Contacts of the helix formed by residues 241 - 262 (chain T) in PDB entry 3FKS
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 241 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T PHE 4.4 0.7 - - - -
79T GLY* 4.0 36.1 - - - +
239T SER 3.7 0.8 + - - -
240T GLU* 1.3 79.5 - - - +
242T ALA* 1.3 66.8 + - - +
243T PRO* 3.4 12.6 - - + -
244T LEU* 3.3 24.5 + - + +
245T GLN* 3.5 8.0 + - - +
287W THR* 4.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241T ALA* 1.3 71.0 - - - +
243T PRO* 1.3 68.0 - - + +
245T GLN* 3.0 8.4 + - - +
246T TYR* 3.0 26.3 + - - +
279T ALA* 3.8 19.4 - - + +
282T GLN* 3.6 35.4 - - - +
283T LEU* 3.8 18.8 - - + -
287W THR* 4.5 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 243 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T GLY* 5.4 0.7 - - - +
76T VAL* 3.6 25.1 - - + -
77T LEU 3.0 25.1 - - - +
78T PHE* 3.6 20.9 - - + -
241T ALA* 3.5 11.9 - - + -
242T ALA* 1.3 94.8 - - + +
244T LEU* 1.3 56.2 + - - +
245T GLN 3.3 0.2 - - - -
246T TYR* 3.8 9.2 - - + +
247T LEU* 3.1 31.2 + - - +
283T LEU* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T PHE* 3.5 45.1 - - + +
79T GLY* 5.3 1.1 - - - -
111T ASP* 5.3 5.6 - - + +
112T ALA* 3.2 37.9 - - + +
113T LEU* 4.5 13.5 - - + -
236T ALA* 3.5 5.4 - - + +
240T GLU* 3.1 37.2 - - + +
241T ALA* 3.3 27.1 + - + +
242T ALA 3.1 0.8 - - - -
243T PRO* 1.3 78.8 - - - +
245T GLN* 1.3 57.9 + - - +
248T ALA* 3.2 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208T VAL* 3.9 15.2 - - + +
209T GLY* 3.5 16.8 + - - -
236T ALA* 3.4 27.8 - - + +
237T THR 2.8 23.2 + - - +
238T ALA* 3.5 13.5 + - - +
240T GLU* 3.5 17.3 + - + -
241T ALA 3.7 7.6 + - - +
242T ALA* 3.0 6.3 + - - +
244T LEU* 1.3 74.6 - - - +
246T TYR* 1.3 60.4 + - - +
247T LEU 3.3 0.4 - - - -
248T ALA* 4.0 1.2 - - - +
249T PRO* 3.1 23.9 - - - +
275T LYS* 4.1 12.6 - - - +
276T GLN* 3.7 7.0 - - - +
279T ALA* 4.2 12.7 - - + +
286W ALA* 6.0 2.3 - - - +
287W THR* 4.6 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64T MET* 5.1 16.0 - - + +
78T PHE* 6.0 1.8 - + - -
132T GLN* 4.0 7.5 + - - -
242T ALA 3.0 15.3 + - - +
243T PRO* 3.9 14.8 - - + +
244T LEU 3.4 0.2 - - - -
245T GLN* 1.3 79.2 - - - +
247T LEU* 1.3 75.2 + - + +
250T PHE* 3.2 23.9 - + - -
276T GLN* 3.3 15.3 + - + -
279T ALA* 4.5 7.1 - - + +
280T TYR* 3.4 42.9 - + + +
283T LEU* 4.7 12.1 - - + -
303T LEU* 3.5 22.0 - - + -
306T ARG* 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64T MET* 5.3 3.8 - - - -
78T PHE* 3.6 29.6 - - + -
97T VAL* 5.0 17.5 - - + -
99T VAL* 5.6 2.0 - - + -
112T ALA* 4.7 7.0 - - + +
113T LEU* 4.7 8.1 - - + -
131T ALA* 4.3 17.3 - - + -
132T GLN* 4.6 10.3 - - + +
243T PRO 3.1 18.1 + - - +
244T LEU 4.6 1.3 - - - +
246T TYR* 1.3 91.4 - - + +
248T ALA* 1.3 67.1 + - - +
249T PRO* 3.2 2.9 - - - -
250T PHE* 2.9 21.2 + - + +
251T THR* 2.9 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112T ALA* 3.8 14.3 - - + +
206T VAL* 4.5 5.2 - - + -
208T VAL* 4.3 8.5 - - + -
234T VAL* 4.0 12.1 - - + +
236T ALA* 3.8 19.1 - - + +
244T LEU 3.2 21.3 + - - +
245T GLN 4.0 2.2 - - - +
247T LEU* 1.3 75.1 - - - +
249T PRO* 1.3 67.5 - - + +
251T THR* 3.2 5.9 + - - -
252T ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 249 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206T VAL* 4.4 6.5 - - + -
208T VAL* 3.9 13.5 - - + -
245T GLN 3.1 18.8 - - - +
246T TYR 3.6 4.5 - - - +
247T LEU 3.3 4.0 - - - -
248T ALA* 1.3 91.7 - - + +
250T PHE* 1.3 55.3 + - - +
252T ALA* 3.3 4.0 + - + +
253T ALA* 3.0 27.7 + - - +
270T TYR* 3.7 32.7 - - + -
273T LEU* 4.8 2.9 - - + -
276T GLN* 3.2 32.5 - - + +
307T LEU* 3.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131T ALA* 3.4 19.5 - - + +
132T GLN* 3.2 30.1 - - - -
246T TYR* 3.2 32.8 - + - -
247T LEU* 2.9 13.3 + - + +
249T PRO* 1.3 80.2 - - - +
251T THR* 1.3 59.6 + - - +
253T ALA* 3.0 18.5 + - - +
254T SER* 3.2 14.0 + - - -
276T GLN* 3.6 16.6 - - - -
303T LEU* 3.6 25.8 - - + -
306T ARG* 3.4 40.6 - - + -
307T LEU* 3.8 19.1 - - + -
310T ARG* 3.6 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99T VAL* 3.6 21.7 - - + +
111T ASP 4.7 0.2 + - - -
112T ALA* 3.0 32.7 + - - +
131T ALA* 3.6 17.7 - - + -
234T VAL* 4.1 5.9 - - - +
247T LEU* 2.9 34.3 + - + +
248T ALA* 3.2 9.7 + - - -
250T PHE* 1.3 75.1 - - - +
252T ALA* 1.3 62.1 + - - +
254T SER* 3.4 12.1 + - - -
255T ILE* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204T VAL* 3.7 17.9 - - + +
206T VAL* 3.8 25.4 - - + -
234T VAL* 4.0 20.9 - - + -
248T ALA 3.0 18.9 + - - +
249T PRO 3.7 4.3 - - - +
251T THR* 1.3 75.8 + - - +
253T ALA* 1.3 61.4 + - - +
254T SER 3.2 0.7 - - - -
255T ILE* 3.7 8.0 + - - -
256T GLY 3.4 14.4 + - - -
268T ILE* 3.9 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249T PRO 3.0 11.9 + - - +
250T PHE 3.0 12.3 + - - +
252T ALA* 1.3 78.3 - - - +
254T SER* 1.3 58.5 + - - +
255T ILE 3.4 0.2 - - - -
256T GLY* 3.6 3.5 + - - +
257T GLU* 3.2 28.9 + - - +
268T ILE* 5.1 2.7 - - - -
270T TYR* 3.5 20.2 - - - +
307T LEU* 4.2 5.8 - - + +
310T ARG* 3.7 25.4 - - + +
323T LEU* 4.5 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99T VAL* 4.0 12.8 - - - -
101T VAL* 3.6 16.5 - - - +
129T SER* 4.4 8.4 + - - -
130T ARG 2.7 28.1 + - - -
131T ALA* 3.3 10.9 - - - -
250T PHE 3.2 3.2 + - - -
251T THR 3.6 9.3 + - - -
253T ALA* 1.3 76.9 - - - +
255T ILE* 1.3 63.3 + - - +
256T GLY 3.1 1.6 - - - -
257T GLU* 3.3 14.9 + - - +
258T TRP* 3.5 8.3 + - - +
310T ARG* 3.2 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99T VAL* 5.7 1.6 - - + -
100T PRO 4.4 4.3 - - - +
101T VAL* 4.0 15.5 - - + -
102T GLY 5.0 2.2 - - - +
105T LEU* 3.8 26.9 - - + -
110T VAL* 5.1 6.1 - - + -
204T VAL* 4.5 10.5 - - + -
232T ILE* 3.6 35.9 - - + -
234T VAL* 3.8 29.2 - - + -
251T THR* 3.3 15.7 + - - +
252T ALA* 3.7 8.3 + - - +
253T ALA 3.4 0.2 - - - -
254T SER* 1.3 76.1 - - - +
256T GLY* 1.3 60.0 + - - +
258T TRP* 3.7 6.8 + - - +
259T PHE* 3.4 21.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204T VAL* 4.6 7.2 - - - +
252T ALA 3.4 11.8 + - - -
253T ALA 3.6 4.0 + - - -
254T SER 3.1 0.4 - - - -
255T ILE* 1.3 78.1 - - - +
257T GLU* 1.3 62.6 + - - +
258T TRP 3.2 0.4 - - - -
259T PHE* 3.4 7.4 + - - +
260T ARG* 3.3 17.7 + - - +
266T ALA* 3.9 13.3 - - - +
268T ILE* 5.5 0.2 - - - -
323T LEU* 4.1 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129T SER* 4.9 2.9 + - - -
133T VAL* 3.5 24.2 - - - +
134T LYS 4.7 1.9 - - - +
253T ALA 3.2 10.2 + - - +
254T SER* 3.3 10.8 + - - +
256T GLY* 1.3 75.5 - - - +
258T TRP* 1.3 60.1 + - - +
259T PHE 3.3 0.4 - - - -
260T ARG* 3.4 44.4 + - - +
261T ASP* 2.9 39.5 + - - +
310T ARG* 3.2 51.3 + - + +
323T LEU* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 258 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101T VAL* 4.4 24.9 - - + -
102T GLY* 4.4 11.5 - - - +
103T PRO* 3.1 39.7 - - + -
126T ALA* 4.6 15.2 + - + +
254T SER 3.5 9.2 + - - +
255T ILE 3.7 11.2 - - - +
256T GLY 3.2 0.4 - - - -
257T GLU* 1.3 79.0 - - - +
259T PHE* 1.3 94.8 + + - +
261T ASP* 3.9 3.0 + - - -
262T ASN* 2.9 60.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 259 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102T GLY 4.6 6.1 - - - -
103T PRO* 4.8 3.4 - - + -
106T LEU* 3.8 25.1 - - + -
202T TYR* 3.4 53.8 - + + -
204T VAL* 5.7 3.1 - - + -
232T ILE* 4.4 15.0 - - + -
255T ILE* 3.4 21.1 - - + -
256T GLY* 3.4 1.0 + - - +
257T GLU 3.3 0.4 - - - -
258T TRP* 1.3 105.1 - + - +
260T ARG* 1.3 60.7 + - - +
262T ASN* 4.0 2.9 - - - -
263T GLY 3.3 26.0 + - - +
265T HIS 4.4 4.8 + - - +
266T ALA* 3.6 28.9 - - + +
322T SER 3.8 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133T VAL* 5.3 4.2 - - - +
134T LYS 5.6 0.6 + - - -
136T PRO* 3.5 29.4 - - - +
256T GLY 3.3 11.8 + - - +
257T GLU* 3.1 41.6 + - - +
259T PHE* 1.3 77.2 - - - +
261T ASP* 1.3 86.6 + - - +
262T ASN 3.2 0.4 - - - -
263T GLY* 3.3 12.3 + - - -
310T ARG 2.9 27.4 + - - -
312T ALA* 4.7 6.5 - - - +
314T LEU* 3.5 35.3 - - + +
319T GLY 6.0 0.3 - - - -
320T SER 4.3 4.0 + - - +
322T SER* 3.8 31.0 + - - +
323T LEU* 4.2 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 261 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257T GLU* 2.9 18.5 + - - +
258T TRP* 4.6 3.1 - - - +
260T ARG* 1.3 107.5 + - - +
262T ASN* 1.3 66.8 + - - +
263T GLY 3.3 2.7 + - - -
314T LEU* 3.8 11.5 - - - +
318T GLU* 4.2 14.3 - - - +
319T GLY* 5.6 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197T GLU* 5.5 0.9 - - - +
258T TRP* 2.9 66.7 + - + +
259T PHE* 4.0 3.8 + - - +
260T ARG 3.2 0.8 - - - -
261T ASP* 1.3 86.1 - - - +
263T GLY* 1.3 65.8 - - - +
----------------------------------------------------------
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