Contacts of the helix formed by residues 296 - 329 (chain A) in PDB entry 3C6G
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 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A TYR* 3.1 14.5 + - - -
284A MET* 3.5 13.0 - - - -
294A THR 3.5 5.9 + - - -
295A PHE* 1.3 74.5 - - - +
297A LYS* 1.3 58.5 + - - +
298A GLU* 3.2 22.2 + - - +
299A ASN* 2.9 27.6 + - - +
300A LEU 3.0 23.4 + - - -
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Residues in contact with LYS 297 (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 SER* 5.4 6.5 - - - -
261A ILE* 6.5 1.3 - - + -
262A GLU* 4.6 22.7 + - - +
281A LEU* 6.6 0.2 - - + -
284A MET* 3.7 14.2 - - + +
296A SER* 1.3 73.9 - - - +
298A GLU* 1.3 72.2 + - - +
300A LEU* 3.4 12.7 + - + +
301A ILE* 3.3 36.5 + - + +
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Residues in contact with GLU 298 (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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120A LYS* 5.0 14.0 + - + +
254A TYR* 3.9 22.2 - - - +
296A SER* 3.5 16.2 + - - +
297A LYS* 1.3 94.2 + - + +
299A ASN* 1.3 58.7 + - - +
301A ILE* 3.1 5.9 + - - +
302A PHE* 3.0 46.5 + - + -
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Residues in contact with ASN 299 (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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119A THR 4.9 0.2 - - - +
122A GLY* 3.7 9.1 - - - -
123A GLY* 2.9 26.0 + - - +
136A HIS* 3.6 9.5 - - - +
280A TYR* 3.0 19.5 + - - +
294A THR* 2.8 25.5 + - - +
296A SER* 2.9 17.6 + - - +
298A GLU* 1.3 76.5 - - - +
300A LEU* 1.3 52.2 + - - +
302A PHE* 3.9 13.4 - - - +
303A SER* 2.5 36.2 + - - -
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Residues in contact with LEU 300 (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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261A ILE* 3.7 29.8 - - + -
276A PHE* 4.0 7.4 - - + -
277A VAL* 4.5 7.9 - - + +
280A TYR* 3.3 48.7 + - + -
281A LEU* 4.1 23.1 - - + -
284A MET* 5.5 0.2 - - - -
296A SER 3.0 13.5 + - - +
297A LYS* 3.5 16.8 - - + +
298A GLU 3.2 0.2 - - - -
299A ASN* 1.3 75.0 - - - +
301A ILE* 1.3 61.1 + - - +
303A SER* 3.8 0.4 - - - -
304A VAL* 3.0 51.0 + - + +
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.4 54.5 - - + +
257A LEU* 3.8 27.0 - - + +
258A SER* 3.5 27.1 - - - -
261A ILE* 3.7 20.6 - - + -
297A LYS* 3.3 24.2 + - + +
298A GLU 3.1 6.6 + - - +
300A LEU* 1.3 78.3 - - + +
302A PHE* 1.3 56.5 + - - +
304A VAL* 4.0 0.5 - - - +
305A GLY* 2.9 27.4 + - - -
701A VD3 4.3 2.6 - - + +
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Residues in contact with PHE 302 (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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118A MET 3.2 25.4 - - - -
119A THR* 3.7 36.1 - - + -
120A LYS* 5.2 15.5 - - + -
123A GLY* 4.1 15.0 - - - -
254A TYR* 3.5 31.4 - + - -
298A GLU* 3.0 38.0 + - + +
299A ASN* 3.9 13.5 - - - +
301A ILE* 1.3 78.0 - - - +
303A SER* 1.3 52.4 + - - +
305A GLY 3.4 0.2 + - - -
306A GLU* 2.8 43.0 + - - +
701A VD3 3.2 26.3 - - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY* 3.9 6.3 - - - -
124A LEU* 4.4 7.2 + - - +
136A HIS* 3.3 23.1 - - - -
276A PHE* 4.3 21.3 - - - -
280A TYR* 4.6 0.2 - - - -
299A ASN 2.5 25.0 + - - -
300A LEU* 3.8 4.9 - - - -
302A PHE* 1.3 76.0 - - - +
304A VAL* 1.3 57.1 + - - +
306A GLU* 3.3 11.2 + - - +
307A LEU* 2.8 39.4 + - - +
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Residues in contact with VAL 304 (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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195A ILE* 4.0 20.0 - - + -
196A PHE* 3.7 17.7 - - + -
257A LEU* 4.1 8.5 - - + -
261A ILE* 3.9 16.6 - - + -
276A PHE* 4.0 8.3 - - + -
277A VAL* 4.3 2.0 - - + -
300A LEU* 3.0 40.2 + - + +
301A ILE 4.0 2.5 - - - +
303A SER* 1.3 76.3 - - - +
305A GLY* 1.3 59.1 + - - +
307A LEU* 3.4 6.4 + - - +
308A ILE* 2.8 53.1 + - + +
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Residues in contact with GLY 305 (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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214A PHE* 3.2 23.7 - - - -
257A LEU* 3.5 27.5 - - - +
301A ILE 2.9 14.0 + - - -
302A PHE 3.8 1.1 - - - -
304A VAL* 1.3 77.8 - - - +
306A GLU* 1.3 56.2 + - - +
308A ILE* 4.5 1.3 - - - -
309A ILE* 2.9 25.5 + - - +
701A VD3 3.9 2.0 - - - -
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Residues in contact with GLU 306 (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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119A THR* 3.6 26.7 + - - +
122A GLY 4.2 2.1 - - - +
123A GLY 3.9 0.3 - - - -
124A LEU* 2.8 19.8 + - + +
125A LEU* 2.8 50.7 + - + +
126A ASN* 3.9 11.3 + - - +
302A PHE* 2.8 27.7 + - - +
303A SER* 3.7 3.1 - - - +
305A GLY* 1.3 72.9 - - - +
307A LEU* 1.3 57.2 - - + +
309A ILE* 3.5 7.2 - - - +
310A ALA* 2.9 35.0 + - - +
601A HEM 5.2 2.7 - - + -
701A VD3 3.8 20.5 - - + +
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Residues in contact with LEU 307 (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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124A LEU* 4.2 12.3 - - + -
140A ALA* 4.3 5.6 - - + -
144A PHE* 3.7 34.8 - - + -
191A THR* 4.4 4.0 - - - +
195A ILE* 4.1 13.0 - - + -
276A PHE* 3.9 36.6 - - + -
303A SER* 2.8 24.7 + - - +
304A VAL* 3.8 4.3 - - - +
306A GLU* 1.3 72.9 - - + +
308A ILE* 1.3 62.3 + - - +
310A ALA* 3.9 4.6 - - - +
311A GLY* 3.1 19.6 + - - -
449A LEU* 4.1 11.9 - - + -
601A HEM 3.8 34.4 - - + +
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Residues in contact with ILE 308 (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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188A SER* 5.7 0.9 - - - -
191A THR* 4.6 8.6 - - + -
192A ASN* 4.5 10.1 - - - +
195A ILE* 3.7 15.3 - - + -
196A PHE* 3.6 24.5 - - + -
207A PHE* 4.8 7.4 - - + -
210A MET* 4.8 5.8 - - + -
211A ILE* 4.1 27.1 - - + -
214A PHE* 5.0 5.8 - - + -
257A LEU* 3.9 13.5 - - + -
304A VAL* 2.8 42.1 + - + +
305A GLY* 3.8 4.3 - - - +
307A LEU* 1.3 72.3 - - - +
309A ILE* 1.3 63.0 + - + +
311A GLY* 3.7 0.5 + - - -
312A THR* 2.9 35.4 + - - +
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Residues in contact with ILE 309 (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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125A LEU* 5.5 0.7 - - + -
211A ILE* 4.6 9.6 - - + +
214A PHE* 3.7 47.8 - - + -
215A SER* 4.0 10.1 - - - +
218A VAL* 3.7 22.7 - - + -
305A GLY 2.9 19.5 + - - +
306A GLU* 3.5 9.6 - - - +
308A ILE* 1.3 79.1 - - + +
310A ALA* 1.3 72.5 + - + +
312A THR* 5.0 4.7 - - + -
313A GLU* 3.1 43.0 + - + +
701A VD3 4.2 19.4 - - + +
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Residues in contact with ALA 310 (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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125A LEU* 4.5 9.9 - - + -
306A GLU 2.9 19.8 + - - +
307A LEU 3.9 1.3 - - - +
309A ILE* 1.3 81.6 - - - +
311A GLY* 1.3 53.3 + - - +
314A THR* 2.6 37.5 + - - +
601A HEM 3.4 43.0 + - + +
701A VD3 4.3 12.3 - - + -
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Residues in contact with GLY 311 (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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187A VAL* 4.0 5.1 - - - +
191A THR* 4.7 6.7 - - - -
307A LEU 3.1 12.9 + - - -
308A ILE 4.1 0.9 - - - -
310A ALA* 1.3 80.0 - - - +
312A THR* 1.3 61.0 + - - +
315A THR* 3.2 32.4 + - - -
601A HEM 3.5 28.0 - - - -
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Residues in contact with THR 312 (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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184A THR* 3.3 35.7 - - + +
187A VAL* 4.3 5.6 - - - -
188A SER* 3.2 29.7 - - - +
191A THR* 5.8 1.4 - - - -
211A ILE* 3.9 20.8 - - + +
308A ILE* 2.9 20.0 + - - +
309A ILE* 4.5 4.7 - - + -
311A GLY* 1.3 73.1 - - - +
313A GLU* 1.3 67.2 + - - +
316A THR* 2.7 35.4 + - - +
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Residues in contact with GLU 313 (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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180A LYS* 6.2 0.2 - - - -
211A ILE* 6.0 0.3 - - - +
215A SER* 2.6 34.0 + - - -
218A VAL* 4.0 22.9 - - + +
309A ILE* 3.1 34.4 + - + +
312A THR* 1.3 81.1 - - - +
314A THR* 1.3 60.0 + - + +
316A THR* 4.1 0.7 - - - -
317A ASN* 2.6 45.0 + - - -
488A THR* 2.9 25.5 + - - +
490A GLN* 4.2 8.8 + - - -
701A VD3 4.0 12.6 - - + -
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Residues in contact with THR 314 (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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310A ALA 2.6 25.8 + - - +
311A GLY 3.5 0.3 + - - -
312A THR 3.4 0.2 - - - -
313A GLU* 1.3 74.8 - - - +
315A THR* 1.3 75.1 + - - +
317A ASN* 2.9 13.3 + - - +
318A VAL* 3.0 14.9 + - - +
374A ILE* 3.8 10.8 - - - +
375A VAL* 4.0 13.2 - - + -
488A THR* 4.3 3.4 - - + -
601A HEM 3.0 39.2 - - + +
701A VD3 3.7 33.4 - - + -
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Residues in contact with THR 315 (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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187A VAL* 3.6 22.0 - - + -
311A GLY 3.2 15.3 + - - -
314A THR* 1.3 82.9 + - - +
316A THR* 1.3 64.1 + - - +
318A VAL* 3.2 3.3 + - - +
319A LEU* 3.2 24.9 + - + +
454A ALA* 4.0 6.6 - - - +
457A GLU* 3.9 33.0 + - + +
458A MET* 4.3 17.5 - - + -
601A HEM 3.6 25.7 - - - +
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Residues in contact with THR 316 (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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180A LYS* 4.4 2.0 - - + +
183A ILE* 3.6 23.5 - - + +
184A THR* 3.6 36.3 - - + +
187A VAL* 3.7 13.1 - - - +
312A THR* 2.7 26.9 + - - +
313A GLU* 4.1 1.8 - - - -
314A THR 3.2 0.6 - - - -
315A THR* 1.3 76.5 - - - +
317A ASN* 1.3 59.5 + - - +
319A LEU* 3.2 5.9 + - - +
320A ARG* 2.9 43.3 + - - +
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Residues in contact with ASN 317 (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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180A LYS* 5.8 0.5 - - - -
313A GLU* 2.6 39.6 + - - +
314A THR 2.9 5.1 + - - +
316A THR* 1.3 76.3 - - - +
318A VAL* 1.3 68.5 + - - +
320A ARG* 3.0 18.7 + - - +
321A TRP* 2.8 29.8 + - + -
374A ILE* 4.0 6.7 - - + +
488A THR* 3.5 15.6 + - - -
489A LEU 3.9 13.8 + - - +
490A GLN* 3.1 31.2 - - + +
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Residues in contact with VAL 318 (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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314A THR 3.0 11.0 + - - +
315A THR 3.5 7.2 - - - +
317A ASN* 1.3 77.0 - - - +
319A LEU* 1.3 59.8 + - + +
321A TRP* 3.3 3.3 + - - +
322A ALA* 2.9 28.6 + - + +
365A LEU* 5.3 4.5 - - + -
368A VAL* 3.8 12.4 - - + +
369A LEU* 3.6 20.2 - - + -
374A ILE* 3.6 23.3 - - + +
458A MET* 3.8 32.8 - - + -
601A HEM 3.5 30.5 - - + -
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Residues in contact with LEU 319 (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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165A PHE* 6.3 1.3 - - + -
183A ILE* 4.1 16.8 - - + -
187A VAL* 4.0 26.5 - - + -
315A THR* 3.2 15.3 + - + +
316A THR 3.6 7.4 - - - +
318A VAL* 1.3 79.3 - - + +
320A ARG* 1.3 57.8 + - - +
322A ALA* 3.2 4.6 + - + +
323A ILE* 2.9 39.7 + - + +
365A LEU* 5.5 1.8 - - + -
458A MET* 3.9 33.0 - - + +
461A PHE* 3.8 24.0 - - + -
462A PHE* 4.0 26.0 - - + +
465A LEU* 6.5 1.1 - - + -
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Residues in contact with ARG 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 4.5 4.9 + - - -
179A PHE* 5.6 0.9 - - + -
180A LYS* 3.8 41.8 - - - +
183A ILE* 3.8 20.6 - - + -
316A THR* 2.9 33.1 + - + +
317A ASN* 3.0 18.1 + - - +
319A LEU* 1.3 77.4 - - - +
321A TRP* 1.3 61.2 + - - +
323A ILE* 4.7 0.2 - - - -
324A LEU* 3.1 10.9 + - - +
490A GLN* 3.1 36.6 + - - +
491A PRO* 3.4 37.1 + - + +
492A GLN 3.9 10.3 + - - -
493A PRO* 4.4 8.1 - - - +
494A TYR* 2.5 36.6 + - - +
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Residues in contact with TRP 321 (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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317A ASN 2.8 23.2 + - - -
318A VAL 3.7 6.1 - - - +
320A ARG* 1.3 74.5 - - - +
322A ALA* 1.3 64.7 + - - +
324A LEU* 3.3 24.3 + - + +
325A PHE* 3.0 53.1 + + - -
368A VAL* 3.9 5.4 - - + -
372A CYS* 3.7 27.3 - - + +
374A ILE* 3.9 17.4 - - + +
481A LEU* 3.7 27.8 - - + -
483A PRO* 3.9 20.6 - - + -
489A LEU* 3.0 29.7 + - + +
490A GLN* 3.6 8.9 - - - +
491A PRO* 3.5 32.3 - - + +
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Residues in contact with ALA 322 (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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318A VAL* 2.9 18.7 + - + +
319A LEU* 3.2 9.4 + - + +
321A TRP* 1.3 72.3 - - - +
323A ILE* 1.3 67.0 + - - +
325A PHE* 3.2 4.4 + - - +
326A MET* 2.9 30.3 + - - +
364A VAL* 5.8 0.2 - - + -
365A LEU* 4.9 8.1 - - + -
368A VAL* 4.1 24.2 - - + +
462A PHE* 4.0 25.4 - - + -
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Residues in contact with ILE 323 (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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165A PHE* 5.6 0.4 - - + -
179A PHE* 3.8 12.6 - - + -
183A ILE* 3.4 33.0 - - + -
319A LEU* 2.9 21.5 + - + +
320A ARG* 4.7 0.9 - - - -
322A ALA* 1.3 77.4 - - + +
324A LEU* 1.3 64.5 + - - +
326A MET* 3.1 8.0 + - - +
327A ALA* 3.1 21.1 + - - +
462A PHE* 5.5 5.8 - - + -
465A LEU* 3.8 29.8 - - + -
466A LEU* 6.3 0.2 - - + -
471A LEU* 4.1 14.5 - - + +
494A TYR* 3.7 9.9 - - + +
496A ILE* 3.0 33.9 - - + -
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Residues in contact with LEU 324 (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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320A ARG 3.1 14.7 + - - +
321A TRP* 3.5 32.5 - - + +
322A ALA 3.2 0.2 - - - -
323A ILE* 1.3 78.1 - - - +
325A PHE* 1.3 57.5 + - + +
327A ALA 3.3 0.3 + - - -
328A LEU* 3.0 28.2 + - - +
473A PHE* 3.7 25.3 - - + -
479A PRO* 4.4 9.4 - - + -
480A ASP 4.2 5.6 - - - +
481A LEU* 3.4 30.3 - - + -
491A PRO* 3.9 15.7 - - + -
494A TYR* 3.5 37.7 + - + -
496A ILE* 4.9 0.4 - - - -
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Residues in contact with PHE 325 (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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321A TRP* 3.0 54.9 + + - +
322A ALA* 3.8 5.2 - - - +
324A LEU* 1.3 81.2 - - + +
326A MET* 1.3 69.4 + - + +
328A LEU* 3.6 6.3 - - + +
329A TYR* 2.9 59.0 + + + +
368A VAL* 5.3 2.0 - - + -
371A PHE* 3.7 29.4 - + - -
372A CYS* 4.0 10.1 - - - -
420A PHE* 3.8 39.3 - + + -
481A LEU* 4.2 23.3 - - + -
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Residues in contact with MET 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ALA* 2.9 22.7 + - - +
323A ILE* 3.1 6.7 + - - +
325A PHE* 1.3 89.1 - - + +
327A ALA* 1.3 61.0 + - - +
329A TYR 3.5 17.1 - - - -
330A PRO 3.6 0.9 - - - -
332A ILE* 3.6 26.2 - - + -
333A GLN* 2.9 53.3 + - + +
336A VAL* 4.4 2.9 - - - -
364A VAL* 3.7 19.3 - - + -
368A VAL* 5.8 0.4 - - + -
420A PHE* 4.7 5.4 - - + -
462A PHE* 3.8 31.2 - - + -
466A LEU* 4.2 9.2 - - + -
471A LEU* 4.9 5.6 - - + -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE 3.1 5.3 + - - -
324A LEU 3.8 2.2 - - - +
326A MET* 1.3 74.5 - - - +
328A LEU* 1.3 64.5 + - - +
329A TYR 3.6 0.2 + - - -
330A PRO* 3.7 9.4 - - - +
333A GLN* 4.1 0.4 - - - +
471A LEU* 3.6 20.8 - - + +
472A HIS* 4.0 13.1 - - - +
473A PHE* 3.5 36.8 - - + -
496A ILE* 3.8 20.6 - - + -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU 3.0 16.7 + - - +
325A PHE* 3.6 11.0 - - + +
327A ALA* 1.3 78.7 - - - +
329A TYR* 1.3 88.4 + - + +
330A PRO* 3.3 7.9 - - - +
473A PHE* 3.6 8.7 - - + -
479A PRO* 4.6 19.5 - - + -
481A LEU* 3.5 42.6 - - + -
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Residues in contact with TYR 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 2.9 50.7 + + - +
326A MET* 3.5 5.5 - - + +
327A ALA 3.3 0.2 - - - -
328A LEU* 1.3 104.9 - - + +
330A PRO* 1.4 59.5 - - - +
331A ASN* 3.2 3.6 - - + -
332A ILE* 2.9 39.2 + - + +
333A GLN 3.2 8.1 + - - -
420A PHE* 4.3 21.8 - + + +
481A LEU* 5.4 2.1 - - - +
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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