D SER* 5.6 5.6 - - - -
203D PRO* 6.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.1 37.0 - + - -
237C MET 3.2 0.6 - - - -
238C GLU* 1.3 81.0 - - - +
240C VAL* 1.3 61.4 + - + +
242C ASP* 3.5 16.0 + - + +
243C THR* 3.0 28.2 + - - -
162D SER* 4.6 9.0 - - - -
199D PRO* 3.2 63.6 + - + +
200D GLU* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 4.5 8.7 - - + -
209C LEU* 3.7 26.0 - - + -
212C PHE* 3.8 38.6 - - + -
218C LEU* 3.8 18.2 - - + -
228C VAL* 4.6 0.4 - - + -
232C ALA* 3.8 11.0 - - + -
237C MET* 3.2 18.8 + - + +
238C GLU 3.2 0.4 - - - -
239C HIS* 1.3 76.6 - - + +
241C VAL* 1.3 65.8 + - - +
243C THR* 3.2 6.7 + - - -
244C CYS* 2.9 29.9 + - - -
200D GLU* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C MET* 3.9 16.9 - - + +
232C ALA* 3.7 7.4 - - + -
233C MET* 3.5 37.0 - - + +
237C MET 3.2 15.6 + - - +
238C GLU* 3.1 11.8 + - - +
240C VAL* 1.3 77.7 - - - +
242C ASP* 1.3 63.1 + - - +
244C CYS* 3.2 7.5 + - - +
245C ARG* 3.0 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLU* 3.0 21.3 + - - +
239C HIS* 3.7 16.1 - - + +
240C VAL 3.3 0.2 - - - -
241C VAL* 1.3 77.9 - - - +
243C THR* 1.3 61.4 + - - +
245C ARG* 2.5 40.3 + - - +
246C LYS* 3.1 21.8 + - - +
162D SER* 3.8 25.9 - - - -
163D ARG* 3.8 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 4.4 15.7 - - - +
3C PHE* 3.4 29.1 - - + -
218C LEU* 4.2 12.1 - - + -
220C LEU* 4.7 4.9 - - + -
239C HIS* 3.0 25.6 + - - -
240C VAL* 3.2 8.7 + - - -
242C ASP* 1.3 73.4 - - - +
244C CYS* 1.3 66.2 + - - +
246C LYS* 3.3 7.3 + - + +
247C PHE* 3.1 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C LEU* 4.7 0.9 - - - -
220C LEU* 4.0 17.0 - - - -
225C ILE* 3.1 31.1 - - + +
228C VAL* 3.8 28.3 - - - -
229C MET* 3.8 31.2 - - + -
240C VAL* 2.9 23.0 + - - -
241C VAL 3.2 8.5 + - - +
243C THR* 1.3 77.5 - - - +
245C ARG* 1.3 62.6 + - - +
247C PHE* 3.2 1.5 + - - -
248C ILE* 3.2 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C MET* 4.1 16.8 - - - -
241C VAL* 3.0 31.4 + - - +
242C ASP* 2.5 39.1 + - - +
243C THR 3.2 0.2 - - - -
244C CYS* 1.3 75.8 - - - +
246C LYS* 1.3 63.1 + - - +
248C ILE* 3.1 21.8 + - + +
249C LYS* 3.3 10.4 + - - +
163D ARG* 5.7 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ASP 3.1 13.5 + - - +
243C THR* 3.8 9.9 - - + +
244C CYS 3.2 0.4 - - - -
245C ARG* 1.3 76.7 - - - +
247C PHE* 1.3 56.9 + - - +
249C LYS* 3.0 28.5 - - + +
250C ALA* 3.2 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU* 3.9 36.3 - - + -
221C ARG* 4.4 4.0 - - - -
222C GLU* 4.4 36.1 - - + -
225C ILE* 3.0 37.5 - - + -
243C THR* 3.1 13.5 + - + +
244C CYS 3.2 1.8 + - - +
246C LYS* 1.3 76.7 - - - +
248C ILE* 1.3 57.9 + - - +
250C ALA* 3.1 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ILE* 3.9 22.2 - - + -
226C MET* 3.6 30.3 - - - -
229C MET* 4.2 18.6 - - + -
244C CYS 3.2 14.6 + - - +
245C ARG* 3.1 11.1 + - + +
247C PHE* 1.3 76.5 - - - +
249C LYS* 1.3 62.4 + - - +
250C ALA 3.5 6.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
245C ARG 3.3 5.8 + - - +
246C LYS* 3.0 21.7 + - + +
248C ILE* 1.3 79.2 - - - +
250C ALA* 1.3 54.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C GLU* 5.1 7.4 - - - +
246C LYS 3.2 8.4 + - - +
247C PHE* 3.1 30.7 + - + +
248C ILE* 3.6 6.1 - - - +
249C LYS* 1.3 78.7 - - + +
----------------------------------------------------------
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