Contacts of the helix formed by residues 292 - 323 (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 THR 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 5.7 2.3 - - - +
286A GLU* 4.5 0.2 - - - -
291A LEU* 1.3 73.4 - - - +
293A ARG* 1.3 70.2 + - + +
294A GLU* 4.1 18.2 - - + +
295A ASN* 2.9 32.7 + - - +
296A VAL* 3.0 13.8 + - - +
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Residues in contact with ARG 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ILE* 6.3 0.2 - - - -
263A ARG* 3.8 22.7 - - - +
286A GLU* 3.6 28.3 - - - +
291A LEU 3.9 2.0 + - - -
292A THR* 1.3 75.9 - - + +
294A GLU* 1.3 95.5 + - - +
296A VAL* 3.1 3.8 + - - +
297A ASN* 3.1 35.0 + - - +
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Residues in contact with GLU 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 3.7 32.8 + - + +
292A THR* 3.1 15.0 - - + -
293A ARG* 1.3 103.9 + - - +
295A ASN* 1.3 61.4 + - - +
297A ASN* 3.2 18.4 + - - +
298A GLN* 3.4 11.4 + - - +
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Residues in contact with ASN 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU 5.3 1.1 - - - +
130A LYS* 2.6 43.0 - - + +
140A LEU* 3.7 29.7 - - - +
144A THR* 4.3 8.4 + - - +
291A LEU* 4.0 23.6 - - - +
292A THR* 2.9 27.6 + - - +
294A GLU* 1.3 75.2 - - - +
296A VAL* 1.3 65.2 + - - +
298A GLN* 3.4 3.9 + - - +
299A CYS* 3.2 25.8 + - - -
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Residues in contact with VAL 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ARG* 4.1 9.9 - - - +
282A LEU* 4.2 19.5 - - + +
283A ILE* 4.3 7.2 - - + -
286A GLU* 3.9 20.9 - - + +
291A LEU* 3.8 25.6 - - + -
292A THR 3.0 16.1 + - - +
293A ARG 3.3 7.4 - - - +
295A ASN* 1.3 74.0 - - - +
297A ASN* 1.3 66.7 + - - +
298A GLN 2.9 6.4 + - - -
299A CYS* 2.9 19.5 + - - +
300A ILE* 3.1 33.6 + - + +
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Residues in contact with ASN 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LYS* 5.3 7.3 - - - -
255A ILE* 4.7 5.2 - - - +
256A GLU* 3.2 38.3 + - - +
259A ILE* 3.6 25.5 - - + +
263A ARG* 3.6 17.0 + - - -
293A ARG* 3.1 31.4 + - - +
294A GLU* 3.2 11.3 + - - +
296A VAL* 1.3 77.4 - - - +
298A GLN* 1.3 58.8 + - - +
300A ILE* 4.1 7.2 - - - +
301A LEU* 3.4 21.8 + - - +
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Residues in contact with GLN 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLY 3.2 19.6 + - - +
127A MET* 3.4 18.6 - - - +
130A LYS* 4.1 13.4 + - + +
131A GLY* 3.7 22.7 - - - +
220A TYR* 3.2 24.0 + - - -
252A LYS* 3.2 28.6 + - - -
294A GLU 3.4 10.3 + - - +
295A ASN 3.7 9.0 - - - +
296A VAL 3.0 1.2 - - - -
297A ASN* 1.3 76.0 - - - +
299A CYS* 1.3 55.8 - - - +
300A ILE 3.3 0.2 - - - -
301A LEU* 3.1 9.7 + - - +
302A GLU* 2.6 46.8 + - - +
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Residues in contact with CYS 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS 4.2 4.7 - - - -
131A GLY* 4.7 2.5 - - - -
144A THR* 3.5 32.8 - - - -
148A PHE* 3.6 25.2 - - + -
278A PHE* 4.0 2.2 - - + -
282A LEU* 3.8 20.4 - - + -
291A LEU* 6.1 0.7 - - - -
295A ASN* 3.2 22.2 - - - -
296A VAL* 2.9 7.7 + - - +
298A GLN* 1.3 77.0 - - - +
300A ILE* 1.3 52.6 + - - +
302A GLU* 3.5 3.4 - - - -
303A MET* 2.6 37.8 + - - +
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Residues in contact with ILE 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 4.7 13.0 - - + -
255A ILE* 4.3 11.2 - - + -
259A ILE* 3.6 33.7 - - + -
278A PHE* 4.2 7.9 - - + -
279A ALA* 4.1 33.2 - - + +
282A LEU* 4.0 13.7 - - + -
283A ILE* 4.7 4.3 - - + -
296A VAL* 3.1 35.3 + - + +
297A ASN 4.3 2.9 - - - +
299A CYS* 1.3 76.4 - - - +
301A LEU* 1.3 61.9 + - - +
303A MET* 4.1 1.7 - - - +
304A LEU* 3.3 32.0 + - + +
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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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220A TYR* 3.8 28.3 - - + +
251A LEU* 3.8 22.2 - - + -
252A LYS* 4.0 34.1 - - + +
255A ILE* 3.8 24.7 - - + -
297A ASN 3.4 14.6 + - - +
298A GLN* 3.1 16.9 + - - +
300A ILE* 1.3 76.6 - - - +
302A GLU* 1.3 68.6 + - + +
304A LEU* 3.1 3.0 + - - +
305A ILE* 3.0 45.3 + - + +
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Residues in contact with GLU 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 3.1 36.7 - - + +
131A GLY* 3.2 19.0 - - - -
132A ILE* 2.6 27.6 + - - +
133A ILE* 3.0 36.4 + - + +
134A PHE 4.2 0.7 + - - -
148A PHE* 4.5 7.1 - - + -
298A GLN* 2.6 33.6 + - - +
299A CYS* 3.8 5.8 - - - +
301A LEU* 1.3 72.1 - - + +
303A MET* 1.3 60.6 + - - +
305A ILE* 3.9 8.4 - - + +
306A ALA* 3.5 22.9 + - - +
600A HEM 5.5 1.7 - - - +
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Residues in contact with MET 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PHE* 3.4 34.1 - - + -
151A ALA* 4.5 1.6 - - + -
152A LEU* 3.9 28.5 - - + -
199A SER* 4.1 9.0 + - - -
203A PHE* 3.6 39.0 - - + -
278A PHE* 3.4 41.7 - - + -
299A CYS 2.6 21.5 + - - +
300A ILE* 4.1 4.0 - - - +
302A GLU* 1.3 73.0 - - - +
304A LEU* 1.3 64.5 + - + +
306A ALA* 4.3 1.2 + - - -
600A HEM 4.2 17.2 - - - +
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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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196A LEU* 4.3 18.1 - - + +
199A SER* 4.0 27.7 + - - +
200A ASN* 4.0 17.9 - - + +
203A PHE* 5.6 3.1 - - + -
204A LEU* 3.9 29.8 - - + -
208A LEU* 5.2 6.1 - - + -
213A ILE* 6.0 3.1 - - + -
217A ILE* 4.8 2.7 - - + -
255A ILE* 4.5 22.0 - - + -
258A LEU* 5.6 2.0 - - + -
300A ILE* 3.3 22.3 + - + +
301A LEU* 3.1 5.4 + - - +
303A MET* 1.3 79.1 - - + +
305A ILE* 1.3 62.9 + - + +
306A ALA 3.2 2.5 + - - -
307A ALA 3.9 0.3 + - - -
308A PRO* 2.9 27.5 - - - +
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Residues in contact with ILE 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 4.5 4.7 - - + -
133A ILE* 5.0 1.8 - - + -
217A ILE* 3.8 28.7 - - + -
220A TYR* 3.7 31.2 - - + -
224A TRP* 3.9 14.4 - - + -
251A LEU* 3.8 19.3 - - + -
255A ILE* 5.5 0.9 - - + -
301A LEU* 3.0 32.0 + - + +
302A GLU* 3.9 10.5 - - - +
304A LEU* 1.3 77.3 - - + +
306A ALA* 1.3 56.9 + - - +
308A PRO* 3.3 2.8 - - - +
309A ASP* 2.8 55.2 + - - +
601A G29 4.0 3.6 - - - +
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Residues in contact with ALA 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 5.1 1.1 - - + -
302A GLU 3.5 16.3 + - - +
303A MET* 4.3 2.7 - - - +
304A LEU 3.2 1.8 + - - -
305A ILE* 1.3 78.8 - - - +
307A ALA* 1.3 64.1 + - - +
310A THR* 3.1 31.5 + - - +
600A HEM 3.6 36.8 - - + -
601A G29 3.2 24.9 - - + +
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Residues in contact with ALA 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 3.6 17.8 - - + +
199A SER* 3.4 18.2 - - - +
304A LEU 3.9 1.0 + - - -
306A ALA* 1.3 74.8 - - - +
308A PRO* 1.4 72.3 - - + +
310A THR 3.1 0.3 + - - -
311A MET* 2.7 38.9 + - - +
446A MET* 4.1 18.6 - - + -
600A HEM 3.8 15.4 - - + +
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Residues in contact with PRO 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 4.0 23.5 + - + +
195A MET* 3.7 16.8 - - + +
196A LEU* 3.7 29.4 - - + -
199A SER* 4.2 0.2 - - - +
214A VAL* 5.9 1.6 - - + -
217A ILE* 4.1 19.7 - - + -
304A LEU 2.9 29.8 - - - +
305A ILE 3.3 5.2 - - - +
307A ALA* 1.4 85.7 - - + +
309A ASP* 1.3 57.2 + - - +
312A SER* 2.4 30.1 + - - +
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Residues in contact with ASP 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 4.9 3.0 + - - +
217A ILE* 4.0 12.7 - - - +
218A GLN* 5.5 0.9 - - - -
220A TYR* 5.6 0.2 - - - -
221A PHE* 3.4 34.9 - - - +
224A TRP* 4.0 2.4 - - - -
305A ILE* 2.8 44.0 + - - +
306A ALA 3.4 5.8 - - - +
308A PRO* 1.3 76.9 - - - +
310A THR* 1.3 63.6 + - + +
313A VAL* 3.3 23.0 - - - +
601A G29 2.9 37.8 - - + +
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Residues in contact with THR 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ALA 3.1 17.4 + - - +
309A ASP* 1.3 76.4 - - - +
311A MET* 1.3 65.0 + - - +
312A SER 3.3 1.8 - - - -
313A VAL* 3.4 3.9 + - - +
314A SER* 2.9 30.9 + - - -
369A VAL* 4.7 3.7 - - - +
370A VAL* 5.0 3.6 - - - -
600A HEM 3.6 35.3 - - + +
601A G29 3.3 59.7 - - + -
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Residues in contact with MET 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 3.6 16.4 - - + -
307A ALA* 2.7 20.1 + - - +
310A THR* 1.3 73.7 + - - +
312A SER* 1.3 58.7 + - - +
314A SER* 4.4 2.9 - - - -
315A LEU* 2.8 47.3 + - + +
443A ALA* 3.9 16.2 - - - +
446A MET* 3.5 46.4 - - + -
447A MET* 3.3 35.0 - - + +
600A HEM 3.7 34.1 - - + -
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Residues in contact with SER 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 4.3 3.4 - - - -
191A LEU* 3.2 36.8 - - - +
192A ARG* 3.4 32.5 + - - +
195A MET* 4.2 2.3 - - - +
307A ALA 3.6 2.0 + - - -
308A PRO* 2.4 28.5 + - - -
309A ASP 3.8 1.6 + - - -
311A MET* 1.3 79.5 - - - +
313A VAL* 1.3 70.4 + - - +
315A LEU* 4.9 0.7 - - - -
316A PHE* 2.9 23.3 + - - +
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Residues in contact with VAL 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 4.4 5.4 - - + -
192A ARG* 3.6 24.2 - - - +
309A ASP 3.3 19.3 - - - +
310A THR 3.4 5.7 + - - +
312A SER* 1.3 81.5 + - - +
314A SER* 1.3 61.7 + - - +
316A PHE* 3.5 6.9 - - - +
317A PHE* 3.1 24.9 + - + -
369A VAL* 3.7 21.3 - - + -
480A HIS* 3.7 15.3 - - + -
481A PRO* 3.6 28.0 - - + -
601A G29 3.9 11.7 - - + -
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Residues in contact with SER 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A THR* 2.9 21.7 + - - -
311A MET* 3.8 6.3 - - - -
313A VAL* 1.3 73.6 - - - +
315A LEU* 1.3 61.9 + - - +
317A PHE* 3.2 7.1 + - - +
318A MET* 3.1 28.3 + - - +
364A MET* 4.6 12.5 - - - +
369A VAL* 3.4 24.5 + - - +
447A MET* 4.6 7.9 - - - -
600A HEM 4.3 23.4 - - - +
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Residues in contact with LEU 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU* 3.7 15.9 - - + -
195A MET* 4.5 6.7 - - - -
311A MET* 2.8 49.8 + - + +
312A SER* 4.9 1.3 - - - -
314A SER* 1.3 72.3 - - - +
316A PHE* 1.3 57.3 + - - +
318A MET* 3.3 21.2 + - + +
319A LEU* 2.9 33.8 + - + +
447A MET* 3.6 26.9 - - + -
450A ILE* 3.3 42.2 - - + -
451A LEU* 3.9 13.2 - - + -
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Residues in contact with PHE 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 3.7 22.4 - - + -
188A LEU* 3.5 29.2 - - + -
191A LEU* 3.6 9.3 - - + +
312A SER 2.9 18.9 + - - +
313A VAL 3.5 4.5 - - - +
314A SER 3.2 0.2 - - - -
315A LEU* 1.3 77.6 - - - +
317A PHE* 1.3 77.7 - + - +
319A LEU* 3.2 15.2 + - - +
320A PHE* 3.2 49.7 + + - -
471A ILE* 4.1 7.9 - - + -
481A PRO* 3.7 26.7 - - + -
488A LEU* 3.4 34.5 - - + -
490A MET* 5.3 0.4 - - - -
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Residues in contact with PHE 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A VAL* 3.1 10.5 + - + -
314A SER 3.2 7.4 + - - +
316A PHE* 1.3 83.9 - + - +
318A MET* 1.3 65.8 + - + +
320A PHE* 3.1 7.0 + - - +
321A LEU* 3.0 27.8 + - + +
363A SER* 6.1 0.7 - - - -
367A GLN* 3.5 42.8 - - + +
368A PRO 3.8 7.2 - - - -
369A VAL* 3.7 21.3 - - + -
468A VAL* 3.9 15.7 - - + +
471A ILE* 4.8 9.0 - - + -
473A LYS* 4.4 14.1 - - + -
479A LEU* 3.4 25.4 - - + -
480A HIS* 4.4 0.4 - - - -
481A PRO* 3.9 33.0 - - + -
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Residues in contact with MET 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A SER* 3.1 24.9 + - - +
315A LEU* 3.3 25.5 + - + +
317A PHE* 1.3 77.5 - - + +
319A LEU* 1.3 57.0 + - - +
321A LEU* 3.3 5.1 + - - +
322A ILE* 2.9 26.0 + - - +
359A PHE* 3.2 22.3 - - + -
360A ILE* 3.8 36.3 - - + +
363A SER* 3.4 28.0 - - - +
364A MET* 5.8 3.4 - - - +
447A MET* 4.3 9.9 - - + +
451A LEU* 3.7 28.0 - - + -
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Residues in contact with LEU 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 3.8 25.1 - - + -
191A LEU* 4.7 6.7 - - + -
315A LEU* 2.9 20.9 + - + +
316A PHE* 3.4 9.9 - - - +
317A PHE 3.0 0.6 - - - -
318A MET* 1.3 74.5 - - - +
320A PHE* 1.3 56.9 + - - +
321A LEU 3.1 4.7 - - - -
322A ILE* 4.4 2.9 - - + +
323A ALA* 3.1 29.1 + - - +
450A ILE* 6.4 0.2 - - + -
451A LEU* 4.2 17.0 - - + -
454A LEU* 3.8 33.4 - - + -
455A LEU* 4.5 15.5 - - + -
460A VAL* 4.0 11.3 - - + +
490A MET* 3.6 26.9 - - + +
492A PHE* 4.8 1.6 - - + -
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Residues in contact with PHE 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A PHE* 3.2 53.0 + + - +
317A PHE* 3.1 8.7 + - - +
319A LEU* 1.3 75.7 - - - +
321A LEU* 1.3 59.6 + - - +
323A ALA* 4.0 6.4 - - - -
324A LYS* 3.6 25.8 + - - +
462A THR* 3.7 24.2 - - - -
463A LEU 5.6 0.2 - - - -
466A GLN* 4.0 13.7 - - + -
467A CYS* 3.9 15.3 - - - -
468A VAL* 4.1 22.9 + - + +
471A ILE* 3.6 21.3 - - + -
487A MET 4.4 4.5 - - - -
488A LEU* 3.9 7.0 - - - -
489A GLU 3.7 17.9 - - - -
490A MET* 3.5 22.2 - - + -
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Residues in contact with LEU 321 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 3.0 21.5 + - + +
318A MET* 3.5 8.3 - - - +
319A LEU 3.1 0.2 - - - -
320A PHE* 1.3 78.1 - - - +
322A ILE* 1.3 64.1 + - - +
323A ALA 3.2 1.3 - - - -
324A LYS 3.4 0.2 + - - -
325A HIS* 2.9 37.8 + - - +
359A PHE* 4.1 11.4 - - + -
363A SER* 3.4 31.9 - - - +
366A TYR* 4.5 5.4 - - + -
367A GLN* 4.4 11.7 - - + -
413A PHE* 3.5 40.6 - - + -
468A VAL* 4.0 27.8 - - + -
469A GLU* 5.6 0.2 - - - +
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Residues in contact with ILE 322 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A MET 2.9 13.1 + - - +
319A LEU* 3.5 5.3 + - + +
321A LEU* 1.3 76.3 - - - +
323A ALA* 1.3 61.8 + - - +
324A LYS 3.3 0.7 + - - -
325A HIS* 3.5 20.3 + - - +
326A PRO* 4.5 0.5 - - - +
328A VAL* 4.9 2.0 - - + -
329A GLU* 3.5 35.7 - - + +
332A ILE* 4.2 11.7 - - + -
359A PHE* 3.3 39.0 - - + -
451A LEU* 4.0 11.2 - - + -
455A LEU* 3.4 39.3 - - + -
460A VAL* 3.9 15.0 - - + -
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU 3.1 18.5 + - - +
320A PHE* 4.4 5.4 - - - +
321A LEU 3.2 0.4 - - - -
322A ILE* 1.3 79.0 - - - +
324A LYS* 1.3 64.3 + - - +
325A HIS 3.6 0.4 - - - -
326A PRO* 5.7 0.6 - - - +
329A GLU* 4.8 1.1 - - - -
460A VAL* 3.3 34.7 - - + +
461A LYS* 4.4 1.9 - - - -
462A THR* 3.8 26.4 - - + +
490A MET* 5.2 1.8 - - - -
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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
------------------------------------------------------------
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