Contacts of the helix formed by residues 278 - 316 (chain A) in PDB entry 2Y01
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 278 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ARG* 1.3 54.1 + - - +
280A VAL* 3.0 17.2 - - - +
281A MET* 2.7 52.7 + - - +
282A LEU* 3.4 5.9 + - - +
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Residues in contact with ARG 279 (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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278A SER* 1.3 72.0 + - - +
280A VAL* 1.3 64.2 + - + +
282A LEU* 3.5 9.2 + - - +
283A MET* 3.1 50.1 + - + +
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Residues in contact with VAL 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 2.9 13.6 + - - +
279A ARG* 1.3 81.2 - - + +
281A MET* 1.3 65.9 + - + +
283A MET* 3.4 7.7 + - - +
284A ARG* 3.1 35.2 + - + +
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Residues in contact with MET 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 2.7 37.5 + - - +
280A VAL* 1.3 76.2 - - + +
282A LEU* 1.3 59.0 + - - +
284A ARG* 3.5 31.0 + - - +
285A GLU* 3.2 32.6 + - - +
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Residues in contact with LEU 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN* 3.4 54.1 - - + +
278A SER 3.4 7.4 + - - +
279A ARG* 3.5 10.5 + - - +
281A MET* 1.3 76.0 - - - +
283A MET* 1.3 61.4 + - + +
285A GLU* 3.5 15.5 + - - +
286A HIS* 3.1 48.1 + - + +
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Residues in contact with MET 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 3.1 49.1 + - + +
280A VAL* 3.6 7.2 - - - +
282A LEU* 1.3 77.2 - - + +
284A ARG* 1.3 57.7 + - - +
286A HIS* 3.3 9.5 + - - +
287A LYS* 2.9 28.2 + - - +
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Residues in contact with ARG 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A VAL* 3.1 25.2 + - + +
281A MET* 3.8 31.1 - - - +
282A LEU 3.4 0.4 - - - -
283A MET* 1.3 76.5 - - - +
285A GLU* 1.3 60.4 + - + +
287A LYS* 3.6 12.4 + - + +
288A ALA* 3.3 20.8 + - - +
348A ASP* 6.0 1.8 - - - -
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Residues in contact with GLU 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLN* 5.4 0.9 - - - +
281A MET* 3.2 23.8 + - - +
282A LEU* 3.8 19.1 - - - +
283A MET 3.3 0.4 - - - -
284A ARG* 1.3 78.7 - - + +
286A HIS* 1.3 64.6 + - + +
288A ALA* 3.4 7.6 + - - +
289A LEU* 3.1 31.0 + - + +
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Residues in contact with HIS 286 (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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143A ILE* 6.1 0.2 - - + -
234A ALA* 3.0 35.5 + - + +
237A GLN* 3.3 23.7 + - + -
282A LEU* 3.1 42.4 + - + +
283A MET* 3.3 12.2 + - - +
285A GLU* 1.3 80.1 - - + +
287A LYS* 1.3 65.5 + - - +
288A ALA 3.3 0.2 - - - -
289A LEU* 3.9 15.6 - - + +
290A LYS* 3.1 24.8 + - - +
502A 2CV 5.9 0.3 - - - +
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Residues in contact with LYS 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A MET 2.9 17.6 + - - +
284A ARG* 3.7 14.1 - - + +
286A HIS* 1.3 76.5 - - - +
288A ALA* 1.3 61.1 + - - +
290A LYS* 3.3 3.1 + - - -
291A THR* 3.0 27.2 + - - +
345A ARG* 3.2 54.1 + - - +
346A SER* 5.7 0.9 - - - -
347A PRO* 4.8 11.4 - - + -
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Residues in contact with ALA 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ARG 3.3 11.3 + - - +
285A GLU* 3.6 11.2 - - - +
286A HIS 3.3 0.2 - - - -
287A LYS* 1.3 79.7 - - - +
289A LEU* 1.3 60.0 + - - +
291A THR* 3.2 11.7 + - - -
292A LEU* 3.2 26.6 + - + +
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Residues in contact with LEU 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG* 3.8 42.4 - - + +
143A ILE* 4.2 15.0 - - + -
230A VAL* 4.3 13.7 - - + -
234A ALA* 4.1 25.4 - - + -
285A GLU* 3.1 19.0 + - + +
286A HIS* 3.9 15.9 - - + +
287A LYS 3.3 0.2 - - - -
288A ALA* 1.3 72.7 - - - +
290A LYS* 1.3 60.0 + - - +
292A LEU* 3.1 10.9 + - + +
293A GLY 2.8 24.1 + - - -
502A 2CV 3.5 22.9 - - + +
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Residues in contact with LYS 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A HIS 3.1 17.7 + - - +
287A LYS* 3.3 7.6 + - - +
289A LEU* 1.3 75.6 - - - +
291A THR* 1.3 58.0 + - - +
293A GLY* 3.2 3.4 + - - +
294A ILE* 2.8 45.7 + - + +
345A ARG* 3.7 22.3 - - - +
502A 2CV 4.7 8.9 - - + +
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Residues in contact with THR 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LYS* 3.0 15.5 + - - +
288A ALA* 3.3 11.6 + - - -
289A LEU 3.2 0.2 - - - -
290A LYS* 1.3 75.2 - - - +
292A LEU* 1.3 58.6 + - + +
294A ILE* 3.2 6.4 + - - +
295A ILE* 3.0 31.8 + - - +
342A ILE* 4.0 28.7 - - + +
343A TYR* 4.3 19.5 - - + -
345A ARG* 2.9 29.9 + - + +
346A SER* 5.6 4.9 + - - +
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Residues in contact with LEU 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR* 4.5 11.2 - - + -
80A ILE* 4.1 23.6 - - + -
135A ILE* 4.0 22.2 - - + -
139A ARG* 3.9 34.1 - - + -
288A ALA* 3.2 14.1 + - + +
289A LEU* 3.1 13.6 + - + +
291A THR* 1.3 75.9 - - + +
293A GLY* 1.3 63.3 + - - +
295A ILE* 3.3 13.5 + - + +
296A MET* 3.0 40.9 + - + +
343A TYR* 5.6 2.5 - - + -
502A 2CV 4.4 4.0 - - + -
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Residues in contact with GLY 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU 2.8 16.9 + - - -
290A LYS* 3.2 4.9 + - - -
292A LEU* 1.3 72.0 - - - +
294A ILE* 1.3 56.6 + - - +
296A MET* 3.3 7.3 + - - +
297A GLY* 2.8 28.1 + - - -
502A 2CV 4.2 22.2 - - - +
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Residues in contact with ILE 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LYS* 2.8 31.5 + - + +
291A THR* 3.5 7.0 - - - +
292A LEU 3.2 0.2 - - - -
293A GLY* 1.3 72.9 - - - +
295A ILE* 1.3 60.8 + - - +
297A GLY* 5.0 0.9 - - - -
298A VAL* 2.9 39.9 + - + +
342A ILE* 3.9 27.1 - - + -
345A ARG* 3.8 39.3 - - - +
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Residues in contact with ILE 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 6.0 0.9 - - + -
83A LEU* 4.4 3.6 - - + -
132A LEU* 3.7 25.6 - - + -
135A ILE* 6.2 0.2 - - + -
291A THR 3.0 20.5 + - - +
292A LEU* 3.3 17.7 + - + +
294A ILE* 1.3 74.0 - - - +
296A MET* 1.3 57.9 + - - +
298A VAL* 4.0 1.4 - - - +
299A PHE* 3.0 29.6 + - + +
335A ASN* 5.0 0.2 - - - +
339A ASN* 3.2 44.6 - - + +
342A ILE* 3.6 29.8 - - + -
343A TYR* 3.7 25.1 - - + +
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Residues in contact with MET 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.7 33.9 - - + +
135A ILE* 3.9 21.1 - - + -
136A ALA* 3.9 13.0 - - + -
223A MET* 3.8 38.2 - - + +
227A ALA* 4.3 12.1 - - + -
292A LEU* 3.0 19.3 + - + +
293A GLY* 3.6 6.1 - - - +
295A ILE* 1.3 75.0 - - - +
297A GLY* 1.3 61.0 + - - +
299A PHE* 3.6 6.4 + - - +
300A THR* 2.9 32.9 + - - -
502A 2CV 3.9 24.9 - - + -
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Residues in contact with GLY 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLY 2.8 20.5 + - - -
294A ILE* 3.8 1.3 - - - -
296A MET* 1.3 70.1 - - - +
298A VAL* 1.3 59.8 + - - +
300A THR* 3.3 6.6 + - - -
301A LEU* 2.9 36.6 + - - +
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Residues in contact with VAL 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ILE* 2.9 33.3 + - + +
295A ILE 4.1 2.5 - - - +
297A GLY* 1.3 75.7 - - - +
299A PHE* 1.3 50.9 + - - +
301A LEU* 3.2 14.9 + - + +
302A CYS* 2.8 36.3 + - - -
335A ASN* 3.8 7.6 - - - +
338A MET* 3.6 37.5 - - + -
339A ASN* 5.7 0.9 - - - +
342A ILE* 4.2 12.3 - - + -
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Residues in contact with PHE 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.0 10.3 - - + -
128A SER* 3.5 24.5 - - - -
129A ILE* 3.7 45.5 - - + -
132A LEU* 3.6 22.4 - - + -
216A PHE* 4.3 12.1 - + - -
220A LEU* 5.3 0.2 - - + -
223A MET* 5.6 0.2 - - - -
295A ILE* 3.0 20.7 + - + +
296A MET 3.8 4.7 - - - +
298A VAL* 1.3 77.4 - - - +
300A THR* 1.3 67.0 + - - +
302A CYS 3.4 0.7 + - - -
303A TRP* 3.1 51.7 + + - +
335A ASN* 3.3 32.7 + - - +
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Residues in contact with THR 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PHE* 5.3 1.1 - - - -
220A LEU* 3.5 33.3 - - + +
223A MET* 3.5 10.0 - - - +
224A ILE* 5.3 6.3 - - + +
296A MET 2.9 19.2 + - - -
297A GLY* 3.6 6.7 - - - -
299A PHE* 1.3 79.2 - - - +
301A LEU* 1.3 61.2 + - + +
304A LEU* 2.8 59.6 + - + +
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Residues in contact with LEU 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A GLY 2.9 21.6 + - - +
298A VAL* 3.6 16.6 - - + +
300A THR* 1.3 78.5 - - + +
302A CYS* 1.3 59.6 + - - +
304A LEU* 5.2 0.4 - - - -
305A PRO* 3.2 25.1 - - - +
331A LEU* 4.0 6.5 - - - +
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Residues in contact with CYS 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A VAL* 2.8 26.3 + - - +
299A PHE 3.9 3.4 - - - +
300A THR 3.2 0.2 - - - -
301A LEU* 1.3 76.6 - - - +
303A TRP* 1.3 61.0 + - + +
305A PRO* 4.2 2.1 - - - +
306A PHE 5.1 0.7 + - - -
328A PHE 4.1 4.0 - - - +
331A LEU* 3.6 31.7 - - - +
332A GLY* 3.5 18.2 + - - -
335A ASN* 3.7 24.7 - - + -
338A MET* 3.7 37.7 - - - -
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Residues in contact with TRP 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASP* 4.3 9.9 - - - -
125A VAL* 3.6 26.7 - - + +
216A PHE* 3.7 17.5 - - + -
299A PHE* 3.1 53.8 + + - +
302A CYS* 1.3 80.6 - - + +
304A LEU* 1.3 68.2 + - - +
305A PRO* 3.3 2.7 - - - -
306A PHE* 3.1 24.8 + + + +
307A PHE* 3.0 43.3 + + + -
329A ASN* 3.6 27.1 - - - -
332A GLY* 3.3 42.3 + - - -
333A TYR* 3.9 11.4 - + - -
335A ASN* 4.5 4.0 - - - +
601A Y00 5.3 1.3 - + - -
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Residues in contact with LEU 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PHE* 3.7 27.9 - - + -
217A TYR* 4.1 12.3 - - + -
220A LEU* 4.3 9.9 - - + -
300A THR* 2.8 42.8 + - + +
301A LEU* 5.2 0.4 - - - -
303A TRP* 1.3 72.7 - - - +
305A PRO* 1.4 60.6 - - + +
307A PHE 3.2 0.3 + - - -
308A LEU* 2.8 62.4 + - + +
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Residues in contact with PRO 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A THR 3.9 0.2 - - - +
301A LEU* 3.2 26.0 - - - +
302A CYS 4.2 1.1 - - - +
303A TRP 3.5 3.8 - - - +
304A LEU* 1.4 94.5 - - + +
306A PHE* 1.3 61.7 + - - +
308A LEU* 3.5 9.2 + - + +
309A VAL* 3.0 28.9 + - - +
328A PHE* 3.8 35.7 - - + -
331A LEU* 4.6 9.0 - - + -
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Residues in contact with PHE 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A CYS 5.1 0.4 + - - -
303A TRP* 3.1 21.9 + + + +
305A PRO* 1.3 78.8 - - - +
307A PHE* 1.3 92.9 + + - +
309A VAL* 3.4 4.3 + - - +
310A ASN* 3.0 30.3 + - - +
325A PHE* 3.3 37.4 - + - -
328A PHE* 3.8 26.4 + - - +
329A ASN* 3.6 33.2 - - + -
601A Y00 3.4 44.9 - + + -
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Residues in contact with PHE 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.1 13.2 - - + -
212A SER* 3.7 21.5 - - - -
215A SER* 5.5 1.3 - - - -
216A PHE* 3.5 62.6 - + + -
217A TYR* 3.0 17.0 + - + +
303A TRP* 3.0 47.4 + + - +
304A LEU 4.0 0.7 - - - +
306A PHE* 1.3 90.2 - + - +
308A LEU* 1.3 64.3 + - - +
310A ASN* 3.3 4.5 + - - +
311A ILE* 3.1 21.3 + - - +
601A Y00 3.6 43.1 - + - -
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Residues in contact with LEU 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR* 3.2 15.9 + - + +
304A LEU* 2.8 51.2 + - + +
305A PRO* 3.8 8.7 - - + +
307A PHE* 1.3 75.5 - - - +
309A VAL* 1.3 59.8 + - + +
311A ILE* 3.3 7.3 + - + +
312A VAL* 3.0 32.1 + - + +
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Residues in contact with VAL 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A PRO 3.0 19.5 + - - +
306A PHE 3.8 1.3 - - - +
308A LEU* 1.3 74.8 - - + +
310A ASN* 1.3 65.4 + - - +
312A VAL* 3.2 6.6 + - + +
313A ASN* 3.0 34.4 + - - +
320A VAL* 3.7 35.2 - - + -
325A PHE* 3.3 31.6 - - + -
328A PHE* 3.7 24.9 - - + -
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Residues in contact with ASN 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A THR* 5.5 0.7 + - - -
208A ALA* 4.1 17.9 + - - +
212A SER* 3.0 23.6 + - - +
306A PHE* 3.0 27.4 + - + +
307A PHE* 3.3 14.5 - - - +
308A LEU 3.3 0.4 - - - -
309A VAL* 1.3 78.3 - - - +
311A ILE* 1.3 65.0 + - - +
313A ASN* 3.7 10.7 + - - +
314A VAL* 3.8 13.5 + - - +
325A PHE* 3.9 18.1 - - + -
601A Y00 3.4 27.2 + - - -
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Residues in contact with ILE 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA 4.5 1.3 - - - +
209A ILE* 4.5 23.6 - - + +
212A SER* 3.8 31.0 - - - +
213A ILE* 5.7 2.0 - - + -
217A TYR* 3.5 21.1 - - + +
307A PHE 3.1 13.5 + - - +
308A LEU* 3.5 8.1 - - + +
310A ASN* 1.3 76.8 - - - +
312A VAL* 1.3 65.7 + - + +
314A VAL* 2.9 25.3 + - - +
315A PHE* 3.7 22.6 - - + -
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Residues in contact with VAL 312 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.0 23.6 + - + +
309A VAL* 3.2 8.7 + - + +
311A ILE* 1.3 79.5 - - + +
313A ASN* 1.3 59.9 + - - +
315A PHE* 3.1 8.9 + - + +
316A ASN* 2.8 37.0 + - + +
319A LEU* 3.9 30.5 - - + -
320A VAL* 4.7 13.9 - - + -
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Residues in contact with ASN 313 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 4.5 0.2 + - - -
309A VAL* 3.0 30.7 + - - +
310A ASN* 3.8 8.6 + - - +
311A ILE 3.1 0.4 + - - -
312A VAL* 1.3 74.1 - - - +
314A VAL* 1.3 67.2 + - + +
315A PHE 3.1 0.7 + - - -
316A ASN 3.5 16.8 + - - +
317A ARG* 3.5 33.7 + - + +
320A VAL* 4.9 7.8 - - - +
325A PHE* 3.8 37.8 - - - +
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Residues in contact with VAL 314 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 2.6 60.3 + - + +
208A ALA* 3.9 18.8 - - + -
209A ILE* 3.6 40.2 - - + -
310A ASN 3.8 10.1 + - - +
311A ILE* 2.9 14.9 + - - +
313A ASN* 1.3 78.0 - - + +
315A PHE* 1.3 63.7 + - + +
503A 2CV 3.6 18.4 - - + -
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Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 5.0 7.4 - - + -
311A ILE* 3.7 33.2 - - + -
312A VAL* 3.1 8.5 + - + +
313A ASN 3.0 0.4 - - - -
314A VAL* 1.3 88.1 - - + +
316A ASN* 1.3 63.1 + - + +
317A ARG* 4.1 5.4 + - - -
503A 2CV 3.4 70.2 + - + -
152B LEU* 4.3 16.6 - - + -
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Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 2.8 24.1 + - + +
313A ASN* 3.5 6.6 + - - +
315A PHE* 1.3 77.6 - - + +
317A ARG* 1.3 66.9 + - - +
318A ASP* 3.0 24.7 + - - +
319A LEU* 3.3 54.3 + - + +
320A VAL 4.6 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) + - + + + + + -
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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