Contacts of the helix formed by residues 249 - 260 (chain C) in PDB entry 2JC6
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 SER 249 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU* 2.4 39.7 + - - -
247C ASP 4.1 0.2 + - - -
248C ILE* 1.3 76.9 - - - +
250C ASP* 1.3 65.5 + - - +
251C SER* 3.0 9.6 - - - -
252C ALA 3.2 21.3 + - - -
253C LYS* 3.4 15.5 + - - +
278C TRP* 4.0 0.2 - - - -
283C THR 3.7 12.2 + - - -
285C LEU* 4.0 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE 4.7 0.9 - - - +
249C SER* 1.3 74.2 - - - +
251C SER* 1.3 58.6 + - - +
253C LYS* 3.9 20.8 + - - +
254C ASP* 3.0 29.8 + - - +
257C ARG* 4.9 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C SER* 3.0 9.8 - - - -
250C ASP* 1.3 79.8 - - - +
252C ALA* 1.3 60.7 + - - +
254C ASP* 3.4 4.8 + - - +
255C PHE* 3.1 18.0 + - - +
276C HIS* 3.4 23.6 - - - -
277C PRO* 4.4 1.0 - - - +
278C TRP* 3.7 3.4 + - - +
283C THR* 2.5 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU* 4.0 0.7 - - - +
215C LEU* 3.5 30.1 - - + -
248C ILE* 3.6 17.0 - - + -
249C SER* 3.2 7.7 + - - +
251C SER* 1.3 77.4 - - - +
253C LYS* 1.3 62.4 + - - +
255C PHE* 3.3 4.7 + - - +
256C ILE* 3.1 29.4 + - - +
278C TRP* 3.5 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 3.6 46.1 - - + +
245C TRP* 2.9 47.2 + - + +
246C ASP* 4.9 3.2 + - - +
248C ILE* 3.6 22.7 + - + -
249C SER 3.4 8.7 + - - +
250C ASP* 3.9 19.4 + - - +
251C SER 3.3 0.4 - - - -
252C ALA* 1.3 76.5 - - - +
254C ASP* 1.3 56.7 + - - +
256C ILE* 3.4 1.1 + - - -
257C ARG* 2.9 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ASP 3.0 19.7 + - - +
251C SER* 3.6 7.0 - - - +
253C LYS* 1.3 73.7 - - - +
255C PHE* 1.3 61.7 + - - +
257C ARG* 3.6 18.6 + - - +
258C ASN* 2.8 41.6 + - - -
268C TYR* 5.2 0.2 + - - -
276C HIS* 3.0 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ILE* 3.6 25.4 - - + -
129C LEU* 4.1 2.9 - - + -
211C ALA* 3.9 10.1 - - + -
251C SER 3.1 14.5 + - - +
252C ALA* 3.5 11.2 - - - +
254C ASP* 1.3 75.6 - - - +
256C ILE* 1.3 69.6 + - + +
258C ASN* 3.3 14.2 + - - +
259C LEU* 3.3 42.7 + - + +
268C TYR* 5.2 1.3 - + - -
273C ALA* 3.6 18.2 - - + -
276C HIS* 3.6 37.4 + + + -
278C TRP* 3.7 27.8 - + + -
279C ILE* 3.5 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C GLY* 4.1 4.9 - - - +
211C ALA* 4.0 23.6 - - + +
212C TYR* 3.8 16.8 - - + +
215C LEU* 4.2 6.5 - - + -
238C TYR* 4.1 8.1 - - + +
240C PHE* 4.1 15.0 - - + -
245C TRP* 3.7 34.8 - - + -
252C ALA 3.1 20.5 + - - +
253C LYS 3.4 3.8 + - - +
255C PHE* 1.3 75.8 - - + +
257C ARG* 1.3 57.7 + - - +
259C LEU* 3.1 4.9 + - - +
260C MET* 2.6 62.2 + - + +
278C TRP* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 3.6 17.7 - - + +
240C PHE* 3.5 33.2 - - + -
250C ASP* 4.9 2.4 + - - +
253C LYS* 2.9 40.4 + - - +
254C ASP* 3.7 19.5 + - - +
256C ILE* 1.3 75.1 - - - +
258C ASN* 1.3 61.2 + - - +
260C MET 3.5 14.4 - - - +
261C GLU* 3.7 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ASP* 2.8 37.8 + - - -
255C PHE 3.7 3.8 - - - +
256C ILE 3.2 1.0 - - - -
257C ARG* 1.3 79.5 - - - +
259C LEU* 1.3 58.3 - - - +
261C GLU* 3.7 4.2 - - - +
266C LYS 4.6 3.3 - - - +
267C ARG* 3.5 9.2 - - - -
268C TYR* 2.9 79.1 + - + -
276C HIS* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 5.1 1.8 - - + -
204C CYS* 3.1 41.5 - - + +
205C TRP* 3.5 9.2 - - - -
207C ILE* 4.1 11.4 - - + -
208C GLY* 3.6 22.7 - - - +
255C PHE* 3.3 49.5 + - + +
256C ILE 3.1 3.9 + - - +
258C ASN* 1.3 75.6 - - - +
260C MET* 1.3 56.8 + - - +
261C GLU 3.1 10.8 + - - -
267C ARG* 3.2 22.8 + - - -
268C TYR* 4.0 11.9 - - + +
273C ALA* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TRP* 3.6 22.6 - - + +
208C GLY* 3.8 27.8 - - - +
209C VAL* 3.9 13.2 - - + +
212C TYR* 4.3 6.5 - - - -
220C PRO* 3.5 19.7 - - + -
221C PHE* 3.4 37.9 - - + -
236C ALA* 5.0 1.7 - - - +
238C TYR* 3.3 40.3 + - + +
256C ILE* 2.6 36.5 + - - +
257C ARG 3.5 7.5 - - - +
259C LEU* 1.3 69.2 - - - +
261C GLU* 1.3 57.5 + - - +
262C LYS 4.1 0.7 + - - -
----------------------------------------------------------
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