Contacts of the helix formed by residues 248 - 270 (chain C) in PDB entry 5TIN
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 248 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 3.9 27.6 - - + -
250B PRO* 5.2 2.5 - - + -
244C ILE* 4.1 6.7 - - + -
245C ASN* 3.0 20.2 + - + +
247C ASP* 1.3 74.0 - - - +
249C ALA* 1.3 64.5 + - - +
250C PRO* 3.4 6.3 - - - -
251C ALA* 3.3 10.2 + - + -
252C ARG* 3.1 23.4 + - - +
301C TYR* 4.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ASP 3.0 10.3 + - - +
248C ALA* 1.3 71.7 - - - +
250C PRO* 1.3 65.7 - - + +
252C ARG* 3.9 0.2 - - - -
253C VAL* 2.9 38.6 + - + +
301C TYR* 3.1 24.6 - - + +
305C ASN* 4.1 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PRO* 4.2 28.3 - - + -
247C ASP 4.8 1.1 - - - +
248C ALA* 3.6 4.5 - - - -
249C ALA* 1.3 96.1 - - + +
251C ALA* 1.3 55.6 + - - +
253C VAL* 4.3 4.4 - - + +
254C ALA* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 4.2 1.8 - - + -
250B PRO* 4.0 25.9 - - + +
253B VAL* 3.8 26.5 - - + +
244C ILE* 4.4 5.6 - - + -
248C ALA* 3.3 22.6 + - + +
249C ALA 3.2 0.2 - - - -
250C PRO* 1.3 81.0 - - - +
252C ARG* 1.3 57.8 + - - +
254C ALA* 3.4 4.8 + - - +
255C LEU* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C SER* 3.0 60.6 + - - +
242C PHE* 3.6 6.9 - - - +
244C ILE* 3.1 25.6 + - + -
245C ASN 3.5 22.2 + - - -
246C MET* 4.2 1.6 - - - +
248C ALA 3.1 8.8 + - - +
251C ALA* 1.3 77.0 - - - +
253C VAL* 1.3 63.4 + - - +
255C LEU* 3.6 7.1 + - - +
256C GLY* 3.2 17.7 + - - -
298C LEU* 4.7 3.3 - - - +
300C GLU* 3.9 6.3 + - - -
301C TYR* 3.0 61.1 - - + +
304C VAL* 5.0 0.4 - - - +
323C ASP* 2.6 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ALA* 2.9 24.8 + - + +
250C PRO* 4.3 4.5 - - + +
252C ARG* 1.3 74.8 - - - +
254C ALA* 1.3 59.2 + - - +
256C GLY* 3.2 1.6 + - - +
257C ILE* 2.8 50.1 + - + +
298C LEU* 4.4 14.4 - - + +
301C TYR* 3.9 21.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
253B VAL* 5.2 0.7 - - + -
254B ALA* 6.0 4.5 - - + -
257B ILE* 3.8 14.8 - - + -
250C PRO 3.0 21.0 + - - +
251C ALA* 3.6 6.5 - - - +
253C VAL* 1.3 76.5 - - - +
255C LEU* 1.3 59.0 + - - +
257C ILE* 4.5 8.3 - - - +
258C THR* 2.8 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 4.0 11.9 - - + -
257B ILE* 3.9 20.2 - - + -
298B LEU* 4.9 1.3 - - + -
237C LEU* 3.2 44.0 - - + +
238C SER* 5.0 3.3 - - - +
240C VAL* 3.6 23.1 - - + -
241C SER* 3.7 26.5 - - - +
244C ILE* 4.4 9.4 - - + -
251C ALA 3.0 17.2 + - - +
252C ARG* 3.6 10.5 - - - +
253C VAL 3.3 0.2 - - - -
254C ALA* 1.3 76.5 - - - +
256C GLY* 1.3 58.3 + - - +
258C THR* 3.5 1.0 + - - -
259C THR* 2.8 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C SER* 6.1 0.9 - - - -
241C SER* 5.9 0.2 - - - -
252C ARG 3.2 8.3 + - - -
253C VAL 3.2 6.1 + - - -
255C LEU* 1.3 77.3 - - - +
257C ILE* 1.3 64.0 + - - +
259C THR* 3.2 4.9 + - - -
260C VAL* 3.1 30.0 + - - +
294C VAL 5.1 1.1 - - - -
297C ALA* 6.3 0.9 - - - -
298C LEU* 4.0 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C VAL* 2.8 44.9 + - + +
254C ALA* 3.9 6.7 - - - +
256C GLY* 1.3 73.6 - - - +
258C THR* 1.3 64.1 + - + +
260C VAL* 3.5 4.3 - - - +
261C LEU* 2.8 53.0 + - + +
298C LEU* 4.4 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 3.3 35.1 - - + +
258B THR* 6.3 0.7 - - + -
261B LEU* 3.8 12.3 - - + +
237C LEU* 5.3 0.7 - - - +
254C ALA* 2.8 25.5 + - + +
255C LEU* 3.5 6.2 + - - +
257C ILE* 1.3 84.3 - - + +
259C THR* 1.3 62.0 + - - +
261C LEU* 4.1 5.5 - - + +
262C THR* 2.8 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 5.8 0.2 - - - -
234C ILE* 3.6 33.0 - - + +
237C LEU* 3.9 23.3 - - + -
238C SER* 3.9 20.3 - - - +
255C LEU 2.8 22.8 + - - +
256C GLY* 3.2 8.3 + - - -
258C THR* 1.3 76.1 + - - +
260C VAL* 1.3 60.7 + - - +
262C THR* 4.6 0.2 - - - -
263C MET* 3.0 31.0 + - - +
294C VAL* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C GLY 3.1 20.7 + - - +
257C ILE* 3.5 4.9 - - - +
259C THR* 1.3 77.4 + - - +
261C LEU* 1.3 70.6 + - + +
263C MET* 3.3 5.2 + - - +
264C THR* 3.1 26.9 + - + +
291C LEU* 3.8 8.2 - - + +
294C VAL* 3.4 22.2 - - + +
295C PHE* 3.8 42.4 - - + -
298C LEU* 4.6 9.2 - - + -
233D LEU* 5.8 3.8 - - + +
234D ILE* 5.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 2.8 42.1 + - + +
258C THR* 4.1 5.6 - - + +
260C VAL* 1.3 74.7 - - + +
262C THR* 1.3 65.3 + - - +
264C THR* 2.6 23.0 + - - +
265C THR* 3.2 13.5 + - + +
234D ILE* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 3.4 27.4 - - + +
264B THR* 5.2 5.2 - - - +
265B THR* 6.6 0.4 - - + -
234C ILE* 3.7 30.3 - - + -
258C THR 2.8 23.4 + - - -
259C THR 4.0 2.9 - - - -
261C LEU* 1.3 75.6 - - - +
263C MET* 1.3 57.5 + - - +
265C THR* 2.9 10.8 + - - +
266C GLN* 2.8 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C SER* 3.5 22.0 - - - +
234C ILE* 4.0 26.5 - - - -
235C VAL* 5.1 2.0 - - - -
259C THR 3.0 18.0 + - - +
260C VAL* 3.4 6.1 - - - +
261C LEU 3.2 0.4 - - - -
262C THR* 1.3 78.5 - - - +
264C THR* 1.3 56.8 + - - +
266C GLN* 3.5 10.3 - - + +
267C SER* 3.0 27.4 + - - -
287C MET* 3.4 35.4 - - - +
290C CYS* 3.7 21.5 - - + +
291C LEU* 3.7 37.3 - - + +
294C VAL* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C VAL* 3.1 16.4 + - + +
261C LEU* 2.6 27.2 + - - +
263C MET* 1.3 74.0 - - - +
265C THR* 1.3 61.3 + - - +
267C SER* 3.3 7.5 + - - -
268C SER* 3.0 26.5 + - - -
291C LEU* 4.1 21.8 - - + -
230D PRO* 5.1 22.0 - - + +
233D LEU* 5.3 4.0 - - + -
234D ILE* 4.7 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LEU* 3.2 11.3 + - + +
262C THR* 2.9 23.4 + - - +
264C THR* 1.3 76.1 + - - +
266C GLN* 1.3 56.1 + - - +
268C SER* 3.1 8.7 + - - -
269C GLY* 2.8 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 5.6 4.3 + - - -
226C GLN 3.9 13.9 + - - -
227C MET* 4.1 9.2 + - - +
230C PRO* 3.8 27.6 - - - +
231C SER* 4.3 7.0 - - - -
234C ILE* 4.8 3.6 - - - +
262C THR* 2.8 32.5 + - - +
263C MET* 3.5 28.3 - - + +
265C THR* 1.3 77.4 + - - +
267C SER* 1.3 61.2 + - - +
269C GLY* 3.8 1.5 - - - -
270C SER* 3.1 23.6 + - - -
287C MET* 4.0 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C MET 3.0 19.0 + - - -
264C THR* 3.4 8.5 - - - -
265C THR 3.2 0.2 - - - -
266C GLN* 1.3 74.5 - - - +
268C SER* 1.3 62.9 + - - +
270C SER* 2.6 22.3 + - - -
271C ARG* 3.3 26.4 + - - -
287C MET* 4.0 28.5 - - - +
291C LEU* 5.6 7.1 - - - +
225D ILE* 5.3 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C THR 3.0 13.2 + - - -
265C THR* 3.1 13.9 + - - +
267C SER* 1.3 75.2 + - - +
269C GLY* 1.3 63.8 + - - +
271C ARG* 3.2 27.4 + - - +
272C ALA* 3.4 11.7 + - - +
226D GLN* 3.5 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C MET* 4.6 6.4 - - - +
265C THR 2.8 21.9 + - - -
266C GLN* 3.8 2.9 - - - -
268C SER* 1.3 75.1 + - - +
270C SER* 1.3 58.8 + - - +
271C ARG 3.1 1.5 + - - -
272C ALA* 3.4 20.5 + - - +
273C SER 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C PHE* 4.3 7.4 - - - -
227C MET* 3.9 30.2 - - - +
266C GLN 3.1 13.3 + - - -
267C SER 2.6 20.0 + - - -
269C GLY* 1.3 74.7 - - - +
271C ARG* 1.3 66.2 + - - +
272C ALA 3.6 0.2 - - - -
273C SER 5.4 0.2 - - - -
274C LEU* 3.9 13.7 - - - +
283C ILE* 3.9 27.8 - - - +
284C ASP* 4.5 0.5 + - - -
287C MET* 4.0 12.6 - - - +
----------------------------------------------------------
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