Contacts of the helix formed by residues 241 - 261 (chain C) in PDB entry 3OFN
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY* 6.2 3.1 - - - -
77C LEU* 3.6 24.7 - - + +
78C PHE* 4.1 19.3 + - - +
79C GLY* 4.5 6.3 - - - +
239C SER 3.8 1.4 + - - -
240C GLU* 1.3 76.0 - - - +
242C ALA* 1.3 68.1 + - - +
243C PRO* 3.3 2.7 - - + -
244C LEU* 3.0 23.1 + - + +
245C GLN* 3.6 3.1 + - - +
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Residues in contact with ALA 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C GLU 3.5 3.2 + - - -
241C ALA* 1.3 70.7 - - - +
243C PRO* 1.4 64.8 - - + +
245C GLN* 2.9 12.9 + - - +
246C TYR* 2.8 26.7 + - - +
279C ALA* 3.6 23.1 - - + +
282C GLN* 3.9 31.8 - - + +
283C LEU* 3.5 17.0 - - + +
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Residues in contact with PRO 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLY 5.3 2.0 - - - +
64C MET* 5.8 1.1 - - - -
76C VAL* 3.4 35.4 - - + -
77C LEU 3.5 15.9 - - - +
78C PHE* 3.4 23.1 - - + -
241C ALA* 3.3 6.3 - - + -
242C ALA* 1.4 93.0 - - + +
244C LEU* 1.3 57.2 + - - +
246C TYR* 3.4 11.0 - - + +
247C LEU* 2.8 33.1 + - - +
283C LEU* 3.7 16.8 - - + -
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 3.3 56.5 - - + +
111C ASP* 6.0 4.5 - - + +
112C ALA* 3.1 34.2 - - + +
113C LEU* 4.3 17.3 - - + +
236C ALA* 3.0 16.8 - - + +
240C GLU* 3.4 32.3 - - + +
241C ALA* 3.0 15.4 + - + +
243C PRO* 1.3 74.4 - - - +
245C GLN* 1.3 60.2 + - - +
247C LEU* 5.2 1.3 - - + -
248C ALA 3.3 9.0 + - - -
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Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 3.5 16.2 - - + +
209C GLY* 3.2 25.9 + - - -
236C ALA* 3.5 18.4 - - + +
237C THR 3.5 17.3 + - - +
238C ALA* 3.6 10.9 + - - +
240C GLU* 3.2 22.4 + - + +
241C ALA 3.9 8.7 - - - +
242C ALA* 2.9 9.5 + - - +
244C LEU* 1.3 75.3 - - - +
246C TYR* 1.3 65.8 + - - +
248C ALA* 3.7 0.5 + - - +
249C PRO* 3.4 17.3 - - - +
275C LYS* 4.6 5.7 - - - +
276C GLN* 3.5 8.9 - - - +
279C ALA* 3.7 14.8 - - + +
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Residues in contact with TYR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C MET* 4.6 12.9 - - + +
66C LEU* 4.8 10.3 - - + +
132C GLN* 4.3 7.0 + - - -
242C ALA 2.8 15.6 + - - +
243C PRO* 3.4 10.8 - - + +
245C GLN* 1.3 76.7 - - - +
247C LEU* 1.3 81.6 + - + +
249C PRO* 3.5 1.6 - - - +
250C PHE* 3.4 13.7 - + - -
276C GLN* 3.1 28.4 + - - -
279C ALA* 3.9 7.7 - - + +
280C TYR* 3.8 29.2 - + + +
283C LEU* 3.7 28.0 - - + -
303C LEU* 3.4 32.1 - - + -
306C ARG* 3.8 18.9 + - - -
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C MET* 4.0 19.3 - - + -
78C PHE* 3.9 20.9 - - + -
97C VAL* 3.5 29.8 - - + -
112C ALA* 4.7 4.7 - - + +
113C LEU* 4.1 13.9 - - + -
131C ALA* 4.7 7.0 - - + -
132C GLN* 5.7 3.1 - - + +
243C PRO* 2.8 13.4 + - + +
244C LEU* 4.3 6.1 - - + +
245C GLN 3.3 0.2 - - - -
246C TYR* 1.3 105.0 - - + +
248C ALA* 1.3 56.6 + - - +
249C PRO* 3.4 0.7 - - - -
250C PHE* 2.8 32.3 + - + +
251C THR* 3.1 24.8 + - + -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA* 4.0 10.5 - - + +
206C VAL* 3.5 13.7 - - + +
208C VAL* 4.3 3.8 - - + -
234C VAL* 3.9 6.3 - - + +
236C ALA* 3.5 22.2 - - + +
244C LEU 3.3 18.7 + - - +
245C GLN 4.0 2.2 - - - +
246C TYR 3.5 0.2 - - - -
247C LEU* 1.3 77.8 - - - +
249C PRO* 1.4 67.6 - - + +
251C THR* 3.8 6.8 + - - -
252C ALA* 3.1 24.6 + - - +
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Residues in contact with PRO 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C VAL* 3.9 9.2 - - + -
208C VAL* 3.9 13.7 - - + -
245C GLN 3.4 14.1 - - - +
246C TYR 3.5 6.5 - - - +
247C LEU 3.5 1.8 - - - -
248C ALA* 1.4 92.1 - - + +
250C PHE* 1.3 57.4 + - - +
252C ALA* 3.9 0.6 - - + +
253C ALA* 3.1 19.8 + - - +
270C TYR* 3.4 29.3 - - + -
273C LEU* 4.5 3.4 - - + -
276C GLN* 3.5 28.5 - - + +
307C LEU* 3.4 23.6 - - + +
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Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ALA* 3.3 17.4 - - + +
132C GLN* 3.4 34.5 - - - +
246C TYR* 3.4 23.8 - + - -
247C LEU* 2.8 14.4 + - + +
249C PRO* 1.3 77.9 - - - +
251C THR* 1.3 62.6 + - - +
253C ALA* 3.2 17.0 - - - +
254C SER 3.3 5.5 + - - -
276C GLN* 3.4 23.8 - - - -
303C LEU* 3.3 34.8 - - + -
306C ARG* 3.8 14.8 - - + -
307C LEU* 3.5 27.8 - - + -
310C ARG* 3.3 26.2 + - - +
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 5.0 3.4 - - + -
98C ASP 5.0 0.9 - - - -
99C VAL* 3.4 31.7 - - + +
112C ALA* 2.7 23.2 + - - +
113C LEU* 5.3 0.7 - - + -
131C ALA* 3.5 29.8 - - + +
234C VAL* 4.9 2.1 - - - +
247C LEU* 3.1 23.4 + - + +
248C ALA* 3.8 4.5 + - - -
250C PHE* 1.3 71.7 - - - +
252C ALA* 1.3 62.0 + - - +
254C SER* 3.4 9.5 + - - -
255C ILE* 3.0 32.6 + - - +
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C VAL* 4.2 3.5 - - + +
206C VAL* 3.5 28.5 - - + -
234C VAL* 3.8 17.5 - - + +
248C ALA 3.1 19.1 + - - +
249C PRO 3.9 2.0 - - - +
250C PHE 3.3 0.4 - - - -
251C THR* 1.3 77.9 + - - +
253C ALA* 1.3 66.4 + - - +
255C ILE* 3.2 14.4 + - - +
256C GLY* 2.9 19.2 + - - -
268C ILE* 3.5 8.2 - - + +
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Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C PRO 3.1 14.8 + - - +
250C PHE* 3.2 12.3 - - - +
252C ALA* 1.3 74.5 - - - +
254C SER* 1.3 50.1 + - - +
256C GLY* 2.7 7.3 + - - -
257C GLU* 2.6 38.4 + - - +
268C ILE* 3.4 11.1 - - - +
270C TYR* 4.0 13.0 - - - +
307C LEU* 4.4 3.8 - - + -
310C ARG* 3.6 25.1 - - + +
323C LEU* 4.3 9.0 - - + +
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 4.0 8.1 - - - -
101C VAL* 3.6 10.5 - - - +
129C SER* 3.7 19.3 + - - -
130C ARG 2.5 29.5 + - - -
131C ALA* 3.6 0.5 + - - -
133C VAL* 4.0 0.5 - - - +
250C PHE 3.3 6.4 + - - -
251C THR 3.4 8.5 - - - -
253C ALA* 1.3 76.5 - - - +
255C ILE* 1.3 63.7 + - - +
257C GLU* 3.2 22.0 + - - +
258C TRP 3.4 8.1 + - - -
310C ARG* 2.7 19.7 + - - +
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 4.6 9.4 - - + -
100C PRO 3.8 11.9 - - - +
101C VAL* 3.7 10.7 - - + +
102C GLY 5.0 2.6 + - - +
105C LEU* 3.7 36.6 - - + -
110C VAL* 4.4 6.1 - - + -
111C ASP 5.8 0.2 - - - +
114C GLY* 5.4 2.7 - - - -
204C VAL* 4.3 5.8 - - + -
232C ILE* 3.8 26.2 - - + -
234C VAL* 3.5 29.4 - - + -
251C THR* 3.0 21.6 + - - +
252C ALA* 3.3 9.0 - - - +
253C ALA 3.2 0.2 - - - -
254C SER* 1.3 75.6 - - - +
256C GLY* 1.3 61.2 + - - +
258C TRP* 3.6 15.8 - - - +
259C PHE* 3.8 9.0 - - - -
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Residues in contact with GLY 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C VAL* 4.2 14.1 - - - -
252C ALA 2.9 9.9 + - - -
253C ALA* 2.7 10.5 + - - -
255C ILE* 1.3 71.9 - - - +
257C GLU* 1.3 62.5 + - - +
258C TRP 3.2 0.2 - - - -
259C PHE* 3.2 19.5 + - - +
260C ARG* 3.7 2.8 + - - +
266C ALA* 3.5 17.3 - - - +
268C ILE* 5.4 0.7 - - - -
323C LEU* 3.9 18.4 - - - +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C SER* 5.6 2.0 + - - +
133C VAL* 3.6 15.5 - - - +
134C LYS 4.3 5.0 - - - +
253C ALA 2.6 17.0 + - - +
254C SER* 3.2 11.0 + - - +
256C GLY* 1.3 70.3 - - - +
258C TRP* 1.3 53.4 + - - +
260C ARG* 3.1 40.0 + - - +
261C ASP* 2.8 45.0 + - - +
310C ARG* 3.0 56.9 + - - +
323C LEU* 4.0 13.7 - - + -
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Residues in contact with TRP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 4.3 15.0 - - + -
102C GLY* 3.9 27.6 - - - +
103C PRO* 3.6 33.2 - - + -
126C ALA* 4.2 13.8 - - + +
129C SER* 5.7 1.5 + - - +
254C SER 3.4 7.3 + - - +
255C ILE 3.6 13.7 - - - +
256C GLY 3.2 0.2 - - - -
257C GLU* 1.3 77.4 - - - +
259C PHE* 1.3 90.5 + + + +
261C ASP* 3.3 5.2 + - + -
262C ASN* 2.9 55.4 + - + +
264C LYS* 3.7 37.2 - - + -
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Residues in contact with PHE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLY 4.4 10.1 - - - -
103C PRO* 4.5 3.1 - - + -
106C LEU* 3.9 32.1 - - + -
202C TYR* 3.5 42.4 - + + -
204C VAL* 5.3 1.8 - - + -
232C ILE* 3.9 20.4 - - + -
255C ILE 3.8 12.3 - - - -
256C GLY* 3.2 17.6 + - - +
257C GLU 3.2 0.6 - - - -
258C TRP* 1.3 103.2 - + - +
260C ARG* 1.3 62.1 + - - +
262C ASN 3.2 5.9 + - - -
264C LYS* 3.0 38.5 + - + +
266C ALA* 3.8 25.6 - - + +
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Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 5.4 3.2 - - - +
134C LYS 5.0 3.8 + - - -
136C PRO* 3.2 34.0 - - - +
256C GLY 3.7 1.6 + - - +
257C GLU* 3.1 38.4 + - - +
259C PHE* 1.3 78.6 - - - +
261C ASP* 1.3 86.5 + - - +
262C ASN 3.3 1.4 + - - -
263C GLY 3.9 1.6 + - - -
264C LYS 3.6 8.5 + - - -
310C ARG 2.7 28.0 + - - -
312C ALA* 4.1 6.9 - - - +
314C LEU* 3.4 32.0 - - + +
318C GLU 4.7 1.0 - - - +
321C GLY* 3.3 20.1 + - - -
322C SER* 3.6 22.1 + - - +
323C LEU* 3.6 29.6 - - + +
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Residues in contact with ASP 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C GLU* 2.8 20.8 + - - +
258C TRP* 3.8 6.7 - - - +
259C PHE 3.2 0.6 - - - -
260C ARG* 1.3 110.4 + - - +
262C ASN* 1.3 69.0 + - - +
263C GLY 3.9 0.9 - - - -
314C LEU* 4.0 9.7 - - - +
318C GLU 4.5 8.8 - - - +
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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) + - + + + + + -
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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