Contacts of the helix formed by residues 241 - 268 (chain A) in PDB entry 4GL5
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 TYR 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A CYS* 5.0 10.3 - - - -
227A LEU* 4.3 5.6 - - + -
234A PHE* 3.6 36.1 - + + -
235A PHE* 3.0 54.3 + + - +
237A ILE 4.4 0.2 - - - -
238A SER* 3.8 27.2 - - - -
240A LEU* 1.3 80.7 - - - +
242A LYS* 1.3 67.1 + - + +
243A LYS* 3.1 4.0 - - - +
244A TYR* 2.9 19.8 + - + +
245A GLU* 2.9 48.5 + - + -
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Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A SER* 3.4 36.7 + - - +
239A TRP* 4.0 28.2 - - + +
240A LEU 3.9 0.6 - - - +
241A TYR* 1.3 77.9 - - - +
243A LYS* 1.3 62.7 + - - +
245A GLU* 3.3 17.8 + - - +
246A LYS* 3.0 24.8 + - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP 5.1 8.7 + - - +
240A LEU* 4.4 20.5 + - - +
241A TYR* 4.7 1.8 - - - +
242A LYS* 1.3 79.7 - - - +
244A TYR* 1.3 82.2 + - + +
246A LYS* 3.1 20.7 + - - +
247A SER* 3.1 18.5 + - - +
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A CYS* 5.4 0.2 - - - -
219A GLY 5.6 0.2 - - - -
222A ASP* 4.4 10.3 - - + -
223A ALA* 3.7 30.5 - - + +
226A ALA* 3.5 26.0 - - + +
227A LEU* 3.7 34.8 - - + -
230A LYS* 5.2 4.3 + - - -
234A PHE* 4.7 5.8 - + - -
240A LEU 4.3 11.2 - - - -
241A TYR* 2.9 19.1 + - - +
243A LYS* 1.3 94.7 - - + +
245A GLU* 1.3 64.8 + - - +
247A SER* 3.5 4.4 + - - +
248A VAL* 3.3 29.0 + - - +
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Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A CYS* 4.4 21.6 - - - +
241A TYR* 2.9 42.0 + - + +
242A LYS* 3.3 18.7 + - + +
244A TYR* 1.3 77.1 - - - +
246A LYS* 1.3 60.1 + - - +
248A VAL* 4.0 4.7 - - - +
249A LYS* 3.5 19.8 + - - +
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS 3.0 15.7 + - - +
243A LYS* 3.1 6.9 + - - +
245A GLU* 1.3 78.1 - - - +
247A SER* 1.3 60.5 + - - +
248A VAL 3.3 0.4 - - - -
249A LYS* 3.8 12.7 - - + +
250A ASP* 3.1 52.4 + - - +
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LYS* 4.6 2.3 - - - +
219A GLY* 3.6 32.8 + - - -
220A TYR 4.4 7.3 + - - -
223A ALA* 4.7 0.7 - - - -
243A LYS* 3.1 16.8 + - - +
244A TYR* 3.5 9.7 + - - -
246A LYS* 1.3 75.5 + - - +
248A VAL* 1.3 65.6 + - - +
250A ASP* 3.6 10.0 - - - +
251A LEU* 3.5 18.4 + - - +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A CYS* 3.6 19.7 - - - +
125A ILE* 3.9 41.7 - - + +
220A TYR* 4.1 21.1 - - + -
223A ALA* 4.3 6.7 - - + -
244A TYR 3.3 17.2 + - - +
245A GLU* 4.0 6.3 - - - +
247A SER* 1.3 74.4 - - - +
249A LYS* 1.3 67.5 + - - +
251A LEU* 3.2 5.9 + - - +
252A LYS* 2.9 34.5 + - + +
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU 3.5 16.2 + - - +
246A LYS* 3.8 14.4 - - + +
248A VAL* 1.3 80.5 - - - +
250A ASP* 1.3 56.8 + - - +
252A LYS* 4.4 5.8 - - - -
253A ASP* 2.7 66.8 + - - +
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Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LYS* 4.0 31.0 + - + +
246A LYS* 3.1 47.9 + - - +
247A SER* 3.6 10.6 - - - +
249A LYS* 1.3 76.8 - - - +
251A LEU* 1.3 62.0 + - - +
253A ASP* 4.0 3.8 - - - +
254A ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 4.2 12.6 - - + -
216A LYS* 3.9 17.2 - - + +
217A ILE* 3.7 32.3 - - + +
220A TYR* 3.7 33.2 - - + -
247A SER 3.5 7.2 + - - +
248A VAL 3.2 7.1 + - - +
250A ASP* 1.3 75.3 - - - +
252A LYS* 1.3 58.8 + - - +
254A ALA* 3.2 4.9 + - - +
255A ILE* 2.9 47.0 + - + +
301A LEU* 3.8 17.3 - - + -
305A ILE* 3.8 20.9 - - + -
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE 3.6 17.8 + - - -
126A GLY* 3.9 9.1 - - - -
130A LYS* 4.5 9.6 - - - +
248A VAL* 2.9 27.6 + - + +
249A LYS* 3.8 5.4 - - - +
251A LEU* 1.3 77.6 - - - +
253A ASP* 1.3 60.8 + - - +
255A ILE* 3.2 2.9 + - - +
256A GLU* 2.8 52.6 + - - +
297A ASN* 5.3 7.2 - - - -
298A GLN* 3.2 26.1 + - - +
301A LEU* 4.0 21.7 - - + +
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Residues in contact with ASP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LYS* 2.7 61.6 + - - +
250A ASP* 4.0 3.8 - - - +
252A LYS* 1.3 77.9 - - - +
254A ALA* 1.3 61.8 + - - +
256A GLU* 3.7 7.9 + - - +
257A VAL* 3.5 24.6 + - - +
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 3.8 24.9 - - + +
216A LYS* 4.3 15.3 - - + +
250A ASP 3.1 18.0 + - - +
251A LEU* 3.2 7.6 + - - +
253A ASP* 1.3 78.9 - - - +
255A ILE* 1.3 60.0 + - + +
257A VAL* 3.6 17.5 - - - +
258A LEU* 3.2 17.3 - - - +
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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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213A ILE* 5.5 4.9 - - + -
251A LEU* 2.9 45.3 + - + +
252A LYS* 3.9 4.5 - - - +
254A ALA* 1.3 77.2 - - + +
256A GLU* 1.3 61.9 + - - +
257A VAL 3.0 2.0 - - - -
258A LEU* 2.8 32.9 + - + +
259A ILE* 2.8 21.2 + - + +
297A ASN 4.7 5.8 - - - +
300A ILE* 4.3 24.2 - - + -
301A LEU* 3.8 33.7 - - + +
304A LEU* 4.5 17.3 - - + -
305A ILE* 5.5 1.1 - - + -
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LYS* 2.8 42.5 + - - +
253A ASP* 3.7 10.0 + - - +
255A ILE* 1.3 74.8 - - - +
257A VAL* 1.3 55.0 + - + +
259A ILE* 3.4 16.9 - - + +
260A ALA* 3.1 28.9 + - - +
297A ASN* 3.2 38.0 + - - +
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ASP 3.5 12.2 + - - +
254A ALA* 3.6 14.4 - - - +
255A ILE 3.0 0.2 - - - -
256A GLU* 1.3 79.3 - - - +
258A LEU* 1.3 66.1 + - + +
260A ALA* 3.6 6.7 + - - +
261A GLU* 3.4 20.1 + - - +
264A ARG* 5.1 1.2 + - - -
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Residues in contact with LEU 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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204A LEU* 3.9 20.0 - - + -
206A ILE* 3.8 32.9 - - + +
207A PRO 4.1 2.0 - - - +
208A LEU* 3.7 44.0 - - + -
213A ILE* 4.6 12.1 - - + -
254A ALA 3.2 21.5 - - - +
255A ILE* 2.8 26.5 + - + +
257A VAL* 1.3 81.0 - - + +
259A ILE* 1.3 60.0 + - + +
261A GLU* 3.2 5.9 + - - +
262A LYS* 3.0 25.4 + - - +
304A LEU* 5.6 2.0 - - + -
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Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 5.0 5.2 - - + -
255A ILE* 2.8 27.3 + - + +
256A GLU* 3.4 28.5 - - + +
258A LEU* 1.3 70.6 - - + +
260A ALA* 1.3 66.3 + - + +
262A LYS* 3.7 8.6 - - + +
263A ARG* 3.0 56.2 + - - +
283A ILE* 5.0 3.5 - - + +
293A ARG* 6.3 0.2 - - - -
297A ASN* 3.6 29.4 - - - +
300A ILE* 3.6 47.6 - - + -
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU 3.1 21.5 + - - +
257A VAL* 3.7 8.7 - - - +
258A LEU 3.1 0.4 - - - -
259A ILE* 1.3 81.8 - - + +
261A GLU* 1.3 60.4 + - - +
263A ARG* 3.4 15.9 + - - +
264A ARG* 3.4 35.9 + - - +
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 4.1 15.7 - - + -
257A VAL 3.4 9.0 + - - +
258A LEU* 3.2 7.2 + - - +
260A ALA* 1.3 76.2 - - - +
262A LYS* 1.3 66.7 + - - +
263A ARG 3.3 0.2 + - - -
264A ARG* 2.6 49.2 + - - +
265A ARG* 2.8 65.6 + - - +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.1 36.6 + - + +
205A ARG* 3.9 13.3 + - - +
206A ILE* 3.8 20.1 - - + +
258A LEU 3.0 14.6 + - - +
259A ILE* 3.3 11.0 + - + +
261A GLU* 1.3 77.8 - - - +
263A ARG* 1.3 58.5 + - - +
265A ARG* 3.5 7.3 + - + +
266A ILE* 3.0 33.7 + - + +
277A ASP* 3.1 36.5 + - - -
279A ALA* 4.2 5.8 - - + -
280A THR* 3.5 11.7 + - - -
283A ILE* 4.0 17.5 - - + -
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Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 3.0 49.8 + - - +
260A ALA* 3.7 7.7 - - - +
261A GLU 3.2 0.2 - - - -
262A LYS* 1.3 75.6 - - - +
264A ARG* 1.3 64.2 + - - +
266A ILE* 3.3 8.0 + - - +
267A SER* 3.1 24.8 + - - -
283A ILE* 4.0 31.4 - - + +
286A GLU* 2.6 36.0 + - - -
287A LYS* 5.5 4.6 - - - +
293A ARG* 3.8 18.7 - - - +
296A VAL* 4.1 9.9 - - - +
297A ASN* 3.6 15.4 + - - -
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL 5.1 1.4 + - - -
260A ALA* 3.4 32.3 + - - +
261A GLU* 2.6 54.7 + - - +
263A ARG* 1.3 76.1 - - + +
265A ARG* 1.3 64.5 + - + +
266A ILE 3.1 0.2 + - - -
267A SER* 2.9 24.2 + - - -
268A THR* 3.3 15.9 + - + +
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG 4.1 4.8 + - - -
206A ILE* 3.6 26.5 - - + +
207A PRO* 3.7 32.1 - - - +
261A GLU* 2.8 46.2 + - - +
262A LYS* 3.9 11.2 - - + +
263A ARG 3.3 0.4 - - - -
264A ARG* 1.3 76.2 - - + +
266A ILE* 1.3 60.2 + - + +
268A THR* 3.8 15.3 - - - +
269A GLU* 3.0 16.3 - - - +
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Residues in contact with ILE 266 (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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262A LYS* 3.0 25.6 - - + +
263A ARG* 4.1 3.8 - - - +
264A ARG 3.1 0.6 - - - -
265A ARG* 1.3 76.4 - - + +
267A SER* 1.3 63.0 + - - +
268A THR 3.1 5.9 + - - -
269A GLU* 3.3 34.7 - - + +
272A LEU* 5.5 5.5 - - + +
280A THR* 3.8 39.0 - - + +
283A ILE* 3.8 37.9 - - + -
284A LEU* 4.9 14.6 - - + -
287A LYS* 6.3 4.0 - - - -
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ARG 3.1 14.0 + - - -
264A ARG* 2.9 23.2 + - - -
266A ILE* 1.3 76.5 - - - +
268A THR* 1.3 64.3 + - - +
269A GLU 3.8 1.5 + - - -
287A LYS* 5.7 8.7 - - - +
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 3.3 16.4 + - + +
265A ARG* 3.8 12.2 + - - +
266A ILE 3.1 0.6 - - - -
267A SER* 1.3 85.6 - - - +
269A GLU* 1.3 60.3 + - - +
270A GLU 4.0 1.0 + - - -
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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