Contacts of the helix formed by residues 241 - 262 (chain B) in PDB entry 3OEE
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU 4.4 0.7 - - - +
78B PHE* 4.2 4.9 - - - -
79B GLY* 3.8 40.2 - - - +
80B SER* 4.8 0.4 - - - +
239B SER 4.0 0.2 + - - -
240B GLU* 1.3 76.6 - - - +
242B ALA* 1.3 68.5 + - - +
243B PRO* 3.2 11.2 - - + -
244B LEU* 2.8 20.8 + - + +
245B GLN* 3.4 6.8 + - - -
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLU 3.6 3.1 + - - -
241B ALA* 1.3 69.0 - - - +
243B PRO* 1.3 66.0 - - + +
245B GLN* 3.0 10.0 + - - +
246B TYR* 2.8 27.3 + - - +
279B ALA* 3.6 29.2 - - + +
282B GLN* 3.3 40.7 - - + +
283B LEU* 4.8 6.1 - - + +
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Residues in contact with PRO 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY* 5.5 3.1 - - - +
76B VAL* 3.2 35.2 - - + -
77B LEU 3.3 20.2 - - - +
78B PHE* 3.9 15.2 - - + -
241B ALA* 3.3 8.3 - - + -
242B ALA* 1.3 93.5 - - + +
244B LEU* 1.3 55.1 + - - +
246B TYR* 3.4 14.0 - - + -
247B LEU* 2.9 32.1 + - - +
282B GLN* 5.5 0.2 - - - +
283B LEU* 4.2 13.9 - - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.4 51.4 - - + +
79B GLY* 5.2 0.7 - - - -
111B ASP* 5.5 6.7 - - + +
112B ALA* 3.2 31.7 - - + +
113B LEU* 4.3 16.4 - - + +
236B ALA* 3.4 11.4 - - + +
240B GLU* 3.6 29.8 - - + +
241B ALA* 2.8 18.5 + - + +
243B PRO* 1.3 74.8 - - - +
245B GLN* 1.3 57.9 + - - +
247B LEU* 3.5 1.1 + - + -
248B ALA 3.1 22.3 + - - -
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Residues in contact with GLN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 3.4 22.5 - - + +
209B GLY* 3.5 21.2 + - - +
236B ALA* 3.5 27.8 - - + +
237B THR 3.4 16.7 + - - +
238B ALA* 4.0 8.4 + - - +
240B GLU* 2.8 29.8 + - + -
241B ALA 3.4 5.3 + - - +
242B ALA* 3.0 9.8 + - - +
244B LEU* 1.3 75.4 - - - +
246B TYR* 1.3 65.8 + - - +
247B LEU 3.1 0.4 + - - -
248B ALA* 4.1 0.2 - - - +
249B PRO* 3.4 12.5 - - - +
275B LYS* 4.6 5.7 - - - +
276B GLN* 3.7 2.6 - - - +
279B ALA* 3.8 18.0 - - + +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 5.4 16.5 - - + +
78B PHE* 5.6 2.5 - + - -
132B GLN* 3.6 10.8 + - - +
242B ALA 2.8 12.5 + - - +
243B PRO* 3.4 21.5 - - + +
245B GLN* 1.3 75.4 - - - +
247B LEU* 1.3 93.6 + - + +
249B PRO* 3.8 0.3 - - - +
250B PHE* 3.5 12.1 - + - -
276B GLN* 3.1 33.3 + - - -
279B ALA* 4.2 3.2 - - - +
280B TYR* 3.2 51.6 - + + +
283B LEU* 4.7 9.9 - - + -
303B LEU* 3.8 17.9 - - + -
306B ARG* 3.6 19.5 + - - -
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 6.1 2.2 - - - -
78B PHE* 4.0 16.6 - - + -
97B VAL* 4.0 13.0 - - + -
112B ALA* 4.0 13.9 - - + +
113B LEU* 3.6 33.2 - - + -
131B ALA* 3.8 26.2 - - + -
132B GLN* 5.0 2.7 - - - +
243B PRO 2.9 17.8 + - - +
244B LEU* 4.0 3.4 - - + +
246B TYR* 1.3 98.7 - - + +
248B ALA* 1.3 55.9 + - - +
250B PHE* 2.7 33.9 + - + +
251B THR* 3.2 15.3 + - + -
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 3.6 17.9 - - + +
206B VAL* 4.0 15.7 - - + -
208B VAL* 4.2 2.5 - - + -
234B VAL* 4.0 8.8 - - + +
236B ALA* 3.8 16.6 - - + +
244B LEU 3.1 16.6 + - - +
245B GLN 4.1 1.8 - - - +
247B LEU* 1.3 74.0 - - - +
249B PRO* 1.3 73.1 - - + +
250B PHE 3.0 0.5 + - - -
251B THR* 3.2 4.6 + - - -
252B ALA* 2.8 23.4 + - - +
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Residues in contact with PRO 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 4.2 4.5 - - + -
208B VAL* 3.7 18.2 - - + -
245B GLN 3.4 13.2 - - - +
246B TYR 3.8 3.1 - - - +
247B LEU 3.7 2.9 - - - -
248B ALA* 1.3 93.0 - - + +
250B PHE* 1.3 55.2 + - - +
252B ALA* 3.8 0.8 - - + +
253B ALA 3.0 21.7 + - - -
270B TYR* 3.6 26.4 - - + -
273B LEU* 4.5 4.5 - - + -
276B GLN* 3.8 24.2 - - + +
307B LEU* 3.3 31.3 - - + +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA* 3.4 23.0 - - + +
132B GLN* 3.3 35.9 - - - +
246B TYR* 3.5 25.6 - + - -
247B LEU* 2.7 20.0 + - + +
249B PRO* 1.3 69.6 - - - +
251B THR* 1.3 63.1 + - - +
253B ALA* 3.1 13.5 + - - +
254B SER* 3.1 14.9 + - - -
276B GLN* 3.4 22.7 - - - -
303B LEU* 3.5 28.3 - - + -
306B ARG* 3.8 19.7 - - + -
307B LEU* 3.7 32.5 - - + -
310B ARG* 4.0 10.8 - - - +
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 5.1 0.2 - - + -
98B ASP 4.7 4.0 - - - +
99B VAL* 3.4 36.4 - - + +
112B ALA* 2.5 33.4 + - - +
113B LEU* 5.4 0.2 - - + -
131B ALA* 3.8 20.2 - - + +
234B VAL* 4.6 2.4 - - - +
247B LEU* 3.2 18.0 + - + -
248B ALA* 3.2 11.8 + - - -
250B PHE* 1.3 76.1 - - - +
252B ALA* 1.3 59.1 + - - +
254B SER* 3.5 2.6 + - - -
255B ILE* 3.3 29.4 + - - +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 3.8 9.8 - - + +
206B VAL* 3.3 33.7 - - + -
234B VAL* 4.0 14.7 - - + +
248B ALA 2.8 20.2 + - - +
249B PRO 3.8 2.9 - - - +
251B THR* 1.3 74.5 + - - +
253B ALA* 1.3 56.3 + - - +
255B ILE* 3.5 8.5 + - - +
256B GLY 2.9 21.0 + - - -
268B ILE* 3.2 13.0 - - + +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PRO 3.0 10.0 + - - +
250B PHE 3.1 8.8 + - - +
252B ALA* 1.3 74.6 - - - +
254B SER* 1.3 54.2 + - - +
256B GLY* 3.3 1.5 + - - -
257B GLU* 2.6 39.7 + - - +
268B ILE* 3.9 7.2 - - - +
270B TYR* 3.6 18.8 - - - +
307B LEU* 4.4 4.7 - - + +
310B ARG* 3.8 26.9 - - + +
323B LEU* 4.2 10.0 - - + +
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.2 7.0 - - - -
101B VAL* 3.4 11.9 - - - +
129B SER* 3.7 19.8 + - - -
130B ARG 2.8 27.5 + - - -
131B ALA* 3.6 1.7 + - - -
133B VAL* 4.9 0.2 - - - -
250B PHE 3.1 10.3 + - - -
251B THR* 3.9 6.2 + - - -
252B ALA 3.4 0.4 - - - -
253B ALA* 1.3 73.8 - - - +
255B ILE* 1.3 66.3 + - - +
257B GLU* 3.6 12.9 - - - +
258B TRP* 3.2 17.2 + - - +
310B ARG* 3.0 12.2 + - - +
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.8 7.6 - - + -
100B PRO 3.7 13.9 - - - +
101B VAL* 3.9 7.6 - - + +
102B GLY 5.3 2.2 + - - +
105B LEU* 3.3 31.9 - - + -
110B VAL* 4.6 6.5 - - + -
114B GLY* 5.7 2.2 - - - -
204B VAL* 4.3 7.6 - - + -
232B ILE* 3.4 35.0 - - + -
234B VAL* 4.0 24.7 - - + -
251B THR* 3.3 17.2 + - - +
252B ALA* 3.6 7.4 - - - +
254B SER* 1.3 81.3 - - - +
256B GLY* 1.3 61.8 + - - +
258B TRP* 3.5 10.9 + - - +
259B PHE* 3.6 14.0 - - + -
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Residues in contact with GLY 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 4.0 15.3 - - - -
252B ALA 2.9 15.7 + - - -
253B ALA 3.5 3.4 - - - -
254B SER 3.2 0.2 - - - -
255B ILE* 1.3 75.4 - - - +
257B GLU* 1.3 62.9 + - - +
258B TRP 3.3 0.9 + - - -
259B PHE* 3.3 9.8 + - - +
260B ARG* 3.6 6.9 + - - +
266B ALA* 3.7 15.0 - - - +
268B ILE* 5.0 0.2 - - - -
323B LEU* 3.8 23.1 - - - +
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B SER* 5.6 1.0 - - - -
133B VAL* 3.7 19.7 - - - +
134B LYS 5.3 0.2 - - - +
253B ALA 2.6 19.8 + - - +
254B SER* 3.6 10.1 - - - +
255B ILE 3.2 0.4 - - - -
256B GLY* 1.3 71.8 - - - +
258B TRP* 1.3 58.6 + - - +
259B PHE 3.2 0.2 - - - -
260B ARG* 3.0 41.9 + - - +
261B ASP* 2.8 38.5 + - - +
310B ARG* 2.3 59.6 + - - +
323B LEU* 4.5 7.9 - - + -
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Residues in contact with TRP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.2 17.0 - - + -
102B GLY* 3.9 19.7 - - - +
103B PRO* 3.4 35.9 - - + -
126B ALA* 4.2 15.9 - - + +
129B SER* 6.0 0.2 - - - +
254B SER 3.2 11.3 + - - +
255B ILE 3.7 11.7 - - - +
256B GLY 3.3 0.4 - - - -
257B GLU* 1.3 74.7 - - - +
259B PHE* 1.3 97.7 + + + +
261B ASP* 3.3 3.9 + - - -
262B ASN* 2.6 58.4 + - + +
264B LYS* 3.9 28.3 - - + -
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLY 4.7 3.6 - - - -
103B PRO* 4.5 10.3 - - + -
106B LEU* 3.5 33.9 - - + -
202B TYR* 3.6 36.8 - + + -
204B VAL* 5.0 3.1 - - + -
232B ILE* 3.8 18.4 - - + -
255B ILE 3.6 20.9 - - - -
256B GLY* 3.3 9.8 + - - +
257B GLU 3.2 0.2 - - - -
258B TRP* 1.3 103.2 - + + +
260B ARG* 1.3 63.4 + - - +
262B ASN 3.1 8.5 + - - -
264B LYS* 3.0 36.9 + - + -
265B HIS 4.3 4.5 - - - -
266B ALA* 3.8 23.1 - - + -
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Residues in contact with ARG 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 5.3 5.9 - - - +
134B LYS 5.3 0.6 + - - -
136B PRO* 3.3 31.4 - - - +
256B GLY 3.6 2.8 + - - -
257B GLU* 3.0 42.6 + - - +
259B PHE* 1.3 77.6 - - - +
261B ASP* 1.3 83.8 + - - +
262B ASN 3.3 1.0 + - - -
263B GLY 3.8 1.4 + - - -
264B LYS 3.7 8.9 + - - -
310B ARG 2.7 31.0 + - - -
312B ALA* 4.6 5.8 - - - -
314B LEU* 3.6 28.0 - - + +
318B GLU 4.7 0.9 - - - +
321B GLY* 3.3 21.3 + - - -
322B SER* 3.7 18.0 + - - +
323B LEU* 3.7 29.4 - - + +
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Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLU* 2.8 26.6 + - - +
258B TRP* 3.3 5.3 + - - +
259B PHE 3.3 0.4 - - - -
260B ARG* 1.3 104.9 + - - +
262B ASN* 1.3 66.9 + - - +
263B GLY 3.6 2.1 + - - -
314B LEU* 4.1 10.4 - - - +
318B GLU 4.8 6.7 - - - +
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Residues in contact with ASN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TRP* 2.6 74.1 + - + +
259B PHE 3.1 2.7 + - - +
261B ASP* 1.3 86.5 - - - +
263B GLY* 1.3 62.0 + - - +
264B LYS* 3.2 20.0 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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