Contacts of the helix formed by residues 273 - 286 (chain C) in PDB entry 3F98
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 273 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C HIS* 1.6 66.8 - - - +
274C PHE* 1.5 51.3 + - - -
276C GLY 2.8 21.8 + - - +
277C ALA 3.1 3.1 + - - -
295C LEU 2.7 13.9 + - - -
296C ASP* 2.9 21.6 + - - -
298C TRP* 3.1 24.3 + - - +
322C PHE* 4.6 1.3 - - - -
351C HIS* 5.0 2.2 - - - -
473C NTJ 1.6 57.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LEU* 3.7 17.7 - - + +
183C SER* 3.8 19.1 - - - -
218C ARG* 3.9 15.9 - - - -
221C GLN* 3.4 39.5 - - + -
222C VAL* 4.1 5.4 - - + -
225C ARG* 3.6 33.9 - - - -
272C HIS 3.3 0.4 + - - -
273C SER* 1.5 51.6 + - - -
275C GLY* 1.3 57.2 + - - +
277C ALA* 3.3 4.8 + - + +
278C THR* 2.9 28.7 + - - -
298C TRP* 3.7 30.5 - + + +
301C PRO* 3.5 26.7 - - + -
473C NTJ 2.7 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C SER* 3.3 31.9 - - - -
151C HIS 3.5 3.0 + - - -
225C ARG* 3.7 1.1 - - - -
271C GLY* 3.5 8.7 - - - -
272C HIS 2.8 21.3 + - - -
274C PHE* 1.3 71.8 - - - +
276C GLY* 1.3 56.8 + - - -
278C THR* 3.3 2.9 + - - -
279C VAL* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C GLY 3.8 12.6 - - - -
272C HIS 3.4 6.3 - - - -
273C SER 2.8 16.0 + - - -
275C GLY* 1.3 68.6 - - - +
277C ALA* 1.3 62.5 + - - -
279C VAL* 3.2 13.2 + - - +
280C ILE* 3.3 17.7 + - - +
294C ALA* 3.8 17.0 - - - +
297C ALA* 3.9 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C VAL* 3.8 14.4 - - + -
273C SER 3.1 5.7 + - - -
274C PHE 3.5 9.0 - - - +
276C GLY* 1.3 75.1 - - - +
278C THR* 1.3 57.8 + - - +
280C ILE* 3.1 3.0 + - - +
281C GLN* 3.0 24.8 + - - +
297C ALA* 4.2 2.3 - - - +
298C TRP 3.1 27.0 + - - +
301C PRO* 4.3 10.1 - - + -
302C LEU* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C SER* 3.5 17.9 - - - +
222C VAL* 3.8 9.8 - - - +
225C ARG* 3.1 45.7 + - + +
226C ALA 4.0 0.7 - - - +
229C CYS* 3.7 23.3 - - - -
269C VAL* 5.3 0.4 - - + -
274C PHE 2.9 14.7 + - - -
275C GLY 3.3 9.9 - - - -
276C GLY 3.2 0.2 - - - -
277C ALA* 1.3 74.0 - - - +
279C VAL* 1.3 57.5 + - - +
281C GLN* 3.7 1.4 - - - +
282C THR* 2.7 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C VAL* 3.8 16.2 - - + +
270C ILE* 3.4 13.5 - - - +
271C GLY 3.3 30.3 - - - +
275C GLY 2.9 14.3 + - - +
276C GLY* 3.4 11.0 - - - +
278C THR* 1.3 75.7 - - - +
280C ILE* 1.3 58.5 + - - +
282C THR* 3.3 1.4 + - - -
283C LEU* 2.9 32.7 + - + +
292C GLY* 3.7 28.7 - - - -
293C ILE 3.5 11.9 - - - +
294C ALA* 4.6 1.6 - - + +
314C LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLY 3.3 13.0 + - - +
277C ALA 3.1 7.4 + - - +
279C VAL* 1.3 75.4 - - - +
281C GLN* 1.3 65.4 + - - +
283C LEU* 3.4 4.1 + - - +
284C SER* 3.1 22.3 + - - -
294C ALA* 5.0 1.1 - - + -
297C ALA* 4.9 0.9 - - + -
299C MET* 3.6 37.5 - - + -
302C LEU* 3.8 16.6 - - + -
306C VAL* 3.8 9.2 - - + -
307C TYR* 5.0 2.2 - - + -
310C ILE* 3.4 25.3 - - + +
314C LEU* 3.9 23.8 - - + -
316C PHE* 3.9 18.2 - - + -
334C CYS* 4.3 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ASN* 4.8 3.1 + - - -
222C VAL* 3.7 27.9 - - + +
223C ARG* 4.2 24.0 - - - +
226C ALA* 3.4 21.1 - - + -
277C ALA 3.0 15.4 + - - +
278C THR 3.8 3.4 - - - +
280C ILE* 1.3 76.0 - - - +
282C THR* 1.3 62.6 + - - +
284C SER* 2.7 26.9 + - - -
285C GLU* 2.8 39.7 + - - +
302C LEU* 3.7 10.0 - - + +
303C GLY 5.0 0.2 + - - -
305C GLU* 4.7 3.1 + - - +
306C VAL* 3.5 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ALA* 3.4 24.4 - - - +
229C CYS* 3.8 19.2 - - + +
230C SER* 4.2 8.5 - - - +
269C VAL* 4.4 9.4 - - + -
278C THR* 2.7 30.9 + - - +
279C VAL 3.7 3.6 - - - -
281C GLN* 1.3 72.4 - - - +
283C LEU* 1.3 64.0 + - - +
285C GLU* 3.0 4.2 + - - -
286C ASP* 2.9 23.7 + - - +
289C PHE* 3.3 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C VAL* 3.8 12.6 - - + -
279C VAL* 2.9 27.3 + - + +
280C ILE* 3.8 5.6 - - - +
281C GLN 3.4 0.2 - - - -
282C THR* 1.3 76.3 - - - +
284C SER* 1.3 61.3 + - - +
285C GLU 3.2 1.2 + - - -
286C ASP 3.6 5.7 + - - -
287C GLN* 3.5 6.9 + - - -
289C PHE* 3.9 11.4 - - + +
291C CYS 3.7 25.6 - - - +
292C GLY* 3.9 20.4 - - - +
310C ILE* 3.8 25.6 - - + -
312C GLN* 3.0 44.1 + - + +
313C PRO 4.4 5.4 - - - +
314C LEU* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ILE 3.1 5.6 + - - -
281C GLN* 2.7 23.1 + - - -
282C THR 3.2 0.2 - - - -
283C LEU* 1.3 76.2 - - - +
285C GLU* 1.3 63.7 + - - +
287C GLN* 5.2 1.8 + - - -
306C VAL* 3.2 40.9 - - - +
309C ARG* 3.6 37.1 + - - +
310C ILE* 3.7 8.3 - - - +
583C FMT 4.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ARG* 4.7 0.5 + - - +
226C ALA* 3.8 12.7 - - - +
227C LYS* 4.5 2.1 + - - -
230C SER* 5.2 3.9 + - - +
281C GLN* 2.8 38.4 + - - +
282C THR* 3.0 5.6 + - - +
284C SER* 1.3 86.2 - - - +
286C ASP* 1.3 60.7 - - + +
287C GLN* 4.2 1.9 + - - -
566C FMT 2.8 35.8 - - - +
573C FMT 3.2 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C SER* 2.7 30.0 + - - +
282C THR 2.9 13.2 + - - +
283C LEU 3.6 4.3 + - - -
285C GLU* 1.3 81.6 - - + +
287C GLN* 1.3 58.8 + - - +
288C ARG* 2.8 55.9 + - - +
289C PHE* 3.3 30.8 + - + +
312C GLN* 3.7 8.7 + - - -
----------------------------------------------------------
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