Contacts of the helix formed by residues 249 - 263 (chain C) in PDB entry 1FSJ
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
----------------------------------------------------------
206C ASN* 3.4 28.3 - - - -
247C PHE* 4.1 0.5 - - - +
248C LYS* 1.3 81.2 - - - +
250C PHE* 1.3 65.1 + - - +
251C ASP* 3.5 7.3 + - - +
252C ASP* 3.1 26.5 + - - +
253C PHE 3.2 8.3 + - - -
314C TYR* 2.9 20.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
205C ARG* 2.9 58.8 + - + +
206C ASN* 4.3 0.4 - - - +
249C SER* 1.3 73.1 - - - +
251C ASP* 1.3 59.9 + - - +
253C PHE* 3.1 22.8 + + - +
254C ARG* 2.9 27.6 + - + +
301C LEU* 3.9 41.3 - - + -
303C HIS* 3.6 20.6 - + - -
313C VAL* 3.2 38.6 - - + -
314C TYR* 3.3 8.0 + + - -
319C ILE* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C SER* 3.2 6.9 + - - +
250C PHE* 1.3 81.4 - - - +
252C ASP* 1.3 56.0 + - - +
254C ARG* 2.9 43.7 + - - +
255C LYS* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C GLU 4.7 1.0 - - - +
247C PHE* 3.6 14.1 - - - -
248C LYS* 2.9 50.1 + - + +
249C SER* 3.1 22.4 + - - +
251C ASP* 1.3 75.2 - - - +
253C PHE* 1.3 62.0 + - - +
255C LYS* 3.4 17.2 + - - +
256C ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ALA* 4.0 16.8 - - + -
234C ILE* 5.2 3.8 - - + -
242C LEU* 3.7 20.6 - - + -
247C PHE* 3.7 30.4 - + + -
249C SER 3.2 1.8 + - - -
250C PHE* 3.1 27.5 + + - +
252C ASP* 1.3 77.1 - - - +
254C ARG* 1.3 68.6 + - - +
256C ALA* 3.1 4.2 + - - +
257C VAL* 2.9 43.4 + - + +
301C LEU* 4.2 7.2 - - + -
314C TYR* 3.8 29.2 - + + -
316C MET* 3.9 22.2 - - + -
319C ILE* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C PHE* 2.9 17.7 + - + +
251C ASP* 2.9 45.4 + - - +
253C PHE* 1.3 75.7 - - - +
255C LYS* 1.3 84.6 + - - +
257C VAL* 3.2 3.4 + - - +
258C TRP* 3.2 39.1 + - + +
282C GLY 2.8 27.2 + - - -
283C TYR* 3.9 4.2 - - - +
284C SER* 3.0 33.0 + - - +
299C TYR 5.8 0.7 - - - -
301C LEU* 3.8 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ASP* 3.0 35.8 + - - +
252C ASP* 3.5 14.7 + - - +
253C PHE 3.2 0.2 - - - -
254C ARG* 1.3 83.8 - - - +
256C ALA* 1.3 57.3 + - - +
258C TRP 3.2 2.1 + - - -
259C GLU* 2.9 47.9 + - - +
281C LYS 4.6 6.3 - - - +
282C GLY* 3.5 35.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
242C LEU* 4.0 12.6 - - + -
247C PHE* 3.4 33.7 - - + -
252C ASP 3.1 8.0 + - - +
253C PHE 3.1 6.8 + - - +
255C LYS* 1.3 74.0 - - - +
257C VAL* 1.3 65.1 + - - +
259C GLU* 3.8 13.1 - - - +
260C GLU* 3.0 31.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
222C TRP* 5.9 2.7 - - + -
234C ILE* 4.5 20.0 - - + -
235C PRO* 6.2 1.1 - - + -
238C ILE* 4.5 11.3 - - + +
242C LEU* 3.7 14.1 - - + +
253C PHE* 2.9 50.3 + - + +
254C ARG* 3.2 10.3 + - - +
256C ALA* 1.3 77.6 - - - +
258C TRP* 1.3 75.3 + - + +
260C GLU* 3.3 2.3 + - - +
261C VAL* 2.9 35.8 + - + +
301C LEU* 4.6 9.0 - - + -
321C VAL* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C TRP* 4.5 10.5 - + - -
223C LEU* 4.4 11.2 - - + -
254C ARG* 3.2 36.4 + - + +
255C LYS 3.9 4.9 - - - +
257C VAL* 1.3 81.4 - - + +
259C GLU* 1.3 67.3 + - - +
261C VAL* 3.2 29.7 + - + +
262C SER 2.9 18.9 + - - -
271C LEU* 5.7 0.7 - - + -
279C VAL* 3.3 25.5 - - + +
282C GLY 4.3 4.3 - - - +
283C TYR 3.9 15.9 - - - +
284C SER* 3.3 27.0 + - - -
285C PRO* 3.5 30.5 - - + -
299C TYR* 3.8 26.1 + + + -
301C LEU* 4.8 12.8 - - + +
321C VAL* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C LYS* 2.9 40.3 + - - +
256C ALA* 3.8 13.6 - - - +
258C TRP* 1.3 76.6 - - - +
260C GLU* 1.3 61.7 + - + +
262C SER* 2.6 22.5 + - - +
263C LYS* 3.2 21.0 + - + +
279C VAL 3.4 7.8 + - - +
280C SER 4.2 9.4 - - - +
281C LYS 4.3 6.1 - - - +
282C GLY* 3.7 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ILE* 3.6 22.5 - - + +
241C LYS* 2.7 47.6 + - + +
242C LEU* 3.9 20.6 - - + +
245C LYS* 5.1 6.1 + - - -
256C ALA* 3.0 22.4 + - - +
257C VAL 3.8 1.8 - - - +
259C GLU* 1.3 74.2 - - + +
261C VAL* 1.3 65.9 + - - +
263C LYS* 3.2 35.7 + - - +
264C ASP* 3.2 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C TRP* 4.0 22.9 - - + -
223C LEU* 6.1 0.4 - - + -
238C ILE* 3.9 18.2 - - + -
257C VAL* 2.9 23.5 + - + +
258C TRP* 3.2 33.2 + - + +
260C GLU* 1.3 75.2 - - - +
262C SER* 1.3 63.6 + - - +
264C ASP* 3.1 24.4 + - - +
267C LEU* 4.1 23.3 - - + +
268C SER* 3.3 3.3 + - - -
271C LEU* 4.3 19.7 - - + -
279C VAL* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C TRP 2.9 7.9 + - - -
259C GLU* 2.6 18.8 + - - +
260C GLU 3.2 0.2 - - - -
261C VAL* 1.3 76.7 - - - +
263C LYS* 1.3 63.6 + - - +
264C ASP 3.3 1.3 + - - -
268C SER* 3.9 13.3 + - - -
276C LYS 4.6 1.6 - - - -
279C VAL* 3.4 29.8 - - - +
280C SER* 3.4 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LYS* 4.7 8.9 + - - +
259C GLU* 3.3 20.4 + - + +
260C GLU* 3.2 42.2 + - - +
261C VAL 3.1 1.0 - - - -
262C SER* 1.3 82.1 - - - +
264C ASP* 1.3 58.5 + - - +
265C PRO* 3.4 10.6 - - - +
----------------------------------------------------------
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