Contacts of the helix formed by residues 243 - 258 (chain C) in PDB entry 2B5F
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 TRP 243 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LYS* 4.6 22.2 - - + +
165C LEU* 4.2 31.6 - - + -
239C TRP 4.7 1.2 + - - -
240C ASP 3.4 23.9 + - - -
241C ASP* 4.1 1.3 - - - +
242C GLN* 1.3 80.2 - - - +
244C ILE* 1.3 87.8 + - + +
246C TRP* 3.1 8.2 + - - +
247C VAL* 2.9 53.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
155C VAL* 4.1 23.8 - - + -
161C LYS* 4.3 24.2 - - + +
164C ALA* 4.2 11.0 - - + +
165C LEU* 3.9 30.1 - - - +
168C GLU* 4.3 4.0 - - + +
241C ASP* 3.3 17.9 - - + +
243C TRP* 1.3 115.6 - - + +
245C PHE* 1.3 71.2 + - + +
246C TRP 3.1 0.4 - - - -
248C GLY* 2.9 29.1 + - - -
249C PRO* 3.4 1.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
153C ASN* 3.8 38.1 - - + -
154C SER 3.2 25.8 - - - -
155C VAL* 5.2 2.7 - - + -
164C ALA* 5.6 0.2 - - + -
168C GLU* 3.5 40.6 - - + -
217C THR* 3.9 7.6 - - + -
221C ILE 6.0 0.2 - - - +
222C ASN 4.6 0.3 - - - -
223C PRO* 3.4 25.3 - - - +
226C SER* 3.3 31.4 - - - +
241C ASP* 3.5 27.4 - - + -
242C GLN* 3.0 16.4 + - - +
244C ILE* 1.3 84.3 - - + +
246C TRP* 1.3 62.0 + - + +
249C PRO* 3.4 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 4.8 5.2 - - + -
123C MET* 5.6 4.0 - - + -
127C CYS* 3.8 22.4 - - - -
223C PRO* 3.5 32.5 + - + -
227C PHE* 3.8 30.5 - + + +
242C GLN* 3.0 44.0 + - + +
243C TRP* 3.1 9.2 + - - +
245C PHE* 1.3 81.2 - - - +
247C VAL* 1.3 63.4 + - + +
248C GLY 3.4 0.7 - - - -
249C PRO* 3.6 0.9 - - - +
250C PHE* 3.0 59.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 4.3 11.0 - - + -
243C TRP* 2.9 42.6 + - + +
246C TRP* 1.3 80.2 - - + +
248C GLY* 1.3 68.5 + - - +
250C PHE* 4.0 3.5 - - - +
251C ILE* 3.1 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 3.5 18.4 - - - +
168C GLU* 4.2 10.8 - - - -
169C ILE* 3.6 20.4 - - - +
244C ILE 2.9 15.5 + - - -
247C VAL* 1.3 79.7 - - - +
249C PRO* 1.3 60.3 - - - +
251C ILE 3.3 0.2 + - - -
252C GLY 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA* 3.8 15.7 - - + -
168C GLU* 4.1 9.6 - - + +
172C THR* 3.3 35.0 - - + +
221C ILE* 4.0 15.3 - - - +
222C ASN 4.1 2.9 - - - +
223C PRO* 4.0 9.6 - - + -
244C ILE 3.4 11.4 - - - +
245C PHE* 3.4 25.4 - - - +
246C TRP 3.6 3.1 - - - +
248C GLY* 1.3 87.8 - - - +
250C PHE* 1.3 55.9 + - - +
252C GLY 3.3 0.2 + - - -
253C ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 4.1 15.9 - - + -
103C ALA* 4.4 3.6 - - - -
106C PHE* 3.5 53.9 - + + -
123C MET* 4.0 28.5 - - + -
223C PRO* 3.8 23.1 - - + -
246C TRP* 3.0 41.8 + + - +
247C VAL* 4.1 4.3 - - - +
249C PRO* 1.3 77.3 - - - +
251C ILE* 1.3 58.3 + - + +
253C ALA* 3.5 1.0 + - - +
254C ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 5.4 4.0 - - + -
169C ILE* 4.0 29.4 - - + -
247C VAL* 3.1 36.8 + - + +
248C GLY 3.6 3.6 - - - +
250C PHE* 1.3 74.2 - - + +
252C GLY* 1.3 62.1 + - - +
254C ALA* 3.2 5.6 + - - +
255C VAL* 2.9 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 3.3 32.8 - - - -
172C THR* 4.3 0.9 - - - -
173C PHE* 3.7 16.2 - - - -
248C GLY 2.9 13.1 + - - -
249C PRO 3.3 2.4 + - - -
251C ILE* 1.3 77.8 - - - +
253C ALA* 1.3 56.4 + - - +
255C VAL* 3.5 3.9 + - - +
256C ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA* 3.4 27.8 - - + +
106C PHE* 4.2 5.6 - - + -
107C GLY* 4.2 11.4 - - - +
172C THR* 4.1 1.4 - - - +
176C VAL* 4.0 21.4 - - + +
249C PRO 2.9 17.7 + - - +
250C PHE 3.7 4.3 - - - +
252C GLY* 1.3 73.7 - - - +
254C ALA* 1.3 61.0 + - - +
256C ALA* 3.3 2.1 + - - +
257C ALA* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PHE* 4.5 4.0 - - + -
110C LEU* 3.3 30.3 - - + +
250C PHE 3.0 17.2 + - - +
251C ILE* 3.2 6.5 + - - +
253C ALA* 1.3 74.1 - - - +
255C VAL* 1.3 66.9 + - + +
257C ALA* 3.3 1.0 + - - +
258C ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 5.2 6.1 - - + -
173C PHE* 3.6 21.0 - - + -
251C ILE* 2.9 35.2 + - + +
252C GLY* 3.7 6.7 - - - +
254C ALA* 1.3 78.9 - - + +
256C ALA* 1.3 62.9 + - - +
258C ALA* 3.6 6.6 + - - +
259C TYR* 3.3 17.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 3.5 21.3 - - + +
176C VAL* 3.6 24.9 - - + -
177C TYR* 3.8 15.9 - - - +
180C PHE* 4.5 6.1 - - - -
252C GLY 3.0 18.1 + - - +
253C ALA 3.5 4.9 - - - +
255C VAL* 1.3 74.7 - - - +
257C ALA* 1.3 68.6 + - - +
259C TYR* 2.7 21.0 + - - +
260C HIS* 3.6 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLY 3.8 22.2 - - - +
110C LEU* 4.3 15.7 - - + -
111C ALA* 5.0 4.7 - - + +
180C PHE* 3.5 18.6 - - + -
253C ALA 2.8 17.3 + - - +
254C ALA* 3.3 5.4 + - - +
256C ALA* 1.3 70.8 - - - +
258C ALA* 1.3 52.6 + - - +
259C TYR 2.7 3.6 - - - -
260C HIS* 2.4 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ALA 2.9 17.7 + - - +
255C VAL* 3.7 7.9 - - - +
256C ALA 3.3 0.2 - - - -
257C ALA* 1.3 73.7 - - - +
259C TYR* 1.3 54.5 + - - +
260C HIS 3.1 2.9 - - - -
261C GLN* 3.4 25.6 - - + +
262C TYR* 3.9 6.4 + - - +
----------------------------------------------------------
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