Contacts of the helix formed by residues 241 - 262 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LEU 3.5 21.1 - - - +
78A PHE* 3.4 27.1 + - - +
79A GLY* 4.6 6.3 - - - +
239A SER 3.8 2.0 + - - -
240A GLU* 1.3 76.1 - - - +
242A ALA* 1.3 69.0 + - - +
243A PRO* 3.2 3.1 - - + -
244A LEU* 3.0 22.0 + - + +
245A GLN 3.7 2.3 + - - -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU 3.5 2.7 + - - -
241A ALA* 1.3 69.0 - - - +
243A PRO* 1.3 72.5 - - + +
244A LEU 2.8 1.7 + - - -
245A GLN* 2.9 21.5 + - - +
246A TYR* 3.0 11.6 + - - +
279A ALA* 3.6 23.2 - - - +
282A GLN* 3.5 40.6 + - + +
283A LEU* 3.9 10.1 - - + -
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Residues in contact with PRO 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 5.4 1.3 - - + -
76A VAL* 3.6 22.4 - - + -
77A LEU 3.4 24.0 - - - +
78A PHE* 3.7 20.9 - - + -
241A ALA* 3.2 7.9 - - + -
242A ALA* 1.3 92.9 - - + +
244A LEU* 1.3 50.3 + - - +
246A TYR* 3.3 10.0 - - + +
247A LEU* 2.8 41.0 + - + +
283A LEU* 3.4 24.9 - - + -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.6 44.0 - - + +
111A ASP* 5.9 3.4 - - + +
112A ALA* 3.4 33.7 - - + +
113A LEU* 4.0 28.3 - - + -
236A ALA* 3.5 6.1 - - + +
240A GLU* 4.1 32.5 - - + +
241A ALA 3.0 10.7 + - - +
242A ALA 2.8 1.6 + - - -
243A PRO* 1.3 76.6 - - - +
245A GLN* 1.3 59.9 + - - +
247A LEU* 3.3 3.0 + - + +
248A ALA 2.9 23.7 + - - -
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Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL* 3.7 14.9 - - + +
209A GLY* 3.2 29.1 + - - -
236A ALA* 3.6 16.4 - - + +
237A THR 3.4 16.1 + - - +
238A ALA* 3.7 11.3 + - - +
240A GLU* 3.0 21.5 + - + +
241A ALA 3.8 7.0 - - - +
242A ALA* 2.9 12.2 + - - +
244A LEU* 1.3 71.8 - - - +
246A TYR* 1.3 65.6 + - - +
248A ALA* 3.5 1.9 + - - +
249A PRO* 3.3 19.9 - - - +
275A LYS* 4.8 2.6 - - - +
276A GLN* 3.6 5.9 - - - +
279A ALA* 3.7 19.4 - - + +
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 5.7 2.3 + - - -
64A MET* 5.3 9.2 - - - -
66A LEU* 5.4 9.0 - - + +
132A GLN* 3.9 10.2 + - - +
242A ALA 3.0 12.0 + - - +
243A PRO* 3.3 16.4 - - + +
245A GLN* 1.3 78.3 - - - +
247A LEU* 1.3 78.1 + - + +
250A PHE* 3.4 15.1 - + - -
276A GLN* 3.2 29.8 + - + -
279A ALA* 4.0 2.7 - - - +
280A TYR* 3.4 40.3 + + + +
283A LEU* 4.0 22.0 - - + -
303A LEU* 3.2 31.6 - - + -
306A ARG* 3.9 17.5 + - - -
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 6.0 1.1 - - - +
64A MET* 3.9 18.6 - - - -
78A PHE* 4.2 15.5 - - + -
97A VAL* 3.4 29.8 - - + -
112A ALA* 4.8 5.2 - - + +
113A LEU* 4.3 5.6 - - + -
131A ALA* 3.7 28.5 - - + -
132A GLN* 4.6 9.9 - - + +
243A PRO* 2.8 22.6 + - + +
244A LEU* 3.3 7.2 + - + +
245A GLN 3.3 0.2 - - - -
246A TYR* 1.3 91.6 - - + +
248A ALA* 1.3 69.8 + - - +
249A PRO 3.4 0.2 - - - -
250A PHE* 3.1 6.3 + - + +
251A THR* 3.0 25.3 + - - +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA* 4.4 6.0 - - + +
206A VAL* 3.9 10.5 - - + -
208A VAL* 4.0 11.2 - - + -
234A VAL* 4.3 9.1 - - + +
236A ALA* 3.7 19.5 - - + +
244A LEU 2.9 16.8 + - - +
245A GLN 3.7 4.7 - - - +
246A TYR 3.4 0.2 - - - -
247A LEU* 1.3 78.2 - - - +
249A PRO* 1.4 73.8 - - + +
250A PHE 3.0 0.2 + - - -
251A THR* 3.0 6.3 + - - +
252A ALA* 3.0 21.3 + - - +
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 4.0 4.5 - - + -
208A VAL* 4.0 13.5 - - + -
245A GLN 3.3 16.2 - - - +
246A TYR 3.6 1.3 - - - +
248A ALA* 1.4 89.5 - - + +
250A PHE* 1.3 54.5 + - - +
252A ALA* 3.6 0.5 + - - +
253A ALA* 3.0 23.0 + - - +
270A TYR* 3.2 36.4 - - + -
273A LEU* 4.0 9.6 - - + -
276A GLN* 3.2 36.6 - - + +
307A LEU* 3.5 14.6 - - + -
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA* 3.1 23.3 - - + +
132A GLN* 3.5 35.7 - - - +
246A TYR* 3.4 33.9 - + - -
247A LEU* 3.1 8.5 + - + +
249A PRO* 1.3 74.1 - - - +
251A THR* 1.3 66.2 + - - +
253A ALA* 3.3 5.2 + - - +
254A SER* 3.2 23.9 + - - -
276A GLN* 3.4 22.4 - - - -
303A LEU* 3.3 28.0 - - + -
306A ARG* 4.3 11.4 - - + -
307A LEU* 3.5 38.4 - - + -
310A ARG* 3.5 10.8 + - - +
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 5.1 3.5 - - - +
98A ASP 5.1 1.0 + - - -
99A VAL* 3.5 33.4 - - + +
111A ASP 4.9 0.9 - - - +
112A ALA* 2.6 32.1 + - - +
113A LEU* 4.9 1.6 - - - +
131A ALA* 3.8 17.3 - - - +
234A VAL* 4.8 5.8 - - + -
247A LEU* 3.0 21.4 + - - +
248A ALA 3.5 4.0 - - - +
250A PHE* 1.3 77.9 - - - +
252A ALA* 1.3 64.6 + - - +
254A SER* 3.2 6.9 + - - -
255A ILE* 3.2 24.9 + - + +
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 3.9 5.3 - - + +
206A VAL* 3.5 31.4 - - + -
234A VAL* 3.7 19.7 - - + -
248A ALA 3.0 12.9 + - - +
249A PRO 4.0 0.9 - - - +
251A THR* 1.3 77.5 - - - +
253A ALA* 1.3 57.8 + - - +
255A ILE* 3.1 15.0 + - - +
256A GLY 2.8 25.6 + - - -
268A ILE* 3.5 11.2 - - + +
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Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PRO 3.0 20.2 + - - +
250A PHE* 3.4 9.2 - - - +
252A ALA* 1.3 77.3 - - - +
254A SER* 1.3 56.0 + - - +
256A GLY* 3.6 1.1 + - - +
257A GLU* 3.0 32.1 + - - +
268A ILE* 3.6 9.3 - - - +
270A TYR* 3.4 16.2 - - - +
307A LEU* 4.2 4.0 - - + -
310A ARG* 3.6 25.1 - - + +
323A LEU* 4.4 7.0 - - + +
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 3.8 15.5 - - - -
101A VAL* 3.7 9.2 - - - +
129A SER* 3.9 15.6 + - - -
130A ARG 2.7 26.9 + - - -
131A ALA* 4.1 0.2 - - - -
133A VAL* 4.0 1.4 - - - +
250A PHE 3.2 8.7 + - - -
251A THR 3.2 9.2 + - - -
253A ALA* 1.3 73.7 - - - +
255A ILE* 1.3 66.9 - - - +
257A GLU* 3.1 20.8 + - - +
258A TRP 3.2 10.2 + - - -
310A ARG* 2.9 14.6 + - - +
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 3.9 18.8 - - + -
100A PRO 3.7 16.8 - - - +
101A VAL* 4.1 8.1 - - - -
102A GLY 5.1 2.3 + - - +
105A LEU* 3.6 23.8 - - + -
110A VAL* 4.6 3.8 - - + -
204A VAL* 4.4 7.6 - - + -
232A ILE* 3.6 32.8 - - + -
234A VAL* 3.8 27.1 - - + -
251A THR* 3.4 14.6 - - + +
252A ALA* 3.1 9.4 + - - +
254A SER* 1.3 78.4 - - - +
256A GLY* 1.3 60.1 + - - +
258A TRP* 3.6 9.7 + - - +
259A PHE* 3.3 16.5 - - + -
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Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 4.2 9.4 - - - -
252A ALA 2.8 14.3 + - - -
253A ALA 3.9 2.5 - - - -
255A ILE* 1.3 75.8 - - - +
257A GLU* 1.3 63.1 + - - +
259A PHE* 3.3 24.6 + - - +
260A ARG* 3.3 8.5 + - - +
266A ALA* 3.6 9.8 - - - +
268A ILE* 5.4 0.4 - - - -
323A LEU* 4.0 21.6 - - - +
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A SER* 6.0 0.2 - - - -
133A VAL* 3.6 17.2 - - - +
134A LYS 4.7 0.7 - - - +
253A ALA 3.0 16.1 + - - +
254A SER* 3.1 10.5 + - - +
256A GLY* 1.3 76.2 - - - +
258A TRP* 1.3 56.2 + - - +
260A ARG* 3.3 46.9 + - - +
261A ASP* 2.8 43.9 + - - +
310A ARG* 2.4 55.3 + - - +
323A LEU* 4.5 8.3 - - + -
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Residues in contact with TRP 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 4.1 31.6 - - + -
102A GLY* 3.9 10.1 - - - +
103A PRO* 3.4 40.4 - - + -
126A ALA* 4.3 14.4 - - + +
254A SER 3.2 7.2 + - - +
255A ILE 3.7 11.2 - - - +
256A GLY 3.3 0.2 - - - -
257A GLU* 1.3 76.8 - - - +
259A PHE* 1.3 95.2 + + - +
261A ASP* 3.6 3.9 + - - -
262A ASN* 2.6 52.2 + - - +
264A LYS* 3.3 32.3 - - + -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY 4.6 3.4 - - - -
103A PRO* 4.5 7.0 - - + -
106A LEU* 4.4 15.0 - - + -
202A TYR* 3.8 43.1 - + + -
204A VAL* 4.8 3.1 - - + -
232A ILE* 4.0 26.9 - - + -
255A ILE* 3.3 24.0 - - + -
256A GLY* 3.4 14.6 - - - +
257A GLU 3.1 0.4 - - - -
258A TRP* 1.3 101.5 - + + +
260A ARG* 1.3 65.6 + - - +
261A ASP 3.1 1.6 - - - -
262A ASN* 2.9 13.4 + - - -
264A LYS* 3.1 31.4 + - + +
266A ALA* 3.8 24.5 - - + +
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Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 5.3 3.2 - - - +
134A LYS 5.4 2.0 + - - -
136A PRO* 3.3 26.3 - - - +
256A GLY 3.3 2.4 + - - +
257A GLU* 3.0 40.5 + - - +
259A PHE* 1.3 79.2 - - - +
261A ASP* 1.3 88.6 + - - +
262A ASN 3.4 0.3 + - - -
263A GLY 3.9 0.3 + - - -
264A LYS 3.6 9.2 - - - -
310A ARG 2.7 35.4 + - - -
312A ALA 4.1 9.2 - - - +
314A LEU* 3.6 24.4 - - + +
318A GLU 5.0 0.3 - - - +
321A GLY* 3.3 20.6 - - - +
322A SER* 3.7 16.5 + - - +
323A LEU* 3.6 28.3 - - + +
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Residues in contact with ASP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLU* 2.8 25.5 + - - +
258A TRP* 4.0 6.1 - - - +
260A ARG* 1.3 114.9 + - - +
262A ASN* 1.3 65.6 + - - +
263A GLY 3.6 2.3 + - - -
314A LEU* 4.3 8.4 - - - +
318A GLU 4.2 11.9 - - - +
319A GLY* 5.6 0.2 - - - -
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Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A TRP* 2.6 55.7 + - + +
259A PHE 2.9 4.5 + - - +
261A ASP* 1.3 86.6 - - - +
263A GLY* 1.3 64.0 + - - +
264A LYS* 3.2 29.8 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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